WO2018226590A1

WO2018226590A1 - Peptides as biomarkers in the diagnosis, confirmation and treatment of a neurological disorder and immunoprofiling in neurodegenerative disease

Info

Publication number: WO2018226590A1
Application number: PCT/US2018/035870
Authority: WO
Inventors: David Sulzer; Alessandro Sette; Cecilia Lindestam ARLEHAMN; John Pham; Bjoern Peters
Original assignee: The Trustees Of Columbia University In The City Of New York; La Jolla Institute For Allergy & Immunology; The Research Foundation For Mental Hygiene, Inc.
Priority date: 2017-06-05
Filing date: 2018-06-04
Publication date: 2018-12-13
Also published as: US20200095296A1

Abstract

The present invention provides methods for assessing whether a subject is at risk of developing a neurological disorder, diagnosing or confirming whether a subject is afflicted with a neurological disorder, assessing a neurological disorder is developing in a subject who has been identified as being at risk of developing the neurological disorder, assessing whether a subject afflicted with a neurological disorder is likely to benefit iron a therapy, assessing whether a subject afflicted with a neurological disorder has benefited from a therapy, treating a subject afflicted with a neurological disorder, and prophylactically treating a subject who has been identified as being at risk, of developing a neurological disorder. The present invention also provides epitopes, compounds and compositions relating to these methods.

Description

PEPTIDES AS BIOMARKERS IN THE DIAGNOSIS, CONFIRMATION AND TREATMENT OF A NEUROLOOICAL DISORDER AND IMMUNOPROFILING IN NEURODEGENERA'i'IVE DISEASE

This application claiats priority of U,S, Provisional Application Numbers 62/637,303, filed March 1, 20iS, 62/586,597, filed N embe 15, 2017, 62/568,039, filed October 4, 2017, 62/522,043, filed June 20, 2017, 62/519,558, filed June 14, 2017, €2/518,285, filed June 12, 2017, and 62/515,429, filed June 5, 2017, the entire contents of which are hereby incorporated by reference herein. This application incorporates -by-reference nucleotide and/or amino acid sequences which are present in the file uajned ^Ώ1δ0604_88451~¾~ PCT Sequence Listing AWS,txt", which is 193 kilobytes in size, and which was created June 4, 2018 in the IBM-PC machine format, having an operating system cosrtpatibiiit with MS-Windows, which is contained in the text file filed June , 2010 as part of this application. hroughout this application, various publications are referenced, including referenced in parenthesis. Full citations for publications referenced in parenthesis may foe found listed at the end of the specification inBusdiateiy preceding the claims. e disclosures of all referenced publications in their entireties are hereby incorporated by reference into this application in order to raore fully describe the state of the art to which this invention pertains. Background o£ Invention

Alz eimer's Disease

Alzheimer's disease (AD) affects about 11% of people aged 65 or older and about 32% of those aged 85 or older. Merck Manual, Parkinson's Disease, last full review/revision August 2007 by David Sidelberg and Michael Pou la.: , available at roerekmanuals , com/boms/brain, ~spinal~cord, -and- n8rve~disorders d8liriuiu~an<J~cleisentia/aXz eiHter~ciiseas (hereinafter ^¾Merck Manual") .

What causes ΆΏ is unclear. According to one theory, several speci ic gene abnormalities m y he involved (Merck Manual) . One gene abnormality affects apoiipoprotein E (ape E) - the protein part of certain lipoproteins, which transport cholesterol through the bloodstream (Merck Manual) . There are three types of apo Si Epsi.ion™4, Epsilon-2, and spsilon-3 (Merck Manual . Patients with the epsiion~4 type develop Alzheimer disease more comrooniy and at an earlier age than others, whereas patients with the epsilon-2 type seem to be protected against Alzheimer disease, and patients with the epsiion-3 type are neither protected nor more likely to develop the disease (Merck Manual) , However, genetic testing for apo E type cannot determine whether a specific person will develop Alzheimer disease (Merck Manual) .

Alzheimer disease may cause the following abnormalities to develop in brain tissue: (1) accumulation of beta-amyloid, an abnormal, insoluble protein, which accumulates because eel Is cannot process and remove it {beta-ajuyloid deposits); {2} clum s ot dead nerve cells around a core ot beta-amyloid (senile or neuritic plaques); (3) twisted strands of insoluble proteins in the nerve ceil (neurofibrillary tangles); and/or (4) increased levels of Tan, an abnormal protein that is a component of neurofibrillary tangles and beta-amyloid (Merck Manual) . The abnormal proteins in Alzheimer disease {beta-amyloid and Tau) are m sfolded and cause other proteins to roisfoid, and na cause the disease to progress (Merck Manual.) .

Improved and novel methods for diagnosing, confirming, providing biojnarkers for, and treating AD are needed.

Pa kinson' Disease

Parkinson's disease (PD) affects about 1 of 250 people older than 40, about 1 of 100 people older than 65, and about 1 of 10 people older than 80, Merck Manual, Parkinson's Disease, last full review/revision August 2007 by David Eidelberg and Michael Pour far, available at merek araials , com/home/brain spinal cord and nerve disorders/movement dis orders/parkinsons_^disease .html {hereinafter "Merck Manual"), What causes 3?D is unclear. According to one theory, Parkinson's disease m r sult from abnormal deposits of synuclein (a protein in the brain that helps nerve ceils communicate) (Merck Manual) . These deposits, called Lewy bodies, can accu ulate in several regions of the brain, particularly in the substantia nigra (deep within the cerebrum} and interfere with brain function (Merck Manual) . Lewy bodies often accumulate in other parts of the brain and nervous system, suggesting that they stay be involved in other disorders (Merck Manual , In Lewy body dementia, Lewy bodies form throughout the outer layer of the brain {cerebral cortex) . Lewy bodies ma also be involved in Alzheimer's disease (Merck Manual),

Improved and novel methods for diagnosing, confirming, p oviding biomarkers for, and treating PD are needed,

Tauopathies are a group of neurodegenerative diseases characterized by the pathological accumulation of insoluble clusters of hyperphosphoryiated fau protein in neurons and glial cells (Tacik et al , , 2015) . Tauopathies are divided into primary Tauopathies and secondary Tauopathies ,

In primary Tauopathies, fau inclusions are the major neuropathoiogicai abnormality. In secondary Tauopathies, au pathology occurs in association with another, more specific, pathology, Tauopathies include Amyotrophic Lateral Sclerosis, Alzheime 's disease, Cerebrotendinons xanthomatosis, Agyrophilic Grain disease, Corticobasal Degeneration, Myotonic Dystrophy Type 1 and 2, Famil al Creutsfeldt-Jacob disease, Fatal Familial Insomnia, Frontotemproal Lovar Degeneration, Frontotemporal Dementia, Gerstmann- Straussier-Scheinher syndrome, Hiemann-Picfc disease, Parkinson's disease, Progressive Supranuclear Palsy, X-linked parkinsonism Kith spasticity, Sialic acid storage disease, Hereditary cerebral amyloid angiopathy, Kofs disease, 18q deletion syndrome, ^aurodegeneration with brain iron accumulatio , and Christiansen syndro e (facile et ai,, 2015} . Improved and novel methods for diagnosing, confirming, idin biomarkers for, and treating Tenopathies are needed, amyotro hic Lateral Sclerosis

Amyotrophic Lateral Sclerosis (ALS) is the most common form of motor neuron disease. Merck Manual, Amyotrophic lateral Solerosis and Other Meter Neuron Diseases, last full review/revision August 2007 by David Eidelberg and Michael Pou far, available at

K w.aercfanaiiuais . eonv2nome/brain, -spinal -cord,™and~nerve- disorders/peripheral-nerve-disorders/amyotrophic-late ai~selerosis~and~ ether-motor-nenrcn-diseases (hereinafter "Merck Manual*'} . k¾at causes .S is unclear. The ma ority of ALS cases (90 percent or mo e) are considered sporadic and about 5% to ? of people who have a motor neuron, disease have a hereditary type (Merck Man al} . According to one theory, about 25 to 40 percent of ail familial cases (and a small percentage of sporadic cases} are caused by a defect in chromosome 9 open reading frame 72, or C90RF72. National Institute of Neurological Disorders and. Stroke, Amyotrophic Lateral Solerosis {ALS} Pact Sheet, available at www , ninds . nih»gov/Disorders/Patient~Caregxver~Education/Fact~

Sheets/Arayotrophic-Latera1.-Sclerosis-ALS-Fact-Sheet, last updated October 18, 2004 (hereinafter "MIHDS Fact Sheet"} , According to another theory, another 12 to 20 percent of familial cases result f om mutations in the gene that provides instructions for the production of the enzyme copper-zinc superoxide dism.utase 1 (SOD!) ( i YS Fact Sheet) .

Amyotrophic Lateral Sclerosis ma result in degeneratation or death of both the upper motor neurons and the lower motor neurons, which stop sending messages to the muscles (MINDS Fact Sheet) . Eventually, the brain loses its ability to initiate and control voluntary rovements (NI-MDS Fact Sheet) . Improved and novel methods for diagnosing, conf rming, providing bioma kers for, and treating »S are ne ded. In various neurodegenerative diseases, it has been observed that aberrant protein expression and/or aberrant protein functio and/or aberrant protein macro-structure (such as protein aggregates) can be found to be associated with the disease predisposition and/or presence and/^*or progress .

For example, the major pathological features of Parkinson'^' s disease (PD) , a neurodegenerative movement disorder, are the death of dopaminergic neurons of the substantia nigra (a basal ganglia structure located in the jsidbrain that plays an important role in reward and atoveisent) , and the presence of intraneuronai protein aggregates known as Lewy bodies that are composed of a~synuelein (a-syu) [Spiliantini et ai , , Proc . Natl Acad. So I . USA 95, 6469-6473 (1998) 1 <

Alzheimer' s disease <AD) is characterized clinically by a progressive and gradual decline in cognitive function and neuropathologieal ly by the presence of neuropil threads, specific neuron loss, and synapse loss in addition to the hallmark protein aggregates in the form of an accumulation of extracellular beta amyloid Αβ) plaques and the fiar?te~ shaped neuro ib illary tangles of the microtubule binding protein tau [Cruts U, Van Broeekhoven C\ (1998) Ann Med 30; 560-565; Ruis J , (2008) Rev. Infirm. 143: 14-15; Hsiao K, et al . (1996) Science 274:99- 102],

Other diseases also have protein aggregates associated with the disease; in Creutsfeldt-Jafcob disease (CJD) there are aggregates of prion protein Sikorska et al,, Subcell Biochem, 2012; 65; 457-96], in sporadic ALS patients there are aggregates of TDP-43 [Aral , et al. _f Biochem, Biophys, Res, Commun, 2006; 351 : 602 -611 ] , and in frontotemporal lobar degenerations (FTLD) there are aggregates of tau, TDP-43, fused in sarcoma/translocated in liposarcoiaa (F s/ LS) and/or ubiquitin [Nonaka et al,, Ceil Rep. 2013 Jul 21; 4(1): 124-34? Neumann et al,_f Science, 2006; 314 : 130-133] . Recent evidence das also suggested, a roie of the innate imsrune system in neurodegenerative diseases.

For x m le, recent evidence has suggested that cytokine profiles have implicated the activation of the innate immune system, suggesting a roie tor the acquired immune system in patients with PD fCebrian et ai . , Curr, Top, Behav. Neurosci. 22, 237-270 {2015} ], including T cell infiltration into the substantia nigra [Brochard, V» et ai. J- Ciin. Invest, 119, 1S2-192 (2009)]. Experimental , genetic and epidemiological data also indicate a crucial role for activation of the innate immune system as a diseas -promoting factor in AD, where the sustained formation and deposition of Α aggregates causes chronic activation of the immune system and disturbance of microglial clearance functions Heneka et al . , Nature Instmnology 16, 223-236 (2015)].

Practical systems, processes and methods for diagnosing, confirming, and/or providing biomarkers for neurodegenerative diseases are still needed,

Smama of he Indentio

This Summary is provided to introduce a selection of concepts in a simplified form that are further described below in the Detailed Description . This Summary is not intended to identify key aspects or essential aspects of the claimed subject matter.

In the present disclosure, the invention proposed can be implemented in numerous ways, including as a process; an apparatus; a system; a co position of matter; a computer program product embodied on a computer readable storage edi m; and/or a processor, such as a processor con igured to execute instructions stored on and/or provided by a memory coupled to the processor, in this specification, these implementations, or any other form that the invention may take, may be referred to as techniques, in general, the order of the steps of disclosed processes may be altered within the scope of the invention, Unless stated otherwise, a component such as a processor or a memory described as being configured to perform a task may be implemented as a general component that is temporarily configured to perform the task at a given time or a specifi component that is manufactured to perform the task. As sed herein, the te m "processor" refers to one or more devises, circuits, and/or processing cores configured to process data, such as computer program instructions .

The present inventors propose a working model where T-cell recognition of peptides derived from proteins associated with neurodegenerative diseases may be a potential element in the neurodegenerative disease predisposition or presence thereof, and/or responsiveness to therapeutic treatment of the disease. Such proteins m y be, for example, proteins that have an aberrant protein expression and/or aberrant protein function and/or aberrant protein macrostructure (such as protein aggregates) . The present disclosure relates to processes, methods and systems, which make use of this working model. Accordingly, it is proposed that protein antigens can act as autoantigens in neurodegenerative diseases such that such antigens can be the source of biomarkers and diagnostics.

The present invention provides jsethods for assessing whether a subject is at risk of developing, or for diagnosing or confirming whether a subject is afflicted with an fi-synuclsinopathy, a Tauopathy, Parkinson' s disease (PD) , amyotrophic lateral sclerosis (ALS } , Lewy Body dementia {LBD} , or Alzheiiser' s disease (AD) comprising

a)

x) obtaining leukocytes from the subject?

ii) contacting the leukocytes with an epitope peptide;

iii} determining whether the leukocytes have increased activation after contact with the epitope peptide; and

iv} identifying the subject as at risk of developing, or as afflicted Kith the -synucieinopath , PD, ALS, LBD or AD if in step iii) the leukocytes are determined to have increased activation after contact with the epitope peptide, and identifying the subject as not at risk of developing, or as not afflicted with the ot^'~ synaclsinopathy, F-£y ALS, LBD or AD if in step iii) the leukocytes are determined to not have increased activation after contact with the epitope peptide, or b)

1) obtaining leukocytes from the subject;

11} separating the leukocytes into 2 or more pools of leukocytes and contacting each pool with an epitope peptide, wherei each pool- is contacted with a different epitope;

iii) determi ing whether each pool has increased activation after contact with the epitope peptide; and

iv) identifying the subject as at risk of developing, or as afflicted with the s-synucieinopathy, Tauopathy, PD, ALS , LBD, or AD if and only if in step iii} 1 or more pools is determined to have increased activation after contact with the epitope peptide.

The present invention also provides a method for assessing whether an of-synucieinopathy, a Tauopathy, Parkinson's disease (PD) , amyotrophic lateral sclerosis (ALS) , Lewy Body dementia {LBD} , or Alzheimer's disease (AD) has progressed or is developing in a subject afflicted with or who has been identified as being at risk of developing the σ-synucleincpafhy, PD, ALS , LBD or AD comprising

a) performing each of the following steps 1} to iii) :

i) obtaining leukocytes frois the subject;

ii) contacting the leukocytes with an epitope peptide that was previously identified to increase activation of the leukocytes; and

iii) determining the level of activation of the leukocytes after contact with the epitope peptide at a first and a second point in ti;ne, and then

iv) concluding that the o-synucleinopathy, PD, ALS, LBD or AD has progressed or is developing in the subject if the leukocytes are determined to be more activated in step iiij performed at the second point in time compared to the level of activation in step iii} performed at the first point in time, or

b) performing each of the following steps 1} to iii) :

i) obtaining leukocytes from the subject; iii separating the leukocytes into two or more pools of leukocytes and contacting each pool with an epitope peptide, wherein eac pool- is contacted, with a different epitope;

iii) determining whether each pool has increased, activation after contact with the epitope peptide at a first and a second point in time, and then

concluding that the o-synueieinopathy, PD, ALS, LBD or AD has progressed or is developing in the subject if more pools of leukocytes are determined to he activated in step iii) perforated at the second point in time compared to the number of pools that are determined to be activated in step iii) performed at the first point in time.

The present invention also provides methods for assessing whether a subject afflicted -with an o-synueieinopathy, a Tauopathy, Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) , Lewy Body dementia (LBD) , or Alzheimer's disease {M» is likely to benefit frois a therapy, wherein the therapy is directed to leukocytes that are activated by an epitope peptide, the method comprising

a)

i) obtaining leukocytes from the subject?

ii contacting the leukocytes with the epitope peptide;

iii) determi ing whether the leukocytes have increased activation after contact with the epitope peptide; and

iv) identifying the subject as likely to benefit from the therapy if in step iii) the leukocytes are determined to have increased activation after contact with the epitope peptide, and identifying the subject as unlikely to benefit from the therapy if in step iii) the leukocytes are determined to not have increased activation after contact with the epitope peptide, or

b)

i) obtaining leukocytes from the subject?

ii) contacting the leukocytes with the epitope peptide;

iii) determining whether the leukocytes have increased activation after contact with the epitope peptide; and 2.0 iv¾ identifying the subject as having benefited, from the therapy if in step iii) if the lsukocyt.es are determined to have increased, activation after contact, with the epitope peptide, and identifying the subject as not having benefitted frosn the therapy if in step iii) the ieuhocytes are determined to not have increased activation after contact with the epitope peptide.

The present invention also provides methods for assessing whether a subject afflicted with a disease or condition involving an inflammatory response or related to nflammation, or a neurodegenerative disease or disorder is likely to benefit or has benefitted from a therapy, wherein the therapy comprises administration of an effective amount, of a τ ceil, receptor for a particular antigen; HC complex, the met od comprising: a) (i) obtaining leukocytes from the subject;

(ii) contacting the leukocytes with the antigen bound to an MHC molecule;

(iii) determining whether the leukocytes have increased activation after contact with the antigen bound to an MHC molecule; and (iv) identifying the subject as likely to benefit froiR the therapy if in step (iii) the leukocytes are determined to have increased activation after contact with the antigen bound to an MHC molecule, and identifying the subject as unlikely to benefit from the therapy if in step (iii) the leukocytes are determined to not have increased activation after contact with the antigen bound to an MHC molecule; or b)

(i) obtaining leukocytes from the subject?

(ii contacting the ieuhocytes with the antigen bound to an MHC molecule; II

<iii) deter ining whether the leukocytes have increased activation after contact with the antigen bound to an MHC molecule; and

(iv) identifying the subject as having benefited from the therapy if in step siii) the leukocytes are determined to have increased activation after contact with the antigen bound to an MHC molecule, and identifying the subject as not having benefitted from the therapy if in step (iii) the leukocytes are determined, to not have increased activation after contact with the antigen bound to an A■ H c molecule .

The present invention also provides methods for treating a subject afflicted with an of-synucleinopathy, a Tauopathy, Parkinson' s disease (PDj, amyotrophic lateral sclerosis ALS , Lewy Body dementia (LED), or Alzheimer's disease (AD) comprising

a) administering to the subject a compound that is approved for use in treating subjects afflicted with the a- synueXeinopathy _f PD, ALS, LBD or AD, wherein the subject has been diagnosed or confirmed to be afflicted with a~ synudeinopathy, PD, ADS, LBD or AD;

b) diagnosing or confirming the subject to be afflicted with the a~synucieinopathy,. PD,. ALS, LBD or AD according to the method, and administering to the subject a compound that is approved for use in treating subjects afflicted -with cf~ synucleinopathy, PD, ALS , LBD or AD;

c) administering to the subject a therapy that is directed to leukocytes that are activated by an epitope peptide, wherein leukocytes of the subject have been determined to have increased activation after contact with the epitope peptide; d) administering an ^immunosuppressant therapy to the subject, wherein the subject has been identified as being likely to benefit therefrom by the methods; or

e) administering an ija unosuppressant therapy to the subject, wherein the subject has been identified as being likely to benefit from a therapy directed to leukocytes that are activated by an epitope peptide according to the rtiethods .

The present invention also provides methods for assessing whether leukocytes of a subject afflicted -with an fi-synucleinopathy, a Tenopathy, Parkinson's disease (PD) _t amyotrophic lateral sclerosis (ALS) , Lewy Body dementia (LBD) , or Alzheimer's disease {AD) are activated by an epitope peptide _t comprising

i) obtaining leukocytes frois the subject;

ii) contacting the leukocytes with the epitope peptide;

ill) determining whether the ieuhocytes have increased activation after contact with the epitope peptide; and

iv¾ identifying the leukocytes of the subject as activated by the epitope peptide if in step ill) the leukocytes are determined to have increased activation after contact with the epitope peptide, and identifying the leukocytes of the subject as not activated by the epitope peptide if in step iii) the .1ex5kocyt.es are determined to not have increased activation after contact with the epitope peptide, wherein

a, the epitope peptides is represented by an amino acid sequence selected from the group of Tan derived sequences represented by SEQ ID MO: i-bv or 240-376,

h. wherein the epitope peptide is represented by the amino acid sequence selected from the group of a~synuciein derived sequences GKTKEGvLYVGSK K (SEQ ID NO; 487} _f KTKEGVLYYG5 KE {SEQ ID NO: 488) , MPVDE-DNE&YEMPSE {SEQ ID ®Q: 89), DNEAYEMPSSEGYQD (SEQ ID NO: 490), EMPSEEGYQDYEPEA (SEQ ID SO: 491},· SEEGYQDYEPEA (SEQ ID HO; 492} , GVLYVGSKTK {SEQ ID MO: 493), VLYVGS T (SEQ ID NO: 494} _f or vLYVGSK KK (SEQ ID NO: 495), or.

c, wherein the epitope peptide is represented by the amino acid sequence selected from the group of TDP43 derived sequences represented by SEQ ID NO: 56-239, The present invention also provides methods for assessing whether a test compound comprises an epitope peptide to which leukocytes of a subject suffering from a neurological disorder are responsive comprising

i) obtaining leukocytes from the subject;

it) contacting the leukocytes with the test compound? iii) determining whether the leukocytes has increased activation after contact with the test compound; and iv) identifying the test compound as comprising an epitope peptide to which the leukocytes are responsive if in step iii) the leukocytes are determined to have increased activation after contact with the test compound, and identifying the test compound as not comprising an epitope to which the leukocytes are responsive if in step iii) the leukocytes are determined to not have increased activatio after contact with the test compound, wherein a. the epitope peptides is represented by an amino acid sequence selected from the group of Tan derived sequences represented by SEQ ID HO : 1-55 or 240-376,

b. wherein the epitope peptide is represented by the amino acid sequence selected from the group of or-synuciein derived sequences GKTKEGVLYYGSKTK (SEQ ID NO: 48?}, K KSGVLYvGS TKE (SEQ ID HO: 488), MPVDPDNSAYE PSS { SEQ ID NO; 489} , DNEAYEMPSEEGYQD (ESQ IB NO: 490), EMPSSEGYQDYEPEA (SEQ ID NO; 491), SSEGYODYSPEA {SEQ ID NO : 492), GVLYVGSKfK ⁽SEQ ID HO : 493), VLYVGSKTK (SEQ ID SO: 494) , Or YLYVGS TKK (SEQ ID UGx 495),■ or.

c. wherein the epitope peptide is represented by the amino acid sequence selected from the group of TDP43 derived sequences represented by SEQ ID HO: 56-239.

The present invention also provides for compounds for treating an «~ synucleinopathy, a Tenopathy, Parkinson's disease (PD) , amyotrophic lateral sclerosis (ALS) , Lewy Body dementia (LBD), or Alzheimer's disease (AD) , comprising i) a major bistocompatibility complex (MHC) Tetramer having four HC molecules, wherein eac MHC molecule is associated with an epitope peptide, and ii) a toxin, wherein a. the epitope peptides is represented by an amino acid sequence selected from the group of Tax- derived sequences represented by SEQ ID NO; 1™55 or 240-376,

b. wherein the epitope peptide is represented by the amino aoid sequence selected from the group of a-synuclein derived sequences GKT SGVLYVGSKT (SEQ ID NO: 487}, ETKSGVLYVGSKTKE (SEQ ID O I 488) , PVDPDKEAYE¾PSE (SEQ ID NO; 489), DNEAYEMPSSEGYQD {SEQ ID NO: 490), EMDSEEGYQDYEPSA <SEQ ID NO : 491} _f SEEGYQDYEPEA (SEQ ID SO: 492} _f GVLYVGSKTK (SEQ ID NO; 493), VLYVGSETK (SEQ ID HO : 494), or VLYVGSKT K (SEQ ID NO : 495), or,

c. wherein the epitope peptide is represented by the amino aoid sequence selected from the group of TBP43 derived sequences represented by SEQ ID HO: 56-239,

The present invention also provides processes for assessing whether a subject is at risk of developing an ~synucleίnopathy, a Tenopathy, Parkinson's disease (PD) , amyotrophic lateral sclerosis (ALS), Le y Body dementia {LBD}, or Alzheimer's disease (AD), which involves an array of testing, the improvement comprising including in the array of testing the steps of:

a)

i) obtaining leukocytes from the subject;

ii) contacting the leukocytes with an epitope peptide;

iii} determining whether the leukocytes have increased activation after contact with the epitope peptide; and iv) identi tying the subject as at risk of developing et~ synucieinopathy, PD, ALS, LBD or AD if in step iii) the leukocytes are determined to have increased activation after contact with the epitope peptide, and identifying the subject as not at risk of developing the cf~ syrmcleinopathy, PD, ALS , LBD or AD if in step iii) the leukocytes are determined, to not have increased activation after contact with t e epitope peptide, wherein

a. the epitope peptides is represented tay an amino acid sequence seiected from the group of Tax- derived sequences represented by SEQ ID KiO: 1.-55 or 240-376,

b. wherein the epitope peptide is represented by the amino acid sequence selected from the group of -synuciein derived sequences GKTKEGvLYVGSKTE {SEQ ID NO: 487), KTEE YLYVGS E (SEQ IB O: 48S) , PVDPDNSAΥΈΜΡ3E (SEQ ID NO: 489) , DMEAYE¾PSESGY^"QD (SEQ ID HO: 490) , EMPSSEGYQDYEPSA (SEQ ID NO: 491), SEEGYQDYEPEA I SEQ ID HO; 492), GVLYVGSKTK (SEQ ID NO: 493), YLYVGSKTK (SEQ 10 SO: 494) , or VLYVGSKTEK (SEQ ID NO : 495) , or.

c. wherei the epitope peptide is represented by the atiioo acid sequence seiected from the group of TDP 3 derived sequences represented by SEQ ID NO; 56-239

h i

i) obtaining leukocytes from the subject;

ii) separating the leukocytes into 2 or more pools of leukocytes and contacting each pool with an epitope peptide, wherein each pool is contacted with a different epitope;

iii) determining whether each pool has increased activation after contact with the epitope peptide; and

iv) identifying the subiect as at risk of developing the cf~ syn cleinopathy, PD, ALS, LBD or ¾D if in step iii) 1 or more pools is determined to have increased activation after contact with the epitope peptide, wherein a. the epitope peptides is represented, by an amino acid sequence selected from the group of Tau derived sequences represented by SEQ ID NO; 1-55 or 240-376, b. wherein the epitope peptide is represented by the amino acid sequence selected from the group of a~synuclein derived sequences GKTKEGVLYYGSKTK (SEQ ID NO; 4S7) , T SGVLYVGSKT S (SEQ ID NO: 488), MFVDPD SAYE PSS {SEQ ID NO; 489} , DNSA^'fEMPSEEGYQD (SEQ ID SiO: 490) , E¾PSEH!GYQDYEPEA

(SEQ ∑D NO: 491), SEEGYQDYEPEA {SEQ ID MO: 492), GVLYVGSKTK {SEQ ID NO: 493} , YLYVGSKTK (SEQ ID NO; 494} , or VLYVGS ΪΚΚ

(SEQ ID HO : 495} , or c. wherein the epitope peptide is represented by the amino acid sequence selected from the group of TDP 3 derived sequences represented by SEQ D SO 56-239.

The present invent ion also provides processes for diagnosing or confirming whether a subject is afflicted "with an o-synucleinopathy, a auopathy, Parkinson's disease (PD) , amyotrophic lateral sclerosis (ALS) , Lewy Body demen ia {LBD}, or Alz e mer's disease (AD), which involves an array of testing, the improvement comprising including in the array of testing the steps of:

a)

i) obtaining leukocytes from the subject;

ii} separating the leukocytes into 1 or more pools of leukocytes and contacting each pool with an epitope peptide, wherein each pool is contacted with a different epitope peptide;

iv) identifying the subject as afflicted with the cf~ synucieiftopathy, PD, ALS, LBD or AD if and only if in step iii) 1 or more pools is determined to have increased activation after contact with an epitope peptide, or bp

i) obtaining leukocytes from the subject; 1? χ separating the leukocytes into 1 or sore pools of leukocytes and contacting each pooi with an epitope peptide, wherein each pool is contacted with a different epitope peptide;

xi} determining whether each pooi has increased activation after contact with the epitope peptide; and

v) identifying the subject as afflicted with the et~ synucieinopathy, PD, ALS , LBD or AD if and only if in step iii) 1 or more pools is determined to have increased activation after contact with an epitope peptide, wherein a. the epitope peptides is represented by an amino acid sequence seiected frois the group of Tau derived sequences represented by SEQ ID HO: 1-55 or 240-376, b. wherein the epitope peptide is represented by the .amino acid sequence selected front the group of a- synuciein derived sequences GKTKBGVLYVGSKTK (SEQ ID NOi 487) , K KSGVLYvGSKT S (SEQ ID NO: 488) , PVDPDNSA EMPSE (SEQ ID HO: 489} _f DNEAYEMPSESGYQD (SEQ ID SO: 490) , E PSEEGYQDYEPEA (SEQ ID NO; 491} , SEEGYQDYEPEA (SEQ ID HO; 492), GVLYVGSKTK (SEQ ID NO : 493} , VLYVGSKT (SEQ ID NO; 494), or VLYvGS TE (SEQ ID NO; 495} _t or.

c. wherein the epitope peptide is represented by the amino aoid sequence seiected from the group of TDP43 derived sequences represented by SEQ ID NO; 56-239.

The present invention also provides for pharmaceutical compositions or treating an a-synucleinopat , a auopathy, Parkinson' s disease (PD> , amyotrophic lateral sclerosis {ADS} , Lewy Body dementia (LBD) , or Alzheimer's disease {AD) , comprising a protein comprising n amino acid sequence selected from the group of

a. the epitope peptides is represented by an amino acid sequence selected from the group of au derived sequences represented by SEQ ID HO: 1-55 or 240-376,· b. wherein the epitope peptide is represented by the amino acid sequence selected from the group of et~ synuciein derived sequences GKTEEGVLYVGSKTK (SEQ ID MO; 487), KTKEGVLYVGSKTKE (SEQ ∑D HO; 488) , MFVDFDNEAYEMPSE (SEQ ID ®Qx 489), DNEAYE PSEEGYQD (SEQ ID MO: 490}, E PSEEGYQDYEPE& (SEQ ID HO; 491), SEEG^'fQDYEFEA (SEQ ID NO: 492} , GVLYVGSKTK ( SEQ ID SO: 493), VLYVGSKTK (SEQ i!) HO: 494} , or VLYVGS T K (ESQ ID NO: 495), or,

c. wherein the epitope peptide is represented by the amino acid sequence selected from the group of TDP 3 derived sequences represented by SEQ IB HO: 56-239, and ii} a pharmaceutically acceptable carrier.

The present invention also provides a method comprising:

a. providing a biological sample f om a subject;

b. processing the biological sample to determine presence of a T cell receptor TCR specific to a peptide, wherein the peptide is a fragment from a protein associated with said neurodegenerative disease.

The present invention also provides a method comprising:

a) providing a biological sample from a subject;

b) processing the biological sample to determine presence of a human leukocyte antigen (HLA) capable of presenting a peptide, wherein the peptide is a fr gment from a protein associated with said ne rodegenerative disease; and

c) processing tl-e biological sample to determine resence of a cell receptor (TCR} specific to said peptide,

As embodied and broadly described herein, the present disclosure relates to a method comprising: providing a biological sam le iron a subject; processing the biological sam le to determine presence of a τ ceil receptor (TCR) specific to a peptide, wherein the peptide is a fragment f om a protein having an aberrant protein expression and/or aberrant protein function and/or aberrant protein nacrostructure in a patient having a neurodegenerative; disease.

As embodied and broadly described herein, the present disclosure relates to a method comprising; providing a biological sample from a subject; processing the biological sample to determine presence of a human leukocyte antigen (HLA) capable of presenting a peptide, wherein the peptide is a fragment f om a protein having an aberrant protein expression and/or aberrant protein function and./or aberrant protein maerostrueture in a patient having a neurodegenerative disease; and processing the biological sample to determine presence of a τ cell receptor {TCR) specific to said peptide.

In one embodiment, the peptide is a fragment from a protein that forms aggregates in a patient having the neurodegenerative disease.

As embodied and. broadly described, herein, the present disclosure relates to a system for processing biological data, comprising; one or more processors; and one or more RieiRcri s coxspied to the one or more processors, The one or more memories are configured to provide the one or mors; processors with instructions which when executed cause the one or more processors to receive first and second biological data elements for an individual from a biological data source_f wherein the first biological data element comprises data pertaining to the individual' s human leukocyte antigen (BLA) typing and the second, biological data element comprises data pertaining to the individual's T ceil receptor {TOR} repertoire. Further, the one or more memories are configured to provide the one or mor processors with instructions which when executed cause the one or more processors to merge the f rst and second biological. data elements from the biological data source to obtain a set of merged biological data associated with the individual, including to identify data in the first and second biological data elements that indicates a reciprocity, the identified data corresponding to a reciprocal, presence of an HXA typing value in the first biological data element and of a TCR repertoire value in the second biological data element; compare the identified data with at least one of an element of BLA typing values and TCR repertoire values stored on the one or more memories, said values stored on the one or mors; memories being associated with reference individuals; and determine a likelihood or predisposition score based on at least the identified data and on the comparison. Further, the one or more memories are configured to provide the one or more processors with instructions «hich, when executed, cause the one or mors; processors to display the likel hood or predisposition score in a graphical user interface (GUI) .

in one non-limiting embodiment, the neurodegenerative diseases may include at least one of alpha~synuciei.nopa.thy, Parkinson's disease (PD) , Lewy Body dementia (LSD), and Alz eimer' s disease (AD).

Ail features of exemplary embodiments which are described in this disclosure and are not mutually exclusive can be combined with one another. Elements cf one embodiment can be utilised in the other embodiments without further mention. Other aspects and features of the present invention will become apparent to those ordinarily skilled in the art upon review of the following description of specific embodiments in conjunction with the accompanying Figures, ®£ Description of the D i

Fig, X: Tan-specific responses for Parkinson'^' s Disease donors as compared to healthy control, donors for each of the HC Young (donors under 35 years old) and HC Age-Matched (donors above 50 years old) cohorts.

Fig, 2A: Analysis of response magnitude per donor for each of the Parkinson's Disease, HC Young {HC<35} and HC Age-Matched (BC>5G) cohorts. Response magnitude for IFN~y IFNg), IL-5 and the um of both cytokine is shown.

Fig, 2B: Analysis of response magnitude for each individual peptide for each of the Parkinson's Disease, HC Young (BC<35) and HC Age-Hatched (BC>5G) cohorts. T e responses observed in each donor against each individual peptide are plotted for IFN-y IFNg) , IL-5 and the sum of both cytokines.

Fig, 3&: Overall response as plotted against age. Overall responses are not correlated with age in either controls or PD patients.

Fig, 3B; Total reactivity as a function of time since onset of symptoms, Fig, 3C: Intercellular Cytokine Staining analysis of cytokine response for each of the Parkinson's Disease, HC Young (HC<35) and HC Age-Matched (BC>50) cohorts.

Fig, 3D: ELISPOT analysis of cytokine response for each of the Parkinson'^' s Disease, HC Young (HC<35) and HC Age-Matched (HO50) cohorts,

Fig, 4&: Breadth of response per donor. The u ber of epitopes responded to per donor is plotted, for each of the Parkinson's Disease, HC Young <HC<35> and HC Age-Matched (HO50) cohorts.

Fig, 4B; Magnitude of response per epitope per donor. The magnitude of response per epitope per donor is plotted for each of the Parkinson' s Disease, HC Young (HC<35) and HC Age-Hatched (HO50) cohorts.

Fig, 5; Tau-specific response as compared to α-syn specific response, Tau-specifio cytenkine response was plotted in comparison to a-syn specific response. Fig, 6&: et-Syn autoiHtmune responses are directed against two regions. Sequence of ot-syn. Antigenic regions are highlighted with dashed lines with amino acids ¥39 and 3129 in bold. Fig, 68: et-Syn autoirrtirrune responses are directed against two regions, Magnitude of IFMy responses expressed as (SFC/ 10^s PBMC) per peptide/ a ticipant combination. Left panels; response to ail overlapping native ¾-syn 15.mer peptides in PD (n∞733) and Control. {n∞3?2) . Right panels indicate responses against specific XSisers. Grey shading indicates antigenic region containing Y30, As many participants showed no response, ma y points are at the limit of resolution (100 SFC) -

Fig, fi : a-Syn autoimmune responses are directed against two regions, Magnitude of IL~5 responses expressed as {SFC/10^s PBMC) per pe tide/particίpant combination. Left panels; response to all- overlapping native ζί-syn ISraer peptides in PD <n∞733) and Control {n∞372} , Right panels indicate responses against specific ISmers, Grey shading indicates antigenic region containing As many participants showed no response, ma points are at the limit of resolution (100 SFC) .

Fig, SB: a-Syn auto.immune responses are directed against two regions. Magnitude of total {1FNy & IL~5) response expressed as (SFC/ 10^s PBMC) per peptide/participanf combination. Left panels; response to ail- overlapping native ζϊ-syn ISraer peptides in PD <n∞733) and Control (n™372) . Right panels indicate responses against specific ISmers, Grey shading indicates antigenic region containing Y39. As many participants showed no response, many points are at the limit of resolution (100 SFC) .

Fig, fil: a-Syn autoimmune responses are directed against two regions, Magnitude of ΣΕ¾γ responses. Left panels; responses to all native and phosphorylated S129 a-syn iorrter peptides in PD (n=150) and Control {n∞72) . Right panels; responses against specific 8129 peptides. Closed, circles, PD {n~lS, indicated by *, ail other n~25) ; open circles, Control (n^:«I2 participants). Two-tailed Mann Whitney, ns, not significant. As isany participants snowed no response, many points are at the limit of resolution (100 SFC) ,

Fi . 6F; ci-Syn aufcinrntune responses are directed against two regions, Magnitude of IL-5 responses. Left panels; responses to all native and phospncrylated S129 o:™syn iSster peptides in PD {n—150) and Control {n=72) . Right panels; responses against specific S129 peptides. Closed. Circles, PB {n^:«19, indicated, by *, all other n^»25) ; open circles, Control. {n∞l2 participants) . Two-tailed Mann Whitney, ns, not significant. As many participants showed no response, many points are at the limit of resolution (100 SFC) ,

Fig, &»i a-Syn antoiramune responses are directed against two regions. Magnitude of total < IFNy & IL-5) response. Left panels; responses to ail native and phcsphorylated S123 o:-syn ISster peptides in PD (n^:«i50; and Control n∞7£) . Right panels; responses against specific S12S peptides. Closed circles, PD (n™19, indicated by *, ail. other n∞25) ; open circles, Control (n™12 participants) . Two-tailed Mann yihitney, ns, not. significant. As .many participants showed no response, many points are at the limit of resolution (100 SFC) .

Fig, 7¾; T ceil reactivity against a~syn peptides {-wild type and posttransiationaliy modified) . Magnitc.de of responses, expressed as the total magnitude (SFC/10* PEMC of IFNy response per peptide/participant co bination . Responses against any o:-syn 1 ,¾aer peptide spanning SI.23 and Y39, ^wany peptide", PD (x\~2Q9) , Control {n~132), and responses against individual ¾-syn ISster peptides spanning SI.29 and Y39, Each dot represents a peptide/ participant combination. Closed circles, PD open circles, Control. {n»12) . Two-tailed Mann Whitney, *, p<0-05, **, p<0.01, ***, p O.OOi.

Fig, 7B; T cell reactivity against o:~syn peptides (wild type and posttransiationali modified) . Magnitude of responses, expressed as the total magnitude SFC/10^¾ PBMCj of IL-5 response per peptide/participant contbination . Responses against any a~syn 1 outer peptide spanning 3129 and Y39, "any peptide", PD (n^∞209) , Control in~132} , and responses against individual x-syn ISm.er peptides spanning S129 and Y39, Each dot represents a peptide/ participant combination. Closed circles, PD ^• :v--l 9} ; o en circles, Control ίη=^«1.2) . Two-tailed Mann Whitney, ^' p 0.05, **, p<0.0X, ***, p<0.00X.

Fig, 7C; T ceil reactivity against a~syn peptides {-wild type and posttransiationaliy modified) . Magn tude of responses, expressed as the total mag itude (SFC/IO PBMC) of total (IFNy and IL-5 com ined response per peptide/participant combinat ion. Responses against any a-syn ISm.er peptide spanning 3129 and Y39, ^any peptide",. PD (n=209) , Control (n^:«132) , and responses against individual cx-syn 15.mer peptides spanning SI 29 and Y39. Eaoh dot represents a peptide/ participant cornbination. Closed circles, PD fn=19} ? open circles, Control {n~12} . Two-tailed Mann Whitney, *, p<0,05, **, p<0,01, **% p<0.001.

Fig, 8A; Reactivity to native and modified a-syn peptides in PD patients. Magnitude of IFNy responses against native and modified a-syn ISiiser 3129 and Y39 region peptides as (SFC/10⁶ PBMC), Each point represents a peptide/participant combination. Closed circles, PD {n∞4G3 peptide/participant combinations "any peptide", KTKEGVLYVGSKTKE n^63 participants (^A> , modified peptides marked with * are tested in 19 participants, unmodified peptides are tested in n-41} ; open circles, control {n^∞228 any peptide, ^Λ n^∞36, *n^∞12 and unmodi ied peptides rt~24) ,

Fig, 8B: Reactivity to native and modified a~syn peptides in PD patients. Magnitude of IL-5 responses against native and modified -syn 15.mer S129 and Y39 region peptides as (SEC/iO* PBHC) . Each point represents a peptide/participant combination. Closed. circles, PD (n=403 pe tide/part icipant combinations "any peptide", KTKEGVLYVGSKTKE n™63 participants {"^'} , modif ed peptides marted with * are tested in IS participants, unmodified, peptides are tested in n^» 1. ) open circles, control in=228 any peptide, ^Λ n~36, *n™12 and -unmodified peptides n∞2 5. Fig, 8C: Reactivity to native and modified et~syn peptides in PD patients, Magnitude of total ( FHy & IL-5 combined) responses against native and modified o:~syn lorrter S129 and Y39 region peptides as <SFC/10* PB C) . Each point represents a peptide/participant combination. Closed circles, PD {n=403 peptide/participant coK&inations "any peptide"; TKEGVLYVGSKTKE n^:«63 participants ( ) , m di ied peptides marked with * are tested in 19 participants, unmodified peptides are tested in _v=41 } t open circles, control (n^:™228 any peptide, ^Λ ·ν·- 3€ , *n=<12 and unmodified peptides n™24j , Fig, 8D; Reactivity to native and modified ¾™syn peptides in PD patients. Com ined IL-5 and IFNy responses against individual native and modified o:-syn peptides by PD, Black points, IF^!y responses; red points, IL-5 responses. Two-tailed Mann Whitney, *, p<0.O5, **, p<0.0i, ***, p<0.001. As many participants showed no response, many points are at the limit of resolution (100 SFC) .

Fig, 9>A: Characte ization of oo-syn specific responses in PD, Gating strategy, T ceils were gated based on CD3 expression. Boolean gating was used to define cytckine-p educing cells expressing CB4 and/or CDS.

Fig, 9 : Characterisation of a-syn specific responses in PD. Percent total cytokine detected from CD3÷ T ceils in response to ce~syn peptides. Each point represents one participant (n™9) ; median ± interquartile range is indicated. Dotted line indicates 0,05% cut-off for specific cytokine production by CD3-f- T cells.

Fi . 9C: Characterization of o:-syn specific responses in PD, Percentage of total cytokines produced for IFNy, IL~4, IL-I0, and IL-17, Each point represents one participant that exceeded the cut-off (n™6) , median ± interquartile range is indicated.

Fig, 9Di Characterisation of -syn specific responses in PD, Percentage of total cytokines produced by CD4÷, CD8÷, CD4-CD8-, or CD4+CD8+ T ceils. Each point represents one participant (n™6) , median ± interquartile range is indicated. Figure 10: Specific ceil reactivity against native or fibrilized a- syn, Magnitude of responses _f expressed as t e average spots per 10^s DBMC, Of response per protein/PD participant or peptide PD participant combination {n-12 PD participants, each represented by a different symbol) . The lines connect discrete values from each individnal participant and are present to provide a means to compare responses within and between individuals. The difference between response to unstimulated compared to peptides, the native a~syn and PFF groups is significant by the ilcoxon one-tailed test (values are shown in the figure) . Ho significant difference (Wilcoxon two-tailed test) in response to PFF and native protein was apparent in this relatively smal 1 sarfi ie . Fig. HLA-DR surface expression across DRB1 *15 ; 01-f- or DRB1*15:01-

DD and HC participants. Gating strategy tor FACS analysis. After eliminating non-lymphocytes and doublet cells by forward- and side- scatter, ceils were gated based on HLA-DR expression, Fig, X1B: HLA-DR surface expression across DRBX*X5:0X÷ or DRBl*X5iGX~ PD and HC participants. HLA-DR and CD3 expression of participant ceils {black; HLA-DR antibody, red; isotype control) of PD patients that carry in- 3 · DRBX*i5;01 allele, Fig, 11C: HLA-DR surface expression across DRBi*15:Gii or DRB1*15:01- PD and HC participants. HLA-DR and CD3 expression of participant cells (black; HLA-DR antibody, red; isotype control) of PD patients that do not carry (n-5) DEBl*15tOX allele, Fig. ilD; HLA-DR surface expression across DRBl*i5;01÷ or DRBl * 15:01- DD and HC participants. HLA-DR and CD3 expression of participant cells (black; HLA-DR antibody, red; isotype control) of HC that carry (n-3) DRB1*15:01 allele Fig, 111: HLA-DR surface expression across DRBX*X5:0X÷ or DRBl*X5iGX~

PD and EC part cipants. HLA-DR and CD3 expression of participant ceils (black; HLA-DR antibody, red; is ype control) of HC that do not carry in- 3 · DRBi*I5;01 allele.

Fig, IIP ; HLA-DR surface expression across DRBi*15:GM or DRB1*15:01- PD and HC participants. 721,221 cells arc used as controls that do not express HLA class II. Fig, 11G : HLA- R. surface expression across DRB1*15 s Ql-f or DRB1*15:01- PD and HC participants. R 3 ceils are used as controls that do express HLA class II.

Fig. 11B: HLA-DR surface expression across DBBl*15tOX* or DBB1*15;01~ PD and HC participants. Mean fluorescent intensities (MFI) ± standard deviations of HLADR expression for each participant cohort.

Fig. ill; HLA-DR surface expression across DBBl*15iOX* or DRB1*15;01~ PD and HC participants. Percentage of living cells that express HLA-DR, ise n ± SD.

Fig. X2Ac HLA class I surface expression across BRBX*X5: 01* or DRB1* 15:01- PD and HC participants. Gating strategy for «¾CS analysis. After eliminating non-lymphocytes and doublet ceils by forward- and side- scatter, cells were gated based on ELA-ABC expression.

Fig, 12B: HLA class I surface expression across DRBl*I5:01 or

DEBl*15iOX~ PD and HC participants. HLA-ABC and CD3 expression of participant cells (black: HLA-ABC antibody, red: isotype control) of PD patients that, carry <Λ~5 ) DRB1*I5:01 allele.

Fig, ISC: HLA class I surface expression across BRRl*X5;01÷ or DRBi*15:01~ PD and HC participants, HLA-ABC and CD3 expression of participant cells (black: HLA-ABC antibody, red: isotype control.) of P patients that do not carry (n^«5 ) DRBX*X5:0l allele. Pig, I2D: HLA class I surface expressio across DRBi*15;01÷ or DRB1*15:01~ H> and HC participants, HLA-ABC and CD3 expression of participant cells (black: HLA-ABC antibody, red: isotype control) of BC that carry (n-3 DRBl*15:0l allele,

Fig, 12E: HLA class I surface expression across BRBX*X5: 01* or

D B1* 15:01- PD and HC participants, HLA-ABC and CD3 expression of participant cells (black: HLA-ABC antibody, red; isotype control) of HC that do not carry l) Bi*15:01 allele.

Fig. 12F; HLA class I surface expression across DF.B1*15 : 014· or

DKB1*15:01 PD and BC participants, 721,221 cells are used as controls that do not express HLA class I.

Fig, 12Q HLA class I surface expression across DRBl*15i01* or

DKB1*15:01 PD and. BC participants, RM3 cells are used as controls that do express HLA class I . Fig, 12H: HLA class I surface expression across DRB1*1S : 01÷ or DRBi*^:15101- PD and HC participants. Mean fluorescent intensities ( FI ) ± standard deviations of HLAABC expression for each participant cohort,

Fig, 13K HLA association of ¥39 epitope and identi ication of A*1X;01 restricted 9-10aa length ¥39 epitopes. Overlapping but largely independent associations between DRSl*X5i01_/ DQSl*03t04 and A*11:0X for PD (13 participants) responding to the Y39 epitope.

Fig, 13B; H; A association of ¥39 epitope and identification of A*I1:01 restricted 9-10aa length Y39 epitopes. Magnitude of responses by PD {n=19) _f as (SFC/XG^S PBHC) of response per peptide/ participant combination to o:-syn 9-10mer peptides spanning the protein. In soste cases, response to overlapping peptides are confined, with additional residues of the longer peptide in parentheses, top panel, FMy; .middle, IL-5; bottom, total IFMy & IL~5 eorsibined) response. As many participants showed no T cell response, many points are at the limit of resolution (100 SFC) .

Fig. 13C: HLA association of Y39 epitope and identification of I : ⁽V; restricted 9-i0aa length Y39 epitopes. Magnitude of Total < IFNy & IL-5 combined) responses by control, participants (n>∞12) , as (SFC/10- P C) of response per peptide/ participant combination to «~syn 9-lGiue peptides spanning the protein, in some cases, response to overlapping peptides are combined, with additional residues of the longer peptide in parentheses. As an participants showed no cell response, a y points are at the limit of resolution (100 SF ,

Fig, 14A: Magnitude of IFKiy responses expressed as (SFC/ 10^s PBMC) per peptide/ a ticipant consfcination. Response to selected TDP 3 ISmer peptides by ALS patients and. healthy controls.

Fig, 14B: Magnitude of IL-5 responses expressed as (SFC/ 10^s PBMC) per peptide/participant consfcination. Response to selected TDP 3 ISmer peptides by ALS patients and. healtby controls.

Fig, I C: Magnitude of XL-10 responses expressed as {SFC/10⁶ PBMC) per peptide/participant consfcination. Response to selected TDP 3 X5mer peptides by ALS patients and. healtby controls. Fig, 14D: Magnitude of any cytokine responses expressed as ίSFC/10⁶ PBMCj per peptxde/participant combination. Response to selected TDP 3 XSmer peptides by ALS patients and. healtby controls.

Figure IS: High-level functional block diagram of a system for assessing a neurodegenerative disease patient in accordance with a specific example of implementation of the present invention;

Figure 16; Functional block diagram of an apparatus for generating neurodegenerative disease patient information suitable for use in the system depicted in figure 15 in accordance with a first specific example of im lementation of the present invention.

In the drawings, exemplary embod ments are illustrated by way of exampl . it is to be expressly understood that the descriptio and drawings are only for the purpose of illustrating certain embodiments and are an aid for understanding. They are not intended to be a definition of the limits of the invention .

Abbreviations

··syn , alpha synuciein; SB, Al sheime ' s disease; IM, Activation Induced Marker; MS, amyotrophic lateral sclerosis; p2m, beta 2 microglobulin; Bf brightfieid; BrdU, 5~brofiso~2~deoxyuridine; BS&, bovine seroalbumin? Conk, concananycin A; C &, chaperone-mediated autophagy; CMS, central nervous system; C Ls, cytotoxic T cells

CT L control; Dk, dopamine/dopaminerg c; D s, dendritic ceils; ELXS&, enzyme-linked immunosorbent assay; EXtXSPOT, enzyise~i inJced iHsarunos ot assay; GSE&, Gene Set Enrichment Analysis; HC, healthy control (s) ; hES, hum stem cells; HL&, human leukocyte antigen; XEBB, Insrome Epitope Database; XFH-y, interferon gaatrna; Xi-l^, nterleukin f~beta; XL-6, intsrieukin β; Integrated. Pathway Analysis? Q, knocked out; L€.< locus eoeruleus; L<3H, lateral geniculate nucleus; LPS, iipopoiysaecharide; M&P-2, microtubule associated protein~2; MEC, ajor histocompatibility complex; HC-X, major hίstocompatibility complex class I; MHC-XX, major histocompatibility complex ciass II; Mfci, spinal motor neurons; MEat^«*a^«*syn , mutated (A53T) alpha synuciein; HE, norepinephrine/norepinephrinergic; Hit.~o.~syn, nitrated alpha synuciein; MM, neurorfielanin; 0¥A_f ovalbumin ? PB C, peripheral blood mononuclear cells? PD Parkinson's disease; PET, positron emission tomography? PSP_r progressive supranuclear palsy; FM, post-tr nslationa1 modification; EA S,. Restriofcr Analysis Tool for Epitopes? SIM, standard error of the mean; SFC., spot-forming cells; SM, substantia nigra; CR, T cell receptor; TH, tyrosine hydroxylase? P8KS, Unified Parkinson's Disease Rating Scale; ¥¾h_f vehicle; ¥M, ventral midbrain; S, ventral tegmental area; WGCHA, Gene Co-expression Network Analysis. A detailed description of one or more embodiments of the invention is provided below along with accompanying figures that illustrate the principles of the invention. The invention is described in connection with such embodiments _? but the invention is not limited to any embodiment. The scope of the invention is limited only by the claims. Numerous specific details are set forth in the following description in order to provide a thorough understanding of the nvention. These details are provided for the purpose or non~ limiting exam les and the invention m y be practiced according to th claims without some or ail of these specific details. For the purpose of clarity, technical material that is known n the technical fields related to the invention has not been described in detail so that the invention is not unnecessarily obscured.

The present invention provides methods for assessing whether a subject is at risk of developing, or for diagnosing or confirming whether a subject is afflicted with an fi-synuc einopathy, a Tauopathy, Parkinson' s disease (PD) , amyotrophic lateral sclerosis A.LS } , Lewy Body dementia (LBD) , or Alzhe mer' s disease (AD) comprising

a)

1} obtaining leukocytes from the subject;

ii) contacting the leukocytes with an epitope peptide;

ii i ) determining whether the leukocytes have increased act vation after contact with the epitope peptide; and

iv) identifying the subject as at risk of developing, o as afflicted with the o~synucieinopathy, PD, AL3, LBD or AD if in step iii) the leukocytes are determined to have increased act vation after contact with the epitope peptide, and identifying the subject as not at risk of developing, or as not afflicted with the ot^'~ synucleinopathy, PD, A1S, LBD or AD if in step iii) the leukocytes are determined to not have increased activation after contact with the epitope peptide, or

b)

i) obtaining leukocytes frois the subject;

ii ) separating the leukocytes into 2 or more pools of leukocytes and contacting each pool with an epitope peptide, wherein each pool- is contacted with a different epitope;

iv) identifying the subject as at risk of developing, o as afflicted with the o-synucieinopathy, Tauopathy, PD, ALS , LBD, or AD if and only if in step iii) 1 or more poors is de ermined to have increased activation after contact with the epitope peptide.

The present invention also provides a method for assessing whether an a~synucieinopathy, a Tauopathy, Parkinson's disease (PD), amyotrophic Lateral sclerosis (ALS) , Lewy Body dementia {LBD), or Alzheimer's disease iM)} has progressed or is developing in a subject affixcted with or who has been identified as being at risk, of developing the or-synocieinopathy, PD, ALS, LBD or AD comprising

a) performing each of the following steps i) to iii) :

i) obtaining leukocytes from the subject?

iii) determining the level of activation of the leukocytes after contact with the epitope peptide at a first and a second point in time, and then

iv) concluding that the a~synucieinopathy, PD, ALS, LBD or AD has progressed or is developing in the subject if the leukocytes are determined to be more activated in step iii) performed at the second point in time compared to the level of activation in step iii) performed at the first point in time, or

b) performing each cf the following steps 1} to iii) :

x) obtaining leukocytes frois the subject;

ii) separating the leukocytes into two or more pools of leukocytes and contacting each pool with an epitope peptide, wherein each pool is contacted with a different epitope;

iii) determining whether each pool has increased activation after contact with the epitope peptide at a first and a second point in time, and then

concluding that the s-synucieinopathy, PD,. ALS, LBD or AD has progressed or is developing in the subject if more pools of leukocytes are determined to be activated in step iii) performed at the second point in time compared to the number of pools that are determined to be activated in step iii) performed at the first point in time. The present invention also provides me ods tor assessing whether a subject afflicted with an ™synucieinopathy, a Tauqpathy, Parkinson' s disease (PD) , amyotrophic lateral sclerosis (ALS ) , Lewy Body dementia (LBD) , or Aisheimer' s disease (AD) is likely to benefit from a therapy, wherein the therapy is directed to leukocytes that are activated by an epitope peptide, the method comprising

a)

1} obtaining leukocytes from the sub ect;

ii contacting the leukocytes with the epitope peptide;

iv) identifying the subject as likely to benefit f om the therapy if in step iii) the leukocytes are determined to have increased activation alter contact with the epitope peptide, and identifying the subject as unlikely to benefit from the therapy if in step iii) the leukocytes are determined to not have increased activation after contact with the epitope peptide, or

b)

1} obtaining leukocytes from the subject;

ii contacting the leukocytes with the epitope peptide;

iii) determining whether the leukocytes have increased activation after contact with the epitope peptide; and

iv) identifying the subject as having benefited from the therapy if in step iii) ii the leukocytes are determined to have increased activation after contact with the epitope peptide, and identifying the subject as not having beneiitted from the therapy if in step iii) the leukocytes are determined to not have increased activation after contact with the epitope peptide .

The present invention also provides methods for assessing whether a subject afflicted with a disease or condition involving an inflammator response or related to inflammation,, or a neurodegenerative disease or disorder is likely to benefit or has benefitted from a therapy, wherein the therapy comprises administration of an effective amount of a T ceii receptor for a particular antigen: RC complex, the method comprising: a)

(i) obtaining leukocytes from the subject?

(ii) contacting the leukocytes with the antigen hound to an MHC molecule;

(iii) determining whether the leukocytes have increased activation after contact with the antigen bound to an MHC molecule; and

< iv) identifying the subject as likely to benefit from the therapy if in step (iii) the leukocytes are determined to have increased activation after contact with the antigen bound to an MHC molecule, and identifying the subject as unlikely to benefit frois the therapy if in step (iii) the leukocytes are determined to not have increased activation after contact with the antigen bound to an MHC molecule; or b)

(i) obtaining leukocytes from the sub ct;

(ii) contacting the leukocytes with the antigen bound to an MRC molecule;

(iv) identifying the subject as having benefited from the therapy if in step iii) the leukocytes are determined to have increased activation after contact with the antigen bound to an MHC molecule, and identifying the subject as not having benefitted from the therapy if in step (ill) the leukocytes are determined to not have increased activation after contact with the antigen bound to an A■ H c molecule. In some embodiments, in step ii) the leukocytes are separated into 2,· 3, 4, 5, 6, 7, 8, 9, 10, 11-50 or more pools, and in step iv) the subject is identified as at risk of developing or as afflicted with the et~ synucleinopath , Tauopathy, PB_f AL , LBD or AD if and only if in step iii) 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11-50 or more pools is determined to have increased activation after contact with the epitcpe peptide. in some embodiments, the subject the s bject

a) is at least about 35, 40, 45, 50, 55, 60, 65, 70, 75 or SO years of age;

bj is less than about 35, 40, 45, 50, 55, 60, 65, 70, 75 or 80 years of age;

c) has a sym to that has preceded the onset of the et~ synucleinopathy, Tauopathy, PD, ALS, LBD or AD in subjects who have developed or-synucleinopathy, Ta.uopat.hy, PD, ALS, LBD or AD?

d) has a syntptom that has preceded the onset of the a- synudeinopathy, Tauopathy, PD, ALS, LBD or AD in subjects who have developed the o-synucXeinopatny, Tauopathy, PD, ALS , LBD or AD, wherein the symptom has preceded the onset of the -syniiicieinopatby, Tauopathy, PD, ALS, LBD or AD in the subjects by at least about 5, 10, 15, 20, 25, 30 or 5-30 yea s;

e) is afflicted with cognitive deciine_f constipation or orthostatic hypotension.

f) is afflicted with cognitive decline, and the cognitive decline is reduced spatial reasoning ability and/or reduced memory ability.

g) is afflicted with fasciculations or muscle twitches in the rm leg, shoulder, or tongue, muscle cramps, spasticity or tight and stiff muscles, muscle weakness affecting an arm, a leg, neck or diaphragm, slurred and nasal, speech, and/or difficulty chewing or swallowing; or

h) is afflicted with cognitive decline, and the cognitive decline is reduced language or decision-making. In some embodiments _f the subject is the subject to

a) be monitored store frequently for the a~syn.ucleinopa.thy,, Tauopathy, PD, AL3, LBD or AD; or

b) receive additional diagnostic testing for the ot^'~ synudeinopathy, fauopathy, PD, ALS, LBD or AD,

if the subject is identified as at risk of developing the a- synucleinopat y, fauopathy, PD, ADS, LBD or AD.

In some embodiments tbe presence of at least one huraan leukocyte antigen (BLA) allele, one cell receptor (TC ) allele, or one MAPT allele is determined in tbe subject.

In some e bodiments, tbe subject is identified as at risk of developing the ci-synucieirtcpathy, PD, ALS, LBD or AD or identified as afflicted with the a~syrmcleinopath , PD, ALS , LBD or AD if

a) the leukocytes are determined to have increased activation after contact with tbe epitope peptide, or 1 or more pools is determined to have increased activation after contact with the epitope peptide, and

bp the subject has at least one HLA allele.

In some embodiments, the subject has the BLA allele DRB5*01∑0X_r DRBI*15:0I, DQBi*03;04, A^"*ll;01, BRBi*09;01, DRBl*15, DRBi*04, DQBl *06, DRBX*0l:01, DRBX*04:O4, DRBl*07tGl, DRB1*11:04, DRB3*02:Q2, DQ *05:0l, DQBl*O3:0i, DQBI*03:02, DQB1*03:03, DQBI*04:02, D Bl.*15:0i/DQBi *06:02 or DEBl*04102 DQBX*03: 02. In a further embodiment, the subject has the HLA alleles D B5*0I:Oi, DB.BI*15:01, DQBI*03:04, and A*ll:Qi. in some arctaodiraants, the subject has tbe BLA allele DRBi 04 and the amino acid sequence is SEQ ID NO: IS, the subject has the HLA allele DQB1*03:03 and the amino acid sequence is SEQ ID NO: 31, the subject has the HLA allele DQAX*05:01 and the amino acid sequence is SEQ ID NO: 32, the subject has the HLA allele ^'*01 :01 and the amino acid sequence is SEQ mt 40, the subject has the BLA allele DRBi*04:04 and tbe amino acid sequence is SEQ ID HO; 49, the subject has tbe HLA allele DQB1*04:02 and the amino acid sequence is SSQ IB NO: 52, or tbe subject has the HL& allele DRB3*02t02 and the amino acid sequence is SEQ ID ¾0: 29. in some ersbodimersts the method assesses whether AD, ALS or PD is developing in a subject who has been identified as being at risk of developing AD, ALS or PD, or assesses whether a subject afflicted with AD, ALS or PD is likely to benefit iron a therapy.

The present invention also provides methods for treating a subject afflicted with an a~s nucleίnopathy, a Tenopathy, Parkinson's disease (PD) _f amyotrophic lateral sclerosis (ALS) , Lewy Body dementia (LBD) , or Alzheimer's disease (AD) comprising

a) administering to the subject a compound that is approved for use in treating subjects afflicted with the a- synucnleinopathy, PD, ALS, LED or AD, wherein the subject has been diagnosed or confirmed to be afflicted "with «~ synucleinopathy, PD, ALS, LBD or AD according to the methods; b) diagnosing or confirming the subject to be afflicted with the a-synucleinopathy, PD, ALS, LBD or AD according to the methods, and administering to the subject a compound that is approved for use in treating subjects afflicted with «- synuoieinopathy, PD, ALS, LBD or AD;

c) administering to the subject a therapy that is directed to leukocytes that are activated by an epitope peptide, wherein leukocytes of the subject have been determined to have increased activation after contact with the epitope peptide; d) administering an immunosu essant therapy to the subject, wherein the subject has been identified as being iiheiy to benefit therefrom by the methods; or

e) administering an immunosuppressant therapy to the subject, wherein the subject has been identified as being likely to benefit from a therapy directed to leukocytes that are activated by an epitope peptide according to the methods. in some embodiments, the therapy is tolerication therapy, and the toleriratxon therapy is specific for leukocytes that are activated by the epitope, preferably wherein administering the toieriration therapy comprises admi.nlstering to the subject the epitope peptide in an amount that is effective to reduce activation of leukocytes in the subject by the epitope peptide.

In some embodiments, the therapy comprises selectively killing the leukocytes that are activated by the epitope peptide in the subject, preferably wherein selectively killing the leukocytes that are activated by the epitope peptide in the subject comprises administering to the subject an effective amount of a compound comprising a major histocompatibility complex <MHC) Tetraiser and a toxin to the subject, wherein the HC Tet amer comprises the epitope peptide, in some embodiments, the im_nunosuppressant therapy com rises toierination therapy, selectively killing the leukocytes that are activated by an epitope peptide in the subject, or administering an effective amount of an immunosuppres ive compound to the subject, preferably wherein the immranosuppressive compound is a ealcineurin inhibitor, a compound that blocks a chemokine receptor that is expressed by a leukocyte, a glucocorticoid, a mTOR inhibitor, an an i-metabolic compound, a phosphodiesterase-5 inhibitor, an antibody, or a leukocyte function antigen~3 (LFA~3) /Fc fusion protein.

The present invention also provides methods for assessing whether leukocytes of a subject afflicted -with an fi-synucleinopathy, a Tauopathy,.

Parkinson! s disease (PO) _t amyotrophic lateral sclerosis (ALS), Lewy Body dementia (LBD) , or Alzheimer's disease {AD) are activated by an epitope peptide, comprising

i) obtaining leukocytes frois the subject;

ii) contacting the leukocytes with the epitope peptide;

iv) identifying the leukocytes of the subject as activated by the epitope peptide if in step iii) the leukocytes are determined to have increased activation after contact with the epitope peptide , and identifying the leukocytes of the subject as not activated by the epitope peptide if in step iii) the leukocytes are determined to not have increased activation after contact with the epitope peptide, wherein

a. the epitope peptides is represented by an amino acid sequence selected frost the group of T ¾ derived sequences represented by SEQ ID NO; 1-55 or 240-376,

to, wherein the epitope peptide is represented by the amino acid sequence selected f ΓΟΚ the group of α-synuclein derived sequences GKT SGVLYVGSKT (SEQ ID NO: 487}, ETKSGVLYVGSKTKE (SEQ ID O: 488) _t PVDPDKEAYE¾PSE (SEQ ID NO; 489), DNEAYEMPSEEGYQD (SEQ IB NO: 490), EMPSEEGYQDYEPEA (SEQ ID NO; 491), SSEGYODYSPEA {SEQ ID NO : 92}, GVLYVGSK K (SEQ ID HO : 493), VLY^'VGSK K (SEQ ID SO: 494} , Or VLYVGS T K (SEQ ID W : 495},· or

o. wherein the epitope peptide is represented by the amino acid sequence selected frojn the group of TDS? 3 derived sequences represented by SEQ ID NO: 56-239.

In an embodiment, the assessment is made as to whether the leukocytes of a subject afflicted with AD_r ALS or ΐ'Ό are activated toy the epitope peptide.

In further ernbod sient , the epitope peptide:

a) is or comprises part of a compound that is produced by neurons in subjects afflicted wit the a~synucleinopath , PD, ALS , LBD or AD;

to) comprises consecutive amino acids that are identical to a stretch of consecutive amino acids in a protein that is produced by the neurons;

c) comprises consecutive amino acids that are identical to a stretch of consecutive ami o acids in a Tax: mutant;

d) comprises about 16, at least 15, 5-50, 8-11, or 8—14 amino acids; e) is phosphorylated, acetyiatsd, nitrated, or dopamine modified;

t^") comprises a phosphorylated serine or a phosphorylated tyrosine;

g) comprises a phosphorylated serine or a phosphorylated tyrosine,, wherein the phospho yl ted ser ne or phosphorylated. tyrosine is within a stretch of consecutive amino acids that is identical to a stretch of consecutive amino acids comprising the serine at position 193, 202, 214, 262, 356, or 422 of au or the tyrosine at position 181, 205, 212, 231, or 262 of Tau.

h) is or comprises part of a compound that is produced by neurons in subjects afflicted Kith the a~syn.ucieinopa.thy, Pi), ALS, LSD or AD, wherein the neurons are in the ventral midbrain, the substantia nigra, the locus eoeruleus, or the ventral teg ental area;

i) is or comprises part of a compound that is produced by neurons in subjects afflicted with the et-symjcieinopathy, PD, ALS, LBD or AD, wherein the neurons are catecholamine neurons; j) comprises consecutive amino acids that are identical to a stretch of consecutive .amino acids in an a-syn mutant;

k) comprises consecutive amino acids that are identical to a stretch of consecutive amino acids in an o:~syn utant, wherein the a~syn mutant is an s-syn A53T or A3OP mutant;

1.) comprises a phosphorylated serine or a phosphorylated tyrosine, wherein the phosphorylated serine or phosphorylated tyrosine is within a stretch of consecutive amino acids that is identical to a stretch of consecutive amino acids comprising the serine at position 129 of o:~syn or the tyrosine at position 39 of c-syn; m) is or comprises part of a compound that is produced by neurons in subjects afflicted with the ALS, wherein the neurons are in the motor area; n) is or comprises part of a com ound that is produced by neurons in subjects afflicted with ALS, wherein the neurons are rector neurons;

o5 comprises consecutive amino acids that are identical, to a stretch of consecutive amino acids in TDD43, FUS, or SOD~l; p) comprises consecutive arainc acids that are identical to a stretch of consecutive amino acids in TDP43 mutant, FUS muta t, or SOD-i mutant;

q) comprises a deamidated asparagine, an oxidized threonine, or a phosphorylated tyrosine.

In further embodiments,, the epitope peptide comprises consecutive amino acids in the sequence set forth as MRGV LVEGILBAPD {SEQ ID NO; 231), LVYVVNYE-KDNKRKM (SEQ ID NO; 233), DMTSDELEBFF8QYC (SEQ ID NO: 236},· ELREHTSyYGDVMDv (SEQ ID NO: 237), EOL∑ IKGISVHISNA (SEQ ID NO; 74), EDDGTVLLSTVTAQF {SEQ ID NO: 229} , &G GHLVYWHYFKD (SEQ ID HO; 232), DVMDWIPKPFRAFA (SEQ ID SiO: 238), Or ElPKPFKAFAFVTFA (SEQ IB NO: 239), in some embodiments, in step iii) the leukocytes are determined to have increased activation after contact with the epitope peptide,

a) if the leukocytes express or release more of at least one cytokine compared to co responding leukocytes not contacted with the epitope peptide;

b) if the leukocytes release at least one cytokine;

c if the leukocytes release at least one cytokine, wherein in step iii) the leukocytes are determined to have released the at least one cytokine if there are over 20 spot-forming ceils (SFC) per million cells as measured by an ELISpot assay comprising the coiorimetric detection of the at least one cytokine.

In s ise embodiments, the leukocytes are T ceils. In a further embodiment, the cytokine is interferon-gamsaa (IFNHJ) or IL~5. In a further embodiment, the cytokine is T Fs, IL-4, IL-17, IL-IO, or IL-21, In a further embodiment, the cytokine is two or more cytokines, therein the two or mors cytokines are at least IFM~ and IL~¾ In a further em odiment, the leukocytes are T cells which are CD4÷ T cells, CD8+ ceils, and/or CD4-fCD8 cells, in a further embodiment, the leukocytes are IL~4 -producing CD4+ T coils, IFN~y~producing CD4÷ T ceils, or IF - y~producing CDSi T cells.

In some embodirents_f the at least one cytokine is at least interferon- gamma {IFM-LJ}, IL~4 or IL-5, wherein the at least one cytokine that is expressed or released from the leukocytes is assayed through a process comprising an enzyme-linked immunosorbent assay (SLISA) , onsyme-lined immucospct (ELI SPOT} , intracellular cytokine staining (ICS), or. Quantitative RT-PCR,

In soae embodiments , the leukocytes are CD4+ T cells.

In some embodiments, determining whether the leukocytes have increased activation comprises

a) contacting the leukocytes with compound comprising a isia or histocompatibility com le (MHC) Tetramer having four BC molecules, wherein each MHC molecule is associated with an epitope peptide; and

b) identifying leukocytes that become bound to the compound as activated.

The present invention also provides methods tor assessing whether a test compound comprises an epitope peptide to which leukocytes of a subject suffering from a neurological disorder are responsive comprising

1} obtaining leukocytes from the subject;

ii contacting the leukocytes with the test compound;

iii) determi ing whether the leukocytes has increased activation after contact with the test compound; and

iv) identifying the test compound as comprising an epitope peptide to which the leukocytes are responsive if in step iii) the leukocytes are determined to have increased activation afte contact with the test compound, and identifying the test compound as not comprising an epitope to which the leukocytes are responsive if in step iii the .1ex5kocyt.es are determined to not have increased activation after contact with the test com ound, wherein a. the epitope peptides is represented, by an amino acid sequence selected from the group of Tau derived sequences represented by SEQ ID MO: i-bv or 240-376,

b. wherein the epitope peptide is represented by the amino acid sequence selected from the group of a~synuciein derived sequences GKTKEGvLYVGSKTK (SEQ ID NO; 487} _f T EGVLYVGS T E {SEQ ID NO: 488) , MPVDPDNSAYEMPSS {SEQ ID ®Q: 89), DMEAYEMPSSEGYQD (SEQ ID NO: 490), EMPSEEGYQDYEPEA (SEQ ID SO: 491), SSEGYQDYEPEA (SEQ ID SO: 492} _f GVLYVGSKTK (SEQ ID NO; 493), VLYVGSETK (SEQ ID HO : 494} _f or VLYVGSKT K (SEQ ID NO : 495), or,

c. wherein the epitope peptide is represented by the amino acid sequence selected from the groxsp of TDP43 derived sequences represented by SEQ ID HO: 56-239,

In an embodiment the test compound is or comprises part of a compound that is produced by neurons in subjects afflicted with an a~ synueleinopath , a Ta opathy, Parkinson's disease (PC) , amyotrophic lateral sclerosis (ALS) , Lewy Body dementia {LED) _t or Alzheimer's disease (AD) .

In a specific embodiment the amino acid sequence is selected from the group of sequences consisting of SEQ ID NO : 136-165. In a further embodiment, the amino acid sequence is selected from the group of sequences consisting of SEQ ID MO: 136-138, SEQ ID NO: 140-143, SEQ ID HO; 145-146, SEQ ID NO: 148-152, SEQ ID SO: 154, and SEQ ID NO; 158-159,

The present invention also provides for a kit. comprising an epitope peptide . The present invention also provides for compounds for treating an «~ synceleinopathy, a Tenopathy, Parkinson's disease (PD) , amyotrophic lateral sclerosis (ALS), Lewy Body deraentia (LSD), or Alzheimer's disease (AD), comprising ί } a ma or histocompatibility compl x (MHC) Tetramer having four MHC molecules, wherein each MHC jsolecule is associated with an epitope peptide, and iij a toxin, wherein a, the epitope peptides is represented by an amino acid sequence seiected from the grocp or fan derived sequences represented by SEQ ID HO: 1-55 or 240-376,

b, wherein the epitope peptide is represented by the amine acid sequence selected from the group of o:™synuciein derived sequences GKTKEGvLYVGSKTK (SEQ ID NO; 487} _f T EGVLYVGS T E {SEQ ID NO: 488) , MPVDE-DNE&YEMPSE {SEQ ID ®Q: 89), DNEAYEMPSSEGYQD (SEQ ID NO: 490), EMPSEEGYQDYEPEA (SEQ ID SO: 491},· SEEGYQDi'EPEA (SEQ ID HO; 492), GVLYVGSKTK {SEQ ID MO: 493), VLYVGS T (SEQ ID NO; 494), or vLYVGSKTKK (SEQ ID NO; 495), or.

c, wherein the epitope peptide is represented by the amino acid sequence selected from the group of TDP43 derived sequences represented by SEQ IB NO: 56-239.

The present invention also provides processes for assessing whether a subject is at risk of developing an o-synucleinopathy, a Tauopathy, Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) , Lewy Body dementia (LSD), or Alzheimer' s disease (AD), which involves an array of testing, the improvement comprising including in the array of testing the steps of;

a)

i) obtaining leukocytes rom the subject;

ii) contacting the leukocytes with an epitope peptide? iiij determining whether the leukocytes have increased activation after contact with the epitope peptide; and i ; identifying the subject as at risk of developing ot- synucleinopathy, PD, ALS, LBD or AD if in step xii) the leukocytes are determined to have increased activation after contact with the epitope peptide, and identifying the subject as not at risk of^" developing the et~ synucieinopathy, PD, ALS, LBD or AD if in step ill) the leukocytes are determined to net have increased activation after contact with the epitope peptide, wherein

a. the epitope peptides is represented by an amino acid sequence selected from the group of au derived sequences represented by SEQ ID HO; 1-55 or 240-376,

. wherein the epitope peptide is represented by the amino acid sequence selected from the group of «~synuc.le.in derived sequences GKTKEGVLYYGSKTK (SEQ ID NO; 4S7) , T SGVLYVGSKT S (SEQ ID NO: 488), MFVDPD SAYE PSS {SEQ ID NO; 489} , DNSA^'fEMPSEEGYQD (SEQ ID SiO: 490) , E¾PSEH!GYQDYEPEA (SEQ ∑D NOi 491), SEEGYQDYEPEA {SEQ ID HOt 492), GVLYVGSKTK (SEQ ID NO: 493} , YLYVGSKTK (SEQ ID NO; 494), or VLYVGS ΪΚΚ (SEQ ID HO : 495) _f or.

c. wherein the epitope peptide is represented by the amino acid sequence selected from the group of TDP 3 derived sequences represented by SEQ D SO: 56-239 or i) obtaining leukocytes from the subject;

ix) separating the leukocytes into 2 or store pools of leukocytes and contacting each poo with an epitope peptide, wherein each pooi is contacted with a different epitope;

iii} determining whether eac pooi has increased activation after contact with the epitope peptide; and

iv) identifying the subject as at risk of developing the ot^'~ synucieinopat y, PD, ALS, LBD or AD if in step iii) 1 or .more pools is determined to have increased activation after contact with the epitope peptide, wherein a. the epitope peptides is represented tay an amino acid seq ence selected from the group of Tax- derived sequences represented by SEQ ID MO: 1.-55 or 240-376, b. wherein the epitope peptide is represented by the amino acid sequence selected from the group of ct-symicleifi derived sequences GKfKEGVEYVGSKTE {SEQ ID NO: 487), TKEGVLY¥GS E (SEQ IB O; 48S) , PVDPDHSAΥΈΜΡ3E (SEQ ID NO : 489} , DNSAYEMPSEEGYQD SEQ ID ISO; 490), EMD3EEGYQDYEPEA (SEQ ID NO: 491} , SESGYQDYEPEA (SEQ ID MO: 492} , GVLYVGSK K

(SEQ ID MO; 493) , VEYVGSKTK (SEQ ID NO; 494), or VLYVGSKTKK {SEQ ID SO: 495) , or c. wherein the epitope peptide is represented by the amino acid sequence selected tram the group of TDP43 derived sequences represented by SEQ ID NO: 56-239,

The present invention also provides processes tor diagnosing or confirming whether a subject is afflicted with an a-synucieinopathy, a Tenopathy, Parkinson' disease {PD) , amyotrophic lateral sclerosis (ALS) , Lewy Body dementia { LED) , or Alzheimer's disease {AD} , which involves n array of testing, the improvement compris ng including in the array of testing the steps of;

a)

i) obtaining leukocytes frost the subject;

ii) separating the leukocytes into 1 o more pools of leukocytes and contacting each pool with an epitope peptide, wherein each pool is contacted with a different epitope peptide;

iv) identifying the subject as afflicted with the a- syn cleinopathy, PD, AES, LBD or AD if and only if in step iii} 1 or aacre pools is determined to have increased activation after contact with an epitope peptide, or b) 1} obtaining leukocytes front the subject;

iij separating the leukocytes into 1 or more pools of leukocytes and contacting each pool with an epitope peptide, wherein each pool is contacted with a different epitope peptide;

iv) identifying the subject as afflicted with the a- synucleinopathyy PD, ALS, LBD or AD if and only if in step iii) 1 or mo e pools is determined to have increased activation after contact with an epitope peptide, wherein a. the epitope peptides is represented by an amino acid sequence selected from the group of Tau derived sequences represented by SEQ ID HO : 1-55 or 240-376,

b. wherein the epitope peptide is represented by the amino acid sequence selected from the group of or-synuciein derived- sequences GKTKEGVLYYGSKTK (SEQ ID NOc 48?}, K KSGVLYvGS TKE (SEQ D HO: 488), MPVDPD¾£AY£ PS£ { SEQ ID NO; 489},· DNEAYEMPSEEGYQD (SSQ IB NO: 490), EMP5SEGYQDYEPEA (SEQ ID NO; 491), SSSGYQDYEPEA {SEQ ID NO : 492}, GVLYVGSKfK ⁽SEQ ID HO : 493), VLYV^'GSK K (SEQ ID SO: 494} , Or YLYVGS TKK (SEQ ID UGx 495},· or,

c. wherein the epitope peptide is represented by the amino acid sequence selected f ojn the group of D 43 derived sequences represented by SEQ ID NO: 56-239. in an embodiment _f the leukocytes have increased activatio after contact with native alpaa-synuclsin protein or fibrilizei aipha-synucleiu protei .

The present invention also provides for pharmaceutical compositions for treating an o-synucXeinopathy, a Tenopathy, Parkinson's disease {PD} , amyotrophic lateral sclerosis (ALS) , Lewy Body dementia (LBD) _f or Alzheimer's disease (ΆΏ) , comprising ί) a protein comprising an amino acid sequence selected from the group of

a. the epitope peptides is represented by an amino acid sequence selected from the group of Tau derived sequences represented by SEQ ID NO; 2.-55 or 240-376, b. wherein the epitope peptide is represented by the amino acid sequence selected rom the group of a~ synuclein derived sequences GKTKEGVLYVGSK K (SEQ ID NO: 48?}, KTKEGVLYVGSKTKE (SEQ ID SO: 488}„ MPVDPDHEAYHM SE (SEQ ID ®Q: 48S), DNEAYEMPSEEGYQD (SEQ ID NO: 490} , EMPSEEGYQDYEPEA (SEQ ID UGx 491) , SEEGYQDYEPEA (SEy ID O: 492), GvLYVGSK K (SEQ ID NO: 493) , VLYVGSKTK {SEQ ID NO : 94 , or VL VGS T K (SEQ ID NO; 495) , or.

c. wherein the epitope peptide is represented by the amino acid sequence selected from the group of TDP43 derived sequences represented by SEQ ID HO: 56-239, and ii) a pharmaceutically acceptable carrier.

In an embodiment, the the amino acid sequence is selected from the group of sequences SEQ ID HO: 74, 139, 144 and 230-239, or wherein the amino acid sequence is selected from the group of sequences SEQ ID NO; 231, 233, 236, and 237, or wherein the amino acid sequence is selected froat the group of sequences SEQ ID NO; 74, 229, 231, 232, 239, or 239.

The present invention also provides a method comprising;

a. providing a biological sample from a subject;

b. processing the biological sample to determine presence of a T cell receptor (ICR) specific to a peptide, wherein the peptide is a fragment from a protein associated with said neurodegenerative disease . In some em odimen s, the processing step includes contacting ϊ cells from said sample with said peptide, and detecting activation of a τ cell having said CR. In a further eKifco is n , the processing step includes performing gene sequencing on at least a cellular fraction of said biological sample: to amplify a gene encoding the TCR specific to said peptide, and detecting presence of said gene encoding said TCR, preferably wherein said at least a cellular fraction of said biological sample includes peripheral blood mononucle r cells { PB C) , preferably leukocytes , In some embodiments, the peptide associated with a neurodegenerative disease is tau, alpha-synuelein, or transactive response DMA binding protein 3 iiDa (TDP~43) - In a further embodiment, the peptide is selected from any one of tables I to

The present invention also provides a method comprising:

a) providing a biological sample from a subject;

b) processing the biological sample to determine presence of a human leukocyte antigen (HLA capable of presenting a peptide, wherein the peptide is a fragment from a protein associated with said neurodegenerative disease; and c processing t e biological sample to determine presence of a

T ceil receptor {TCR} specific to said peptide.

In some embodiments, t e peptide is a fragment from a protein that forms aggregates in a patient having the neurodegenerative disease, in embodiments, the method of step c) for processing the biological sample includes contacting T ceils present in said sample with said peptide, and detecting activation of a T cell having said TCR.

In some embodi ents, the method of step b) for processing the biological sample includes performing gene sequencing on at least a cellular fraction of said biological sample to amplify a gene encoding the HLA capable of presenting said peptide, and defecting presence of said gene encoding said HLA and c) includes performing gene sequencing on at least a cellular fraction of said biological sample to amplify a gene encoding the TCR specific to said peptide, and detecting presence of said gene encoding said TCR. in some embodimen s, at least a cellular fractio of said biological sample includes peripheral blood mononuclear cells (PB C) , preferably leukocytes, in some embodiments, the protein that forms aggregates in a patient having a neurodegenerative disease is tau, alpha-synuciein, or transactive response DMA binding protein 43 kit; <TDD~ 3} . In some e bodiments, the protein is tau, preferably wherein the peptide derived from the tau protein includes a phosphorylated serine and/or tyrosine. In some embodiments, the protein is TDP-43, preferably wherein the peptide derived from the TDD-43 protein includes a phosphorylated serine and/or tyrosine, in further embodiments, the peptide is selected from any one of tables 1 to preferably wherein the peptide is selected from any one of G T EGVLYVGS TK (SEQ ID NO: 487), KTKEGVLYVGS TKE (SEQ ID NO: 488), PVDFDNSA EMPSE (SEQ ID NO: 48S) , D SAYE PSSSGYQD (SEQ ID mt 490) , E PSEEGYQDYEPEA { SEQ ID SO: 491), SEEGYQDYEPEA (SEQ ID NO; 492},· GVLYVGSKTK (SEQ ID HO; 493), VLYVGSKTK (SEQ ID NO: 494) , or VLYVGS T (SEQ ID HO: 495} ,

In some embodiments, the HLft is DRB5* 01:01, DRBl* 15 : 01, )081*03:04, A*U:01, DRBl*0?:0I_f DRBl*09:OI_f or DQBI*03:01.

In some embodiments, the meth d comprises detecting a peptide : HC complex comprising any one of the peptides and any one of the HL&s listed in Table 5. a) In some embodiments, the presence of the TCR and the BLA is

indicative that the subject is predisposed to, at risk of, or has a neurodegenerative disease, preferably wherein the presence of the TCR is indicative that the subject is predisposed to, at risk, of or has a neurodegenerative disease, preferably wherein the neurodegenerative disease or disorder is aipha-synucleinopathy, a Tauopathy, Parkinson's disease (PD) , Lewy Body dementia iLBD), or Alsheimer' s disease (AD} . Amyotrophic Lateral Sclerosis

ALS is often diagnosed by a neurologist who can evaluate symptoms and their severity, national Institute of Neurological Disorders and Stroke, Amyotrophic Lateral Sclerosis (ALS) Fact Sheet, available at www , ninds . nih_^gov/Disorders Patient-Caregiver-Educatioii/Fact-

Sheets/Amyotrophic-Latera1-Sclerosis-ALS-Fact-Sheet, last updated October 18, 2004 (hereinafter "HINDS Fact Sheet") , According to the National institute of Neurological Disorders and Stroke, there is currently no test that can clearly identify the disease (KINDS Fact Sheet) . The presence; of upper and lower motor neuron symptoms strongly suggests the presence of the disease (HINDS Fact Sheet) , Additionally, muscle and imaging tests, laboratory tests, and tests for other diseases and disorders can help doctors decide if a patient has true ALS or some other disorder that resei:¾bies it (MINDS Fact Sheet) .

The present invention provides jnethods for identifying subjects afflicted with ALS that would previously have remained undetected. Aspects of the present invention enable the detection of ALS in presyxspto atic stages. Additionally, the present invention provides methods for identifying those who might eventually develop ALS, ADS has an increased prevalence with age. See, for example, the NINDS Fact Sheet, the entire content of each of which is hereby incorporated herein by reference, without wishing to foe bound by any scientific theory, the peripheral iramane response of ALS may begin in a subject decades before ALS ma be diagnosed by a neurologist, and subjects having the peripherai iiamuue response may be identified for earlier therapy using methods of the invention. The present invention provides methods for diagnosing causes of these symptoms, and be used to identify subjects who iay benefit from prophylactic treatment for ALS,

Aspects of the present invention provide an epitope useful as a test/biomarker for ALS, which could include identifying patients in preclinical stages or in danger of ALS, and to measure disease progression and/or response. As described herein, aspects of the invention provide means to detect these I cells in patient blood. Similar approaches for identifying tuberculosis patients will be known to those skilled in the art. For us of a sirailar test i TB diagnosis, see en , wihipedia . org/wihd/QuantiFERO«, t e entire contents of which are hereby incorporated, by reference.

Additionally,, aspects of the invention define which precise cells and antigens individual patients have, and provide individualized therapy that spare other important immune functions. The test/biomarker test for ALS has already been conducted and is effective, as described in the Exam les disclosed herein.

Without wishing to be bound by any scientific theory, the cells identified in embodiments of the invention may be a step in the disease, The present invention provides means to treat ALS, as blocking these T cells arrest the disease progression. An example would be toierization : particular epitopes the ^s ceils recognize are determined, and patient are exposed to the epitope in a form that alters the immune system to recognise it as self, and halt or reduce making killer ? cells. In addition to TDP43, there are additional .mutant proteins that are detected in ALS, including FUS and SOD~l< These markers are similarly useful for diagnosing, confirming, providing bio arkers for, and treating ALS.

Alzheimer'' s Disease

AD is often diagnosed by a neurologist who oan evaluate symptoms and their severity. Rational Institute on Aging, Alzheimer's disease, available at www . nia . nih ,go /aishelters (hereinafter "HIA"^") . According to the National institute on Aging, there is currently no test that can clearly identify the disease NIA) . Tests of memo y, problem solving, attention, counting, and language can help doctors decide if a patient having memory problems has "possible Alzheimer's disease" (dementia may be due to another cause), "probable Msheijner^? s disease" (no other cause for dementia be found.) , or some other problem (NIA) , Additionally, standard medical tests, such as blood and urine tests, and brain scans, such as computed tomography (CT) , magnetic resonance imaging { RI } , or positron emission tomography (PET) , may be used to identify other possible causes for sym oms (ΝΣ&5 , These tests may be repeated, to give doctors information about how the person's memory and other cognitive functions are changing over tine ( IA) . However, the diagnosis of Alzheimer's disease can be confirmed when a sample of brain tissue is removed (after death, during an autopsy) and examined under a microscope (Merck Manual) . The characteristic loss of nerve cells, neurofibrilla y tangles, and senile plaques containing beta-arayioid can be seen throughout the brain, particularly in the area of the temporal lobe that is involved in forming new memories (Merck Manuel) ,

The present invention provides jnethods for identifying subjects afflicted with AD that would previously nave remained undetected. Aspects of the present invention enable the detection of AD in presyatptoisatic stages. Additionally, the present invention provides methods for identifying those who night eventually develop AD, AD has an increased prevalence with age. See, for example, the N±A; and Mayeaux and stern, (2012) Epidemiology of Alzheimer Disease, Cold Spring Harb Perspect Me , 2 (S) : a006239_f the entire content of each of which is hereby incorporated herein b reference. Without wishing to be bound by any scientific theory, the peripheral iiamune response of AD may begin in a subject decades before AD may be diagnosed by a neurologist, and subjects having the peripheral irajsune response may be identified for earlier therapy using methods of the invention. The present invention provides methods for diagnosing causes of these symptoms, and be used to identify subjects who may benefit from prophylactic treatment fo AD,

Aspects of the present invention provide an epitope; useful as a test bioiiiarker for AD, which could include identifying patients in preclinical, stages or in danger of D, and to reasure disease progression and/or response. As described herein, aspects of the invention provide means to detect these τ cells in patient blood. Similar approaches for identifying tuberculosis patients will be Known to those skilled in the art. For use of a similar test in TB diagnosis, see er wikipedia.org/wiki/QuantiFSRON, the entire contents of which are hereby incorporated by reference.

Additionally, aspects of the invention define which precise τ cells and antigens individual patients have, and provide individualized therapy that spare other important immune functions. The test/biomarker test for

AD has already been conducted and is effective, as described in the Examples disclosed herein. without wishing to be hound by any scientific theory, the ceils identified in embodiments of the invention may be a step in the disease. The present invention provides means to treat AD_f as blocking these cells arrest the disease progression. An example would be tolerisation ; particular epitopes the T ceils recognize are determined, and patients are exposed to the epitope in a form that alters the immune system to recognize it as self, and halt or reduce making killer T cells. In addition to Tau, there are additional mutant proteins that cause AD, including β-aroylcid. These markers are similarly useful for diagnosing, confirising, providing biomarkers for, and treating AD .

Parkinson/ Disease

PD is often diagnosed by a neurologist who can evaluate symptoms and their severity. National institute of Neurological Disorders and Stroke, Parkinson's Disease Backgrounder, available at www, ninds . nih.gov/disorders/parkinsons disease/parkinsons disease back grounde .htm, last updated October 18, 2004 {hereinafter "NIHDS Backgrounder" , According to the National institute of Neurological disorders and Stroke, there is currently no test that can clearly identify the disease, (NINDS Backgrounder). Sometimes people with suspected PD are given anti-Parkinson's drugs to see if they respond {KINDS Backgrounder) , Other tests, such as brain scans, can help doctors decide if a patient has true PD or some other disorder that resembles it <HXNDS Backgrounder) , Microscopic brain structures called Le y bodies, which can be seen only during an autopsy, are regarded as a hallmark of classical PD (NINDS Backgrounder) . Autopsies have uncovered Dew bodies in a surprising number of older persons without diagnosed

PD 8% of people over 50, almost 13% of people over 70, and almost 16% of those over 80, according to one study {NIKDS Backgrounder) . As a result, some experts believe PD is something of an ^¾iceberg; phenomenon, ^w lurking undetected in as m ny as 20 people for eac known Parkinson's patient. (NINDS Backgrounder) . without, wishing to be bound by any scientific theory, a few researchers contend that almost everyone would develop Parkinson's eventually if they lived long enough (NINDS Backgrounder ,

The present invention provides methods for identifying subjects afflicted with PD that would previously have remained undetected. Aspects of the present invention enable the detection of PD in resymptomat c stages. Additionally, the present invention provides met ds for identifying those who might eventually develop PD, PD has an increased prevalence with age. See, for example, the KINDS Backgrounder? and Van Den Sedan et. al . , (2003) incidence of Parkinson'^' s Disease: variation by Age, Gender,, and Race/Ethnicity, ¾au J. Epidemiol . 157 (11); 1015-1022, the entire content of each of which is hereby incorporated herein by reference. PD ranks among the most common late-life neurodegenerative diseases, affecting approximately 1.5% to 2,0% of people aged 60 years and older (Patrick Sweeney, Parkinson' s Disease, Cleveland Clinic? available at cleveiandciinicneded. coj;s/medicaipubs/disease;ianageTf;ent/neurology

/parkinsons-disease/} . ithout wishing to be bound by any scientific theory, the peripheral immune response of PD raay begin in a subject decades before PD may be diagnosed by a neurologist, and subjects having the peripheral irraune response may be identified tor earlier therap using methods of the invention. There are a number of peripheral symptoms associated with PD including orthostatic hypotension and constipation. The present invention provides methods for diagnosing causes of these symptoms, and be used to identify subjects who may benefit from prophylactic treatment tor PD. Aspects of the present invention provide an epitope peptide useful as a test/hiojsarker for PD, which could include identifying patients in preclinical stages or in langer of PD, and to measure disease progression and/or response. As described herein, aspects of the invention provide iseans to detect these T cells in patient blood. Similar approaches for identifying tuberculosis patients will be known to those skilled in the art, For use of a similar test in TB diagnosis, see en , wikipedia , org/wiki/ynanti ^'EROH, the entire contents of which are hereby incorporated by reference.

Additionally, aspects of the invention define which precise T ceils and antigens individual patients have, and provide individualise therapy that spare other important immune functions. The test/biomarker test for PD has already been conducted and is effective, as described in the Examples disclosed herein. without wishing to be bound by any scientific theory, the ceils identified in embodiment of the invention may kill the neurons in PD, and thus be a step in the disease. The present invention provides means to treat PD, as blocking these T cells arrest the disease progression. An example would be tolerizationc particular epitopes the T cells recognise are determined, and patients are exposed to the epitope in a form that alters the immune system to recognize it as self, and halt or reduce making killer T ceils. In addition to cx-synuciein, there are additional mutant proteins that cause PD, including L KK2 and glueocerebrosidase , These markers are similarly useful for diagnosing, confirming, providing biomarkers for, and treating PD,

Each embodiment disclosed herein is contemplated as being applicable to each of the other disclosed embodiments, Thns, ail combinations of the various elements described herein are within the scope of the invention.

It is understood that where a parameter range is provided, ail integers within that range, and tenths thereof, are also provided by the invention. For example, ^Nh).2~5 rag/kg" is a disclosure or 0.2 rag/kg, 0,3 rag/kg, 0,4 .mg/kg, 0.5 mg/kg, 0,6 mg/kg etc. up to 5.0 ra /kg .

Proteins

In the present disclosure, met ods, systems and procedures are presented f om which the person of skill can reasonably predict that various proteins that are associated with a neurodegenerative disease, for example where the protein forms aggregates associated with the disease, may contain epitopes that are recognised as autoantigens by ϊ cells and such proteins or peptides derived there rom may thus be useful in such methods, systems and procedures.

Exam les of proteins that may illustrate the concept underlying the present disclosure are discussed below. For example, these proteins may include peptides that may be useful in the herein described processes, systems and methods that make use of assessing the presence of TCR specific to a given peptide to determine neurodegenerative disease predisposition or presence thereof, and/or to determine responsiveness to therapeutic treatment of the disease.

In one non-limiting embodiment, the TAR DHA~bindiug protein 43 (TDP-43, transactive response DMA binding protein 43 kDa) may represent an example of a protein that jsay contain epitopes that are recognized as autoantigens by cells at least based on one or more of the following observations ;

, hyper-phosphorylated, ubiquit inated and cleaved form, of TDP-43 - known as pathologic TDF 3 - is the major disease protein in ubiguitin-pesitive, tau-, and alpha~synuciein-negative f ontotemporal dementia s FTLD-TDF) and in Amyotrophic lateral sclerosis (ALSj . [Neumann et al., (2006). Science, 314 (5796); 130-3] .

b, Elevated levels of the DP-43 protein have been identified in individuals diagnosed with chronic traumatic encephalopathy, a condition that often airics ALS and that has been associated with athletes who nave experienced multiple concessions and other types of head injury,

c. bnorma ties of occur in an important subset of

Alzheimer' s disease patients, correlating with clinical and neuropathoiogic features indexes. [fremblay et ai„ , {2011} _f J

Neuropathol Exp Neurol . 70 (9); 788-98] .

in one non-limiting enVbodiriient, the tan protein ma re resen another example of a protein that may contain epitopes that are recognized, as a toantigens by cells at least based on one or more of the following observations:

a.Tau is the protein product of the crot taule-asscciated protein tau ( APT) gene. This protein, in highly phosphoryiated aggregates, has long been associated with Alzheimer ^f s disease <AD} , progressive supranuclear palsy (PSP) and other dementias . b. AP has been identified as a risk factor for Parkinson's disease

(PD) by genome-wide association study (GWAS) [Sharma et ai,, Neurology, 2012_f Aug 14; 79 (7) : 659-67] _f but not AD itself.

c. Phospho-tau irnmunolabel can also be high in PD and particularly brain of LBD (Parkinson's disease dementia and dementia with Lew bodies) , while phospho~t.au is higher in AD, and there is often significant overlap in patient brain pathology between the disorders [Arnold et ai , , J Comp Neurol, 2013, Dec 15? 521(18): 4339-55] .

d. Tau and alpha-syn have

parallel features including association with PD by G AS, phosphorylation under disease conditions, presence of both proteins [Baapel et al., Nat Rev Drug Diseov., 2010 Jul; 9(7 ; 560-74; Foulds et ah, Sol Rep,, 2013; 3: 2540; Zefterberg et ai . , Alzheiaers Res Ther,, 2013, Har 28; 5(2); 9], and autoantibodies in blood [Partes et ai,, J Hs roImmunol ,„ 2012, Nov 15; 252 (1-2): 100-5? oehier et al,,

PLoS One, 2013, May 31 ; 8 (5) ; e€ €49] , and similar degradation by chaperone-raediated autophagy (CM¾) that is disturbed by mutation [Wang et al., Bum ¾ol Genet . , 2009, Nov 1; 19(21} ; 4153-70]. They may even form joint oligomers in some patients. [Ssngopta et al. _f Biol Psychiatry, 2015, Sov 15; 78(10} ί 672-83].

e » Pbosphoryiated candidate epitopes are important for tau, which has about 40 potential pbosphoryiated sites (Sharma et al . , 2012; Yin et al._f 2013} of which 20 were identified in AD patients (Buka et al., 2013} / 10 phosphorylated sites we e identified in PD striata (3202, 235, 262, 356, 396/404, 03, 413, 422 and T205, 212); and seven sites in LED <S214, 238, 396/404, 422 and 212, 21?} .

f.In PD patients, there are 3 clusters of phospho~tau (202, 205, 212; 356, 396, 404; and 409, 413, 22).

¾mino acid and nucleotide sequences or tan are accessible in public databases by the NCBI Gene ID: 4137.

In one non-limiting embodiment, the aipha-synuclein protein may represent another example of a protein that may contain epitopes that are recognized as aufoantigens by T ceils at least based on one or more of the following observations:

a. T cells restricted by DRB5*01:01, DRB1*I5:G1, DQBl.*03:04, A*11:G1, DRB1*07:01, DKB1*GS:01, or QB1*03:01 have been shown to recognise speci ically certain aipha-synnelein peptides in PD patients. [Sulzer et al., N ture, in press, doi:10.1038] .

The reader will readily understand that the present disclosure is not limited in terms of practical ίi lementation to the use of any particular protein from the above non-exhaustive list of proteins .

Peptides

In some embodiments, the epitope described herein comprises consecutive .amino acids that are identical to a stretch of consecutive amino acids in the herein described protein. In other words, it is in the form or a peptide.

In some embodiments, the peptide is pbosphoryiated or nitrated. In some embodiments, the epitope comprises a pbosphoryiated serine and/or a phosphorylated tyrosine, In some em odiments, the epitope comprises a p osphorylated serine.

In some embodiments, the peptide comprises consecutive amino acids that are identical to a stretch of consecutive amino acids of the tau protein, where at least one phosphorylated serine arid/or phosphorylated tyrosine is within the stretch of consecutive amino acids, in some embodiments, the stretch of consecutive amino acids of the tau protein comprises the serine at position 195, 198, 202, 214, 235, 237, 238, 262, 356, 396/404, 400, 409, 413, or 422, or the tyrosine at position 181, 184, 205, 212, 217, or 231.

In some embodiments, the; peptide comprises a non-amino acid, polymer that is produced by the neurons. In some embodiments, the peptide is neuroneianin or a portion thereof, Motor symptoms or PD are caused by cell death in the substantia nigra, which may be partly due to oxidative stress. This oxidation may be relieved by neuroiselan n .

In some embodiments, the epitope comprises consecutive amino acids in the peptide sequences derived from tau, as set forth in Table ί .#

Table 1 - peptid sequences derived from Urn

39 SVQIVY PVDLSKVTS 305 320

40 VDLSKVTS CGSLG I 313 328

4! KCOSLOMiHH PGGOQ 321 336

42 HH PGOGQVEV SEI 329 344

43 VEV SEKLDF D VQS 337 352

DF DR VQSK3GSLDNI 345 360

45 IGSLD IXHVPGGGN 353 368

46 THWGGG IETH L 36 ί 376

47 K IETHKX.TF ENAKA 369 384

48 TFREMA A TDHGAEI 377 392

49 TDHGAEiVY SPVVS 385 400

50 VYK3P 3GDTSFRHL 393 408

51 GDTSPRHLSNVSSTGS 401 416

52 S V3STGSIDMVDSPQ 409 424

53 IDMVDSPQLATLADEV 417 432

54 LATLADEVSASLAKQG 425 440

55 ATLADEVSASLAKQGL 426 441 in sosne embodiments, the epitope compr ses consecutive amino acids in the peptide sequences derived from as set forth in Table 2,

Table 2 - peptide seq e ce derived from TDP-43

75 DLH GiSVffiSNAE

76 LilKGISVfflS AEP

77 IIKGISVHISNAEPK

78 IKGiSVHJSNAEP H

79 KGISVHISNAEPKHN

80 GIS VHISN AEP HNf S

ΫΛ !SVHISNAEP HNS

82 SVF!ISMAEPKHNSNR

83 VHISNAEPKHNSNRQ

84 HiSNAEPKHNSNRQL

85 ISNAEPKH S ROLE

80 SNAEPKHNSNRQLER

87 NAEPKHNSNRQLERS

88 AEP HNS RQLERSG

89 EP HNS RQLERSGR

90 PKHN^'SNRQLERSGRF

91 KHNSNRQLERSGRFG

92 HN^'SNRQLERSGRFGG

93 N^'SNRQLERSGRFGGN

94 SNRQLERSGRFGGNP

95 NRQLERSGRFGGNPG

96 RQLERSGRFGGNPGG

97 QLERSGRFGGNPGGF

98 LERSGRFGGNPGGFG

99 ERSGRFGG PGGFGN

1.00 RSGRFGG PGGFG^' Q

101 SGRFGGNPGG FGNQG

102 GRFGGNPGGFGNOGG

103 RFGG PGGFGNOGGF

104 FGGNPGGFGNOGGFG

105 GGNPGGFGNQGGFGN

106 GNPGGFGNOGGFGNS

10? PGGFGNQGGFGNSR

108 PGGFGNQGGFGN8RG

109 GGFGN^'QGGFGNSRGG no GFGN^'QGGFGNSRGGG

1 .1 FGN^'QGGFGNSRGGGA

112 GN^'OGGFGNSRGGGAG

113 N^'OGGFGNSRGGGAGL

114 QGGFGNSRGGGAGLG

115 GGFGNSRGGGAGLGN

116 GGFGNSRGGGAGLGNN

117 FGNSRGGGAGLGNNO

1 8 GNSRGGGAGLGN QG

119 NSRGGGAGLGNNQGS 120 SRGGGAG^'LGNNQGSN

1.2] RGGGAG^'LG QGSNM

122 GGGA.GLGN QGS MG

1.23 GGAGLGN QGS MGG

124 GAGLGNN'OGS MGGG

125 AGLG MO S MGGGM

126 GLGNNQGS MGGGMN

127 LG OGS MGGGMN

128 GNNQGSNMGGGMNFG

129 N QGS MGGGM FGA

1.30 N^'QGSNMGGGM FGAF

131 QGSNMGGGMNFGAFS

1.32 GSNMGGGM FGAFSI

133 SNMGGGM FGAFSIN

1.34 NMGGGM FGAFSINP

135 MGGG NFGAFSINPA m MGGGMNFGAFSINPA

13? GGMNFGAF5INPA M

138 GMM GAFSIMPAMMA

1.39 MNFGAFSINPAMMAA

140 FGAFSINPAMMAAA

14.1 FGAFSINPAMMAAA.Q

142 GAFSMPAMMAAA.QA

1.43 AFSINPAMMAAA.OAA

144 FSI PAMMAAAQAAL

145 SiNPAMMAAAQAALQ

1 6 [NPAMMAAAQAALQ5

147 NPAMMAAAOAALOSS

1 8 PAMMAAAQAALOSSW

149 A MAAAQAALQSSWG

1.50 MAAAQAALQSS GM

151 MAAA.QAALQSSWGMM

1.52 AAA.QAALQSSWG MG

1 S3 AAQAALQSSWGM GM

154 AQAALOSSWGMMGML

155 QAALQSSWGMMGMLA

156 AALQSSWGMMGMLAS

15? ALQSSWGMMGMLASQ

158 LQSSWG MGMLASQO

1.59 QSSWGMMGMLASQQN

160 SSWGM GMLASQQ Q

161 SWG MG XASQQ QS

162 WGMMGMLASOO OSG

163 GMMGMLASOQNQSGP

164 MMGMLASOQNQSGPS 165 MGMLASQQ QSGPSG

166 GMLASQQ QSGPSGN

167 MLASQQ^' QSGPSGN

168 LASQQ QSGPSGN Q

169 ASOONOSGPSGN ON

170 SOONQ8GPSGNNQNQ

171 QQNQSGFSGNNQNQG

172 QNQSGPSGNN^QNQGN

173 NQSGPSG NQ!NGGNM

174 QSGPSGNNQNQGMMQ

175 8GP8GNNQ QG QR

176 GPSGNNQNQGNMQRE

177 PSGN QNQGNMQREP

178 SGN QNQGNMQREPN

179 GNNQMQGNMDREPNQ

180 ONQGMMQREPNOA

18! NQNQGNMQREPNQAF

182 QNQGNMQREPNQAFG

183 NQGNMQREFNQAFGS

184 QGNMQREPNQAFGSG

185 GNMQREPNQAFGSGN

186 N QREPNQAFGSGNN

187 QREPNO AFGSGN S

188 QREPNQAFGSGNNSY

189 REPNOAFGSG NSYS

190 EPNQAFGSGNNSYSG

191 PNQAPGSGNNSYSGS

192 NQAFG8GNNSYSGSN

193 OAFGSGNNSYSGSNS

1 4 AFGSGNNSYSGSNSG

195 FGSGNNSYSGSNSGA

196 GSGNNSYSGS SGAA

197 SGMMSYSGSNSGAAJ:

198 GNNSYSGSNSGAAJG

199 NSYSGSNSGAAIGW

200 NSYSGSNSGAAiOWG

20! SYSGSNSGAAIGWGS

202 YSGSNSGAAIGWGSA

203 SGSNSGAAIGWGSAS

204 GSNSGAAIGWGSAS

205 SNSGAAIGWGSASNA

206 NSGAAIG^'WGSASNAG

207 SG. A AIG WG S AS N AG S

208 G AA J G WGS ASN AGSG

209 AAIGWGSASNAGSGS 6?

In some em odiments, the epitope comprises consecutive amino acids in the peptide sequences derived, from tau, as set forth in Table 3.

240 NATRIPA TPPAPKT

241 AT IPA TFPAP TF

242 TRIPAKTPPAPKTPP

243 MPA TPPAPKTPPS

244 IPAKTPPAPKTPPSS

245 PAKTPPAP TPPSSG

246 AGIGDTPSLEDEAAG 247 AKTPPAFKTPP8SGE

248 KTPPAPKTPPSSCEP

249 TPPAFKTPPSSGEFP

250 PPAPKTPPSSGEPPK

251 PAPKTPPSSGEPPKS

252 APKTPPSSGEPPKSG

253 PKTPPSSGEPPKSGD

254 KTPPSSGEPP SGDR

255 TPPSSGEPPKSGDRS

256 SSGEPP SGDRSGYS

257 SGEFPKSGDRSGYSS

258 GEPPKSGDRSGYSSP

259 EPPKSGDRSGYSSPG

260 PPKSGDR3GYS3PGS

261 PKSGDR3GYS3PGSP

262 KSGDRSGYS&PGSPG

263 SGDRSGYSSPGSPGT

2(54 GDRSGYSSPGSPGTP

265 DRSGYSSPGSPGTPG

266 RSGYSSPG3PGTPGS

26? SGYSSPGSPGTPGSR

268 GYSSPGSPGTPGSRS

269 YSSPGSPGTPGSRSR

270 SSPGSPGTPGSRSRT

271 SPGSPGTPGSRSRTP

272 PGSPGTPGSRSRTPS

273 GSPGTPGS SRTPSL

274 SPGTPGSRSRTPSLP

275 PGTPGSRSRTPSLPT

276 GTPGSRSRTPSLPTP

277 TPGSRSRTPSLPTPP

278 PGSRSRTPSLPTPPT

279 GSR.SRTPSLPTPPTR

280 SR.SRTPSLPTPPTRE

281 RSRTPSLPTPPTREP

282 SRTPSLPTPPTREP

283 RTPSLPTPPTREP K

284 TPSLFTPPTREP V

285 PSLPTPPTREPKKVA

286 SLPTPPTREPKKVAY

28? TPPTREP KVAWRT

288 PPTREPKKVAVVRTP

289 PTREFKKVAVVRTPP

290 TREP KVAWRTPPK

291 REP KVAVVRTPP S 292 EPKKVAVVRTPPKSP

293 P KVAVV TPP SPS

294 KVAVVRTPP SPSS

295 KVAVVRTPP SPSSA

296 VAVVRTPP SPSSA

29? AVY TPP SPSSAKS

298 VYRTPP SPSSA SR

299 VRTPP SPSSAKSRL

300 RTPP SPSSAKSRLO

301 TPPKSPSSA SRLOT

302 VPMPDLKNVKSKIGS

303 PMPDLKNVKS IGST

304 MPDL NVKSKIGSTE

305 PDLKNVKSKiGSTEN

306 DLKNVKS IGSTENL

307 LKNVKSKJGSTENL

308 KNYKS IGSTENLKH

309 NY S IGSTENLKHQ

310 V S IGSTENLKHQP

311 KSKIGSTE LRHQPG

31.2 SKIGSTE L HQPGG

313 KIGSTE L HQPGGG

31.4 IGSTENL HQPGGGK

315 GSTEMLKHQPGGG V

316 STENLKHQPGGG VO

31? EKLDFKDRVOSKiGS

318 KLDFKDRVQSKIGSL

319 DFKDRVQSKIGSLDN

320 F DI V'OSKIGSLDNI

32? DRVQSKIGSLDNIT

322 DRVQSKIGSLD ITH

323 RVQS IGSLDNITHV

324 VQSKMGSLD ITHVP

325 OSKMGSLD ITHVPG

326 S GSLDNITHVPGG

327 GSLDNITHVPGGG

328 iGSLDNITHVPGGGN

329 GSLDNFFeVPGGG K

330 SLD JTHVPGGGNK

331 A AKTDHGAEIVYKS

332 AKTDHGAEIVYKSP

333 A TDHGAEIVYKSPV

334 TDBGAEIVYKSPVV

335 T HGAEIVYKSPWS

336 DHGAEiVYKSPWSG 33? HGAEJVYKSPWSGD

338 GAF3YYKSPVYSGDT

339 AEJVYKSPVYSGDTS

340 EJVYKSPWSGDTSP

3 1 IVYKSPVVSGBTSPR

342 VYKSP SGDTSPRH

343 Y SPWSGDTSPRHL

344 KSPWSGDTSPRHLS

345 SPWSGDTSPRHLSN

346 PWSGDTSPRHLSNV

347 VVSGDTSPRHLSNVS

348 VSGDTSPRHLSNVSS

349 SGDTSPRHLS VSST

350 GDTSPRHLS VSSTG

351 DTSPRHLS VSSTGS

352 TSPRHLSNVSSTGSI

353 SPRHLSNVSSTGSSD

354 PRBLSNVS8TGSID

355 RHLS VSSTGSID V

356 HLSNVSSTGSIDMVD

35? LSNVSSTGSIDMVDS

358 SNVSSTGSiDMVDSP

359 NVSSTGSiDMVDSPQ

360 VSSTGSiDMVDSPQL

361 SSTGSIDMVDSPQLA

362 STGSiDMVDSPQLAT

363 TGSIDMVDSPQLATL

364 GSIDMV'DSPQLATLA

365 S1DMVDSPQLATLAD

366 IDMVDSPQLATLADE

367 DMYDSPQLATLADEV

368 MYDSPQLATLADEVS

369 VDSPQLATLADEVSA

370 DSPOLATLADEVSAS

371 SPQLATL ADE V S ASL

372 VAYYRTPPKSPSSAK

373 PAPKTPPSSGEPPKSG

374 PMPDL NV SKIGSTE

375 DF DRVQSKIGSLDNI

376 DRSGYSSPGSPGTPGS

In some embodiments, the epitope comprises consecutive amino acids in the peptide sequences derived from alph.a-synuclein _r as set forth in Table Table 4 - peptide seq ences derived from aipha-synuclem

Seq ID Peptide

377 VF KGLSKA

378 DVFMKGLSKA

379 GWAAAEKTK.

380 VAAAEKTKQGVAEAP

381 YAAAEKTKQGVAEAA

382 AGKTKEGVL

383 PGKTKEGYL

384 AGKTKEGVLY

385 APGKT EGVL

386 GVAEAAGKTK

387 KQGVAEAPGKTKEGV

388 PG TKEGVLYVGSKT

389 KTKEGVLYVGSKTKK

390 KQGVAEAAGKTKEGV

391. AGKTKEGVLYVGSKT

392 VLYVGSKTK

393 LYVGSKTKK

394 YVGSKTKEGV

395 VLYVGSKTK

396 GVLYVGSKTK

39? LYVGSKTKEG

398 KTKKGWHGV

399 KTKKGWHG

400 YVGSKTKKGWHGVA

401 KTKEGVLYVGSKTKE

402 VTNVGGAW

403 GWHGVTTV

404 EEGAPQEG!

405 GSIAAATGFV

406 SIAAATGFVK

40? AGSiAAATGF

408 LAAATGFVE:

409 APQEGILEDM

410 EEGAPQEGiL

41 i VF GLSKAK

412 AEAAGKTKEG

413 YVGSKTKEGVVHGVT

414 IAAATGFVK

45? GVAEAPGKXK

458 K^' CEOVVHO

459 YVGSKTKEGVVHGVA

460 AVVTGVTAV

461 QVTNVGGAV

462 KT EOVTNV

463 NVGGAWTGV

464 GAVVTGVTAV

465 GVTAVAQ TV

466 EQVT VGGAV

467 VATVAEKTKE

468 GVVHGVATV

469 EG HOVTTVAEKT

470 TTVAEKT EQVTNVG

471 KG VVHGV ATVAEKTK

472 EGWHGV ATVAEKTK

473 ATVAEKT EOVTNVG

474 S1AAATGFV

475 AAATGFV .

476 KTVEGAGSI

477 GSIAAATGF

478 NEEGAPQEGi

479 AATGFVKKDQ

480 FVK DQLG

481. PVDFDNEAY

482 MPVDPO EA

483 DPDNEAYEM

484 EGILEDMPVD

485 MPVDPDNEAY

486 QEGILEDMPV

48? GKTKEGVEYVGSK K

488 KTKEGVLYVGSKTKE

489 MPVDPDNEAYEMPSE

490 ONE A YEMPSEEG YQD

491 EMPSEEGYQDYEPEA

492 SEEGYQDYEPEA

493 GVLYVGS T

494 VLYVGS TK

495 VLYVGS T K

496 MDVFM GLSKAKEGV

497 KGLSKAKEGVVAAAE

498 AKEGVVAAAEKTKQG 499 VAAAE .TKQGVAEAA

500 KTKOGVAEAAGKTKE

501 KQGVAEAAO T EGV

502 VAEAAGKTKEGVLYV

503 AGKT EGVLYVGS T

504 GYLYVGSKTKEGVYH

505 YVGSKTKEGWHGVA

506 GSKTKEGVVHGVA.TV

SO? EGVVHGVATVAE TK

508 GVATV'AEKTKEO^'V'TN

509 ATVAEKT EOVT3STVG

510 AE .TKEQVT VGGAV

51 1 EOVT VGGAWTGVT

512 VGGAVYTGVTAVAOK

513 VTGVTAVAQ TVEGA

514 AVAQKTVEGAGSIAA

515 TVEGAGSIAAATGFV

516 GSIAAATOFVKKDQL

51? ATGFV DQLGK EE

518 KKDQLG NEEGAPQE

51 GKNEEGAPOEGILED

520 GAPQEGILEDMPVDP

521 GILEDMPVDPD EAY

Bion-asrjcer Process[ing

in a. practical implementation, a method is described whereby a biological sample is processed to determine the presence of a TCR specific to an epitope contained in a protein associated with a neurodegenerative disease, as previously discussed. For example, in one em odim nt, the protein may fo m aggregates in a subject, where the aggregates are associated with the neurodegenerative disease. The person of skill will recognise that there are various practical approaches to making such determination,

in a first variant, the person of skill can determine the presence of the TCR specific to such epitope by detecting an increase activation of .lexskocytes contained in the sample, after contacting the leukocytes with the epitope or test compound. For example, t e epitope or compound may include at least one peptide derived frosxx the protein associated with the neurodegenerative disease. In another example, the epitope or compound may include at least one peptide derived froiR the protein that forms aggregates in the subject, where the aggregates are associated with the neurodegenerative disease, in another example, the epitope may include at least one of the peptides listed in any one of Tables 1 to

In s me embodiments, the peptide nay he linked or associated to a carrier, for exasrtple, a major histocompatibility complex (MHC) molecule or an inert carrier, such as streptavidin or avidin beads. General methods for linking a peptide to such carrier are readily available to the person of skill and will, thus, not be further discussed here.

General methods for assaying whether a leukocyte has increased activation are known to those of skill in the art, and may include techniques such as EL Spot assay Western Blot Analysis and ELISA for detecting / assessing cytokine release of activated leukocytes; cell counting and fluorescence-activated cell sorting (FAGS) for assaying increased proliferation and di ferentiation of activated leukocytes; PCR, RT-F-CR, Northern Blot Analysis, and raicrcar ay analysis for assaying differential gene expression o activated leukocytes; and the like. For sake of conciseness, and since such techniques are readily available to the person of skill, these techniques are not further discussed here, in a second variant, the person of skill can determine the presence of the TCR specific to such epitope by detecting the presence of the particular TCR using a gene detection approach. For example, the person or skill m make use of technigues such as PGR, RT~PCR_f Northern Blot Analysis, and the like. Such techniques are readily available to the person of skill. Once a particular TCR specific to a particular peptide is known, the person of skill can desig and / or use particular primers or probe for detecting the presence of the TCR in a particular biological sample, a cell fraction thereof, or a cell culture derived therefrom. Again, for sake of conciseness, and since such technigues are readily available to the person of skill, these techniques are not further discussed here. In other e_s oli_?te∑its of the present invention, there is provided a jnethod comprising; providing a biological sample from a subject; processing the biological saxaple to determine presence of a human leukocyte antigen ( HLA) capable of presenting a peptide, wherein the peptide is a fragrant from a protein having an aberrant protein expression and/or aberrant protein function and/or aberrant protein maerostrueture in a patient having a neurodegenerative disease and the HLA allele is associated with a neurodegenerative disease, identification of the HLAs expressed in a sample or by a patient, i.e. ^HLA typing" can he done using methods known in the art, including ge s detection approaches, in certain embodiments, the present method determines detecting the presence of one or more of the following HLAs; DRB5*01.:0I, DRBl* 15:01, DQB1*03:G4, A* II: 01, DRBI*07;0I, DRBi*09;01, Or DQBI*03:O1..

In a practical implementation, a method is described whereby the presence of the TCR specific to such epitope or the HLA capable of presenting such peptide is indicative of the patient being predisposed, at risk, of or having a neurodegenerative disease or being a potential candidate for treatment of neurodegenerative disease, Non-li ting examples of therapies that are directed to leukocytes that are activated by an epitope include administration of a compound that selectively kills leukocytes that are capable of becoming activated when they are contacted with the epitope, and toierization therapy. For example, toieriration therapy may be implemented by exposing the patient to the particular epitope in a form that alters the immune system to recognise it as self, and halt or reduce making killer ϊ cells.

Such practical implementation may be based, without being limited to any particular theory, on the following scientific rational. The specificity of T cells towards their target antigens is determined by their heterodi eric, hyper-variable T ceil receptor (TCR) molecules, which recognise antigenic peptides that are presented by BC molecules. In imm.une defense situations, the MHC molecules are of ^¾seif"-origin, whereas the antigenic peptides are '-non-self", i,e. they are derived from, viral or m.erobiai peptides. Typically, class~I EC molecules present peptides of intracellular (viral) origin to CDS* T cells, whereas class-II MHC molecules present phagoeytosed (microbial) peptides to CD4+ cells, in addition, ^¾seif" hC moiecxsles also present ^¾seif" peptides, but these are normally ignored, because of T ceil tolerance. It is assumed that in autoimmune diseases the tolerance is broken and recognition of ^seif" peptides results in chronic inflammation, disturbed organ function or tissue destruction.

In further embodiments, t e present methods comprising detecting the presence of both, (i) a. human leukocyte antigen (HLA) capable of presenting a peptide, wherein the peptide is a fragment from a protein having an aberrant protein expression and/or aberrant protein function and/or aberrant protein maerostructure in a patient having a neurodegenerative disease and the B LA allele is associated ¾?ith a neurodegenerative disease and (ix) a ICR specific to an epitope contained in the peptide associated with a neurodegenerative disease, in certain embodiments , the methods comprises (i) providing a biological sample from a subject; processing the biological sample to determine presence of a human leukocyte antigen {BLA} capable of presenting a peptide, wherein the peptide is a fragment from a. protein having an aberrant protein expression and/or aberrant protein function and/or aberrant protein maerostructure in a patient having a neurodegenerative disease; (iij if the HLft is detected in the biological sample, contacting cells in the sample with the peptide to expand the leukocytes and determine the presence of a TCR specific to the epitope. in certain embodiments, the detection in the patient sample of a HLA allele associated with neurodegenerative disease in combination with detection of a TCR specific to an epitope contained in a protein associated with a neurodegenerative disease indicative of the patient being predisposed, at risk of or having a neurodegenerative disease or being a potential candidate for treatment of neurodegenerative disease,

In specific embodiments of the present method, the method comprises determining in the biological, patient sample the presence of an BLA allele listed in Table 5 and the presence of a TCR that binds an epitope listed in Table 5, wherein the presence of such an ELA allele and such a TCR is indicative of the patient being predisposed, at risk of or having a neurodegenerative disease or being a potential candidate for treatment of ne rodegenerative disease,

Table 5

so hkdiag detected,; ad: so doae.

Mso provided is a method for assessing whether a subject afflicted with a disease or condition involving an inflammatcsry response or related, to inf laismation is l iJceiy to benefit or has benefitted from a therapy, wherein the therapy comprises administration of a T cell receptor for a particular antigen :MHC complex ( .g. as provided on a oell through adoptive ϊ cell therapy) , the method comprising, consisting, or alternatively consisting essentially of a) (i> obtaining leukocytes from the subject; (ii) contacting the leukocytes with the antigen bound to as MHC juoieeule; <iii) determining whether the leukocytes have increased activation a ter contact with the a antigen bound to an HC molecule; and Civ) identifying the subject as iibely to benefit ree* the therapy if in step (iii) the leukocytes are determined to have increased activation after contact with the antigen bound to an MHC jsolecule, and identifying the subject as unlikely to benefit from the therapy if in step {ixi} the leukocytes are determined to not have increased activation after contact with the antigen bound to an MHC molecule; or (b) (i) obtaining leukocytes fxovx the subject; (ii) contacting the leukocytes with the antigen bound to an MHC molecule; (iii) determining whether the leukocytes have increased activation after contact with the antigen bound to an MHC molecule; and (iv) identifying the subject as having benefited from the therapy if in step (iii) the leukocytes are determined to have increased activation after contact with the antigen bound to an MHC molecule, and identifying the subject as not having benefitted from the therapy if in step (iii) the leukocytes are determined to not have increased activation after contact with the antigen bound to an MHC molecule .

in some embodiments, provided herein is a method for assessing whether a subject afflicted with a neurodegenerative disease or disorder is likely to benefit or has benefitted from a therapy, wherein the therapy comprises administration of an effective amount of a f ceil receptor for a particular antigen;MHC complex {e.g. as provided on a cell through adoptive ϊ ceil therapy) _f the jnethod comprising, consisting, or alternatively consisting essentially f: { a) (i) obtaining leukocytes from the subject; (ii) contacting the leukocytes with the antigen bound to an MHC molecule; (iii) determining whether the leukocytes have increased activation after contact with the antigen bound to an MHC molecule; and {iv} identifying the subject as likely to benefit from the therapy if in step (iii) the leukocytes are determined to have increased activation after contact with the antigen bound to an MHC molecule, and identifying the subject as unlikely to benefit frois the therapy if in step (iii) the leukocytes are determi ed to not have increased activation after contact with the antigen bound to an MHC molecule; or {£>} (i) SO obtaining leukocytes from, the subject; (ii) contacting the leukocytes with the antigen bound to an MHC .molecule; (iii) determining whether the leukocytes have increased activation after contact with the antigen bound to an MHC molecule; and (iv) identifying the subject as having benefited from the therapy if in step (iii) the leukocytes are determined to have increased activation after contact with the antigen bound to an MHC molecule, and identifying the subject as not having ene itted from the therapy if in step (iii) the leukocytes are determined to not have increased activation after contact with the antigen bound to an MHC molecule, in certain embodiments , the neurodegenerative disease or disorder is a-synucleinopathy, Parkinson's disease, Lewy Body dementia, or Alzheimer ^f s disease.

The following examples are illustrative of procedures which can be used in various instances in carrying: the disclosure into effect,

In one non-limiting embodiment, the herein described methods, processes, and. systems can be used, alone or in combination with one another, for example as diagnostics.

Systems

The herein described methods, systems and procedures may be useful in practical applications for assisting a medical expert, in assessing whether a subject is predisposed to a neurodegenerative disease or that the subject is afflicted with the disease. The person or skill in view of the teachings of the present text will readily understand how to design and perform a system for making such assessments.

With reference to Fig. 6, there is shown a configuration of a system 1.00 for assessing a neurodegenerative disease patient. The system 100 comprises a user interface 102, an apparatus 101 including a processing unit. 104, and an output unit 106.

The user interface 102 includes any one or a combination of a keyboard, a pointing device, a touch sensitive surface, a speech recognition unit or any other suitable device allowing information to be entered by a user. Alternatively, the user interface 102 may be in the form of a data input device such as, but not limited to, a disk drive, CD-ROM, a port connected to a data stream and flash memory . The user interface 102 enables a user to provide a set of information data elements associatod to a certain neurodegenerative disease patient.

The set of biological in ormation data elements may include information pertaining to the presence of a human leukocyte antigen (KLA) capable of presenting a peptide, wherein the peptide is a fragment fro a protein that forms aggregates in a patient having a neurodegenerative disease. Additionally or alternatively, the set of information data elements may include information pertaining to the presence of a ? ceil receptor (TCR) specific to such peptide.

Optionally, the set of information data elements may also include information derived from cognitive assessment test results associated with suspected AD; measurement of motor manifestations, assessment of ability to perform daily functional activities, and symptomatic response to medication with suspected PD; measurement or assessment of loss of function or gradual, slowly progressive, painless weakness in one or isore regions of the body, without changes in the ability to feel, with suspected ALS; patient age; and the like.

Other suitable in ormation data elements may also be provided through user interface 102 in alternative implementations.

The apparatus 101 is configured to receive the set of information data elements. The apparatus 101 processes the set of information data elements to generate information associated with the neurodegenerative disease patient. In the specific embodiment shown in Figure 15, apparatus 101 includes a processing unit 104, an input 110 and an output 114, Input 110 is operative for receiving signals from the user interface 102 indicative of a set of information data elements associated to the patient. As shown in Fi e 15, the processing unit 104 is in communication with input 110 for receiving the signal or signals indicative of a set of information data elements associated to the patient. As will be described in more detail below, on the basis of the signal or signals received at input 110, the processing unit 104 is operative to generate information associated with the neurodegenerative disease patient. The information conveys the l keli ood of the predisposition or presence of the neurodegenerative disease,

The apparatus 101 releases at output 114 a signal for causing output unit 106 to convey the information to a user. The output unit 106 may be in the form of any suitable device for conveying information to the physician or other health care professional, in a specific example of implementation, the output unit 106 can include a display screen, or in an alternative example of implementation, the output unit 106 can include a printing device for displaying the data in printed form.

As shown in Figure 16, the processing unit 104, in accordance with a first specific embodime t, includes a neurodegenerative disease generation module 210, a memory unit £20 and an output control module 240.

Memory unit 220 stores a plurality of instructions and is configured to provide these instructions to the processing unit 104. When executed, these instructions cause the processing unit 104 to;

(i) receive first and second biological data elements for an individual frojn a bioiogicai data source, wherein the first biological data element comprises data pertaining to the individual's human ieukocyte antigen (HLA) typing and the second biological data element comprises data pertaining to the individual'^' s T ceil receptor (TCR) repertoire?

{11} merge the first and second biological data elements from the biological data source to obtain a set or merged biological data associated with the individual, including to;

1} identify data in the first and second bioiogicai data elements that indicates a reciprocity, the identified data corresponding to a reciprocal presence of an HLA typing value in the first bioiogicai data element and of a TCR repertoire value in the second bioiogicai data element;

2) compare the identi ied data with at least one of an element of HLA typing values and TCR repertoire values stored on S3 the one or more memories, said values stored on the one or more memories being associated with, reference individuals; nd

3) determi e a likelihood or predisposition score based on at least the identified data and on the comparison; and

{iii} display the likelihood or predisposition score in a graphical user interface {GUI) .

Those skilled in the art should appreciate that in some non~ im ting embodiments, all or part of the functionality previously described herein with respect to the components of the system 100 for assessing a neurodegenerative disease patient, to perform operations for providing the TCR and/or HLA im une-prof^"iiing functionality to a user as described throughout this specification, may be implemented as pre-programmed hardware or firmware elements (e,g. , application specific integrated circuits (ASICs) , electrically erasable programmable read-only memories (EEPRGMs) , etc,} , or other related components .

In other non-limiting embodiments, all or part of the functionality previously described herein with respect to the system 100 ior assessing a neurodegenerative; disease patient to perform operations for providing TCR and/or HLA immune-profiiing functionality to a user as described throughout this specification, may be implemented as software consisting oi a series of program instructions for execution by one or more computing units. The series of program instructions can be tangibly stored on one or more tangible computer readable storage media e.g., removable diskette, CD-ROM, ROM, PROM, EPROM or fixed disk) , or tbe instructions can be tangibly stored remotely but transmittable to the one or more computing unit via a modem or other interface device {e.g. , a communications adapter) connected to a network over a transmission medium. The transmission medium may be either a tangible medium (e,g,, optical or analog communications lines) or a medium implemented using wireless techniques {e.g. _f microwave, infrared or other transmission sebem.es) . Those skilled in the art should, further appreciate that the program instructions ni.ay be written in a number of programming languages for use with many computer architectures or operating systems. Terms

Unless otherwise defined, all technical and scientific terms used herein have the sane meaning as conunonXy understood by a person of ordinary skill n the art to which this inventio belongs. As used herein, and unless stated otherwise or required otherwise by context, each of the following terms shall have the definition set. forth below .

As used herein, ^¾about" in the context of a numerical value or range means ±10% of the numerical value or range recited or claimed, unless the context requi es a more limited range.

As used herein, a *subject afflicted with" a condition, e.g, PD, LBD, ALS or AD, means a subject who was been affirmatively diagnosed to have the condition . Embodiments of the present invention relate to determining whether leukocytes have increase activation after contact with an epitope or test compound. It will be understood that the ^increased activation" of the leukocytes is in response to contact with the epitope or the test compound. General methods for assaying whether a ieuhocyte has increased activation will be known to those of ordinary skill in the art. Additionally, assays for determining increased activation that are described for particular epitopes or test compounds in the Examples herein may be applied to other epitopes and test compounds of the invention .

In some embodiments, the leukocytes are determined to have increased activation after contact with the epitope if the leukocytes release a cytokine. In some embodiments, the leukocytes are determined to have increased activation after contact with an epitope or test compound if the leukocytes release a cytokine that is not released by corresponding S5 leukocytes not contacted with the epitope or test compound. In some embodiments, a cytokine is determined to be released if there is a nvinimua of about 5, 10, 15, 20,· 25, 30, 35, 40, 5, 50, 100, or about- 10-50 spot-forming ceils (SFC) per million cells are measured using an ELISpot assay comprising the colorinetric detection of the cytokine. In some embodiments, the leukocytes are determined to have released the at least one cytokine if there are over 20 spot-forming cells {SFC} per million cells as measured by an ELISpot assay comprising the coiorimetrie detection of the at least one cytokine, A person having ordinary skill in the art will readily be able to perform the ELISpot assay in embodiments of the invention using the disclosures herein, ELISpot assays are described in Cserkinsk.y at al . (1988) Reverse ELISpot Assay for Clonal Analysis of Cytokine Production, I. Enumeration of g mma- Interferc-n-Secreting Cells, J. Immunol . Methods, 110 i 29; Sedgwick and Holt, {1983} A Solid-Phase Imnuinoenzyinatic technique for the Enumeration, of Specific Antibody-Secreting Ceils, J. Im unol, Methods, 57; 301; and Cserkinsky et al . (2.383) A Solid-Phase Enzyme-Linked immunespot (ELISPOT} Assay for Enumeration of Specific Antibody Secreting Cells, J. Immunol. Methods,, 65:103, the entire content of each of which is incorporated here n by reference.

In some embodiments, the leukocytes are determined to have increased activation after contact with an epitope or test compound if the leukocytes release store of a cytokine than corresponding leukocytes not contacted Kit the epitope or test compound. In some embodiments, the leukocytes are determined to have increased activation after contact with the epitope or test compound, if the leukocytes release about 1, 2, 3, , 5_f 10, 15, 20, 25, 30, 35,· 40, 45, 50, 55, 60, 65,· 70, 80, 90, 100, ISO, 200, 300, 400, 500, 750, 1,000, or 1-5,000% more of a cytokine than corresponding leukocytes not contacted, with the epitope or test compound. Additional thresholds can be defined based on comparison with reactivity of, for example, non-PD donors (ie, healthy controls) . Methods for assaying increased cytokine release include but are not limited to the ELISpot assay, Western Blot Analysis and ELISA, which will be well understood to those in the art. in some embodiments, the leukocytes are determined to have increased activation after contact with the epitope or test compound if the leukocytes proliferate, and corresponding leukocytes not contacted with the epitope or test com ound do not proliferate. In some eifibodijnents, the leukocytes are determined to have increased activation after contact with the epitope or test compound if the leukocytes proliferate more than corresponding leukocytes not contacted with the epitope or test compound. In some embodiments, the leukocytes are determined to have increased activation after contact with the epitope or test compound if the leukocytes proliferate about 1,· 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 90, 100, 150, or 200% more than corresponding leukocytes not contacted with the epitope or test compound. In some embodiments the leukocytes are determined to have increased activation after contact with the epitope or test, compound if the leukocytes become di ferentiated after contact with the epitope or test compound, and corresponding leukocytes not contacted. Kith the epitope or test compound do not become differentiated. In some embodiments the leukocytes are determined to have increased activation after contact with the epitope or test compound if the leukocytes are jsore differentiated than corresponding leukocytes not contacted with the epitope or test compound. Methods for assaying increased proliferation and. differentiation are well known in the art, and include cell counting and fluorescence—activated cell sorting (FACS) .

In some embodiments, the leukocytes are determined to have increased activation after contact with the epitope o test, compound if the leukocytes express a gene at a higher or lower level than corresponding leukocytes not contacted with the epitope or test compound, in some embodiments, the expression is about 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 90, 100, 150, 200, 300 400, 500, 750, 1,000, or 1-5,000% higher or lower than in the corresponding leukocytes, In some embodiments, the gene encodes a cytokine. Examples of genes which are di ferentially expressed in activated T cells are described in Teague et ai. {1999} Activation changes the spectrum but not the diversity of genes expressed by T cells, ΡΝΛ3 Vol. 96, ¾o, 22,· 12691.-·ί26θδ, the entire content of which is hereby incorporated herein by reference. Met ods for assaying gene expression are well known in the art, and include PCP., RT-PCR, Northern Blot Analysis, and microarray analysis,

The release, proliferation, differentiation or change in expression may be measured at, for example, about 0.5, 1, 2, 3, 4, 5, 6, 10, 12, 18, 24, 30, 36, 42, 48, or 72 hours after the leukocytes are contacted with the epitope or test compound.

As used herein, the term ^w -eell receptor^fi, or ^W C ", is a molecule found on the surface of ΐ cells, or τ lymphocytes, which is responsible for recognising fragments of antigen as peptides bound to jsajor histocompatibility complex { HC) molecules , %^:hen the CR engages with antigenic peptide and HC <peptile/MHC} , the Ϊ lymphocyte is activated through signal, transduction, that is, a series of biochemical events mediated by associated ensymes, co-receptors, specialized adaptor molecules, and activated or released transc iption factors.

As used herein, the terra ^biological sample" includes a biological sample that contains immune cells. Such immune cells are generally isolated from peripheral blood, secondary lymphoid tissue and effector sites of activated immune ceil, populations (e.g. lung, gut, or intestine). The herein described sam le can be obtained by any known technique, ror example by drawing, by non-invasive techniques, or from sample collections or banks, etc. The sample may be processed so as to isolate a cellular fraction thereof. For example, in the case of blood, the cellular fraction can be fractionated from whole blood by centrifugation, using for instance gentle centrifugafion at about 300~800x g for about five to about ten minutes, or fractionated by other standard methods.

As used herein, the terra "peptide" describes a group of molecules consisting of up to 50 amino acids. Peptides may further form dimers, imers and higher oligomers, i.e. consisting of more than one molecule which iuay be identical or non-identical. The corresponding higher order S8 structures a e, consequently, termed, hojno- or heterodijners, homo- or heterot.ri.mers etc. The term ^peptide'' (wherein ^polypeptide" is interchangeably used with ^protein") also refers to naturally modified peptides wherein the modification is effected e.g. by giyeosylation, acetyiation, phosphorylation and the like. Such modifications are well- known in the art. Preferably, the peptides have a inimus; length of at least 4 amino acids, such as for example at least 5, at least 6, at least ?, at least 8, at least 9 or at least 10 amino acids . Also preferred is that, the peptides have a length of at the most 50 amino acids, such as for example at raost 45, such as at most. 40, at most 35, at most 30, at most 25, at most 20 amino acids. Any of the intermediate: numbers not. explicitly Mentioned are also envisaged herein. More preferably, peptides represented by HC class I molecules have a length of between 4 and 20 amino acids. Thus, said peptides may be 4, 5, 6, 7, 8,· 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 1.9 or 20 amino acids in length. Also preferred is that peptides represented by MHC class II molecules have a length of between 4 and 50 ajmino acids. The class ∑I peptides m in principle be infinitely long, because they may reach out from the MHC binding groove at both sides. The epitope itself is normally 8 to 10 amino acids long. Thus, said peptides may be 4, 5, 6, 7, 8, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 33, 40, 41, 42, 43, 44, 45, 46, 47, 4S, 49 or 50 amino acids in length, As used herein, a stretch of ^consecutive .amino acids" means a plurality of amino acids arranged in a chain, each of which is joined to a preceding amino acid by a peptide bond, excepting that the first amino acid in the chain may optionally not he joined to a preceding amino acid. The amino acid of the chain .may be; naturally or non-naturally occurring, or may comprise a mixture thereof. The amino acids, unless otherwise indicated, may be genetically encoded, natural l.y™oceur i g but not genetically encoded, or non-natural ly occurring, and any selection thereof,

in :;:o;·····? embodiments, the epitope peptide may be post-translationaily modified and/or shortened and/or elongated on both sides As used herein a therapy that is "directed to leukocytes that are activated by an epitope" is a therapy tha selectively reduces or prevents the activa ion of the leukocytes by the epitope, it will be understood that selectively reducing or preventing the activation ot^" leukocytes by an epitope includes killing the leukocytes or reducing the viability or proliferation of leukocytes that are capable of becoming activated when they are contacted with the epitope. Non-limiting examples of therapies that are directed to leukocytes that are activated by an epitope include administration of a compound that selectively kills leukocytes that are capable of becoming activated when they are contacted with the epitope, and toleri nation therapy.

As used herein, ^tolerization t erapy" or ^{^}antigen-specific toierization" comprises exposing a subject with an epitope in a way that alters the subject's iisraune system to have reduced activation by the epitope, oieriEation therapy results in a decrease in the activation of a leukocyte of the subject, such as a T ceil, by the epitope, Toisriration therapy is discussed in Coppieters et al. (2013) Clinical I m nology_! 149, 345-355; Biiietta et al, (2012) CUn Immunol, 145 (2) : 94-101; and Lutterotti and Martin (2014) Expert Opinion on Investigations! Drugs, Vol, 23 f No, 1, pages 9-20, the entire content or each or which is hereby incorporated herein by reference, Aspects of the present invention relate to a compound comprising a major histocompatibility complex (MHC) Tetrainer and a .oxin - MBC trainers are complexes of four Major Histocompatibility Complex (MSC) molecules which are each associated with a specific molecule. The specific molecule may he an epitope of the invention, in some embodiments, the four MHC molecules are associated with each other via a tetra.merisat.ion agent, in some embodiments, the MHC Tetranter comprises four MBC monomer fusion proteins, wherein each MBC monomer fusion protein comprises a MBC molecule and biotin. In some embodiments, the tetrasterization agent is strsptavidin or avidin. In the compound, a MHC Tetramer may be coupled to a toxin by, e.g., a covaient bond, a linker, a streptavidin-biotin interaction or a streptavidin-avidin interaction. In some eat odiments , the toxin is covalently bound to the streptavidin or the avidin. There are two types of Tetra ers, Class I and Class II. In some embodiments, the MHC molecules of a Class I

are mutated to rainimize binding of the t¾HC molecule to CD8+ ceil surfaces. These Ciass Ϊ letra ers show diminished CD8~ mediated binding to the general. CD8+ lymphocyte population, but retain MHC peptide-specific binding to ICR thus facilitating targeting of specific ceils that are activated by the epitope, MHC Tetramers are described in 0,8. Patent Application Publication No. 2004/0137642 Al, published July IS, 2004; Bess et al . , (200?) Selective deletion of antigen-specific CDS-*- T ceils by MHC ciass I tetracers coupled to the type I ribosome-inact ating protein saporin. Blood, 106 ; 3300-3307; and at www . eefcmauoouIter. com/¾?srportal/«sr/resea rch-and-discover /products - and~services/fIow~cytojnetry/ciass~I~itag~mhc~tetramer /index . htsi, the entire content of each of which is hereby incorporated by reference.

It will be understood that by ^treating'' a subject there are ultiple possible outcomes. For instance, treating a subject may comprise substantially reducing,- slowing, stopping, preventing or reversing the progression of a disease, particularly a neurological disorder such as PD, LBD, or AD. Additionally, treating a subject may comprise substantially reducing, slowing, stopping, preventing or reversing a symptom of a disease, ∑n the most favorable case, reduction is equivalent to prevention.

As used herein, a ^symptom" associated with PD, DBD, A1S or AD includes any clinical or laboratory manifestation associated with PD, LBD, ALS or AD and is not limited to what the subject can feel or observe. Commo symptoms of PD include but are not limited to tremors, muscle stiffness, difficulty maintaining balance, difficulty .maintaining posture, bradykinesia, akinesia, rigid limbs, a shuffling gait, and a stooped posture. Other symptoms of PD include but are not limited to depression, personality changes, dementia, sleep disturbances, speech impairments, and sexual difficulties. Common symptoms of ALS include but are not limited to fascicuiations {muscle twitches) in the arm, leg, shoulder. or tongue, muscle cramps, tight and stiff muscles ( spasticity) , muscle weakness affecting an arm, a leg, neck o dia hragm, slurred and nasal speech, difficulty chewing or swallowing, muscle atrophy. Other symptoms of ALS include hut are not limited to depression, personality changes, dementia, sleep disturbances, speech impairments, and sexual difflenities.

The term * HC" s used interchangeably with H LA herein. The genetic loci involved in the rejection of foreign organs are known as the major histocompatibility complex (MHC) , and highly polymorphic ceil surface molecules are encoded by the MHC. The human MBC is called the HLA (Human Leukocyte Antigen) system, when the specific HLA gene encoding the MBC recognized by the ΐ cell receptor under investigation is not known, then a preceding experiment may be performed to screen the complete set of all MHc (BLA) molecules expressed from all alleles of the subject, e.g. of a patient, using methods well established in the art, such as for example as discussed in Robinson J, et al, (2003) Nucleic Acids Research, 31:311-314; Bsttinotti et ai. (2003) J. Immunol . Hefh. 275:143-148; Marsh et al (2010) Tissue Antigens 75:291-455,

The term "genetic data*' as used herein refers to information derived from a laboratory assay whereby a biological sample is processed in order to determine genetic data contained therein. For example, such genetic data may include data obtained from sequencing. Methods for sequencing comprise, without being limiting, approaches of seguence analysis by direct sequencing, fluorescent SSCP in an automated A sequencer and pyro-sequencing. These methods are well known in the art, see e.g. Adams et al . (Ed,), *Automated D A Sequencing and Analysis", Academic Press, 1994; phay, " MA Sequencing: From Experimental Methods to Bioinformatics", Springer Verlag Publishing, 1997; Ramon et ai . , J. Transl. Med. 1 {2003) . sub « 9; eng et ai., J, Clin. Endocrinol. Metab, 90 (2005) 3419-3422.

As used herein, the terms ^individual," "subject," and "patient," generally refer to a human subject, unless indicated otherwise. As used herein, the tern ^treating" a subject includes multiple possible outcom.es . For instance, treating a subject may comprise substantially reducing, slowing, stopping, preventing or reversing the progression of a disease, particularly a neurological disorder suc as PO, LBO, or AD, Additionally, treating a subject nay comprise substantially reducing, slowing, stopping, preventing or reversing a s tom of a disease;. In the most favorable case, reduction is equivalent to prevention.

The terms "determining, '"^' "measuring,'' ^evaluating, " "assessing," and ^assaying," as used herein, generally refer to any form of measurement, and include determining if an element is present or not in a biological sample. These terms include both quantitative and/or qualitative determinations, which require sample processing and transformation steps of the biological sample. Assessing may be relative or absolute. The phrase ^assessing the presence; of" can include determining the amount of something present, as well as determining whether it is present or absent ,

The term ^stringent assay conditions" generally refers to conditions that are compatible to produce binding pairs of nucleic acids, e.g., probes and target TCR gene, of sufficient complementarit to provide for the desired level of specificity in the assay while being generally incompatible to the formation of binding pairs between binding members of insufficient complementarity to provide fo the desired specificity. The term '-stringent assay conditions" generally refers to the combination of hybridisation and wash conditions,

A label" or a "detectable moiety" in reference to a nucleic acid, generally refers to a composition that, when linked with a nucleic acid, renders the nucleic acid detectable, for example, by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. Exemplary labels include but are not limited to radioactive isotopes, magnetic beads, metallic beads, colloidal, particles, fluorescent dyes, enzymes, biotin, digoxigenin, haptens, and the like. A "labeled nucleic acid or oligonucleotide probe^fi is generally one that is bound, either covalently, through a linker or a chemical bond, or noncovaiently, through ionic bonds, van de Waals foroes, electrostatic attractions, hydrophobic interactions,■ or hydrogen bonds, to a label such that the presence of the nucleic acid or probe can be detected, by detecting the presence of the label bound to the nucleic acid or probe.

In one non limiting esrfcodiment, the herein described detection agent comprises a nucleic acid primer (or probe) having a sequence f 6-50, or 10-30, or 15-30, or 20-30 contiguous nucleotides of the target TCP,, including any length between the stated ranges . Such primer may be present, if desired, on a microarray.

Primers (or probes) are usually single-stranded for maximum efficiency in amplification/hybridisation,. but nay alternatively be double- stranded. If double-stranded, the primers (or probes) are usually first treated to separate the strands before use; this denaturation step is typically done by heat, but may alternatively be carried out using alkali, followed by neutralization.

By wa of a non-limiting example, the primers (or probes) for detecting a circulating jrderoRHA may be labeled, using labeling techniques that are known to one skilled in the art, to facilitate detection, including but not limited to radioisotope labels or fluorescent iabeis. The primers (or probes) can hybridize to nucleic acid molecules that are either or both strands of the double stranded nucleic acid molecule portion of the jsicroRNA.

A "label" or a ^detectable moiety" in reference to a detecting agent, in particular in the case of primers (or probes), generally refers to a compound that, when linked with at least one detecting agent, renders it detectable, for example, by spectroscopic, photochemical, biochemical, ijxmunoche ieai, or chemical means. An example of a "label" or a ^detectable moiety" includes but is not limited to radioactive isotopes, jsagnetic beads, metallic beads, colloidal particles, fluorescent ayes, enzymes, biotin, digoxigenin, haptens, and the like, in this context, ^¾ labeled" primers (or probe) includes primers (or probe) that are bound, either covaientiy, through a linker or a chemical bond, or noncovalently, through ionic bonds, van der Waals forces, electrostatic attractions, hydrophobic interactions, or hydrogen bonds. to a label such that e presence of the primers (or probe) can be detected by detecting the presence of the label bound to the primers {or probe) .

A detectable label may be included n a amplification reaction. Suitable labels include fiuorochromes , e.g., fluorescein isothiocyanate CFITC} _f rhodamine, Texas Red, phycoerythrin, a1 lopbyeocyanin, 6- carboxyfluorescein ( 6~F¾M) , 2 ' , 7¹ ~di_?te hoxy~ ' , 5¹ ~dichioro~6~ carboxyfiuorescein (JOE) , 6-carboxy~X~rh.odamine <ROX) , 6-carboxy™ 2 ^! , ' , 7 ' , , 7~hexachiorofiuorescein (BEX), 5~carboxy£iuorescein (5~FAM) or N , hi % * ~tetramethyi~6-carboxyrhodamine {TA RA.} , radioactive labels, e.g. 32P, 35S, 3H; etc. The label m be a two stage system, where the ampli ied DMA is conjugated to biotin, haptens, etc. having a high affinity binding partner, e.g., avidin, specific antibodies, etc, where the binding partner is conjugated to a detectable label. The label may be conjugated to one or both of the primers. Alternatively, the pool of nucleotides used in the amplification be labeled, so as to incorporate the label into the amplification product. All of these and other labeis are well known in the art and one can select corresponding snitabie means for defecting such labels without departing from the present invention.

Hybridization primers (or probes) may be coupled to labels for detection. As Kith ampli cation primers, several methods and compositions for derivitizing oligonucleotides with reactive functionalities that permit the addition of a label are known in the art. War example, several approaches are available for biotinylafing probes so that radioactive, fluorescent, c emiluminesce>nt., enzymatic, or electron dense labels can be attached via avidin. See, e.g., Broken ef ai , , Naei, Acids Res, (1378) 5:363-384 which discloses the use of fer ritin-avidin-biotin labels; and Choiiet et al. Noel, Acids Res. (1985) 13:1529-1541 which discloses biotinyiation of the 5' termini of oligonucleotides via an aminoalfcyiphospheramide linker arm. Several methods are also available for synthesizing amino-derivatized oligonucleotides which are readily labeled by fluorescent or other types of compounds derivatised by amino- reactive groups, such as isothiocyanate, N~hydroxysuccinimide, or the like, see,^, e.g., Connolly U987) Nucl, Acids Res, 15:3131-3139, Gibson at al. (1987) .cl . Acids es, 15:6455-646? and U.S. Pat. Sio. 4, 605,735 to Miyoshi et al, Methods are also available for synthesizing suifhyoryi- derivatized oligonucleotides which ca be reacted with thioi-specific labels, see, e.g., U.S. Pat, o. 4,757,141, Connolly et al . (1985) Hue. Acids Res. 13:4485-4502 and Spoat et al. (198?) Nucl . Acids Res. 15:4837- 4848, A comprehensive review of methodologies for labeling D¾ fragments is provided in Matthews et al-, Anal. Rioehea. (1988) 169:1-25,

For example, probes na be flaorescently labeled by linking a fluorescent molecule to the ncn-ligating terminus of the probe. Guidance for selecting appropriate fluorescent labels can be found in Smith et ai,, Meth, Enzymol . (19S?) 155:260-301; arger et al . , Nucl . Acids Res. (1991) 19:4955-4962; Haugland (1989) Handbook of Fluorescent. Probes and Research Chemicals (Molecular Probes, inc. , Eugene, Greg. } . ∑n one eifibodiment, fluorescent labels include fluorescein and derivatives thereof, such as disclosed in U.S. Pat. So, 4, 318,846 and Lee et al,, Cytometry U98S) 10:151-164, and 6-FA , JOE, TAM A, ROX, BEX-l, HEX-2,· ZOE, E -i or A - i, and the like.

Additionally, probes can be labeled, with an acridinium ester (AS) . Current technologies allow the AS label to be placed at any location within the probe. See, e.g., Nelson et ai . (1995) ""Detection of Aeridini rfi Esters by Chexniluminescence" in Nenisotopie Probing, Blotting and Sequencing, Kricka L. J, (ed) Academic Press, San Diego, Calif,; Nelson et al, (1994) ^Application of the Hybridization Protection Assay {HPA} to PCR" in The Polymerase Chain Reaction, Huliis et ai . (eds,) Birkhanser, Boston, Mass.; Weeks et al., Clin. Chem. (1983) 29:1474™ 1479; Berry et al,, Clin. Chem, (1988) 34:2087-2090. An AE molecule can be directly attached to the probe using non-nucleotide-baseo linker m chemistry that allows placement of the label at any location within the probe. See, e.g., rj.S. Pat, Ho . 5,585,481 and 5,185,439.

Hybridisation (e.g., formation of a nucleic acid duplex) refers to the ability of a strand of nucleic acid to join with a complementar strand via base pairing. Hybridization occurs when complementary nucleic acid sequences in the two nucleic acid strands contact one another unde appropriate conditions .

Nucleic acid hybridization is affected by such conditions as salt concentration, tem erature, or organic solvents, in addition to the base composition, length of the complementary strands, and the number of nucleotide base mismatches between the hybridizing nucleic acids, as will bo readily appreciated by t ose skilled in the art. Stringency conditions depend on the length and base composition of the nucleic acid, which can be determined by techniques well hnown in the art. Generally, stringency can be altered or controlled by, for example, manipulating temperature and salt concentration during hybridisation and washing. For example, a combination of high temperature and low salt concentration increases stringency. Such conditions are known to those skilled in the art and can be found in, for example, Strauss, W. . ^Hybridization kdt.h Radioactive Probes," in Current Protocols in Molecular Biology 6.3,1- 6.3.6, (John Wiley & Sons, Y. 2000), Both aqueous and non-aqueous conditions as described in the art can be used.

An ex mple of stringent hybridization conditions is hyb idization in 0.1 x SSC (15 mM sodium chloride /1, 5 mM sodium citrate) at 50 degree C, or higher. Another example of stringent hybridisation conditions is hybridization overnight at 42 degree C, in 50% rorsiamide, 1 κ SSC (150 .mM NaCl, 15 HJM sodium citrate), 50 mM sodium phosphate (pH 7.6) , ox Denhardt's solution, 10% (w/v) de¾tran sulfate, and 20 pg/mX denatured, sheared salmon sperm DNA, followed by washing in 0 , lx SSC at about 65 degree C. Highly stringent conditions can include, for e ample, aqueous hybridization (e.g. , free of formami.de) in 6x SSC (where 20x SSC contains 3,0 M Had and 0,3 sodium citrate), 1% (w/v) sodium dodecyl sulfate (SDS) at 65 degree C, for about 8 hours (or more), followed by one or isore washes in 0.2x SSC, 0,1% SDS at 65 degree C,

Moderately stringent hyb idization conditions permit a nucleic acid to bind a complementary nucleic acid that has at least about 60%, at least about 75%, at least about 85%, or greater than about 90% identity to the complementary nucleic acid. Stringency ot hybridisation is generally reduced by decreasing hyb idization and. washing temperatures, adding 9? tOrmaiaide to the hybridisation buffer, or increasing salt concentration of the w shing buffer, either individually or in combination. Moderately stringent conditions can include, for exam le, aqueous hybridisation (e.g. , free of foraamb.de) in 6x SSC, 1% (w/v) SDS at 65 degree C. for about 8 hours (or more), followed by one or jsore washes in 2x SSC, 0.1% SDS at room temperature . Another exemplary hybridisation under moderate stringency comprises hybridization in 6x SSC, 5x Denhardb's reagent, 0.5% (w/v) SDS, and. optionally 100 pg/ml sonicated salmon or herring sperm DHA, at about 42 degree C, followed by washing in 2JE SSC, 0,1% (w/v) SDS at 65 degree C. Other permutations and possibilities will be readily apparent bo those of ordinary skill in bhe art, and are considered as equivalents within the scope of the instant invention.

As used herein, the terms ^*compleatentary" or contplementarity" are used in reference to ^polynucleotides" and "oligonucleotides" {which are interchangeable terns that refer to a sequence of nucleotides) related by the base-pairing rules. For example, the sequence ^W5'~CAGT~3 * , " is complementary to the seguence "5 * -&CTG-3 ' . " Complementarity can be ^partial" or ^wtotal . " Partial" complementa ity is where one or more nucleic acid bases are not matched according to the base pairing rules, "Total." or ^complete" complementarity between nucleic acids is where each and every nucleic acid base is matched with another base unde the base pairing rules. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands . This is of particular importance in .amplification reactions, as well, as detection methods which depend upon binding between nucleic acids.

In one non-li iting embodiment, substantially complementary nucleic acids have at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% identical nucleotides.

As used herein, the term "about" for example with respect to a value relating to a particular parameter (e.g. concentration, such as "about 100 taM" ) relates to the variation, deviation or error (e.g. determined via statistical analysis) associated with a device or method used to measure the parameter. For exam le, in the case where the value of a parameter is based o a device or raethcd which is capable of measuring the parameter with an error of .-÷---< 10%, about" would encompass the range from less than 10% of the value to more than 10% of the value.

As used herein, ^effective" when referring to an amount of a compound administered to a subject for the treatment of a neurological disease refers to the quantity of the compound that is sufficient to yield a desired therapeutic response without undue adverse side effects (such as toxicity, irritation, or allergic response) commensurate with a reasonabie benefit/risk ratio when used in the manner of this invention,

Amino acid sequence of Tau is accessible in public databases by the accession number P10636-1 and is set forth herein as SEQ ID NO; 522, Nucleotide sequences for tau is accessible in public databases by the accession number J03778.1, which is set forth herein as SEQ ID HO: 523, Amino acid and nucleotide sequences of Tau are also accessible in public databases by the tiCBl Gene ∑D: 4137, The name of the Tau gene is microtubule-associated protein Tau (MAPT) , The amino acid sequence of amyloid β is accessible in public databases by the accession number P 05067-1 and is set forth herein as 5RQ ID NO: 524,

The amino acid sequence of TDP43 is accessible in public databases by the accession number Q13148 and is set forth herein as SEQ ID NO; 525, The amino acid sequence of R^A-binding protein FUS is accessible in public databases by the accession number ϊ3Ρ_004351,1 and is set forth herein as SEQ IB NO: 526. The amino acid sequence of superoxide dismutase is accessible in public databases by the accession number NP 000445,1 and is set forth herein as SEQ ID SO 527.

Amino acid sequences of a-syn are accessible in public databases by the accession nucibers ΝΡ_000336 and NP_00S2S2, which are set forth herein as SEQ ID NOs : 52S and 529 respectively. Nucleotide sequences fo a-syn is accessible in public databases by the accession numbers NM 000345 and NMJ3Q7308, w ich are set forth herein as SEQ ID NOs : 530 and 531 respectively. The amino acid, sequence of ieucine-rich repeat kinase 2 (IiRRK2) is accessible in public databases by the accession num er HP 940980 and is set forth herein as SEQ ID NO: 532, A nucleotide sequence for LRRK2 is accessible in public databases by the accession niH¾foer KIM 198578, which is set fort herein as SEQ ID NO; 533, The amino acid sequence of giaeoeerebrosidase is accessible in public databases by the accession number ΒΆ&02545 and is set forth herein as SEQ ∑D NO: 534, A nucleotide sequence for giucocerebrosidase is accessible in public databases by the accession number D13286, which is set forth herein as SEQ ID NO: 535, Amino acid and nucleotide sequences of tau are accessible in public databases by the NCB∑ Gene ID; 4137, The name of the tau gene is microtubule-associated protein tau (MAPI) , Aspects of the present invention relate to the HLA alieies. Additional information HLA alleles is available in Yokoyajna ef ai , (2016) Association Between Genetic Traits for irfmuine-Mediated Diseases and Alzheimer Disease, JAMA Neurol 73 (6) : 691~6S7_r the entire content of which is incorporated herein by reference. Aspects of the present invention relate to the specific HLA alieies DRB5*0l:01, DRBl*15;0i, DQBl*03iG , A*X1:01, DKB1*Q7:01, DRB1*09:01, or DQBl*O3:0i. The amino acid sequence for the DRB5*0l:01 protein sequence is set forth herein as SEQ ID NO: 536 and the aiEiino acid sequence for the DRB1*15:01 protein sequence is set forth herein as SEQ ID NO; 537, The amino acid sequence for the DQB1*03;04 protein sequence is set forth herein as SEQ ID HO; 538, The amino acid sequence for the A*X1:01 protein sequence is set forth herein as SEQ ID HO; 533. The amino acid sequence for the DRBl^"*0 :01 protein sequence is set forth herein as SEQ ID NO; 540, The amino acid sequence for the DRB1*09:01 protein sequence is set forth herein as SEQ ID O: 541, The aiEiino acid sequence for the DQB1*03:01 protein sequence is set forth herein as SEQ ID KOi 542, Additional information about these and other HLA alleles is available in issemann et ai, {2013} Association of Parhinson disease with structural and regulatory variants in the HLA region. Am 0" Bum Genet, 93:984-993, PMC3824il6, the entire content of which i incorporated herein by reference, Additional information. including sequence information, relating to these alleles and other alleles disclosed herein is available at www , ebi ,ac , uK/ipd/imgt/hia/ailele . tnti . It will be understood that persons skilled in the art are able to identify and obtain sequences and genomic locations tor the HLA alleles disclosed herein using knowledge in the art,

Hon-limiting examples of compounds which may be used in the treatment of AD in embodiments of the invention include hoixnesterase inhibitors {e.g,, dcnepssii, rivaatigmine, galantaraine, and tacrine) , tf-stethy1~d-aspartate receptor antagonist (e.g., me-mantine) , high-dose vitamin E (1000 IU po once/day or bid), selegiline, NSAIDs, Ginkgo bileba extracts, and statins,

Hon-iimiting examples of compounds which raay be used in the treatment or PD in embodiments of the invention include growth factors (e.gv, GDSF) , cell transplantation, deep brain stimulation, anti-inflammatory drugs .

Non~limiting examples of compounds which may be used in the treatment of PD in embodiments of the invention include dopamine precursors (e.g., ievodopa and carbidopa) , dopamine agonists (e.g., bromocriptine, pramipexoie, ropiniroie, apomorphine, and rotigotine) , MftO-B inhibitors (e.g., rasagiline, selegiline, and pargyline) , CQMT inhibitors (e.g., entacapone and toicapone) , anticholinergic compounds (e.g., trihexyphenidyl, benztropine, amitiriptyline and diphenhydramine) antiviral co pounds (e.g., amantadine) , beta-blockers {e.g., propranolol), calcium channel blocker (e.g. isradipine and dihydropyridine) , and antioxidants, Non-i imiting examples of compounds which may be used in the treatment of ALS in embodiments of the invention include riluzcle (Rilutek) and edaravone sRadicava , baclofen, quinine or phenytoin, anticholinergic drug (eg, glyoopyrrclate, amitriptyline, benztropins, trihexyphenidyl, transdermal hyoscine,- atropine, amitriptyline, fluvoxa in , or a combination of dextromethorphan,

Hon-limiting e am les of contpounds which may be used in the treatment of AD, PD or ALS in embodiments of the invention also include isrsmxriosuppressive compounds . In some embodiments, an immunosuppressive compound targets an autoimmune component in AD, PD or ALS, for example T cell, activation or function, Non-limiting examples of approaches for suppressing the immune system, or a component thereof, in embodiments of the subject invention include:

1. Blocking receptors of c emokines such as CCR5 present on cytotoxic T ceils. This can he achieved by using antagonist drugs such as aara?irc>c. It will bo understood that. CCR5 is one of the HIV-1 receptors and such drugs have been in use for years to treat HIV patients ,

2. Administering a glucocorticoid such as prednisone or prednisolone, which are effective immunosuppressive agents. They inhibit the activation of cytotoxic I cells. Additionally, they cross the blood brain barrier and are used to treat multiple sclerosis (MS) .

3. Administering a caicineurin inhibitor such as cyclosporins or tacrolimus, which are potent i munosuppressive agents. They inhibit caicineurin, which blocks phosphatase activity, and thus T cell activation. They are used to inhibit transplant rejection.

4. Administering an inhibitor of HtTOR such as rapanaycin, which blocks cell cycle at Gi>S phase, Rapamaycin inhibits ϊ cell activation and proliferation. It is used to treat transplant rejection,

5. Administeri g an antd.-metabolic drug including azathioprine, micophsnolate or nofetil ho block killer T cells,

6. Administeration of antibodies for LFA~3lgl. fusion protein, which interferes with τ cell activation. This has been used in psoriasis,

7. Administering a phosphodiesterase-^ inhibitor such as sildenafil or paclitaxel, which have been used in melanoma, to lead to cell-mediated I cell imtauxiosupression . General tecimiques and compositions for making dosage forms useful in the present invention are described in the following references: 7 Modern Pharmaceutics, Chapters 9 and 10 (Banker & Rhodes, Editors, 1379); Pharmaceutical Dosage Forms: Tablets {Lieberman et al . , 1381); Ansel, Introduction to Pharmaceutical Dosage Forms 2nd Edition (1376); Remington's Pharmaceutical Sciences, 17th ed, ¾ack. Publishing Company, Easton, Pa., 1985); Advances in Pharmaceutical Sciences (David Ganderton, Trevor Jones, Eds . , 1992); Advances in Pharmaceutical Sciences vol 7, {David Ganderton, Trevor Jones, James McGinity, Eds,, 1995); Aqueous Polymeric Coatings for Pharmaceutical Dosage Forms (Drugs and the Pharmaceutical Sciences, Series 36 (James McGinity, £·.; - , 1389); Pharmaceutical Particulate Carriers: Therapeutic Applications; Drugs and the Pharmaceutical Sciences, vol 61 (Alain Roiiand, Ed,, 1993); Drug Delivery to the Gastrointestinal Tract (Ellis Hcr ood Boohs in the Biological Sciences, Series in Pharmaceutical Technology; J. G, Hardy, s, S. Davis, Ciive G. Wilson, Eds.); Modern Pharmaceutics Drugs and the Pharmaceutical Sciences, Vol, 0 (Gilbert S. Banker, Christopher T, Rhodes, Eds,}. These references in their entireties are hereby incorporated by reference into this application.

As used herein, the term ^¾ bout" for example with respect to a value relating to a particular parameter (e.g. concentration, such as "about 100 Ϊ&Μ") relates to the variation, deviation or error {e.g. determined via statistical analysis) associated with a device or method used to measure the parameter. For example, in the case where the value of a parameter is based on a device or method which is capable of measuring the parameter with an error of . -:— .10%, "about" would encompass the range from less than 10% of the value to more than 10% of the value,

it must be noted that, as used herein and in the appended claims, the singular forms ^wa," "as," and ^""the" include plural referents and plural referents include singular forms unless the context clearly dictates otherwise. Thus, for example, reference to " subject polypeptide" includes a plurality of such polypeptides, reference to the agent" includes reference to one or more agents and equivalents thereof known to those skilled in the art, reference to '-nucleic acid molecules" includes reference to one or more nucleic acid molecules , and reference to "antibodies" includes reference to one or more antibodies and so forth,

With respect to ranges of values, it is contemplated that these encompass the upper and lower limits and eac intervening value between the upper and lower limits of the range to at least a tenth of the upper and lower limit's unit, unless the context clearly indicates otherwise. Further, the invention encompasses any other stated intervening values.

The foregoing is considered as illustrative only of the principles of the invention . Further, since numerous modifications and changes will readily occur tc those skilled in the art, it is not desired to limit the invention to the exact examples and embodiments shown and described,, and accordingly, ail suitable modifications and equivalents may be resorted to, falling within the scope of the claims.

All publications and ether references mentioned herein are incorporated by reference in their entirety, as if each individual publication or reference were specifically and individually indicated to be incorporated by reference. Publications and references cited herein are not admitted to be prior art.

This invention will be better understood by reference to the Experimental Details which follow, but those skilled in the art will readily appreciate that the specific expe iments detailed are only illustrative of the invention as defined in the claims which follow thereafter, Exam les are provided below to facilitate a mere com lete understanding of the invention . The following examples illustrate he exemplary modes. of making and practicing the invention. Howe er, the scope of the invention is not limite to specific bodi nts disclosed in these Examples, which are for purposes of illustration only.

Exasa i® 1. Ph a horjla est as is reco^ai¾¾d as an atstoantigen

Identification of specific Tax- antigens that act as autoantigens , This can be used as the source of biomarkers, diagnostics and therapeutics via tol rizatioxi and related approaches.

Tau_f the protein product of the ΜΛΡΤ gene, in highly phosphoryiated aggregates has long been associated with Alzheimer's disease (AD) , progressive supranuclear palsy (PSP) and other dementias; in addition, MAPT has been identified as a risk factor for Parkinson's disease iPD} by GWAS (Sharia et al,, 20X2} «· but not AD itself. Phospho-Tau iiitunoiabel can also be high in PD and particularly LED brain, while phospho- au is higher in AD, and there is often significant overlap in patient brain pathology between the disorders (Arnold et al., 2013), Tau and a-syn have many parallel features including association with PD by GWAS, phosphorylation under disease conditions, presence of both proteins (Hamper et al,, 2010; Foulds et ai., 2013; Zetterberg et al., 2013), and autoantibodies in blood

(Bartos et al., 2012; Koehier et al,, 2013), and similar degradation by CHA that is disturbed by mutation (Wang et al,, 2009). They may even form joint oligomers in some patients (Sengupta et al,, 2015).

Phosphoryiated Tau is recognised as an autoantigen by ΐ cells in the blood in PD. Without wishing to be bound by any scientific theory, an autoimmune response in Tauopathies such as Alzheimer's and other dementias can be the basis of new means for diagnosis, biomarkers, and clinical therapies. Phospho ylatsd candidate epitopes are important for Tau, which has ~4Q potential phosphorylated sites iSharraa est al, , 2012; Yin et al . , 2013), of which 20 were identified in AD patient (Duha et ai . , 2013) ; 10 phosphoryiated sites were identified in PI) striata (S202, 235, 262, 356, 396/404, 09, 413, 422 and T205, 212}? and seven sites in LBD (3214, 238, 396/404, 422 and 212, 217) . interestingly, in PD there are 3 clusters of phospho~Taa (202 _f 205, 212 ? 356,· 396, 404 ; 40 , 413, 422} . To conduct this assay, 15 mer epitopes were analysed that contain the following phosphorylated residues of Tau, each of which are reported in dementias: iSi, S199, S202, 205, T212, 8214, 231, S262, S356, S422, These peptides were incubated in PBHCs obtained from 3 PD patients and one age-matched control and recorded T cell activation following the Sette lab s published protocols. Each individual including the control was found to have ceil responses to at least some set of these epitopes, The precise antigens are determined in assays as the pooled peptides are segregated, The precise ϊ ceil types and HLA alleles involved are also identified, without wishing to be bound by any scientific theory, the observation that T ceii response is quite common nay underlie the very high population that exhibits AD and related dementias,

Ess ssple 2. Cytokine R@i® ¾¾ in Controla nd PD Patie a

Eiood from age matched controls and PD patients were obtained and mononuclear cells were isolated by gradient centrifligation . Release of the cytokine interferon-gasmna (iFNg) , which measures activation of CD4* and/or CD8+ T cells, and the interieukin, IL~5, which measures activation of CD4÷ cells was measured by ELI SPOT assay. Briefly, the isolated ceils were plated in wells that have eoiorimetrie detection of iFNg and IL~5, and were sti ulated with pools of 95 epitopes of -synuciein that the Sette lab determined would potentially be displayed by MHO-∑ or ΜΗΟΪΙ antigen-presenting proteins in humans♦ After 22 hours of stimulation at 37 c_f the cells were removed and release of cytokines w s measured by coiorimetric detection of spct~forbing ceils (SFC) . Confirmed release of cytokine is determined by the presence of a minimum of 20 SFC per million ceils. Cytokine release was detected in only 15 of 160 stimulations to a- synudein epitopes across controls {n~12), while 43 of 248 stimulations in PD patients had antigenic responses, yielding a probability of p ^:™C 029 that PD patients are a different population (two-tailed Fisher exact test) . Thus, the data shows that PD patients are more likely to have T ceils in blood that recognize and are activated by a-synuciein than una fected individuals ,

Exassple 3, olerization h¾ a v specific for e i o ss of ¾u ate us©f¾l in tr®ati¾Q subieets afflicted wit >,

Epitopes to which T cells are responsive in subjects afflicted Kith AD are identified by

i) obtaining T cells from each subject;

ii} contacting the ceils with a test compound;

iiij determining whether the τ cells have increased activation after contact with the test compound; and

ivj identifying the test compound, as an epitope to which the ceils are responsive if in step ill) the cells are determined to have increased activation after contact with the test compound, and identifying the test compound as not an epitope to which the T cells are responsive if in step iii) the cells are determined to not have increased activation after contact with the test compound . This method is repeated sequentially or in parallel for thousands of test compounds, each having an amino acid sequence identical to a stretch of consecutive amino acids in the fan protein. Epitopes for Tan are identified in individual subjects.

The subjects afflicted with PD are then separated into one of two groups; 1) a test group that receives tolerlEation therapy, or 2} a control group that does not receive toierization therapy, yixthin the test group, an effective amount of a fan epitope is administered orally, nasally, or subontaneously to each subject (i.e., tolerisation therapy specific for the epitope) . Within the control group, a polypeptide having a random sequence is administered, to each subject.

Compared to the control group, subjects in the test group have a statistically significant reduction in sym toms or AD. Additionally, a statistically significant proportion of the subjects have little or no progression of AD.

Less or no activation of ϊ ceils by the epitope is observed in subjects who receive and respond to toIsrination therapy, but not in subjects who do not receive or who do not respond to Polarisation therapy.

Without wishing to be bound by any scientific theory, at least some AD is in part an autoimmune disorder. without wishing to be bound by any scientific theory, the ceils recognise Tau. E as^le S. Parkinson's Bisease is ^sociated_^wit^ HL¾ Class XI Eestrlct-fd

CD4 ϊ Cell es o se arge i g S¾s Tau ntigen

The Tau protein is known to accumulate with age and in a number of different disease conditions. Whether the aggregated proteins are recognised by ? ceil responses is currently unknown, and it is also unknown whether differential recognition occurs between healthy people and patients affected by several different neurodegenerative diseases, such as Parkinson's (PD}_f Alzheime ^f s, Dementia, AL5, Schizophrenia and others. This experiment investigated whether peptides derived from the Tau protein are preferentially recognised in PD patients .

A} Accrual of PD patients and control donor cohorts

Features, diagnosis, recruitment, age, gender are described in Table 6 below. able 6. Demographics of Study Participants

Ca-ueasi&n, % fn) 100 (22) I 85.7 (18) 77.3 (17)

B) Tali-specific f ceils are detected in both PD and control donors, throughout the Tan antigen sequence it «as investigated whether ceil responses against Tan we e detectable in the and healthy control (BC) donors. To this end, a panel of overlapping peptides spanning through the entire sequence of the Tau protein was synthesized. Since it is known that the Tau protein is post- translationaiiy modified {mainly by phosphorylation) , in several instances phosphoryiated peptides were also synthesized, in ail, 55 non- modified 16~raers overlapping b 8 and 24 modified 26~ ers were synthesized.

C Results PD: η∞16, peptides tested 14-16 tines; HC above 50 years o d denominated as age-matched: :ν··1 ; (9-ii times) and HC below 35 years old (BC Young} ; n-13 (10-13 times) . These peptides were tested utilising the following assay strategy. Briefly, PBMC from each donor were stimulated in vitro for 14 days as described (Binz,- D., 2015) wit)- pools of 10 to 16 peptides each. After 14 days, the cell cultures were assayed with lF g/lL™5 dual SLISPOT assays <r £> . Positive pools were deconvoiuted at da 17 to identify the specific individual epitopes recognised.

The results shown i Fig. i for PD, HC Young and HC Age-matched donors show that Tau specific τ ceils were detected in both PD and control donors, throughout the Tau antigen sequence, both in the case or unmodified peptides, as well as the modified versions, also shown in separate panels.

D> Analysis of overall response reveals higher responses in PD ve sus control donors Further analysis showed that while the reactivity of healthy young and age-matched controls was similar, the reactivity of PD donors was higher than the age-matched controls Fig, 2A a d 2B. More specifically, in Fig, 2A responses detected for each donor are shown, reporting separately iFNg, IL5 or the sua of both cytokines. There was a trend for responses in the PD cohort being higher than for either the young or age-raatched controls, A significant difference was actually detected in terms of iFNg responses between the PD and age-matched controls, in Fig, 2 _f the responses observed in each donor against each individual peptide are plotted. By this analysis, no significant difference was seen between the young and age-matched controls. Howeve , significant differences were noted between PD and either group of controls, when the iFHg, ∑L5 or both cytokines combined was considered. E) Phosphoryl tec Sequences Ar M re Kecognized Tha Untnodit^"led Ones

Ne¾t, the magnitude and frequency or responses to unmodified and phosphorylated peptides wer com red. The results are shown in the following le ? tor the seven cases where pair of phosphorylafed and non-phosp orylated peptides were tested and responses were detected in at least four donors against one of the peptide pairs. Strikingly, in seven out of seven cases phosphorylated sequences were recognised .mo e frequently than unmodified ones _f in higher frequencies and /or magnitude.

Table 7, Phosphoryiated Sequences are More Recognized Thai- Unmodified

Ones

Total PD HC>50 ^'::■:· ;35 ion ticsa

BW

To ,¾l Tot T t; -a I Tot Total To Re s port ai espon al Eespori al tiers SFC SFC ders SFC

17? I 107 0 0 1 107 0 0

ΕΡί?Κ8β

26 6 S 146 5 620 12 217

ΕΡί?Κ8β 24 72 7 45

X§3 2 133 1 1X7 1 157 0 0

2 5

9 54S 5 X3S 1 18 3 395

9 0 2

2X7 X 170 1 170 0 0 0 0

7 7

7 4 181 0 0 3 39?

0 3

225 δ 455 5 0 0 0 0

S

23 463 12 224 3 «93 8 169

2 10 7 27

249 o 1S8 5 133 3 SOS 2 368

XCSS E 15 «3 4

X X 110 5 5X7 516 2 720

S3 5 8

DSTOKVQS&X δ 672 2 239 3 433 0 0

7 7 0

DSTOKVQS&X 7 680 4 49 122 X 109

7 0 0 7

409 SHVSSTGSXS 3 176 2 7X0 1 105 0 0 WBS¾ 7 7

SHVSSTGSXS 4 148 4 148 0 0 0 0

€ 4

417 i 173 i 173 a 0 0 0

5 170 i 157 2 943 2 563

3

12

F) Overall responses are not pgrrelated, with age in either controls or PD patients

The potential relationship between age nd Tan reactivity by plotting reactivity for each, donor as a function of age was addressed, in Fig. 3&, the PD donors are shown in red_f while the controls (both age-raatched and young) are shown with black symbols. While there is a mild trend, toward correlation with age, the trend is not significant. We also show a plot, for the PD donors of total reactivity as a fo.nction of time since symp oms onset (Fig, 3B . Here again no significant correlation is detected,

G) JnterceXlolar Cytokine Staining indicates that responses are polarized towards €04, IPHg and IL-4 To further characterise responses, we also analyzed responses using Intercellular Cytokine Staining (ICS) to ascertain whether the three different cohorts differed in the patterns of cytokine produced in response to antigenic stimulation. When using ICS, in all three cohorts IFNy and IL-4 were the predominant cytokines detected ( , 3C) , Notably, no Ilr*10 was produced. Further, the Taa epitope response was produced almost entirely by CD<h cells.

B ) ELISPOT indicates that responses are οlarised towards Ih-5

To further characterize responses, we also analysed responses using Enzyme-Linked immunoSport (ELiSPO ) to ascertain whether the three different cohorts differed in the patterns of cytokine produced in response to antigenic stimulation . When using ELISPOT, in all three cohorts IL~5 was the predominant cytokine detected ( ig. 3D) . I) Differences between the donor cohorts are to be ascribed to breadth, and not per epitope magnitude In the next series of analyses, the basis for the higher responses detected in the PD cohort w s investigated in mere detail. Specifically, it was addressed separately whether the reason tor the higher response was to be ascribed to a larger nuraber of epitopes being recognized (breadth) , a higher magnitude of positive responses (magnitude) or both. It was found that both breadth (Fig. 4A) and magnitude of response/epitope (Fig, 4B> were increased in the PD donors with respect to controls. These results suggest that both factors contribute to the difference in response observed. ) Tau-specific responses are stronger than those against a-syn

Next, the cytokine response as determined by ELISPOT assay to Tau epitopes was compared to the response to ζϊ-syn. It was found that the Tau-specific response was signi icantly stronger than the α-syn. specific response {Fig. 5) .

K) Definition of dominant epitopes and PD specif c ones

The most doisinantly recognised epitopes were defined as those accounting for 90% of the total response; those epitopes are listed in the following able 8, The most dominant epitopes were recognized in ail three cohorts in most cases, in a few cases, the epitopes were selectively recognised in PD donors . The following Table 9 lists the selectivity of the dominant! recognised epitopes.

Table 8. Dominant Epitopes Across All Cohorts

Saquanea Start Modifies i Total Avaraga % of Prequan poaiti on SFC SFC pe total 3f of on per respond aspon reapons along epitop er se a aa. a

KV& RXPPKSPS 225 X-pT 46324 2014 13,2 43.4

SA

PAPKXPP5SGEP P 177 X-pT 42624 1639 12.2

SG

GKVQIINKKLDLS 273 30211 1511 8,6 37.7

HVQ

KTΏΕGASIVTKSP 385 20142 1679 5.7 22.6 vv;i PMFDLKNV SKIG 249 19815 1 S2 5.7 18,9

STE KIE H LfFREM 369 18790 1174 5,4 30.2

A A

BVTQARMVSKS D 121 14677 146S 4,2 18.9

G G

SVQIVYEPVDLSK 305 13838 731 4.0 35.8

VTS

VYKSPVvSGBTSP 393 13408 1915 3.8 13,2 B L

IKHVPGGGSVQIV 297 11875 1319 3,4 17.0

YKP

P BLKNVKSKIG 249 11063 1006 3,2 20.8

ΣΊΈ

VDLS VTS CGSL 313 9361 1409 2 8 1 .2

GHI

GQKGQANA RIPA 1.61 8164 1361 Z ..3 l : , TP

SLEDEAAGHVTQA 113 7698 1283 2 , 2 11.3

RMV

DFKBRvQS IGZL 345 6807 972 1 , 9 Ί^■¾ ^■?

DHI

DFKDRVQS IGSL 345 6727 1345 1.9 9.4

DHI

DRSGYSSPGZPGX 193 X-p , Z-pS 5499 €11 1.6 17.0

PGS

ADGKTEIATPRGA 145 5210 868 1.5 11.3

AFP

ATLADEVSASLA 426 j 4997 999 1 , 4 9,4

QGL

KV& RTPPKSPS 225 4556 911 1.3 9.4

3AK

IGSLDNI BVPG 353 4070 070 1.2 1.9

GGH

TRIPAKTPPAPKT 169 3897 1299 1.1 5.7 PS

GBTSPPHT.RWSS 401 3 98 633 1 , 1 11.3

TGS

LATLADEVSASLA 425 3 93 948 1 , 1 7,5 QG

Table 9. Selectivity in Recognition of Dominant Epitopes

Sequence Start Modi fie:a PD HO50 PB/HC PD/HO posit tion Tot % of Tot % ot >50 50

.1oraI Total ai Total Ratio Ratio long SFC Respon SFC Respon of of %

Tau ders ders Respo Respon nse ders KVAVVRTPPE 225 455 100.0 0 0.0 inf inf

SFSSAK 6

IGSLDNITH 353 407 j 100,0 0.0 inf inf

VPGGGN 0

BVTQARMVSK 121 891 j 50.0 133 5.0 SKDG G 6 !

IKBVPGGGSV 29? 856 44,4 737 33 _* 3 11.6 1,3 QIVY P 5

SLEDEAAGBV 1.13 705 66.7 640 11 2 , 0 fQARMV 8

fRIFAKTPPA 169 145 33.3 160 33.3 8.1 1.0

PKTPPS 0

VDLSKvTSKC 313 671 57.1 897 28.6 7.5 - 0 GSLGNI

DRSGYSSPG2 ; 193 X=pT, 136 55,6 8^ 7 , 3

PGXPGS 3- S 0

KTDHGAE VY i 385 133 58.3 243 j 8.3 r KSPVVS 36 7

DFKDRVQSKI 345 S-pS 449 j 57,1 122 i 28.6 2.0 GSLDNI o i 0

GQRGQANAfR 161 624 j 66,7 177 j 16.7 3,5 4,0 I PAK P 7 ; 0

GKVQI INKKL 273 182 50.0 556 i 20.0 3.3 2 , 5 DLSNVQ 90 0 j

KV&VVRXEPK 225 X*-?.' 224 52.2 698 j 13.0 4.0 SPSSA 10 ?

VYKSPvVSGD i 393 895 42.9 339 i 42.9 2 , 6 1.0 TSPRHL 1 ?

P&PKXPR3SG 177 X=pT 146 34,6 620 19.2 2 , 1,8 EPPKSG 72 7

P PDLKNVKS 249 133 50.0 608 30.0 2 , 2 1,7 KIGSTE 63

IETHKLTF 369 8 9 3.8 569 i 31.3 1.4 1.4 REH KA 0 8 SVQIVY PVD 305 620 36.8 546 42,1 1 , 1 0 , 9 LSKVTS 3 0

PMPDLKNVKS 2 S 2-pS 517 45, 5 516 j 36.4 1 1.3 IGZTE 5 g

ATLA.DSVSAS j 426 219 60.0 280 j 40,0 0.8 1.5 LAKQGL 3 -'

DFKDRvQSKI 345 239 40 , 0 433 60.0 0.6 0.7 GSLD I 7 0

GDTSPRHLSN 401 997 16.7 165 j 50,0 0,6 0 , 3 VSSTGS 7

ADGKT IATP 145 163 00.0 357 50.0 0.5 1.0 RGAAPP 3 7

LATLADEVSA | 425 126 25.0 253 75.0 0.5 0.3 SLAKQG 3 0

A genetic inference approach to attribute potential HLA restriction to specifi epitopes was used (Paul et al,_f 2017), This approach was used to identify potential restriction of Tan epitopes. This analysis allowed, assigning restriction for many of the most prominently recognised epitopes. he results are shown in the following le 10.

Ss s¾3¾p ¾ 6 . Psxth®^ B gp¾K ¾i¾¾¾¾.& WitA &¾tigf-e¾is

Experiments are conducted with an additional 95 non-modifled X6~mer peptides based on Tax: beyond the 55 16-mers used in Example 5, in accordance with the experimental methods used in Exam l 5, Further, additional modified Tan epitopes are tested, including a 16-mer Tau epitope phosphoryiatsd at residue T18, four Tau epitopes nitrated at residues TIB, T29, T197 or 394 and two Tan epitopes aeetylated at residues K280 or 174. Finally,^, full-length wild-type Tau will he tested,^, as well as pre- formed fibrils.

E am le 7. Determination of H«ma.a Leukoc e tatigea Bestriofcion of en ified ISpttopes.

it is hypothesized that recognition of disease associated Tau-derived epitopes in PD patients is dependent on cofactors such as expression of specific HLA molecules that can hind the Tau-derived peptides _f the presence of τ cells expressing specific CRs , and/or the presence of particular Tau hapiotypes (HI vs. H2)

HLA binding predictions are perforated, along with assaying for binding with purified HLA molecules. Restriction is confirmed with HhA transfected ceil lines in selected examples .

Cellular assays and validated genetic inference methods are used to determine the EL& restriction for each epitope. Proliferation of the specific T ceils responding to selected epitope/HLA combination is induced by restirfiuiation with specific epitopes, the τ cell receptors that recognize those specific HLA-epitope coatbinations are determined.

Cellular assays and validated genetic inference methods are used to determine the HLA restriction for each epitope. First, it is determined whether responses are MHC class I or class ∑I restricted. To accomplish this goal, epitope responsive T ceils are studied for their CD4/CD8 phenotype, since a CD4 phenotype is indicative of class ∑I presentation, while a CDS is indicative of class I presentation. It is e pected that isost responses will be class II restricted CD4 T ceils. If, however, CDS class I restricted responses are detected, algorithmic protocols developed for peptides for class I are used (Paul et ai. _f 2013? Kiro et al . , 2014), in this approach, each possible amino acid sequence that can be derived from the entirety of a particular protein, including pathogenic alleles, is predicted for the specific MHC alleles (Paul et al,, £013; Kiat et al,, £0 4} expressed by a particular patient or EC, This approach has been shown to successfully predict MHC~pepti.de binding or >90% of the human population sWeisfcopf et al , , 2013), Each peptide with significant binding potential is synthesized and tested for recognition by the specific donor.

The HLA restriction of Tan epitopes is next confirmed. First, potential HLA restrictions are identified using the genetic inference Restrictor Analysis Tool for Epitope (KATE) approach, which matches likely HLA restriction for class I and class II alleles (Paul et al . , 2015). able 10 above demonstrates Tau alleles for which Tan epitope restriction has been identified. Such inferences are verified b determining which of the potential restricting alleles bind the epitopes in in vitro assays with purified HLA allelic variants (Sidney et al . , 2013), and directly map restricting alleles with cell lines trafts acted with single HLA molecules (Mc inney et al,, 2013).

Methods

Donors are HLA typed by an American Society for Histocompatibility and liamunogeneties {ASHI } -accredited laboratory at the Institute for

& infections Diseases <I∑∑D) , Murdoch University (Western Australia) , HLA typing for class I {HLA A; B; C) and class II CDQAl; DQBl; DRB1 3,4,5; DPBlj is perforreO using loens-specific FCR amplification, on genomic DNA. Friraers used for asrglification employ patient-specific barcoded primers. Amplified products are quantified and pooled by subject and up to 48 subjects are pooled. An unindexed {454 eight lane runs) or indexed {8 indexed MiSeq runs) library is quantified using Kappa universal QPCR library quanti ication kits. Sequencing is performed using either a Roche 54 FLX+ sequencer with titanium chemistry or n IlIuTfiina HiSeq using 2 X 300 paired end chemistry. Reads are quality-filtered and passed through a proprietary alleie-calling algorithm and analysis pipeline using the latest I GT KLA allele database as a reference. The algorithm was developed at I ill) and relies on periodically updated versions of the freely available international

information system and an ASHl-accredited LA aiiele caller software pipeline, HID HLA Analysis Suite.

Potential KLA~epitope restrictions are inferred using the RATE software program (Paul st ai . , 2015} , Briefly, a computational method that infers HLA restriction of epitopes from coil response data in HLA typed subjects is used. RATS infers KLA restrictions by considering the presence or absence of a response to a given epitope as the biological outcome, and calculating the relative frequency of the subjects responding to a given epitope and expressing a given aiiele as compared to the general test population and associated statistical signi icance. Binding predictions are performed using the consensus prediction method publicly available through the Immune Epitope Database (IEDB) Analysis Resource (Kim et al,_f 2012) .

Next, classical competition assays are performed to quantitatively iseasure peptide-binding affinities for HLA class I and II MHC molecules, based on inhibition of binding of high affinity radiolabeled peptides to purified MHC molecules. In brief, 0.1-1 nM of radiolabeled peptide is eo-ineubated at oom temperature or 37 °C with purified MB. in the presence of a cocbtaii of protease inhibitors (and, for Class I,· exogenous human β 2~ microglobulin). Following a two to four day incubation, ^HC-bound radioactivity (c.p.m. } is determined by capturing MHC-peptide complexes on plates coated with either HLA DR (L2 3) , DQ (BBI80), DP {B7/21} or Class ∑ (W6/32) specific monoclonal antibodies. Bound cp.rn. is measured and the concentration of peptide yielding 50% inhibition of binding of the radiolabeled peptide is calculated. Under the conditions used, where [label] < { MHC] and IC50 ·£^■ [MHC], measured IC50 values are reasonable approximations of true d, Bach competitor peptide is tested at six different concentrations covering a 100,900- fold, range, and in three or mere independent experiments. As a positive control, the unlabeled version of the radiolabeled probe is aiso tested in each experiment. A threshold of 1,000 nM binding affinity is associated with intmunogenicity of ΆΪΛ ciass II ceil epitopes, and most epitopes bind in the 1-100 a.¾ range, with affinities in the 1-10 nM considered to be of high affinity.

Results

The HLA hapiotype associated with the recognitio of specific Tau epitopes is identified. Whether the HLA hapiotype is a risk factor for PD and/or is associated with PD disease symptoms is determined.

These experiments focxss on the generation of a hegapool^w of PD peptides, and are tested in either re-stimulation mode, or also directly ex vivo, utilizing intracellular cytokine staining (ICS) or AIM assays (Dan et ai,_f 2016). In these experiments FhCS staining for various markers is incorporated. This establishes whether the responses are mediated as excepted by CD4 responses, and which cytokines in addition fc IL5 and iFHg are released by the Tau-specifio τ cells, thus rtiore precisely establishing their functionality. 1110 is tested, to assess whether T cells with potential regulatory activity can be detected.

Further, epitope, epitope pool or

stimulations are used to confirm the results, in an independent cohort, of the raain findings of higher responses in PI) versus control donors, CD phenotype, and patterns of cytokines secretion. In addition, whole Tau stimulation is used to demonstrate recognition of natural antigen.

E am le 9, C&aracterize t e cell receptor repertoire associated with recogni ion of a¾ epi o e

Recognition of disease associated autoirfinuine epitopes in PD is dependent on expression of specific HLA molecules that bind the aufcinBuune peptides, and presence of T cells expressing specific T cell receptors (TCRs) . Du ing development in the thymus, each cell gene ates a unique TCR stochastically by recombining segments of V, D and J genes, This experiment investigates if the increased frequency of cells responding to specific autoimmune epitopes in PD vs. EC participants is associated Kith the presence of shared, ^public' TCRs in PD patients recognizing these epitopes .

PD patients and EC subjects that show T ceil reactivity to Tau are selected. To identify TCRs recognising Tan-derived epitopes, peripheral blood mononuclear cells (PB-4C) are stimulated with peptide epitopes and culture for 14 days to expand epitope-specifie ceils. The T ceil repertoire; in the expanded culture is compared. with the repertoire of input ceils to determine which TCRs are specifically expanded . Peptides unrelated to PD, e.g., from common bacteria, are used as negative control- stimuli . yihether shared TCRs are present in the Tau~epitope specific T cells in the population is determined, and iraportantly, if these shared TCRs are present in PD but not KC saifiples is determined. This analysis of TCR sharing is perforated both for specific TCR. sequences as well as for motif in the TCR CDR3 regions that are shared between related clonctypes with shared specificities.

Methods

During their maturation, T ceils undergo a stochastic recombination process in which, a unique receptor sequence is formed by recombination of genes to encode a mature TCR consisting of a TCR alpha and beta chain. The antigen-specificity of a ΐ cell is determined by its receptor, but the phenotype of the rao nted. response can change over time as a T cell undergoes differentiation. The formation of memory ceils and their proliferation gives rise to ^clonotypes* of cells that can be tracked bach to a common origin. The CDR3 region of the TCR-beta chain is the most polymorphic, and is in direct contact with the epitope. Thus, sequencing this region aione is sufficient to generate a useful marker of epitope specific colls.

A protocol to determine the an igen-spec! f eity of cell receptors is used, similar to other published approaches {Kiinger et al . , 2015} , hut specifically targeted to roproducibly detect relatively rare antigen- specific C 4+ ? ceils. Briefly, PBMC are stimulated with individual epitopes or epitope pools, driving the proliferation of epitope-specific T ceils. The TCR repertoire is sequenced from the D«A of ceils extracted post-expansion, and cross-compared to the TCR repertoire in PBMC *x vivo, to identify TCRs from T cells that have undergone expansion, and to the TCR repertoire in ceils stimulated with different epitopes to remove potentially unspecific τ cells) . To reliably detect antigen-specific ceils, it is important to run culture repeats, and cross compare proliferation with different antigens, as some T cells will proliferate unspecifreally in a bystander fashion, When comparing the identified TCRs based on this proliferation approach to those obtained by isolating epitope-specific T ceils directly ex vivo using tetramer sorting, it is shown that the vast majority of the identified cells are epitope specific {>95% specificity) . This approach is utilized to identity it there are common TCEs that are found across multiple PD donors, which would suggest that presence of specific TCRs could serve as a diagnostic. If no identical TCR sequences are found, the publicly available Glyph package {Cianviiie et al,_f 2017} is used to search for conserved motifs in the epitope specific TCRs .

Results

The TCR hapiofype associated with the recognition of specific Tau epitopes is identified, hether the TCR haplotype is a risk factor for PD and/or is associated with PD disease symptoms is determined.

E¾:¾ss¾l¾ 10. De e mina io of ethe ΜΆΡ Ba lotypea are Asso ia ed with Res onses t au-derived Epitopes Two major hapiotypes (HI vs. H2> of MAPT have been discovered and associated with different prevalence of neurodegenerative diseases including PD, In this experiment, both PD and HC patients are genotyped to deterrine their MAPT ha lotype . Using these data, it is determined if there is evidence that the recognition of particuiar epitopes in the Tau-protein is associated with particuiar MAPT hapiotypes . This could result from different MAPT having different levels of expression for the various Tau-splice isoforms and their PTMS .

Methods

To determine whether recognition of particular epitopes derived from Tau protein is associated with MAPT hapiotype, eight intragenic polymorphic markers in exons 1, ? and 9 and introns 2_f 3 and 13 are used to infer MAPT hapiotypes (Ghidoni et ai,, 2006} . Polymorphisms of exons 1 (g.75859 g > a) , 7 g.104964 g > a; PI76P) , 9 <g.109929, A227A g.110013 t > c, N255H? g.110058 g > a, P270F) and of introns 2 (g, 85372 c > t> , 3 (g.87889 a > g) and 13 (g.137615 t > c) are analyzed by PGR amplification followed by sequencing .

Results

The MAPT hapiotype associated with the recognition of specific Tau epitopes is identified. Whether the MAPT hapiotype is a risk factor for PD and/or is associated with PD disease symptoms is determined.

In this experiment, 1 ceils that are responsive to Tau epitopes are functionally characteri ed. To do so, epitope-speeific τ cells are analysed by flow cytometry to establish their memory phenotype using CD45RA CCR7 staining {naive, CD45KA+CCR7+; central memory, CD 5RA~CCR7-f; effector memory, CD45R&-CCR?~; effector memory re-expressing CD45RA, CD 5RA÷CCE7~} . The functional characterization utilizes ICS assays to determine the specific pattern of cytokine secretion including IFNy, TMFet, IL-4, IL~I7, IL-10, and IL-21. Additional staining for specific surface markers, such as CP , CCR , CXCR3 , CXCR5, PD~1, CD 0L, and CD6S determines their differentiation state and general phenot pe , To increase sensitivity, the recently described Activation Induced ba te (AIM) assay (Dan et al., 2016} , which was developed to allow capture of rare T ceil subsets and specificities, is utilized,

As a parallel approach to characterize specific T ceils, HLA iriuiti ers are designed, which use specific allele and epitope combinations to measure: the presence of reactive T ceils (Cecconi et al . , 2010). For determined and dominant HLA allele-epitope combinations, multimers are produced, which stain and phenotype reactive cells. This technique could be used as a new means to identify preclinical PD, and by extension may by adapted for other neu odegenerative disorders that show autoimmune features .

Bx vivo analysis is used in cytokine capture assays for IL-5 and other cytokines with the AIM assay and ray1timer staining to characterise responses without in vitro manipulation, and to provide isolation of specific T cells for identification of micro mRM¾~Seq» RSA-Seq {RNA sequencing) uses procedures that allow the study of rare antigen-specific T cells (Arlehamn ef al . , 2014 ), First, mRKlA profiles of PD and EC are compared at the level of bulk, memory subsets. This determines a baseline for comparison with isolated antigen-specific ceils and addresses whether a discriminatory signature is present in bulk subsets. κιΚΝΆ signatures are then compared in bulk subsets with epitepe-specific τ ceils. Distinct mRNA signatures are associated with epitope-specific responses from patient cohorts, mRNA profiles f om epitopespeeific cells are compared for donors to identify genes that are consistently up- or down-regulated, and associated molecular programs and functions are pinpointed by standard gene network analysis.

Methods

RHA-Seq is performed using the LJI Sequencing and Bioiivformatics Core, Following collection of epitope-speoif ic T cells during E¾€S sorting, RllK isolation and libraries are prepared for sequencing by a KiSeg2500 {Xilunina Platform) sequencer, The sequencing data is passed to the Bioinforjsat ios Core at LJI for analysis in their antedated next generation sequencing (HGS) pipeline. Bioinforisatics analysis defines genes significantly u regulated, in the two subsets . Expression levels or housekeeping genes such as β 2 microglobulin {B2M} are compared to ensure consistency and highly reproducible data normalization between samples .

Genes differentially regulated are identified at a E ; <0.05. Pathway analysis of genes significantly u regulated, in the various subsets and the associated gene modules is then performed. For this purpose, the web tool Gens Set Enrichment Analysis (GSSA) is used to determine which pathways are significantly represented (Mootha et a!., 2003; Subra anian et ai,, 2005). GSSA is a computational raethod that determines whether an a priori defined set of genes shows statistically significant differences, in this case between differentially regulated gens set and the gene set represented by the full genome annotated genes, in addition, the Integrated Pathway Analysis' <IPA) software is used to determine in raore detail the directionality of the overrepresented functions and the coismon upstream regulators for the given set of genes (Kramer et ai,_f 2014). A complementary approach follows a modular analysis that identifies clusters of genes that share a similar expression profiles, in particular the Gene Co-expression Network Analysis (WGCNA) algorithm (hangfeider and Horvath, 2008) is used.

Results

The analysis of Tau epitopes by cytokine, AIM assays and. multimer technology determines the number and phenotypes of responsive τ cells in PD and yields insight info their biological roles in neurodegenerative pathogenesis. The ability to isolate epitope specific τ cells also allows for the identification of their nsRN signatures.

These experiments also provide a means to quantify specific autoimmune reactive τ cells in individual patients; the numbers of specific T cells are correlated wit UPDR3 scores to determine if this assay migh provide a progression foiomarker. A battery of multimers provides general screening to identify ^prodromal" individuals and could lead to indi idualized therapies .

E&as&ple 12. ~cells of Parkinson's disease patients recognise ot-svn clein

Atanorraal processing of self-proteins can produce epitopes presented by major histoco patibility complex (MBC) proteins to be recognised by specific T ceils that escaped toierance during thymic selection (Marrack and Kappler, 2012) . Such actions by the acquired iHsarur.e system are implicated in autoimmune disorders including Type~l diabetes {Ti > . k¾iie not considered to possess autoimmune features, neurodegenerative diseases are characterized by altered protein processing. The jsajor pathological features of Parkinson's disease <PD) , the most common neurodegenerative movement disorder, are the death of substantia nigra (SH) dopa.ffiine gic neurons, and the presence of intraneuronal aggregates known as Lewy bodies composed of ζϊ-synuclein <ce -syn) {Spillantini et al„ _t 1998} - Activated croglia have been reported in PD SN for nearly a century sFoxx and Nicolesco, 1925} and cytokine profiles implicate activation of the innate immune system (Cebrian et al., 2015), More recen evidence suggests a role for the acquired ieunune system (Cebrian et al., 2015} , including T cell infiltration to PD SR (Brochard et al,, 2009} . Genome wide association studies associate PD with an inusune hapiotype {Wissemann et al. , 2013} present in --15% of the general population including the MHC class II gene alleles DBB5*01 and DRBl*I5i01 (Greenfoaum et al . _» 2011} , and a polymorphism in a non-coding region that isay increase MBC class II expression (Bamsa e al,, 2010; Kannarbat et al . , 2015} , Antigen presentation by MBC class expression in SM dopamine neurons was reported in adult human brain of PD patients and age matched controls. If was further demonstrated that SN dopamine neurons express MHC class I upon activation by cytokines released from microglia activated by «~syn or neuro eianin, and that CD8+ T ceils kill neurons that present the appropriate cosftbination of MHC ciass I and peptide {Cebrain et ah, 2014), Native {Mor et al,, 2003; Theodore et al., 2008) 1 ? ^fi and. modified (nitrated) synuelein-derived peptides (Benner et ai., 2008} elicit T cell responses in rats and m ce, and Standaert and coworkers recently demonstrated that SN neuronal death in a s-syn overexpression mod l is absent in HC l null mice (Harms et ai . , 2013).

To address if PD is associated with ϊ cell recognition of epitopes derived from α -syn presented by specific MHC alleles, 67 PD participants and 36 age-matched non™PD healthy controls <HC) were recruited. Participants were 46-83 years of age <PD, median 66, range 46-83; EC, median 64, range 52-83} and €6% were male (PD 75%; HC 50%) {Tables 11a, lib, and 12), while -15% of HC carried DRB1 * 15 : 01/ DRB5*01 : 0 1 alleles, -2/3 of PD carried these alleles (difference between PD and HC, p∞0.G3S and 0.022 for DRBl hlS ; 01/ DRB5*0i ; 01) , indicating association of HLA DR allelic variants with PD in our cohort (Table 13) . able 11a. De ographics of st-dy participants

&J Xe lib. Demographics or study participants with Unified Parkinson' s dieease rating seale (ϋPDRS) scores

Parkinson' & cases Controls p-value

(n===58) (n -23) Mean age in years,

65.5 (8,2) 64,9 (8.3) 0 , 754 (SD)

Male, % in) 75.9 ί 44 > 0 , 5539

Rec uitment site, %

Columbia University 100 {58 ^'ί 100 {23)

(n}

Subjects with £a.mily

history of Parkinson-' s

0,21 {12 0,043 {1} 0 , 3714 disease in first- degree relative, % (n)

Mean Parkinson's age-

58 {3,44} H A N/A at-onset, (SD)

Mean UPDRS part XII, 16,87 <S.43) 1.48 (2,06)

<0.0001 (SD) (range 5- 6) {range 0-6)

Table 12. Demographics of additional study participants in

Supplemental figure 8a. **Hote: total ri∞I2; demographics collected only for n~8.

#

Parkinson' s cases

in-8)

Mean age in years, 65.5 (5,4)

<SD)

Male_f % in) 62.5% (5}

Rec u ment site, %

Columbia University 100% {Si

in)

Subjects with fam ly

history of Parkinson-' s

37,5% (3)

disease in first- degree relative, % (n)

Mean Parkinson's age-

55, {5.2}

at-onset, (SD)

Mean UPDRS part III,

17,5 {7)

(SD)

Median UPDRS part ill

Range UPDRS part III Ki ; 7; M s; 28

able 13 , ΧΛ association o£ subjects ,

To determine whether α-syn. derived peptides were recognized by T cells, responses were assayed to pools that each contained - wen 9-IQaa peptides predicted, to bind common H LA class I types 15, and 15aa peptides spanning the protein that could elicit HXA class II responses, PBMCs front PD and HC were stiirrulated for 14 days, and IFNy and IL~5 responses were measured by dual color EL∑SPOT, enabling quantification of responsive cells. Positive pools were deconvolirted to identify the peptides eliciting cytokine responses, I Ε¾γ was used as a representative cytokine to detect CD8+/HLA class 1 and CD4÷ Thl/Class II I cells, and ∑L-5 as a representative cytokine secreted by CD4-i- Th.2/Class I∑ τ ceils. Each pool was tested in an initial cohort in 19-25 randomly selected PD and 12 HC . The majority of PBMC responses to the 15aa peptides produced 11-5 (68% ot total), indicating a prominent CD4+ Th2 phenotype, and the remainder of the responses were to ∑EUy (32%) . No cells producing both IL~5 and IFNy were detected.

Two antigenic regions were identified in ¾~syn, the first near the N terminus, composed of aa31GKT EG LYVGSKTK aa45 and aa32K KSGVLYVGSKTKS &a46 (referred to as the ¥39 region) (Fig Is), which elicited an apparent Class II restricted ∑L~5 and IFNy response (Fig Ib-d) . Residue aa32 is a plassdn cleavage site 16 and chymotrypsin cleavage sites are at aa3i 32 and aa45/46 17.

The second antigenic region was near the C terminus iaali6~1.40) (referred to as the S123 region) (Fig 6a) , and required phosphorylation of amino acid. residue S1.29, The three phosphoryiated aaS129 epitopes {aaX 16HPVDPDNE¾YSMFSEa 130, aal21D¾EAYE PSESGYQDaal 35, aal26EMPSEEGYQDYEPEAaal 0) produced markedly higher IL~5 responses in PD than EC (p=0.02, Fisher's exact test, 300 SFC threshold) (Fi 6e~g) , Phosphcryiated aaS!.29 residues are present at hig levels in PD Lewy bodies {Fukiwara et al,, 2002} , and PD Lewy bodies contain -syn fragments with cleavage sites at approxi ately aallS, 119, 133, and 135 (Anderson et al , , 2006), and include the fragment aa12SSEEGYQDYEPEAaaX40, which is contained within one of the aaS129 epitopes. Caspase-i (Wang et al., 2016} and neurosyn (Kasai et al,, 2008} can cleave a-syn at aaI21_f chyrrtotrypsin and cathepsin can cleave at aa!.16, aal25/126„ and aal35/13€ (Hossain et al.., 2001), proteaSOKES may cleave at aall9/120 (Li et al . , 2005} , and caipain can cleave at aa!22, with resulting fragments identified, in PD brain (Dufty et al , , 200?},

The imm ne responses to aa39 and aal29 region epitopes, including a second cohort of 19 PD and 12 HC assayed for response to additional phosphoryiated and nitrated modifications (Fig 1} , were different between PD and HC for secretion of both IFMy (two-tailed Mann-Whitney test, p<Q.05) and. TL-5 (two-tailed Mann-Whitney test, p<0„00i}, and. combined responses (two-tailed Mann-Whitney test, p<0.00X) {Fig, 8a-c) , While residue aa39 is highly phosphor iated. in PD patients 24, Y39 phosphorylation was not required for antigenic response. The response was primarily polarized cowards IL-5 in PD {71% IL-5 and 29% IFMy; fig, 84} . This polarisation was PI) specific, and the relatively rare EC responses were not similarly polarized (46% IL-5 and 54% IFNy) , To identify specific sets of T cells that respond to a-syn epitopes, we measured response to a pool of the 11 a-syn antigenic peptides by 9 PD participants (Fig, 9}, Approximately 0,2% of CD3 - T cells responded to the a-syn peptides. Of the responsive T ceils, "-50% produced IL- and 50% produced IFNy, with no detectable IL-10 or IL-I7 production. In most cases, responses were mediated by CD4+ τ cells, but response by one PD was mostly mediated by IFNy-producing CD8÷ T ceils. Thus, T cell response to x-syn antigenic peptides was largely .mediated, by IL-4 or IFNy- producing CD4+ T ceils, with potential contributions from CD8÷/lFNy producing T ceils.

To test if the o:~syn epitopes arise frost processing of native and/or fibriiized s-syn, PEMCs were stimulated with s-syn epitopes for 14 days. The cultures were then assayed with -syn peptides, 25 xq/ l fibriiized (PFrj a-syn, 25μ¾/ι¾1 native a-syn_; or stedia alone. Fig. 10 shows that T cells lines specific for the α-syn epitopes -were activated by antigen presenting cells pulsed with native or PFF protein in 7/12 and 11/12 cases. There was significantly higher response to native a-syn (p∞0.004) and PFF a-syn (p=0«0005) than media alone. Thus, T cells can respond to a-syn epitopes arising from natural processing of extracellular native a-syn, which is present in blood, and the fibriiized a-syn associated with PD.

We then identified the HLA alleles that present es-syn peptides by in vitro binding to a panel of HLAs representing the commo alleles expressed in worldwide populations 1, A threshold or 1,000 nM binding affinity is associated with imstunogenicity of HLA class II T cell epitopes, and most epitopes bind in the 1-100 nnt range, with affinities in the 1-10 nM considered to be of high affinity. Of 26 common HLA class IX alleles tested, five bound to aa32KTKEGVLYVGSKTKEaa S (Table 5| . The HLA class ∑l variants DRBl* 15:01 and. DRB5*01:01 bound the epitope with high affinity (2,8 nM and 8.1 nM, respectively) _f while DKB1*G7:01, Bl*09;QX and DQBX*03:GX bound in the 00-250 nM range. The aa32KT EGVLYVGS TKEaaA 6 epitope phcsphorylated at Y39 also bound DRBl*15:0l and DRB5*01:01 with high affinity. Comparison of PD with and without DRBl* 15:01 alleles found no difference in levels of SLA class I or class II protein expression (Fig, 11 & 12) . Inus, epitopes in the ¥39 region of a-s n strongly bind two HLA class II β chain alleles associated with . In contrast, the C terminus peptides spanning S129 and its post- translationai forats ound HLA class II alleles weakly, with the exception of aa 121 DNEAYEMPSEEGYQDaai 35 _f which i both native and phosphoryiated S129 forms strongly bound DQBl*05:0l. The aal 16MPVDPDNEAYS ?SEaal30 epitope bound several. alleles with lower affinity, and the aa 2 GSMPSSEGYQDYEPE&aa1 0 epitope bound DQ81*Q :02 and DQB1*05:OI with low affinity. Thus, antigenic peptides in the C terminus .8129 antigenic region demonstrated relatively little clear restriction, suggesting that they are recognized promiscuously .

DEBl*15:0l and DRB5*01:0I alleles are in linkage disequilibrium, and participants expressing one allele likely express both. Of PB participants, 8/13 responders to the aa32KTEECVLYVGSKTKBaa 6 epitope expressed both DKB1*15:01 and DRB5*01:01, while only 12/45 {DRBl* 15: 01) and 13/43 {DRB5*01:01} non-responders expressed the alleles, indicating association between the alleles and antigenic response (odd ratios of 4,4 and 3,7, p values of 0,04 and 0,05, respectively) {Table 14} . able 14. ΧΛ association of es onses

This analysis detected additional associations, with 2/13 responders expressing DQB1*03:0 (ρ^Ο,Οδ) compared to 0/45 non-responders, as well as the HLA class I allele A* 11: 01, with 8/13 responders expressing A* 12 01 compared to 9/45 non-responders (p-0,0 2) . vfcile A*ll:01 is in relatively mild linkage disequilib ium with DRBl* 15: 01 and DRB1*01:01, the associations were largely independent (Fig 13a) , In general, PD participants showed, a trend towards higher expression of HLA molecules, particularly HLA class II. This is consistent with an inflananatory component of PD, and higher HLA class ∑I expression and induction in PBMCs of PD vs. HC 3. Little or no dif erence in HLA class ii expression was ound between participants expressing DRBX*X5:0X vs. other DRB1 alleles (Fig, 11} . A similar but still less pronounced trend, w s noted for HLA class I (Fig. 12} < This suggests that the association between DRB1*15:01 and PD is not based on differential expression of the protein. We detected negative association between recognition of aa32KTKEGVLY^"VGSKTREaa46 and the DRB3*02:02 allele, suggesting this allele might be protective. The four alleles DRBl*15i 01, DRB5*01:01, DQBl*03t0 and A*1X:0I accounted for every single individual responding to the aa39 epitope (p-0,00007 for PD, able 14), This association was far more significant in PD than HC (p^O.OOS) . The combined association for the four alleles for PB vs. Hi was significant (p^»O,008 two-tailed Fisher's exact test compared to individual DRB!*!5:01, p^™G.05_f and DRB5^"*^:G 1101, o- .03· , Kith - half of the PD (31 with alleles and 27 without carrying one of the four alleles, whereas only -20% of the HC (S with alleles and 26 without) expressed one of the four ( abl© 14} ,

Following detection of association of response to the Y^"39 region with the HC class I allele HLA A*1 X ; 01 , PD responses to shorter es-syn derived peptide candidates were evaluated for class I presentation, it was found that 5/19 PD responded to these short peptides while 0/12 HC responded (Fig, I3B & I3C) (two-tailed Chi sq ared.765, Idf, 0523} . Reactivity occurred mostly on peptides contained within the Y39 region, involving three peptides (aa36GVLYVGS TKaa45, aa37yLYVGSKTKaa.45, aa3?VLYVGSKTKKaa46} predicted as potential A*ll.:01 binders 15. Each peptide was tested for binding to purified HLA A*1X:01 molecules in vitro, and found that the 9mer aa3?VLY¥GS T aa45, which is nested within the two lOiTiers, hound with good affinity {1C50 ™ 161 nM) , while the other two bound po r ^"· y , indicating that the 9raer is responsible for T cell recognition. Reactivity to short peptides was mostly mediated by I F y producing cells and most pronounced for the Ail binding peptides. Thus, intntune responses to of-syn associated with PD have both MRC class i and II restricted, components .

Discuss ion

Genetic studies associate Parkinson's disease with aiieies of the major histocompatibility complex (Greenbau et ai., 2011; Hamsa et al . , 2010; Kannarkat et ai . , 2015) , A defined set of peptides derived from et- synuclein,. a protein aggregated in Parkinson's disease*?, was found, to act as antigenic epitopes displayed by these alieies and drive helper and cytotoxic T cell responses in Parkinson's disease patients. ithout wishing to be bound by any scientific theory_f these responses may explain the association of Parkinson' s disease with alieies of the acquired immune system.

Alleles of over twenty genes a.re associated with familial PD (hernande™. et al . , 2016) , many of which encode proteins implicated in lysosomal degradation pathways including •mitochondrial turnover. For example, mutations in es-syn or dopamine-modif ed s~syn pMartinex-Vincente et al , _f 2008; Cuervo et al,, 2004), and LRKK2 (Orcnstein et al . , 2013) interfere with protein degradation by chaperone-mediated actophagy, a process that becomes less efficient with age, Ext acell lar oiigoKteric ot-syn stay be acquired by brain cells during PD pathogenesis fhuk et ai,, £012) , These reports suggest that altered degradation of proteins including -syn could produce antigenic epitopes that trigger immune reactions during aging and PD,

The results herein indicate that peptides derived from two regions of ce~syn produce immune response in PD patients; their roles in additional synueleinopathies arc untested. Epitopes derived from the Y39 region h-aa31/32 to 45/46) arc specifically displayed by two MHC class l∑ beta chain alleles, DBB5*01:0X and DBB1*15:0I, associated with PD, as well as an additional MHC class 11 allele and an MRC class I allele not previously associated with PD. This response is enacted mostly by secreting CD4-J- cells, as well as FMLi CDS* cytotoxic cells, -Syn is not. to our knowledge endogenous iy expressed by ceils that express MKC class II, but is in CSF (A ik et ai., 20X6} , from where it can be acquired by MKC class II expressing cells. This situation is analogous to the experimental autoissOTune encephalitis model of multiple sclerosis, as myelin proteins used to produce; autoimmunity are not endogenous to BC class II expressing ceils, but are accumulated and processed for MBC class rl display by antigen presenting cells and microglia. The Y39 antigenic region is strikingly close to the ζί-syn mutations that cause PD (A30P, E46K, R50Q, G51D, A53T) (Hernandez et a ; . _t 2016). The second antigenic region encompasses S129 and requires S12S phosphorylation, a fors present in Lewy bodies (Fuji¾?ara et al . , 2002} c antigenic epitopes from that region are not strongly restricted and can drive immune responses in PD patients who do not express ΆΪΛ alleles that recognize the Y3 region.

Approximately 40% of the PD participants in our cohort exhibited immune responses to s-syn epitopes, and these responses may reflect variations in disease progression or environmental factors. The fraction of patients who display such responses in classic autoimmune disorders such as TID, rheumatoid arthritis and multiple sclerosis is often ---20-50% <Pe rich de Marquesini et al . , 2010 ), Without wishing to he bound by any scientific theory, as with TlD, which features epitopes derived

both preproinsulin and additional proteins, it may he that PD-related epitopes are derived from co-syn and additional proteins. In classic autoiia une disorders, MBC class II response stay precede MKC class I (Ma rack et al,, 2012), and it is noted that exposing .microglia, to a- syn triggers MBC class I expression by dopamine neurons (Cehrain et al , , 2014} . Without wishing to be bound by any scientific theory, the > '■>^■ associated proteins parkin and PINK! may regulate antigenic presentation of mitochondrial peptides (Maiheoud et ai,, 2016), and it is possible that an autoimmune presentation of antigenic epitopes unites lysosomal and. mitochondrial mechanisms of PD pathogenesis. A} Study subjects

All participants provided written informed, consent for participation in t e study. Ethical approval xas obtained from the LJ and. Columbia University institutional review boards. 6? participants with PD and. 36 age-matched healthy controls (HCs) were recruited from the greater San Diego (PD_f n-S; BC, n-13) and Hew York City (PD, n-58; HO, n-23) areas. The Hew York cohort was recruited from the Center for Parkinson' s Disease at Columbia University Medical Center through the Spot study 34. PD was defined based on the United Kingdom Parkinson's Disease Brain Bank criteria, without excluding cases with a family history of PD 35, Demographies and disease characteristics were collected including age, age of onset, sex, medications, comorbidities and raotor disease severity as iiieasured by the Unified Parkinson's Disease Rating Scale (0PDRS) motor score (UPDRS~I∑I) . Also, family history of PD i first-degree relatives was collected. The data are reported in fa les 11a & lib. In the San Diego cohort, demographic data was collected and PD was self-reported.

Samples used for additional assays in Fig, 13 and Fig, 10 were collected from consecutive individuals based on the schedule of their appointment ; the demographics and PD characteristics of these participants are displayed in Tables 12 and 13, HCs were recruited through a convenience sample of consecutive non-blood related individuals, and were mostly spouses of PD participants . At Columbia University, PD and EC were recruited only if there was no history of immune modulatory medications {e.g., steroids) or overt autoimmune disorder (e.g., lupus). No significant difference was detected in response rates as a function of sex or geographical, location. Three participants with PD had a history of Crohn's disease and one patient, had a history of Hashimoto's thyroiditis. Two of the three participants with Crohn' a disease showed antigenic response to a-syn and the participant with Hashimoto' s thyroiditis did not. Experimental blinding was accomplished by labeling the blood samples in a coded fashion without information on age/gender or PD status. The cohort was predominantly Caucasian {88,3%} and no firm conclusions between Crohn's {Harms et ai . , 2013} disease and S?D could be drawn because of the Limited auiKber of Crohn's disease patients studied.

Bj Peptides

Peptides were synthesized as crude material, on a small (1 mg) scale by A and A (San Diego, CA} . Peptides were 40 issuers overlapping by 10-14 residues and 70 9- or iOmers predicted to bind common HLA™eiass I alleles. Briefly, each possible 9- and I Outer frost et~syn were scored for their capacity to bind a panel of 27 common HL& class 1 A and B molecules Paul et ai., 2013). For each allele 4 peptides were synthesized (two 9mers and two lOmers, n™61 after removing redundant sequences that were selected for 2 or more alleles) . In addition, any peptide that scored at the 2 percentile level or better for predicted binding, but were not within the 4 selected per allele were synthesized (n™9) , Posttransiationaiiy modified peptides {n=?} were synthesized as purified material (>S5% by reversed phase HPLC) by A and A (San Diego) . Peptides were combined into pools of 1 peptides (range 11-16) .

An alternative mode of stimulation would be to use whole s-syn, but it was opted for synthetic peptides due to their well-characterised and uniform chemical species, in contrast to a~syn preparations that contain varying amounts of different post-translational modifications, and as it is unclear which form s) are processed by APCs during PD, In addition to a lower cost, synthetic peptides better provide apping of specific epitopes and reasurement of HLA binding,

C) PBIC isolation and culture

Venous blood was collected in hepar in-containing blood bags or tubes. Peripheral blood mononuclear cells (PBMC) were purified from whole blood by density-gradient centr ifugation, according to the manufacturer's instructions . Cells were crycpreserved in liquid nitrogen suspended in FBS containing 10% (vol/vol) DMSO . Culturing of PBMCs for in vitro expansion was performed by incubating in R I (Omega Scientific) supplemented wit 5% hum n AB serura (Gemini Bioscience) , 15 GiutaH&X (Gifoco) , and p<gniei 1.1 ίn/st reptomycin (Oraega Scientif ic) at 2 2 106 per L in the presence of individual peptide pools at 5 jig/ml . Every 3 clays, lOtf/ml ∑L~2 in media ware added to the cultures.

D) EL SPOT assays

After 1.4 days of culture with individual peptide pools (Spg/sti), the response to pools and individual peptides {5pg/ml) was measured by IF y and IL-5 dual ELISPOT 37, ELISPOT antibodies,, mouse anti-human IFMy {clone 1-E51K) , mouse anti-human IL-5 (clone TRF 5) , mouse anti-human H¾y~RRF (clone 7~B6~1 , mouse anti-human IL-5 biotinylated (clone 5AI0) were ail from a tech♦ o be considered positive, a response had to match three criteria: 1) elicit at least 100 spot-forming cells (SEC) per 106 PB C, 2) p¾SO,05 by Student* s t-test or by a. Polsson distribution test, 3) stimulation index 5¾2.

For the experiments -with fibrili ed or native s-s n, PBMCs -were stimulated Kith epitopes derived frost co-syn for 14 days. These cultures were then stimulated -with s-syn peptides,. 25 ug/^'ml fibriiized a~syn or 25ug/ l native o:-syn,

E) HhA typing_f restriction,, binding predictions and assays

Participants were HLA typed at the la Jolla Institute or by an ASBI- accredited laboratory at Murdoch University {Western Australia) , Typing at 1J1 was performed by next generation sequencing 38, Specifically, arti l icons ere generate-d from, the appropriate class II locus for exons 2 through by BCR amplification. From these amp!icons, sequencing libraries were generated {lilumina Re tera XT) and sequenced with MiSeq Reagent Kit v3 as per manufacturer instructions (lllumina, San Diego, CA) ,

Sequence reads were matched to HLA alleles and participant genotyping assigned. LA typing in Australia for Class I (HLA A; B; C) and Class II {DQA1 > DQB1, DBSI 3,4,5; DE^>BX) was performed using locus-specific PCR amplification on genomic D13¾, Primers used for amplification employed patientspecifi.c barcoded inters , Amplified products were guantitatec and pooled by subject and up to 48 subjects were pooled. An unindexed ( 5 8- l ne runs) or indexed (8 indexed MiSeq runs) library was then quant itafed using Kappa universal QPCR library quantification kits. Sequencing was performed using either a Roche 454 FLX-f sequencer with titanium chemistry or an liiumina iSeq using 2 x 300 paired-end chemistry. Reads were quality-filtered and passed through a proprietary allele calling algori hm and analysis pipeline using the latest !MGT HLA allele database as a ref rence .

The algorithm was developed by co-authors LP and S and relies on periodically updated versions of the freely available international iifimuuogeneties information system (http://www.ijngt.org) and an ASBI- accredited HLA allele caller software pipeline, HID HLA Analysis Suite {www, iiid. coat,au/labora ory-tes ing/} .

Potential BLA-epitope restrictions were inferred using the RATE program (Paul et al., 2015) . HLA A*ll:01 binding predictions were perforred using the consensus prediction method publicly available through the IHDB Analysis Resource (available at www. iedfo.org) (Vita et al., 2015).

Class leal competition assays to quantitatively measure peptide binding affinities for HLA class I and II HHC molecules, based on inhibition of binding of high affinity radiolabeled peptides to purified MH molecules, were performed as detailed elsewhere 40, Briefly, 0.1-1 nM of radiolabeled peptide was co-incubated at room temperature or 3?°C with purified MHC in the presence of a cocktail of protease inhibitors (and, for class I, exogenous human p2~ icrogiobulin} . Following a two to four day incubation, MHC bound radioactivity (cpm) was determined by capturing MHC/peptide complexes on Lumitrao 600 plates (Greiner Bio-one, Fr ckenl.a sen, Germany) coated with either HLA DR (L243), DQ { B1 SO), DP (B7/2I) or class I S/32) specific monoclonal antibodies. Bound cpm was measured using the TopCount microscintiilation counter (Packard Instrument Co,, eriden, CT) , The concentration of peptide yielding 50% inhibition of binding of the radiolabeled peptide was calculated. Under the conditions utilized, where label] < £ BC] and ∑C50 S^; [MHC] , measured IC50 values are reasonable approximations of true Kd (Cheng and Brusoff, 1973; Gui kota et al,_f 199?} . Each competitor peptide was tested at six different concentrations covering a 100, 000~£old range, and in three or more independent experiments . As a positive control, the unlabeled version of the radiolabeled probe w s also tested in each experiment.

A threshold of 1,000 nM binding a finity is associated with immunogenicity of BLA class II T cell epitopes, and most epitopes bind in the 1-100 nm range, with affinities in the 1-10 nM considered to be of high affinity *Siduey et al . , 2010} ,

F) Int acellular cytokine staining

After 14 days of culture PBMC were stimulated in the presence of 5ug/nti ct-syn peptide peel for 2h in complete RPMI medium; at 37*C with 5% C02. After 2h, 2,5pg/iiii each of BFA and monensin was added for an additional 4h at 37*0. Uns imulated PBMCs were used to assess nonspecific/background cytokine production and PHA stimulation at 5pg/rrti was used as a positive control. After a total of S _t cells were harvested and stained for cell surface antigens CD4 {anti-CD4~AS?C£f 80„ RDA-14, eBioscience), CD3 <anti- CD3-AH^:?00, UCHT1, BD Pharmingen) , CDS (anti-CDS-BVoSO, RPA- 8 _f BioLegend) , CD14 (anti~CDI4~V500, M5E2, BD Bharmingen) _f GDIS (anti~CD13~ V500, ΒΪΒ19, BD Pharmingen) , and fixable viability dye eFl or 506 (eBioscience) . After washing, cells were fixe using 4% paraformaldehyde and permeabiiized using saponin buffer. Cells were stained for IFMy {anti- xFNy-APC, 4S.B3, eBioscience), IL-17 {ant.i~IL~1 ~PECy7, eBioo 'iDEC ll , eBioscience), IL~4 <anti-∑L~4~P£/Dazzle5S4, MP4-25D2, BioLegend) , and XL- 10 (ant.i~IL~10-AF4S8_f JES3-9D?, eBioscience) in saponin buffer containing 10% BBS. Samples were acquired on a BD LSR II flow cytoiseter.

Frequencies of GD3÷ T cells responding to o:~syn peptide pool were quantified by determining the total nuraber of gated C∑)3f and cytokine* cells and background values subtracted {as determined front the medium alone control) using FlowJo X Software <FX© Jo, Ashland, OR) . Consfcinations of cytokine producing colls were determined using Boolean gating.

G) HLA-DR and -ABC expression

PBMCs from I)RBi*15:01- or BRBi*15;01™ PI) (n=5 for both) and EC (n-3 DEBl*15i0l+ and n-5 DRBX*X5:GX~ were assessed for HLA-DR and HLA-ABC (as a control) expression, 721,221. and RM3 ceils (both sourcod from A CC, mycoplasma free) were used as controls for HLA-DR and HLAABC expression, 721,221 cells lack HLA-ABC and express HLA-DR, whereas RM3 cells lack HLA-DR and express HLA-ABC. All cells were stained for cell surface antigens CD1 anti~CD14~APC_f 61D3, Tonbo biosciences},. CD3 (anti~CD3~ AF70O, UCHTi, BD Pharminqec.) _f HLA-ABC (ant i-HL -ABC--AF 88, «6/32; pan HLA class X, BioLegend) , HLA-DR {anti~BLA~DR~PE_f L243; pan HLA-DR, oBiosoionce) , and f ixafoie viability dye erluor 506 (oBioscionoe) or isotype controls for HLA-ABC {AF 88 Mouse IgC2a_r x, catalogue number 400233, BioLegend) or HLA-DR (PE Mouse XgG2a, , catalogue number 12- 4724, ©Bioscience) . After washing, cells were fixed using 4% pa a ormaldehyde . Samples were acquired on a BB LSR ∑∑ flow cytometer, T e fraction of living cells expressing HLA-ABC or HLA-DR was determined using Flo Jo X Software,

H> g-Syn purification and «-syn PFF preparation

Recombinant a-syn monomer was purified as previously described 44, cc-Syn pre-fcrmed fibrils (PFF) were prepared by agitating or-syn monomer in a transparent glass vial with a magnetic stirrer (350 rp at 37 °C) « After 5-7 days of agitation, the clear σ-syn monomer solution became turbid, indicative that ¾~syn fibrils were generated. The s-syn fibrils were then sonicated for 30 seconds at 10% amplitude to generate ot^'-syn PFF (Branson Digital Sonifier, Danbury,. CT, USA) , o-Syn monomer and PFF were aiiquoted and kept at -80 ^CC.

I) Statistics and Reproducibility A power analysis was not conducted, a priori as there was no Hteans to estimate effect size, F tu e validation studios will test whether the Y39 antigenic region is recognized significantly higher in donors with PD co pa ed to EC. The recognition frequency of this peptide was 17% in PD and 3% in EC, which achieves 61% power to detect a response difference between response rates of 14 percentage points. To achieve SG% power in a repeat study to detect a similar effect size, a total of 62 PD and 62 HC should be included. Additionally validation studies will test whether the overall recognition of the peptides is significantly higher in donors with PD compared to HC. Based on our combined cohort data the recognition frequency of a pool of peptides was 37% in PD and 8% in HC, To obtain S0% power in a validation study a cohort size of 43 in both and KC will be required to detect the same effect.

The Fisher's exact (two-tailed) test wa used to evaluate the contingency between carriers and non-carriers of the DRBl*15;01 and DRB5*01:01 alleles in the PD and HC donors (Supplemental Table 13} , between the responses to phosphorylated aaS123 epitopes of PD and HC donors (Fig. le-g) _? and between ORB!*0 ί /DRB5* 01 : 01/DQBi *03 ; 04/A*ll : 01 carriers and non-carriers in PD and HC donors <Table 15) . A n ~para_?tetric test was used because the data is not normally distributed.

Fisher' s exact test that provides exact p values for the analysis of contingency tables and is available in most professional statistical analysis packages,

Che Harm yihitney test (two-tailed) was used to assess whether the number of SFCs of HC donors would be less or greater tha those of PD donors (Fig, 1 b-q, Figure 2, Fig. 3 a-c) , The Mann Whitney test (two-tailed) was used to determine if the number of IFNy SFC was different than XL- 5 SFCs of PD donors (Fig 3d) , A no -parametric test was used because the data is not normally distributed.

T~t.ests ware sed to analyze parametric differences in demographics between PD and HC donors (Table 11a, l b, 12} . The Wilcoxon test was used, to analyze differences in population Hteans of t e repeated jseasureraents of numb r of SFCs induced by raedia and different isoforms of a~syn {Fig. } . A non-parametric test was used because the data is not normall distributed, it was hypothesized that responses to proteins and peptides would he higher than media alone, therefore a one- tailed test was used for those comparisons. Comparison between FFF and native o~syn w s two-tailed.

A power analysis could not be run for this prior to the experiments as there were no means to estimate effect size. Future validation studies will test whether the Y39 antigenic region is recognized significantly higher in donors with PD compared to HC, The recognition frequency of this peptide was 17% in PD and 3% in HC, which, achieves 61% power to detect a response difference between the response rates of 14 percentage points. To achieve 80% power in a repeat study to detect a similar effect size, a total of 62 PD and 62 HC should be included. Additionally, validation studies will test whether the overall recognition of the 11 peptides is significantly higher in donors with PD compared to HC, Based on our combined cohort data the recognition frequency of a pool of peptides was 37% in PD and 8% in HC. To obtain 80% power in a validation study a cohort size of 43 in both PD and. HC will be required to detect the same effect .

The present, invention is useful to diagnose, confirm, provide a foioraarker for, and treat PD.

Aspects of the present invention relate to the surprising discovery that epitope peptides that activate leukocytes are expressed on the surface of neurons in subjects afflicted with PD, Surprisingly, these epitopes are useful in diagnostic and treatment methods for PD. The present invention provides improved and novel. methods for diagnosing, confirming, providing bioisarkers for, and treating PD are needed. Additionally, specific treatments tailored for individual patients are provided herein. Identification of specific TAR DNA binding protein 43 ( DS?43) antigens that act as autoantigens . This can be used as the source of biomarkers, diagnostics and therapeutics via toierization and related approaches.

Amyotrophic lateral sclerosis (M»S) patients undergo an extraordinarily rapid death of neurons, prominently including- mot r neurons, leading to death at a me n duration of three years following diagnosis, yihiie aggregates in the surviving neurons clearly point to a disturbance in normal protein handling during the disease process, despite much research and multiple theories, the field has not identified the means by which these neurons die, in this proposal ¾?e explore a novel hypothesis, that these neurons ma be killed by autoimmune 1 ceils that recognise particular epitopes from isprocessed disease-linked proteins.

The work herein characterizes aufoinvfiune epitopes in ALS patients.

ALS is presently associated with mutations in over twenty genes and m y more are likely to be involved, Mutations in the gene for transactivation response DNA~binding protein 43 (TDP43 } are rare, but there appears to be a convergence during ALS pathogenesis, as 97% of patients diagnosed with ALS feature TDP43 intraneuronal cytosolic aggregates (Neumann et al, , 2006? Aral ef al . _f 2006; Ling et al., 2013). TDM3 is nominally a nuclear ribonucleoprotein implicated in ENA handling, and so the presence of cytosolic aggregates strongly indicates abnormal protein handling and degradation of the protein associated with, the disease (Blok.huis et ai,, 2013} . The TDP43 protein within the aggregates features phosphoryiated, deamidated, and cleaved, residues in the glycine-rieh C terminal region (Kametani et al., 2016). Without wishing to be bound by any scientific theory, methods of the present invention focus on DP 3 due to its near ubiquity in ALS aggregates, its protein modifications associated with disease, and its likely role as a substrate for chaperone-mediated autophagy (Ct-lA) , Without wishing to be bound by any scientific theory, there are multiple additional proteins also found in ALS aggregates that may be important as discussed herein,

Suntfiary

Specific autoittnrune damage in ALS stems from two overall lines of recent findings :

A) Finding 1

Although neurodegenerative disorders of aging are not considered to be autoimmune disorders, recent findings in press at Nature from the collaboration between the Columbia and LJI teams (Sulzar et aL, 2017} show that there are helper cell and cytotoxic CD8+ T cell (CTL) autoiimtune responses in Parkinson' s disease <PD} , and that this is due to specific epitopes, in this case derived from cc-synuciein ( ~syn presented by specific MHO I and II alleles, These epitopes include a phosphorylated residue of -syn, S123, which is the classic component of Lewy bodies, which are PD aggregates with multiple analogies to ALS aggregates. This PD autoimmune response may in turn stem from the decrease in CM& activity that occurs with aging (Cuervo et ai . _f 2005), and the Sulser group in collaboration with Ana Maria Cuervo (Einstein University) introduced CMA as the ;rteans by -which s-syn is degraded and by which pathogenic σ-syn blocks normal protein degradation (Cuervo et ai,, 2004; Martinez-Vincents et ai,, 2008), including for other PD- linked proteins (Orenstein et ai. , 2013). without wishing to be bound by any scientific theory, it is noted that DP 3 possesses a CMA consensus sequence, 134QVK D138, that is extremely close to the a~syn C A sequence, 95VKKDQ99, and that TDF43 is likely to be a CMA substrate as well, CMA has already been shown to be blocked by pathogenic atec anisms such as amino acid atodificat on. Thus, TDP 3 is a strong candidate as an autoarvtigen, in a manner si.milar to -syn, w thout wishing to be bound by any scientific theory, this response could engender both biomarkers and new treatments for ALS patients, it is noted that in a recent publication, the protein annexin A-ll was reported as a relatively rare cause of ALS, and t is protein is already implicated in the classical autoimmune disorders, systemic lupus erythematosus and sarcoidosis (Smith et ai . , 2017).

B) Finding 2

Adult CHS neurons were long thought to not present antigen, hut a recent study demonstrates in human pathological specimens that midbrain dopamine and norepinephrine neurons that die in PD express HC-I (Cebrian et 2014), In rodent models, the MBC-I expression in the neurons is driven by cytokines, pa ticula ly inter fercn-y released frc- activated microglia, and the appropriate combination of I ceils and antigens kill these neurons_* In the specific case; of meter neurons, multiple earlier studies demonstrate MHC-I presentation b nature and aged juotor neurons in rodents 13-15, and a new study confirms MH - \ presentation by rootor neurons in SODX ALS mouse models (Nardo et ai . , 2016), In ALS huisian pathology, multiple publications report activation of microglia and monocytes (Butovsky et al,, 2012; Zhao et ai., 2017), a feature also observed in ALS mouse models (Chiu et ai,_f 2009; Chin et al., 2013). in human ALS, there appear to be variable levels of T ceii infiltration; Appel and collaborators first, suggested autoimmune features of ALS, although with normal numbers of I ceils in most patients 21, while early reports found a 90-fold increase in cytotoxic CDS T cells (CTLs) in ALS spinal cord over age-raatched control patients, and 2?~fold increase in helper ϊ cells (McGreer et ai,, 1993; Kawaraata et ai , , 1992), To our knowledge, there have been no reports of MHO-∑ or ∑i on neurons or astrocytes in human ALS specimens. It is noted that studies of the periphery often assume that MHC-I provides a neuroprotective role, but that in ALS pathology (Chiu et ai , , 2008), as with dopamine neurons and other cells that express MHCI, recognition by CTLs ma lead to cell death.

Without wishing to be bound by any scientific theory, it is hypothesised that aberrant degradation and processing of TDP43, and likely additional proteins, lead to the production of specific TDP 3-derived autoimmune epitopes displayed by MHC-Ϊ I that activates specific helper I cells and by MHO! that activate specific C'TLs . Future work would, determine the role of autoimmune function in neuronal death, if autoimmune response provides ALS bio arkers, and bow blockade of these steps could halt ALS pathogenesis .

Aim of Exporime 111s

C) m I

Ail possible 15~mer peptides of TDP 3 overlapping by 10 amino acid residues covering the entire protein sequence will be produced, corresponding to approximately 40 peptides. Additionally, a smaller num er or peptides will be manufactured that feature deanidated asparaqine and oxidized methionine residues reported in ALS aggregates {Kametani et ai., 2016), yfciie initial focus is on TDP 3 as discussed above, a smaller number (--5 each) of peptide candidates will be determined in FOS and SOD-1, which are less ubiquitous but relatively common additional proteins observed in ALS aggregates (Blokhnis et al„ , 2013), in contrast to anne.in~All , which is only observed in particular familial samples (Smith et ai„, 2017). All of these peptides (approximately 60) will be arranged in 6 pools of approximateiy 10-15 peptides each. Clinical analysis will, be performed and 30 cc fresh blood samples obtained from 40 sporadic ALS and 40 age-matched controls (HC) that will be sent for analysis of specific ΐ cell reactivity. For this purpose, PBHC will be separated by the use of standard magnetic bead protocols (Riitenyi Biofecj , in subsets corresponding to CD4+ T cells including effector and regulatory subtypes, CDS-f- cells, and remaining CD3~ceiis (containing B cells, DC and macrophages to be used as APC) . CD4+ T cells and CD8+ T ceils will be separately stimulated in the presence of APC with the di f rent peptide pools. After in vi tro rest limitation, ϊ cell recognition will be assessed by triple FLUOROSPOT analysis for detection of IL-5 (indicating helper ceils

mainly of the Th2 subset), IL-17 (for Thl7 ceils), XFN~y (for C Ls/helper Thl ceils) and lL-10 (for regulatory T regs to pools of epitopes under conditions in which diagnosis is blinded. Responsive samples will, be decouvoiuted and the specific epitopes responsible identified. T cell lines that undergo activation in response to specific epitopes will be analyzed by flow cytometry assays to confirm their CD /CD8 identity as CTLs or specific helper subtypes, and additional phenotypic cha acterisation will be performed, in terms of patterns of cytokines secreted. Ail data will be examined blind.,^, will not be traceable to donors, and will be considered exempt (under Title 32, Federal Regulations, Part 2X9, Section 101(b) (32 CFR 2X9.101 [b] > . Ai∞ 2

The epitopes identified above derived from TDP43, US and SOD-i will be characterized. Aim 2a) - The correlation will be analysed between 1 ceil recognition and location of the immunogenic

sequences. Without wishing to be bound by any scientif c theory, it is expected that the epitopes will concentrate in particular regions near the carboxy terminus, based on reports of TDF43 fragments found in ALS aggregates (aa252-263, 276-293, 409-414) {Neumann et al., 2006), and recently reported TDP43 amino acid modifications in ALS patients et ai„, 2016), including 18 phosphorylated disease-linked serine residues near the carboxyl terminus (from aa 242 to 403) . Aim 2b) The HLA molecules that act as restriction elements will be determined. For this purpose, HLA typing will be determined by next-generation sequencing methods, and the association between responses to individual alleles and particular HLA molecules determined by genetic inference (Paul et al . , 2015} - The putative restrictions will be independently confirmed by performing quantitative BLA~peptide binding measurements with the HLA raoiecuies expressed in the responding donors. Aim 2c) These confirmed restriction data will, be utilised to produce tetramerie and dejitrameric staining reagents, isolate specific responding ? cells, and determine the patterns of ICR gene expressio (TCR sequencing} , of interest for fhe development of ALS biomarbers.

E) Aim 3 The ALS and. HC samples will be genotyped for HLA alleles and for known causes of familial ALS (including and not limited, to specifi alleles in the TDP 3 gene, TARDBF, HNRMBA.1 , PFNi, C90RF72, UBQIN2, OPTN, VCP, ANXA11, and FUS) . ceil receptors responsible for recognition of specific epitope /HLA combinations will be sequenced. After analysis, the results Kill be unblinded and analysed for the relationship between specific autoimmune responses and disease status, duration, age, sex, and HLA genotype, as wall as known ALS- linked genes.

Piscu sion

F ) Innovation

There have been no analyses to address if ALS has autoinusrune responses to epitopes from specific disease-linked proteins, nor characterization of the HLA alleles, T cells, or cell receptors involved in such responses, indeed, this approach has only become possible with the introduction of new technical approaches to identify specific epitope- allele interactions by the Sette group and collaborators, More broadly, the only publication describing such autoimmune response in neurodegenerative diseases of aging is the recent collaborative paper in PD patients (S izer et ai . , 2017), which relied on work on protein degradation, and the identification of candidate HLAs and epitopes . it is noted that multiple sclerosis is a classic autoimmune degenerative disorder of the nervous system, but that the principal cellular targets of the immune system are oligodendrocytes.)

The an.toin^une responses to m.sfolded and/or aggregated signature proteins in ALS will provide clear consequences for the evelopment of biomarkers and therapy,

Gj Impact

Together, this experimental design provides a clear means to address if ALS has autoimmune responses to epitopes of specific disease-linked proteins. Once specific epitope~BLA restriction patterns are discerned, ALS patients can foe characterized for their specific autoimmune responses using ^ ultimer" technology, which provides a rapid and effective jneans to assay the number of specific reactive ϊ ceils. This would define specific subtypes of ALS, and contribute a valuable and independent means to genetyping . It is noted that many sporadic ALS patients have no known associated disease allele _f and in analogy to our findings from responses to syn-derived epitopes in PD, the autoimmune responses .may show convergence from multiple causes, This may be particularly true for TDP43 epitopes, which would be present in the vast .majority of aggregates of nearly all ALS patients.

The identification of specific autoimmune τ cells ma provide a predictive bioatarker, and may provide a bioatarker for the efficacy of treatments for particular individuals. ∑t is acknowledged that the treatment for autoimmune disorders has been very challenging, and multiple im unosuppress ive drugs (glucocorticoids, cyclophosphamide, azat ioprine, cyciosporine and others) have been ineffective in ALS patients, it is further noted there are however recent developments that provide very effective imstuxiOisoduiatory treatments for many relapsing- remitting multiple sclerosis patients that could be examined for ALS treatment (e,g,, teriffluno ide, dimethyl ruisarate, nataiizuisab) . Perhaps central to the development of effective treatment is that the nsRu osuppressive drugs that to our knowledge have been examined in ALS are not specific for ΐ cell epitope combinations, and there are multiple new approaches under development to specifically modulate epitopespeci ic reactions, Additional approaches may include means to decrease HC presentation by microglia, motor neurons, astrocytes, and. epithelial ceils, h ^personalized" approach based on detection of the antigen-HLA conformation and. T cell receptors of that patient may be required due to the diversity of HLAs, epitopes and Ϊ ceil receptors,

This study would also contribute to the basic knowledge of how neurons die in ALS , a central issue that remains unciear and promises additional, therapeutic development. Given the evidence above for recognition of MHC-ΪΙ epitopes, and the expression by HHC-X by motor neurons, the results from this proposal may provide the means for follow-up studies to specifically test ? cell-mediated responses in animal ALS models, as well, as i.FSC-derived neurons from particular KLB patients with defined HLA alleles and restricted epitope responses, lx ¾le X5, Cjtokin-e BeXgase in Cont ols and LS F tients

Blood from age matched controls nd ALS patients we e obtained and jsononucXear ceils were isolated by gradient centrifugation ,

Release of the cytokines gajana-interferon, which measures activation of €D4* and/or CDS-*- T cells, the interieubin, IL-5, which measures activation of CD4 - T cells, and the interieukin iL-10 were measured by ELlSpot assay. Briefly, the isolated ceils were plated in wells that have coXoriiaetric detection of gam a-interferon, IL-5, and IL-10, and we stimulated with pools of epitopes of TDP40 that the Sette lab determined would potentially foe displayed by MHC-X or MHC-XX antigen-presen ing proteins in humans -

After two weeks of stimulation, the cells were harvested and release of cytokines was measured by colorimetric detection of spot~f©rising ceils CSFC) - Confirmed release of cytokine is determined by the presence of a κιχηχϊταΗη of 20 SFC per isiXXion cells,

Preliminary results indicated that ALS patients have a high reactivity to DP43 peptides than the control groups {Fig Χ4Ά^«-Χ4Β ,

ALS patients are more likely to have T cells in blood that recognise and are activated by TDP 3, FUS or SGD-l than unaffected individuals, gstjagle 16 ol¾ri ¾tion t¾¾r¾jay s -¾ci.fic f ¾ i O ¾g .f roF 3,. Fgg or

SQD~1 are usef l in treating subjects afflicted with ALS,

Epitopes to which cells are responsive in subjects afflicted with ALS are identified by

i) obtaining T ceils from each subject; ii} contacting the ϊ cells with a test compound;

ill.) dete mining whether the T cells have increased activation after contact with the test compound; and

ivj identif ing the test compound, as an epitope to which the cells are responsive if in step iii) the celis are determined to have increased activation after contact with the test compound, and identifying the test compound as not an epitope to which the T celis are responsive if in step iii) the cells are determined to not have increased activatio after contact with the test compound. This method is repeated sequentially or in parallel for thousands of test compounds, each having an amino acid sequence identical to a stretch of consecutive amino acids in the DP43 protein. Epitopes for DP 3 are identified in individual subjects.

i) obtaining T ceils from each subject;

ii) contacting the T cells with a test compound;

iii} determining whether the T celis have increased activation after contact with the test compound; and

iv) identifying the test compound as an epitope to which the T celis are responsive if in step iii) the T ceils are determin d to have increased activation after contact with the test compound, and identifying the test compound as not an epitope to which the cells are responsive if in step iii) the T cells are determined to not have increased activation after contact with the test compound. This method is repeated sequentially or in parallel for thousands of test compounds, each having an amino acid sequence identical to a stretch, of consecutive amino acids in the FUS protein, Epitopes for FUS are identified in individual subjects.

Epitopes to which ϊ ceils are responsive in subjects afflicted with ALS are identified by

i) obtaining T cells frosi each subject;

ii) contacting the T ceils with a test compound;

iii) determining whether the T cells have increased activation after contact with the test compound; and iv) identifying the test compound as an epitope to which the T ceiis are responsive if in step iii) the T ceiis are determined to have increased activation after contact with the test compound, and identifying the test compound as not an epitope to which the ceiis are responsive if in step iii) the T ceiis are determined to not have increased activation after contact with the test compound. This method is repeated sequentially or in parallel for thousands of test com ounds, each having an amino acid sequence identical to a stretch of consecutive amino acids in the SOD-1. protein. Epitopes for SOD-1 are identified in individual subjects.

The subjects afflicted with ALS are then separated into cue of two groups: I) a test group that receives toierination therapy, or 2} a control group that does not receive tolerization therapy, within the test group, an effective amount of an epitope to which τ ceils are responsive in subjects afflicted with ALS is administered orally, nasally, or subcutaneous!y to each subject (i.e., fdenization therapy specific for the epitope) . Within the control group, a polypeptide having a random sequence is administered to each subject.

Compared to the control group, subjects in the test group have a statistically significant reduction in symptOi S of ALS, Additionally, a statistically significant proportion of the subjects have little or no progression of ALS,

Less or no activation of T cells by the epitope is observed in subjects who receive and respond to tolerization therapy, but not in subjects who do not receive or who do not respond to toieri zation therapy, gstjagle 17. A¾¾oi^¾n,¾ F®at r@¾ of Nagrc^s^atijg Disor^rs

Without wishing to be bound by any scientific theory, at least sojne ALS is in part an autoinvfiune disorder.

Without wishing to foe bound by any scientific theory, the cells recogni e TDP 3 , PUS, or SOD-1. Aspects of the present invention relate to the surp ising discovery that epitopes that activate leukocytes are expressed on the surface of neurons in subjects afflicted with Aid; . Surprisingly, these epitopes are useful in diagnostic and treatment methods tor ALS, The present invention provides improved and novel methods for diagnosing, confirming, providing biomarkers for, and treating »S are needed. Additionally, specific treatments tailored for individual patients are provided herein. mtients with Parkinson' s diseas

This ex iTi ie describes a specific epitope screen to identify disease- relevant antigens for Parkinson's disease, it should be understood that these methods can he broadly applied to other neurodegenerative diseases and disorders that involve an infla matory response and/or i flammation, noniiiaiting examples of such are disclosed herein.

Genetic studies have shown the association of Parkinson's disease with alleles of the Htaj r histocompatibility complex (Greenbaum, j, t ai. Functional classification of class ∑∑ human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes, Irrmuinogenetics 63, 325-335 (2011); Bamza, T» H, et al . Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease. Nat. Genet, 42, 781-785 (2010} ,^* Kannarkat, G. Ϊ . et ai . Conraon genetic variant association with altered HLA Expression, synergy with pyrethroid exposure, and risk for Parkinson's Disease: an observational and case- control study. NPJ Parkinson's Dis, l_f 15002 (2015)}.

Described herein is a defined set of peptides that are derived front cf~ synuclein, a protein aggregated in Parkinson' & disease (Spiliantini, , G. , Crowther, R . A , , Jakes, R . , Hasegawa, M , k Goedert, M , et~symiciein in filamentous inclusions of Lewy foodies frora Parkinson's disease and dementia with iewy bodies, Proe. Had Acad. Sci. USA 95,· 6469-6473 (1998)} act as antigenic epitopes displayed by these alleles and drive helper and. cytotoxic T ceil responses in patients with Parkinson's disease, %^'itho t being bound by theory, these responses m y explain the association of Parkinson' s disease with specific isajor histocompatibility complex (MHC) alleles.

Abnormal processing of self-proteins can produce epitopes, which are presented MHC proteins to be recognised by specific T ceils that have escaped tolerance during thymic selection (Harrach, P. & Kappler, J. Do MB.CII -presented neoantigens drive type 1 diabetes and other autoimmune diseases? Cold Spring Barb, Perspect, Med, 2, a007765 (2012}}, Such actions by the acquired immune system have bee implicated in autoimmune disorders, including type-! diabetes. While not considered to possess autoimmnne features, neurodegenerative diseases are characterised by altered protein processing. The major pathological features ot^" Parkinson's disease, the most common neurodegenerative movement disorder, are the death of dopaminergic neurons of the substantia nigra, and. the presence of intranenronal. aggregates known as Lewy bodies that are composed of a~synuclein {of~syn} {Spiliantini, G», Cro thsr, R, A. , Jak.es, R„ , Rasegawa, , & Gcedert, M. or-synuclein in filamentous inclusions of Lewy bodies from Parkinson' s disease and dementia with lewy bodies. Proc, Natl Acad, Sol, USA 95, 6469-6473 {1998} }. Activated microglia have been reported in the substantia nigra of patients with Parkinson's disease for nearly a century and cytokine profiles have implicated the activation of the innate immune system (Cebrian, C, Loike, J, D, & S izer, D. Neuroinfia mation in Parkinson's disease animal models: a cell stress response or a step in neurodegeneration? Curr, fop, Behav, Heurosci. 22, 237-270 (2015)}.

More recent evidence has suggested a role for the acguired immune system (Cebrian, C, Loike, J. D. & Sulzer, D. Neuroinf iamsiatien in Pa kinson' s disease animal models: a ceil stress response or a step in neurodegeneration? Curr. Top. Behav. Neurosci, 22, 237-270 (2015)}, including T cell in ilt ation info the substantia nigra of patients with Parkinson's disease (Brochard, v. et ai . Infiltration of €D * lymphocytes into the brain contributes to neurodegeneration in a mouse model of Parkinson disease. J, Clin. Invest. 119, 182-192 (2009) } , Genonte~wide association studies have shown the association of Parkinson's disease with an imaune ha lotype (kdssem nn, w. T. et ai. Association of Parkinson disease with structural and regulatory variants in the BLA region . nn J , Hum. Genet, 93, 984-993 (2013)} that is present in approximateiy 15% of the general population including the MHC class II gene alleles DKB5*G1 and DRB1 * 15 : 01and a pol morphism in a n n-cod ng region that n y increase MHC class II expression. (Hamza, T. H, et ai . Condon genetic variation in the MLA region is associated with late-onset sporadic Parkinson's disease, Nat. Genet. 42, 781-785 (2010); Kannarkat, G. T, et al. Common genetic variant association with altered B A Expression, synergy with pyrethroid exposure;, and risk for Parkinson'^' s Disease: an observational and case-control study. NPJ Parkinson' s Dis , 1, 15002 (2015) ) . Antigen presentation by t¾HC class I expression in dop mine neurons of the substantia nigra in adult human brains of patients with Parkinson's disease and age-matched controls is reported. It has been further demonstrated that dopamine neurons of the substantia nigra express MHC class I upon activation by cytokines that are released front microglia, which are activated by «~syn or neu one!anin,, and that COB* T cells kill neurons that present the appropriate combination of MHC class I and peptide. (Cebrian, C. et aX. KC~∑ expression renders catecholamine^ ic neurons susceptible to T-cell- ediated degeneration, at, Coiamun . 5, 3633 (2014)}, Hative and modified {nitrated) synuciein- derived peptides { or, F., Quin ana, F,_F Mimran, A, & Cohen, ∑, R, Autoiia une encephalomyelitis and uveitis induced by T ceii immunity to self a-synuciein, J, Immunol, 170, 628-634 (2003); Theodore, S,, Cao, S. _f McLean, P, J, & Standaert, D. G. Targeted overexpression of human or-synuciein triggers microglial activation and an adaptive im u e response in a mou e model of Parkinson disease, J, europathcl , Exp, Meuroi. 67, 1149-1158 {2008}; Eenner, E, J. en ai. Nitrated a-synuciein immunity accelerates degeneration of nigral dopaminergic neurons, PLoS Om 3, e!376 (2008)} elicit Ϊ ceil responses in rats and mice, and it was previously demonstrated that neuronal death in the substantia nigra in an s~syn overexpression model is absent in MHC II null mice {Harms, A, S, et al . MHC11 is required for of.™syn ciein -induced activation of jsicrogl a, CD cell proliferation, and dopaminergic ne rodegeneration . J. Neuroaci . 33, 9592-9600 (2013)} .

To address whether Parkinson'^' s disease is associated wit T cell recognition of epitopes that are derived rom o:~syn presented by specific MHC alleles, 67 participants with Parkinson's disease and 36 age-matched non-Parkinson* s disease healthy controls were recruited. Participants were 46-83 years of age (Parkinson's disease, median 66, range 46-83; healthy controls, median 64, range 52-83) and 66% were male (Parkinson's disease, 75%; healthy controls, 50%) | abl«» lt&, IIB, 12} , Whereas approximately 15% of healthy controls carried D BX*15: DRB5*01:01 alleles, around one-third of patients with Parkinson's disease carried these alleles (difference between patients with Parkinson's disease and healthy controls,. P - 0.036 and 0.022 for DRBl*X5iGX and DRB5*01:0X, respectively}, indicating association of HLA DR. allelic variants with Parkinson' s disease in our cohort (Table 13),

To determine whether o:-syn-derived peptides were recognised by cells, responses to pools that each contained approximately twenty peptides of 9-10 amino acids (a. .) predicted to bind common HLA class I types, (Vita, R, et ai . The mmune epitope database (XEDB 3.0. Nucleic Acids Res. 43, D405-D 12 (2015)) and peptides of 15 amine acids spanning the protein that could elicit ΆΪΛ class IX responses were assayed. Peripheral blood mononuclear ceils fro patients with Parkinson'' s disease and healthy controls were stimulated for 14 days. Interferon~y ( IF y) and inter leirkin-5 (lL-5) responses were me sure by dual-colour enzyme- linked iinmunospot (ELISEOT) assay, enabling quantification of responsive cells. Positive pools were deconvoluted to identify the peptides eliciting cytokine responses, I FNy was used as a representative cytokine to detect CDS' HLA class I and CD4^* T helper 1 class ∑∑ cells, and IE-5 as a representative cytokine secreted by CD4^'- ¾2 class II T ceils. Each pool was tested in an initial cohort of 13-25 randomly selected patients with Parkinson's disease and 12 healthy controls. The jsaj ority of PBMC responses to the peptides of 15 amino acids produced IL-5 (€8% of total responses), indicating a prominent CB4- τ¾2 phenotype. and the remainder of the responses "were to IFNy (32%) . Ho cells producing both XL-5 and IF y were detected.

Two antigenic regions in a~syn were identified, the first near the N terminus, composed of a . a , 3IGKSGVLYvGSKTKa . .45 and a. a.32K£GVLYVGSKTK£a.a. 6 (referred to as the ¥39 region) (FIG. 6¾) , whic elicited an apparent class II restricted IL~5 and I Ε¾γ response (FXGS S -WIG, 60} . 32 is a piasmxn-cleavage site {Kim, K. S. et al . Proteolytic cleavage of extracellular a---synuclein by plasiain : implications for Parkinson disease, J, Biol. Cheis. 287, 24862-24872 (2012)} and chymotrypsin-cleavage digestion sites are at 32 and 45 (ref, 17) , (Hossain, S. et al. Limited proteolysis of MACP o-synuclein. J, Aizheif¾ers Dis. 3_f 577-584 (2001)),

The second antigenic region was near the C terminus (a, , 116-140} (referred to as the S129 region) (FIG. 6&3 and required phospho ylation of amino acid residue SI29, The t ree phosphoryiated S229 epitopes ( , a .116MPVDPDNEAYE PSE3.. a .130, a. a.121DNEAYE PSEEGYQDa .a.135, a < a , 126EHPSBEGYQDYBPEAa . a .140) produced markedly higher IL-5 responses in patients with Parkinson'^' s disease than in healthy controls (P ∞ 0.02, Fisher's exact test, threshold of at least 300 spot-forming ceils {SFC> (FIG. βΕ-PIG, &Q) . Phosphoryiated SI29 residues are present at high levels in Eew bodies of patients with Parkinson's disease, (Fujiwara, H, et al. -synuciein is phosphoryiated in synucieinopath lesions, ^at. Ceil Biol. 4, 160-164 (2002)) and Lewy bodies of patients with Parkinson's disease contain oc-syn fragments wi h cleavage sites approximately at amino acids 115, 119, 133 and 135 (Anderson, J. P. et al . Phosphorylation of Ser-129 is the dominant pathological modification of ce~synuciein in f milial and sporadic Lewy body disease. J, Biol, Chest . 281, 29733-29752 (2006)) and include the fragment . a .1.29SESG^'fQOYEPEAa . a .140, which is contained within one of the S129 epitopes. Caspase~l (Anderson, J. P. et al . Phosphorylation of Ser~129 is the dominant pathological modification of o:~synuclein in familial and sporadic Ee y bod disease. J. Biol. Cheat. 281, 29733-29752 (2006)) and neurosyn (Kasai, T. et al . Cleavage of normal and pathological forms of a-synuciein by near©sin. in vitro. Meurosci. Lett. 436, 52-56 (2008)) can cleave ςί-syn at a. a.121, c ymetrypsin and thepsin D digestion sites a e at a. a .116, a, a, 125 and a, .136 (Hossain, S. at al. Lira!ted. proteolysis of NACP a-synuciein . J, Aizheimers Dis. 3, 577-584 {2001) ) prot.easo.me may cleave between a. a.119 and a. a.120 (Li, w. at ai , Aggregation promoting C~terminai truncation of a-synuciein is a normal cellular process and is enhanced by the familial Parkinson's disease- linked mutations . Proc. Natl Acad, Sci, USA 102, 2162-2107 (2005)) and calpain can cleave at a. a, 122, with resulting fragments that have been identified in brains of patients with Parkinson' a disease (Dufty, B. M. et al, Caipain-cieavage of a-synucleinc connecting proteolytic processing to disease-linked aggregation. Am.. J. Pathol, 170, 1725-1738 (2007) J .

The immune responses to a. a, 39 and a, a.129 region epitopes, which included analysis of a second cohort of 19 patients with Parkinson's disease and 12 healthy controls that were assayed for response to additional phosphorylated and nitrated modifications <FX®. 7) were different between patients with Parkinson'^' s disease and healthy controls for secretion of Jmy (two-failed Mann-Whitney d-test, P < 0.05), 1L-5 (two-tailed Mann-Whitney d-test, P < 0.001) and both combined responses {two-tailed Man -Whitney O-oest, P < 0.001) 8A-8C} . While residue

39 is highly phosphorylated in patients with Parkinson'^' s disease, (Brahraachari, S. et al. Activation of tyrosine kinase c~Abi contributes to ci-synuclein-induced neurodegenerafion , J. Clin, Invest. 126, 2970- 2988 (2016) ) , ¥39 phosphorylation was not required for antigenic response. The response was primarily polarized towards 57-5 in patients with Parkinson's disease (71% IL-5 and 29% I F y; FIG. 80) . This pola zation was specific to patients with Parkinson's disease, and the relatively rare responses in healthy controls were not similarly polarised (46% IL-5 and 54% IFSiy) ,

To identify specific sets of T ceils that respond to a-syn epitopes, the response to a pool of the 11 x-syn antigenic peptides by nine participants with Parkinson's disease was measured (FIG. 9), Approximately 0.2% of CB3- T cells responded to the a-syn peptides. Of the responsive cells, approximately 50% produced IL-4 and 50% produced IFNy, with no detectable IL-IO or XL- 17 production. In most cases, responses were mediated by τ calls, but response by one patient with

Parkinson' s disease was mostly mediated by IFNy-producing CDS* T ceils, Therefore, the T cell response to a-syn antigenic peptides was largely mediated by IL~4 or IFNy-producing CD4* T cells, with potential contributions rom 1 H¾y-producing CDS^'- T cells.

To test whether the s-syn epitopes arise from processing of native and/or fibrili.Ked ot-syn, PBMCs were stimulated with x-sy epitopes for 14 days. The cultures -were then assayed following exposure to a~syn peptides, 25 pg mi^"3- fibrilized {pre- forsted fibrils, PFE a-syrt, 25 pg ml^~'- native -syn or Kte ium alone. FIG, 10 shows that cell lines specific for the s-syn epitopes were activated by antigen-presenting ceils pulsed with native or PFF protein in 7 out of 12 or 11 out of 12 cases, respectively. There was a significantly higher response to native s-syn { ∞ 0.004) and to PFF a-syn (P ^» 0.0005) than to medium alone. Therefore, T ceils can respond to α-syn epitopes arising from natural processing of extracellular native α-syn, which is present in blood, and the fibrilized a-syn associated with Parkinson's disease,

^!ext, the HL¾. alleles that present c-sy peptides by in vitro binding to a panel of HLAs representing the conation alleles expressed in worldwide populations were identified. A threshold of 1,000 nM binding affinity is associated with imis nogenicity or HLA class II T ceil epitopes, and most epitopes bind in the 1-100 nM range, with affinities in the 1-10 nM considered to be of high affinity. Of 26 common HLA class II alleles tested, five bound to a„a .32KTKEGVLY^"VGSKTKEa , a .46 (Table S) . The HLA class 11 variants DRBl*X5iGX and DRB5*0l:01 bound to the epitope with high affinity (2.8 nM and h .1 n¾, respectively), while DKBl*07:0i, DRBX*09:01 and DQB1*03:01 bound in the 80-250 nM range, The a . a .32 T EGVLYVGS TKEa, a. 6 epitope phosphorylated at Y39 also bound DRBitlScOi and DRB5*01:01 with high affinity. Compariso of patients with Parkinson's disease with and without DRB1*15:01 alleles showed that there was no difference i levels of HLA class I or class l∑ protein expression (WIG. 1 & FIG, 9) . Thus, epitopes in the Y39 region of s-syn strongly bind HLA hete odiirte s including two HLA class li s chain alleles associated with Parkinson's disease.

By contrast, the C terminus peptides spanning S12S and its post- translational forms bound ELA class II alleles weakly, with the exception of a. a.121DN£AYSMPSE£GYQDa.a.135, which in both native and phosphoryiated S129 forms strongly bound to DQBI*05J01. he a . a , 116 PVDPDNEAY£MPS£ . .130 epitope bound to several alleles with lower affinity, and the . a, I26E PSEEGYQDYEPEAa . a .140 epitope bound to DQBl*04:02 and DQB1*05:01 with low affinity, Thus,^, antigenic peptides in the C terminus S129 antigenic region demonstrated relatively little clear restriction, suggesting that they are recognized promiscuousl .

DRB1*15:01 and DRS5*G1:01 alleles are in linkage disequilibrium, and participants expressing one allele are likely to express both. Of participants with Parkinson's disease, S out of 13 responders to the a , a , 32 TKEGVLY GSK KEa . a , 46 epitope expressed both DRB1*15:0I and D B5*01:01, while only 12 out of 45 (DRB1*15:01) and 13 out of 43 {DRB5*0l;01} non~responders expressed the alleles, indicating an association between the alleles and antigenic response (odd ratios of 4,4 and 3.7, P values of 0,04 and 0,05,· respectively) ( le 14), This analysis detected additional associations, with 2 out of 13 responders expressing DQB1*03:04 (P ^» 0,05} compared to 0 out of 45 non~responders, as well, as the HLA class I allele A* 11; 01, with 8 out of 13 responders expressing A*ll :G1 compared to 9 out of 45 non-responders (P ~ 0.012), While A*I1;01 is in relatively raild linkage disequilibrium with D .B1*15:01 and DRB1*0I;01, the associations were largely independent ( I¾, 13^,} , ∑n general, participants with Parkinson's disease showed a trend towards higher expression of HLA juoleeules, particularly HLA class II, This is consistent with an infiammatory component of Parkinson's disease, and higher HLA class 1 expression and induction in PBMCs of patients with Parkinson' s disease compared to healthy controls ( annarkat, G. T. et al , Cosrstnon genetic variant association with altered HLA Expression, synergy with pyrsthroid exposure, and risk for Parkinson's Disease; an observational and case-control study, NPJ Parkinson's Dis , 1, 15002 <2015) ) . Little or no difference in HLA class II expression was found, between participants expressing DRB1*15:G1 versus other DRBI alleles (PIG. ) . A similar but still less pronounced, trend w s noted for HLA class I (FIG. 5) , This suggests that the association between DRBl*I5i 01 and Parkinson's disease is not based on differential expression of the protein. A negative association between recognition of a. a , 32KTKEGV^'LYVGS TKEa, a.46 and the DRE3*02:02 allele was detected, suggesting this allele m ght he protective, The four alleles D Bi*15:01, DRB5*01;01, DQB1*03;G4 and AMI: (V; accounted for every single individual responding to the a. a .39 epitope CP ~ 0,00007 for Parkinson's disease, a le 14) , This association was far mo e significant Parkinson's disease than healthy controls {P ·» 0,009), The combined association of the four alleles for Parkinson's disease versus healthy controls was significant (P - 0,008 two-tailed. Fisher's exact test compared to individual DRB1*15:01, P - 0,05? and BRB5*01:01, P = 0.03), with around half of the patients with Parkinson's disease (31 with alleles and 27 without) carrying one of the four alleles, whereas only around 20% of the healthy controls (S with alleles and 26 without) expressed one of the four (Table 14} .

Following detection of association of response to the Y39 region with the MHC class I allele HLA A*ll:01, Parkinson's disease responses to shorte a-syn-der ived peptide candidates for class ∑ presentation were evaluated. 5 out of 19 Parkinson's disease responded to these short peptides, whereas 0 out. of 12 healthy controls responded (PIS, 13B -

,., , ?

liC; (two-taxlea "' -3.765." P-0.0S23..! . Re ct,i.vi. y occurred jeostiy on peptides contained within the ¥39 region, involving three peptides

{a, a.3 VGS Ka . a . 5, a . a .37VLYVGSKTKa . a . 5, a. .37 LYV SK KKa .a. 6) predicted as potential A*ll:01 binders (Vita, E, et al. The iramune epitope database f ISDB} 3.0. Nucleic Acids Res, 3, D405-D412 (2015)),

Each peptide was tested fo binding to pur fied HLA A*11 :01. molecules in vi tro_t and found that the 9-Hter a, a.37VLYVGSKTKa . .45, which is nested within the two 10~mers, bound with good. 50% inhibitory concentration ilC$(i ) ™ 161 nM , while the other two bound poorly, indicating that the 3~mer is responsible for T cell recognition. Reactivity to short peptides was mostly mediated by lFNy~producing cells and most pronounced for the All binding peptides. Therefore, inauune responses to oc~syn associated with Parkinson's disease have; both MHC class I and n restricted components .

Alleles of over twenty genes are associated with familial Parkinson's disease, (Hernandez, D. G., Reed, X. & Singleton, A. B. Genetics in Parkinson disease;; Mendelian versus non-Mendelian inheritance. j. Neuroc en*. 133, 59-74 (2016)} ma or which encode proteins implicated in lysosomal degradation pathways including mitochondrial turnove . For example, mutations in a-syn or dopamine-modif ed cx-syn, (Martinez- Vicente, M, ef al. Dopamine~m;odi fίed a-synuclein blocks chapercne™ isediated autophagy. J. Clin, Invest, 118, 777-788 (2008); Cuervo, A, U,_f Stefanis, L. _t Fredenburg, R., Lansbury, p. T, s Sulzer, D. Impaired degradation of mutant a-synuciein by chaperons-mediated autophagy. Science 305, 1292-1295 (2004)), and LRRK2 (Orenstein, S, J, et al , Interplay of LRR 2 with chaperone-iiiediafed autophagy. Hat. !Searosci. 16,· 394-406 (2013)} interfere with protein degradation by ehaperone-mediated autophagy, a process that becomes less efficient with age. Extracellular oligogenic -syn j¾ay be acquired by brain cells during Parkinson's disease pathogenesis (ink, K. C, et ai. Pathological co-synuciein transmission initiates Parkinson-like neurodegeneration in nontransgenic mice. Science 338, 949-953 (2012)), without being bound by theory, these reports suggest that altered degradation of proteins including a-syn could produce antigenic epitopes that trigger isrctnune reactions during ageing and Parkinson' s disease.

These results indicate that peptides derived from two regions of s-syn produce immune responses in patients with Parkinson's disease; their roles in additional synueleinopathies are untested. Epitopes derived from the ¥39 region {approximately i on a, a, 31/32 to a. a. 5/46) are specifically displayed by two MHC class I∑ cc-chain alleles, DEB5*01:01 and DRBl*15;01, associated with Parkinson' s disease, as well as an additional MHC class l∑ allele and an MHC class I allele not previously associated with Parkinson's disease. The response is enacted mostly by Ih-o-secretiug CD4* T cells, as well as IFMy-sscreting CDS* cytotoxic cells. a~syn is, to our knowledge, not endogenous! expressed by cells that express MHC class XX, but is found fzo whore it can be acquired by MHC class I -expressing cells. This situation is analogous to the experimental autoimmune encephalitis model of multiple sclerosis, as .myel in prot ins used to produce autoimmunity are not endogenous to MHC class Il~expressing ceils, but are accumulated and processed for MHC class II display by antigen-presenting cells and microglia. The Y39 antigenic region is strikingly close to the s-s n flotations that cause Parkinson's disease (Ά30Ρ, E46K, H50Q, G510, Α53ΐ) , (Hernandez, D. G . , Reed, X. & Singleton, A. S, Genetics in Parkinson disease; Hendeiian versus non~Meudeiian inheritance. J. euroc esu 139,· 59-74 (2016)). The second antigenic region encompasses S129 and requires Si 29 phosphorylation, a form present in Lewy bodies {Ftsji ara, H, et al . et~ synuclein is phosphorylated in synucleinopathy lesions. Nat. Cell Biol, , 160-164 {2002}); antigenic epitopes from that region are not strongly restricted and can drive immune responses in patients who do not express ΆΪΛ alleles that recognize the ¥33 region.

Approximately 40% of the participants with Parkinson' s disease in our cohort exhibited immune responses to ζϊ-syn epitopes, and responses m y reflect variations in disease progression or environmental f ctors. The fraction of patients who display these responses in classic autoimmune disorders such, as type-i diabetes, rheumatoid arthritis and multiple sclerosis is often around 20-50% {Petrich de arqoesini, L. G. et ai , IFN-y and IL-!O islet-antigen-specific cell responses in autoantibody- negative first-degree relatives of patients with type 1 diabetes, Diabetologia 53, 1451-1460 (2010); Arif, S. et al. Peripheral and islet interieufcin-l? pathway activation characterIces human autoimmune diabetes and promotes cytckine-mediated β-cell death. Diabetes 60, 2112- 2119 (2011) } . As with type- I diabetes, which features epitopes that are derived f om both preproinsulin and additional proteins, it ma be that epitopes related to Parkinson' s disease are derived from ςϊ-syn and additional proteins. In classic autoimmune disorders, the MHC class 11 response may precede MHC class I, {Marrack, P, & Kappler, J, W. Do MHCII- presented neoantigens drive type 1 diabetes and other autoi mune diseases? Cold Spring Harb, Perspect. ed. 2, a007?65 (2012)} and that exposing microglia to ~syn triggers HC class I expression by dopamine neurons (Cebrian, C. et al. MHC-I expression renders catecholarainergic neurons susceptible to f-celi- ediated degeneration. Mat, ConiOTUXi . 5,· 3633 (2014)}, The Parkinson's disease-associated proteins parkin and ΡΙϊΙΚΙ isiay regulate antigenic presentation of mitochondrial peptides (Matheond, D . at ai . Parkinson's disease-related prc>teins PINK! and Parkin repress mitochondrial antigen presentation. Ceil 166, 314-327 (2016)} and it is possible that an a toirnraune presentation of antigenic epitopes unites lysosomal and mitochond ial echanisms of Parkinson's disease pathogenesis.

Methods

A) Stndy subjects

Ail participants provided written informed consent for participation in the study. Ethical approval was obtained from the LJI and Columbia University. 67 participants with Parkinson's disease and 36 age-matched healthy controls from the greater San Diego (Parkinson's disease_f n ** 9; healthy controls, n ∞ 13} and Sew ^'fork City (Parkinson's disease, n ∞ 58; healthy controls, n =·= 23) areas were recruited. The ^;e« York cohort was recruited fzom the Center for Parkinson's Disease at Columbia University Medical Center through the Spot study (Alealay, R. N . et ai, Giueocerebrosidase activity in Parkinson's disease with and without GBA mutations. Brain 138, 2648-2658 (2015), Blood samples were collected by Dr. Sean Campbell and Suxiao Yang of the Columbia Center ior ranslational imnuinolegy (CC I) Human Studies Core and approved by the CUMC Institutional Review Board, Parkinson's disease was defined based on the UK Parkinson' s Disease Brain Bank criteria, without excluding cases with a family history of Parkinson' s disease {Hughes, A, Jh , Ben- Shiomo, Y,, Daniel, S, E , & Lees, A, j. what features improve the accuracy of clinical diagnosis in Parkinson's disease; a clinioopafhologic study, 1992, Neurology 57, S34-338 (2001)) . We collected demographics and disease characteristics including age, age of onset, se¾, medications, comorbidities and motor disease severity as measured by the Unified Parkinson'^' s Disease Rating Scale (0PDRS) motor score (OPDRS-IIX } , We also collected family history of Parkinson's disease in first-degree relatives . he data are reported in Tables IVk aad 11 . In tl-e San Diego cohort, demographic data was recorded and Parkinson's disease was self-reported. S m les used for additional assays in IG. 13 and I . 10 were collected from consecutive individuals based on the schedule of their appointment; the demographics and Parkinson's disease ch racteristics of these participants are shown in Tables 13 and S. Healthy controls were recruited through a convenience sample of consecutive non-blood related individuals, and were mostly spouses of participants with Parkinson's disease. At Columbia University, Parkinson's disease and healthy controls were recruited only if there was no history of immune modulatory medications (for example, steroids) or overt autoimmune disorder (for example, lupus) . «o significant difference was detected in response rates as a function of sex or geographical location. Three participants with Parkinson's disease had a history of Crohn's disease and one patient, had a history of Hashimoto's thyroiditis, T o of the three participants with Crohn's disease showed antigenic response to -syn and the participant wi h Hashimoto's thyroiditis did not. Experimental blinding was accomplished by labelling the blood samples in a coded fashion without information on age/gender or Parkinson' s disease status. The cohort was predominantly Caucasian (88.3%) and no firm conclusions between Crohn's disease and Parkinson's disease could be drawn because of the limited nuntber of Crohn' s disease patients studied.

B> Peptides

Peptides were synthesized as crude material on a small (1 mg) scale by A and A, LLC (San Diego)♦ Peptides were forty 1.5-mers overlapping by 10- 14 residues and seventy S- or iO~ ers predicted to bind c HBaon HLA class 1 alleles. In brief, each possible 9- and lO-m r from ζϊ-syn was scored for their capacity to bind a panel of 27 comsion HLA class I A and B jsolecules (Paul, 3. et ai . HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and

J. Immunol . 191₁ 5831-5839 (2013)), For each allele four peptides were synthesized (two 9~mers nd two lO- ers,- n ^» 61 after removing redundant sequences that were selected for 2 or raore alleles} . In addition, any peptide that scored at the 2 percentile level or better for predicted binding, but were not within the four selected per allele were synthesized (n ~ 9} . Post-transiationaiiy modified peptides {n = 7) were synthesized as purified material (>95% by reversed phase PLC) by A and A, LLC (San Diego) . Peptides were combined into pools of 14 peptides (range 11-16} .

An alternative mode of stimulation is to use "whole a~syn protein. However, synthetic peptides are preferred owing to their well- characterized and uniform chemical species _t in contrast to a~syn preparations that contain varying amounts of different post- transnational modifications _f and as if is unclear which fornt(s) are processed by antigen presenting ceils Parkinson's disease. In addition to a lower cost, synthetic peptides provide better mapping of specific epitopes and. measurement of HLA binding,

C) PBMC Isolation and cultu e

Venous blood was collected in hepa in-containing blood bags or tubes, PBMCs were purified from whole blood by density-gradient centrifugation, according to the manu acturer' s instructions. Cells were cryopreserved in liquid nitrogen suspended in FBS containing 10% (vol/vol} DM30, Cuituring of PBMCs for in vitro expansion was performed by incubating in RPMI (Omega Scientific) supplemented with 5% human AB se um (Gemini Bioscience} , Gluta AX (Gibco) , and penicillin and streptomycin (Omega Scientific) at 2 x 10^s per ml in the presence of individual peptide pools at 5 pg ml^"1. Every three days, 10 0 ml"¹ IL-2 in medium was added to the cultures .

D) Ell POT assays

After 14 days of culture with individual peptide pools (5 ug ml^"1), the response to pools and individual peptides (5 pg ml^"1) was me sured by IFNy and IL-5 dual ELXSPOT (Oseroff, C. et al. Molecular deter inants of T ceil epitope recognition to the common Timothy grass allergen. J, Iiranunol . 185, 943-955 (2010)), EL1SP0T antibodies, mouse anti-human IFNy (clone 1-DlK) , .mouse anti-human IL-5 (clone TRFK5) , souse anti- human IFMy-HRP {clone 7~B6~1 , mouse anti-human IL~5 biotinylated (clone 5.AI0) were ail from abtach, To be considered positive, a response had to match three criteria: (1) elicit at least 100 spot~forising cells (SFC) per iO⁶ PB C; (2) F < 0,05 by Student's t-test or by a Poisson distribution test; <3> stimulation index ≥ 2,

For the experiments with fi.brili.Ked or native ot-syn, PBMCs were stimulated -with epitopes derived from s-syn for 14 days. These cultures were then stimulated with x-syn peptides, 25 fig nvl^~; fibriH^ed οί-syn or 25 yg r&l~^l native a™syn,

E) HLA typing, restriction, binding predictions and assays

Participants were HLA-typed. at the La Jolla institute or by an American Society for Histocompatibility and Ijnnumogenetics (ASHI) -accredited laboratory at Murdoch University (Western Australia) , Typing at LJI was performed by nest-generation sequencing { cKinney, D. H. et ai , Development and validation, of a sample sparing strategy for HLA typing utilizing next generation sequencing, Husu XnsRunol . 76,· 917-922 (2015)), Specifically, amplieens were generated from the appropriate class II locus for exons 2 through by PGR amplification. From these ampl icons, sequencing libraries were generated (liiumina Siextera XT) and sequenced with MiSeq Reagent Kit 3 as per the manufacturer's instructions (Illumina) , Sequence reads were matched to HLA alleles and participant genotypes were assigned. HLA typing in Australia for class I (HLA A; B; €} and class IX (DQA1; DQS1 , DRBX 3,4,5; DE^>BX) was performed using locus- specific PCR amplification on genomic DNA , Primers used for amplification employed patient-specific barcoded primers, amplified products were quantified and pooled, by subject and up to 48 subjects were pooled. An unindexed (454 eight-lane runs) or indexed {8 indexed MiSeq runs) library was then quantified using Kappa universal QPCP library quantification hits. Sequencing was performed using either a Roche 454 FLX+ sequencer with titanium chemistry or an Illurina MiSeq using 2 x 300 paired-end chemistry. Reads were quality-filtered and passed through a proprietary allele- alling algorithm and analysis pipeline using the latest IMGT HLA allele database as a reference. The algo ithm was developed by E.P. and S.M, and relies on periodically updated versions of the freely available international iramunogenet ics information system {htt : / www , iragt - org} and an ASHl-aecredited HLA allele caller software pipeline, HID HLA Analysis Suite (htt : //www . ii id . om . au/iafeoratory-test ίng/^* .

Potential BLA~epitope restrictions were inferred using the RATE program (Paul, S. et al. A population response analysis approach to assig class II HLA-epitope restrictions. J. Xarounol . 134, 6164-6176 (2015)}, HLA A* 11: 01 binding predictions were performed using the consensus prediction Tfiethod publicly available through the Inunune Epitope Database (∑EDB) Analysis Resource (available at http://www.iedb.org} (Vita, R, et ai. The ii r.un epitope database (IEDB} 3,0. Nucleic Acids Res. 43,· D405-D412 (2015}}.

Classical competition assays to quantitatively measure peptide-binding affinities for HLA class I and II tmc molecules, based on inhibition of binding of high affinity radio-labelled peptides to purified MKC molecules, were performed, as detailed elsewhere (Sidney, J. et. al. Measurement of MHC/peptide interactions by gel filtration or monoclonal antibody capture. Current Protee, In^unci . 18, 18.13 (2013)}, In brief, 0,1-1 nM of radioiabeiled peptide was co~ineubated at room temperature or 37 *C with purified MRC in the presence of a cocktail of protease inhibitors {and, for class I,· exogenous huma α2 -microglobulin ) » Following a two to four day incubation, MHC-hound radioactivity (c.p.s!, ) was determined by capturing MHC-peptide complexes on Lunitrac 600 plates (Greiner Bio-one, Frickenhausen, Germany) coated with either Η .Λ DR ILZ43) , DQ (HB180), DP (B7/21) or class 1 32} specific monoclonal antibodies. Bound c.p. , was measured using the TopCount microscintiliation counter (Packard Instrument Co,), The concentration of peptide yielding 50% inhibition of binding of the radioiabeiled peptide was calculated. Under the conditions used, where [label] < [M C1 and ICs ~ [MHCj , measured IC50 values are reasonable approximations of true ¾ {Cheng, Y . & Frusoff, w. H . Relationship between the inhibition constant {Kl} and the concentration of inhibitor which causes 50 per cent inhibition (150) of an enzymatic reaction. Biochem. Pharmacol. 22, 3099-3108 (1973); Guluko , K., Sidney, J., Sette, A. & DeLisi_f C. Two complementary methods for predicting peptides binding majo histocompatibility complex molecules. J. ?*?oi, Biol. 267, 1258-1267 (1997) . Each competitor peptide was tested at six different concentrations covering a 100, 000-fold range, and i three or more independent experiments. As a positive control, the unlabelled version of the radiolabeled probe was also tested in each experiment, A threshold of 1,000 nM binding affinity is associated with immunogenicity of HLA class II T cell epitopes, and most epitopes bind in the 1-100 nm range, with affinities in the 1-10 nM considered to be of high affinity {Sidney, J, et al. Divergent motifs but overlapping binding repertoires of six HLA-DQ molecules frequently expressed in the worldwide human population. J. Immunol . 185, 4183-4198 (20X0}} .

F) Intracellular cytokine staining

After 14 days of culture, PBMCs were stimulated in the presence of 5 pg mi^"5- a~syn peptide pool for 2 h in complete RFMX medium at 37 ^eC with 5% CO₂. After 2 h, 2,5 pg ml^"*- each of BF& and monensin w added for an additional 4 h at 37 *C. Unstimulated PBMCs were used to assess nonspecific/background cytokine production and ΡΗΆ stimulation at

5 g si^"' was used as a positive control. After a total or 6 h, cells were collected and stained for cell surface antigens CD4 (anti~CD4~ APCeF780, RPA--- 4 , eBioscience) , CDS (anti~CD3-AF700, UCHTI, BD Pharntingen) , CDS {anti-CD8~BV650, EPA-T8, BioLegend) , CDI4 (anti-CD14~ V500, ¾5E2_f BD Fharmingen) , CD19 (anti-CDl 9-V50G _f ΗΣΒ19, BD Fharmingen) , and finable viability dye sFIuor 506 (eBioscience) . After washing, cells were fixed using % paraformaldehyde and permeabiiized using saponin buffer. Cells were stained for IFNy (anti-IFNy-APC, 4S.B3, eBioscience), XL-17 {anti~IL~I7~PBCy7_f eBio64DEC17_f eBioscience), XL- {anti-XL-4- Pg/Daszle594_i MP4-25D2, BioLegend), and 11-10 (anti~IL-10-AF488_f JES3- 3D7, eBioscience} in saponin buffer containing 10% FBS. Saapl s were acquired on a BD L8 11 flow cytometer. Frequencies of CD3* τ cells responding to a~syn peptide pool were quantified by determining the total number of gated CDS* and cytokine" cells and background, values were subtracted (as determi ed from the m dium alone control} using FlowJo X

Software (FlowJo) . Consign tions of cytokine producing cells were determined using Boolean gating,

G) HLA-PR and BLA-ABC express ion

PB Cs ron; DRBl*i5;01÷ or DRBi*15 : 01^" patients with Parkinson's disease {n ∞ 5 for both) and healthy controls in ∞ 3 DRHi * 7 0 I" and n ∞ 5 DRBi hlS i 027) were assessed for H LA-DR and HLA-ABC (as a control) expression, 721,221 and RM3 cells (both sourced from ATCC, mycoplasma free) were used as controls for HLA-DR and HLA-ABC expression. 721.221 cells lack HLA-ABC and express H LA-DR, whereas RM3 cells lack HLA-DR and express HLA-ABC. Aii cells were stained for cell-surface antigens CD1 (anti-CDl4-APC, 61D3, Tonbo biosciences) _f C03 ianti-CI>3-AF700, UCHT1, BD Pharmingen) , HLA-ABC {anti-HLA-ABC--AF488 , &'6/32 an-HLA class 1, BioLegend) , HLA-DR (anti-HLA-DR™PE, L243; pan-HLA-DR, eBioscience) , and fixable viability dye eFlucr 506 (eBioscience) or isotype controls for HLA-ABC (AF488 mouse IgG2a, s, catalogue number 400233, BioLegend) or HLA-DR (PE mouse IgG2a, x, catalogue number 12-4724, eBioscience), After washing, ceils were fixed using 4% paraformaldehyde. Samples were acquired on a BD LSR 11 flow cytometer♦ The fraction of living ceils expressing HLA-ABC or HLA-DR was determined using FlowJo X Software.

H) a-syn purification and a-syn PF preparation

The recombinant a-syn stonomer was purified as previously described (Mao, X, et ai . Pathological a~synuciein transmission initiated by binding lyjaphocyte-activat ion gene 3, Science 353, aah3374 (2016)). a-syn preformed fibrils (PFF) "were prepared by agitating es-syn monomer in a transparent glass vial with a magnetic stirrer (350 r .p.m. at 37 °C) , After 5-7 days of agitation, the clear s-syn monomer solution became turbid, indicative that a-syn fibrils were generated. The -syn fibrils were then sonicated for 30 s at 10% amplitude to generate -syn PFF {Branson Digital Sonifier) . of~syn m omer and PFF were aiiquoted and kept at -80 °C.

Statistics and reproducibility A power analysis was not conducted a priori as there was no means to estimate effect size. Future validation studies will test whether the Y39 antigenic region is recognised significantly higher in patients with Parkinson's disease compared to healthy controis. The recognition frequency of this peptide was 17% in patients with Parkinson's disease and 3% in healthy controls, which achieves 61% power to detect a response difference between response rates of 14 percentage points. To achieve 80% power in a repeat study to detect a similar effect size, a total of 62 patients with Parkinson' s disease and 62 healthy controls should be included. Additionally validation studies will test whether the overall recognition of the 11 peptides is significantly higher in patients with Parkinson'^' s disease compared to healthy controls. On the basis of the combined cohort data, the recognition frequency of a pool of peptides was 37% in patients with Parkinson's disease and 8% in healthy controls. To obtain 80% power in a validation study a cohort size of 43 in both patients with Parkinson's disease and healthy controis will be required to detect the same effect.

The Fisher^fs exact (two-tailed) test was used to evaluate the contingency between carriers and non-carriers of the DBB1*15:0I and DRB5*0X:G1 alleles in the patients with Parkinson* s disease and healthy control, donors (Table 5} , between the responses to phosphorylated S129 epitopes of patients with Parkinson' s disease and healthy control donors (FIG.

, and between DRBI^"*01./DRBS*01 :0i /DQBl.*03 : 04/A*ll : 01 carriers and non-carriers in patients with Parkinson' s disease and healthy controls (Table 14) . A non-parametric test was used because the data are not normally distributed, A Fisher's exact test that provides exact P values for the analysis of contingency tables is available in most professional statistical analysis packages.

The Mann-Whitney test (two-tailed) was used to assess whether the niH¾foer of SFC of healthy control donors would be less or greater than those of donors with Parkinson ^fs disease (FIGS, SB~6¾, a d IG, 7) . The Mann- Whitney U-test (two-tailed) was used to determine whether the nuraber of IF y SFC was different frost the number of 1L-5 SFC in patients with Parkinson' s disease (FIG, 8D) , A non-parametric test was used because the data are not normally distributed. Student ' s t~tesis were used to analyse pararaetrie differences in demographics between patients with Parkinson' s disease and healthy control donors ( ables 12Ά, 128 , aad 13} . The Wilcoxon signed-rank. test was used to analyse differences in population jueans of the repeated measurements of number of SFC induced by .medium and different iseforsts of o:~syn (FIG, 10) . A non-paramet ic test was used because the data are not normally distributed, We hypothesised that responses to proteins and peptides w ld be higher than medium alone, therefore a one—tailed test was used for those comparisons . Co pariso between PFr and native o:™syn was two-tailed.

Ix m Xe 19 ; Determining HIA and C s as biomarkers ,

To develop diagnostic biomarkers for neurodegenerative disease, the following is erfor ed:

a) Eat ents are HLA typed to identify those with an H1A capable of presenting certain disease associated epitopes (e.g. those HLA and epitopes identified using methods as described in Example 18) . bj in parallel cells from these patients expressing those HLA are expanded with the epitope in vitro, the and TCR is deter i ed

Thus individuals are screened based on HLA plus TCR presence and identified as persons with the disease or at risk for it. In addition, this rethod can be used to determine TC s that should be used in therapeutics ,

Other examples of implementations will become apparent to the reader in view of the teachings of the present description and as such, will not be further described here,

here that titles or subtitles ma be used thro ghout the present disclosure for convenience of a reader, but in no way these should limit the scope of the invention. Moreover, certain theories may be proposed and disclosed herein; however, in no way they, whether they are right or wrong, should limit the scope of the invention so long as the invention is practiced according to the present disclosure without regard for any particular theory or scheme of action. All references cited throughout the specification are hereby incorporated by reference in their entirety for ail. purposes.

It will be understood by those of skill in the art that throughout the present specification, the term ^¾a^fi used be ore a terra encompasses embodiments containing one or more to what the term refers. It will also he -understood by those of skill in the art that throughout the present specification, the term ^wcomprising"^", which is synonymous with "including, " *contain ng, " or "c ar cto ized by, " is inclusive or open- ended and does not exclude additional, un-reeited elements or method steps .

Unless otherwise defined, ail technical and scientific teriss used herein have the same meaning as cornraonly understood by one of ordinary skill in the art to which this invention pertains. In the case of conflict, the present document, including definitions will control.

As used in the present disclosure, the terms "sround", ahour ·" or "approximately" shall generally mean within the error margin generally accepted in the art. Hence, numerical quantities given herein generally include suoh error margin such that the terms "around", "about" or ^approximately" can be inferred if not expressly stated.

Although various embodiments of the disclosure have been described and illustrated, it will be apparent to those skilled in the art in light of the present description that numerous modi ications and variations can be m de. The scope of the invention is defined more particularly in the appended claims

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Claims

1. A met od for assessing whether a subject is at risk of developing, or for diagnosing or con irming whether a subject is afflicted with an o-synucleincpathy, a Ta.uopat.hy, Parkinson/ s disease (PD) , amyotrophic lateral sclerosis (ALS) , Le y Body dementia (LSD) , or Alzheime 's disease (AD) comprising

a)

1} obtaining leukocytes from the sub ect;

ii) contacting the leukocytes with an epitope peptide;

iv) identifying the subject as at risk of developing, o as afflicted with the o!-synucXeinopafhy, PD, ALS , LED or AD if in step iii the leukocytes are determined to have increased activation after contact with the epitope peptide, and identifying the subject as not at risk of developing,' or as not afflicted with the cf~ synncieinopathy. Pi), ALS, LBD or D if in step iii) the leukocytes are determined to not have increased activation after contact with the epitope peptide, or

b>

i) obtaining leukocytes from the subject;

iv) identifying the subject as at risk of developing, o as afflicted with the c-synucieinopathy, Tauopathy, PD, ALS, LBD, or AD if and only if in step iii) 1 or more pools is determined to have increased activation after contact with the epitope peptide.

A method for assessing whether an 'a-synucleinopathy, a Tauopathy, Parkinson's disease (PD) _; amyotrophic lateral sclerosis (ALS), Lew Body dementia (LBD), or Alzheimer's disease (AD) has progressed or is developing in a subject afflicted with or who has been identified as being at risk of developing the co-synuclei ncpatny, PD, ¾.LS, LBD or AD comprising

a) performing each of the following steps 1} to iii) ;

i) obtaining leukocytes fr is the subject;

ii) contacting the leukocytes with an epitope peptide that was previously identified to increase activation or the leukocytes; and

iii) determining the level of activation of the leukocytes after contact with the epitop peptide at a first and a second point in time, and then

iv) concluding that the a-synueieinopathy, PD, ALS, LED or AD has progressed or is developing in the subject if the leukocytes are determined to be store activated in step iii) performed at the second point in time compared to the level of activation in step iii} performed at the first point in time_f or

b) performing each of the following steps i) to iii) :

i) obtaining leukocytes from the subject?

iv) concluding that the -synucieinopafhy, PD, ALS, LED or ΆΏ has progressed or is developing in the subject if more pools of leukocytes are determined to be activated in step iii) performed at the second point in time compared to the number of pools that are determined to be activated in step iii) performed at the first point in time.

3, A method for assessing whether a subject afflicted with an «- synucleinopathy, a fauopathy, Parkinson's disease (PD) , amyotrophic lateral sclerosis (ALS) , Lewy Body dementia (LBD) , or Alzheimer's disease (AD) is iikeiy to benefit from a therapy. wherein the therapy is directed, to leukocytes that are activated by a epitope peptide, the method comprising

a)

1} obtaining leukocytes from the sub ect;

ii) contacting the leukocytes with the epitope peptide;

b)

1} obtaining leukocytes from the subject;

ii contacting the leukocytes with the epitope peptide;

iv) identifying the subject as having benefited from the therapy if in step iii) if the leukocytes are determined to have increased activation after contact with the epitope peptide, and identifying the subject as not having benefitted from the therapy if in step iii) the leukocytes are determined, to not have increased activation after contact with the epitope peptide.

4. A method for assessing whether a subject afflicted with a disease or condition involving an inflammatory response or related to inflammation, or a neurodegenerative disease or disorder is likely to benefit or has benefitted from a therapy, wherein the therapy comprises administration of an effective amount of a T cell receptor for a particular antigen :MHC com lex, the method comprising : <i) obtaining leukocytes fr is the subject;

<ii} contacting the leukocytes with the antigen bound to an MKC molecule;;

(ill) determining whet er the leukocytes have increased activation after contact with the antigen bound to an MHC molecule; nd

(iv) identifying the subject as likely to benefit from the therapy if i step (iii) the leukocytes are determined to have increased activation after contact with the antigen bound to an MHC molecule,■ and identifying the subject as unlikely to benefit from the therapy if in step (iii) the leukocytes are determined to not have increased activation after contact with the antigen bound to an MHC molecule; or

(1) obtaining leukocytes from the subject;

(ii) contacting the leukocytes with the antigen bound to an MHC molecule;

(iv) identifying the subject as having benefited f om the therapy it in step (iii) the leukocytes are determined to have increased activation after contact with, the antigen bound to an MHC molecule, and identifying the subject as not having benefitted from the therapy if in step (iii) the leukocytes are determined to not have increased activation after contact with the antigen bound to an MHC molecule.

The isieth d of any one of claims 1-4, wherein a. the epitope peptides is represented, by an amino acid sequence selected from the group of Tau derived sequences represented by SEQ ID MO: i-bv or 240-376,

b. wherein the epitope peptide is represented by the amino acid sequence selected from the group of a~synuciein derived sequences GKTKEGvLYVGSK K (SEQ ID NO; 487} _f TKEGVLYVGS T E {SEQ ID NO: 488) , MPVDE^>DNSA¥£MPSS {SEQ ID ®Q: 89), ONEAYEMPSSEGYQD (SEQ ID NO: 490), EMPSEEGYQDYEPEA (SEQ ID HO: 491},· SEEGYQDYEPEA (SEQ ID HO; 492} , GVLYVGSKTK {SEQ ID MO: 493), VLYVGS T (SEQ ID NO: 494} , or vLYVGSKTKK (SEQ ID NO; 495), or,

c. wherein the epitope peptide is represented by the amino acid sequence selected from the group of TDP43 derived sequences represented by SEQ ID HO: 56-239,

6. The jnethod of any one of claims 1-5, wherein in step ii) the leukocytes are separated into 2, 3, 4, 5, 6, 7 , 8, , 10, 11-50 or more pools, and in step iv) the subject is identified as at risk of developing or as afflicted Kith the a~syrmcleinopat y, Tauopathy, P _r ALS, LED or AD if and only if in step iii} 1, 2, 3,· 4, 5, 6, 7, 8, 9, 10, 11-50 or acre pools is determined to have increased activation after contact with the epitope peptide.

7 . The method of any one of claims 1-6, wherein the subject

a) is at least about 35, 40, 45, 50, 55, 60, 65, 70, 75 or 80 years of age;

b) is less than about 35, 40, 45, 50, 55, 60, 65, 70, 75 or 30 years of age;

c) has a symptom that has preceded the onset of the et~ syuucleinopathy, Tauopathy, PD, ALS, LBD or AD in subjects who have developed Ci-synueieinopathy, Tauopathy, PD,. ALS, LBD Or AD;

d) has a symptom that has preceded the onset of the et~ syuucleinopathy, Tauopathy, PD, ALS, LBD or D in subjects who have developed the of-synucieinopathy, Tauopathy, PD, ALS, LSD or ¾D, wherein the symptom has preceded, the onset of the a~synuc.1einopat , Tauopathy, PD, ALS, LED or AD in the subjects by at lease about 5, 10, 15, 20, 25, 30 or 5-30 years

e) is afflicted with cognitive decline, constipation or o thost tic hypotension

f) is afflicted with cognitive deciine, and the cognitive decline is reduced spatial reasoning ability and/or reduced memory ability.

g) is afflicted with fascicniations or muscle twitches in the arm leg, shoulder, or. tongue, muscle cramps, spasticity or tight and stiff muscles , muscle eakness affecting an axis, a leg, neck or diaphragm, slurred and nasal speech, and/or difficulty chewing or swallowing; or

h) is afflicted with cognitive decline, and the cognitive deciine is reduced language or decisionmaking♦

The method of any one of claims 1-7, further comprising directing the subject to

a) be monitored more frequently for the ζί-synucieinopathy,.

Tauopathy, PD, ALS, LED or AD; or

b) receive additional diagnostic testing for the a- synucleinopathy, Tauopathy, PD, ALS, LBD or D, if the subject is identified as at risk, of developing the a- synucieinopathy, Tauopathy, PD, ADS, LBD or AD,

The method of any one of claims 1~S, further comprising determining the presence of at least one human leukocyte antigen <HLA> allele, one T cell receptor (TCR) allele, or one HAFT allele in the subject.

The method of claim 8, wherein the subject is identified as at risk of developing the o-synucleinopathy, PD, ALS, LBD or AD or identified as afflicted with the cc-synucleinopathy, PD, ALS, LBD or AD if a) the leukocytes are determined to have increased activation after contact with the epitope peptide, or I or more pools is determined to have increased activation after contact with the epitope peptide, and

hi the subject has at least one HLA allele.

The jnethod of claim 10, wherein the subject has the HLA allele DRB$*G1;01, DKBi*15:01, 0081*03:04, A*ll: 0 1 , DRB1*09J O I , DB.B1*15, BRBI*04, DQBl*06, DRB1*0X:01, DRBI*04;04, DBB1*Q7;G1, DRBl*ll:04, DB.B3*02:02, DQA1*O5:01, DQBl*03;0X_f DQBi^"*03:02, DQB1*03:03, BQBl*Q4;02, DKB1*15 : GI/D Bl* 06 : 02 or DRBI* 04 : 02/DQBl *03 : 02, preferably wherein the subject has the HLA alleles DRB5*01iGX, DRBX*I5:01, DQBI*Q3:04, and Α*11:0ί,

The method of

XX, wherein the subject has the HLA allele BRBX*Xl:04 and the amino acid sequence is SSQ ID HO; 13, the subject has the HLA allele 0(281*03:03 and the amino acid sequence is SEQ IB KQi 31, the subject has the HLA allele DQAl*05tOX and the amino acid sequence is SEQ ID HO: 32, the subject has the HLA allele BRBX*0l:01 and the amino acid sequence is SSQ ID HO; 40, the subject has the HLA allele DRB1*0 : 04 and the amino acid sequence is SEQ ID KQi 49, the subject has the HLA allele DQBI*04:02 and the amino acid sequence is SEQ ID NO; 52, or the subject has the HLA allele BRB3*02:02 and the amino acid sequence is SEQ ID HO; 29,

The method of any one of claims 1-12, for assessing whether AD, ALS or PD is developing in a subject who has been identified as being at risk of developing AD, ALS or PD, or for assessing whether a subject afflicted with AD, ALS or PD is likely to benefit from a therapy.

A method for treating a subject afflicted with an o~ synucieinopathy, a Tauopathy, Parkinson'^' s disease (PD) , amyotrophic lateral sclerosis (ALS) , Lewy Body dementia {LSD} , or Alzheimer's disease (AD j comprising a) administering to the subject a compound that is approved for use in treating subjects afflicted Kith the a- synueieinopathy , PD, ALS, LBD or AD, wherein the subject has been diagnosed or confirmed to be afflicted with a~ synudeinopathy, PD, ALS, LBD or AD according to the jsetho of any one of claims 1-12;

b} diagnosing or confirming the subject to he afflicted with the

-synucieinopathy, PD, ALS, LED or AD according to the method of any one of claims 1-12, and administering to the subject a compound that is approved for use in treating subjects afflicted with .~synuc.1eίnopathy, PD, ALS, LBD or AD;

c) administering to the subject a therapy that is directed to leukocytes that are activated by an epitope peptide, wherein leukocytes of the subject have been determined to have increased activation after contact with the epitope peptide; d) administering an immunosuppressant therapy to the subject,■ wherein the subject has been identified as being likely to benefit therefrom by the method of any one of claims 1-12; or e) administering an immunosuppressant therapy to the subject, wherein the subject has been identified as being iibely to benefit from a therapy directed to leukocytes that are activated by an epitope peptide according to the method of any one of claims 1-1.2.

The method of claim 14, wherein the therapy is toierization therapy, and the toierization therapy is specific for leukocytes that are activated by the epitope, preferably wherein administe ing the toierization therapy comprises administering to the subject the epitope peptide in an amount that is effective to reduce activation of leukocytes in the subject by the epitope peptide.

The raethcd of claim 1$, wherein the therapy comprises selectively killing the leukocytes that are activated by the epitope peptide in the subject, preferably wherein selectively killing the leukocytes that are activated by the epitope peptide in the subject comprises administering to the subject an effective amount of a compound comprising a major histocompatibility com lex (MB.C) Tetra er and a toxin to the subject, wherein the MHC Tetramer comprises the epitope peptide.

17. The met od of claim. 16, wherein the immunosuppressant therapy comprises toXerization therapy, selectively killing the leukocytes that are activated by an epitope peptide in the subject,, or administering an effective amount of an iiiSTinnoauppressive compound to the subject, preferably wherein the immunosuppressive compound is a caieineurin inhibitor, a compound that blocks a che okine receptor that is expressed by a leukocyte, a glucocorticoid, a raTOR inhibitor, an anti -metabolic compound, a phosphodiesterase-.? inhibitor, an antibody, or a leukocyte function antigen~3 {LFA- 3}/Fc fusion protein.

18. A method for assessing whether leukocytes of a subject afflicted with an a-synucieinopathy, a Tanopathy, Parkinson's disease {PD) , amyotrophic lateral sclerosis (ALS) , Lewy Body dementia (L D) , or Alzheimer's disease (AD) are activated by an epitope peptide, compri.sing

i) obtaining leukocytes from the subject?

ii) contacting the leukocytes with the epitope peptide;

iv) identifying the leukocytes of the subject as activated by the epitope peptide if in step iii) the leukocytes are determined to have increased activation after contact with the epitope peptide, and identifying the leukocytes of the subject as not activated by the epitope peptide if i step iii) the leukocytes are determined to not have increased activation after contact with the epitope peptide, wherein

a. the epitope peptides is represented by an amino acid sequence selected from the group of Tau derived sequences represented by SEQ ID HO : 1-55 or 240-376, b. wherein the epitope peptide is represented by the amino aoid sequence selected frcm the group of a-synuclein derived sequences GKT SGVLYVGSKT (SEQ ID NO: 487), ETKSGVLYVGSKTKE {SEQ ID NO: 488) , :PVDPI)KEAYE¾PSE (SEQ ID NO; 489), DNEAYEMPSSEGYQD {SEQ ID NO: 490), EMP3SEGYQDYEPEA <SEQ ID NO : 491} _f SEEGYQDYEPEA (SEQ ID SO: 492} _f GVLYVGSKTK (SEQ ID NO: 493), VLYVGSETK (SEQ ID HO : 494), or VLYVGSKT K 03EQ ID NO : 495), or,

c. wherein the epitope peptide is represented by the amino aoid sequence selected from the group of TBP43 derived sequences represented by SEQ ID NO; 56-239. , The method of claim IB, for assessing whether leukocytes of a subject afflicted with AD, ALS or PD are activated by the epitope peptide , , The method of any one of claims 1-19, wherein the epitope peptide a) is or comprises part of a compound that is produced by neurons in subjects afflicted with the a~synuclei nopath , PD, ALS , LBD or AD;

b comprises consecutive amino acids that are identical to a stretch of consecutive amino acids in a protein that is produced by the neurons;

c) comprises consecutive amino acids that are identical to a stretch of consecutive amino acids in a Tau crutant; d) comprises about 16, at least 15, 5-50, 8-11, or 8—14 amino acids;

e is phosphorylated, aeetylated, nitrated, or dopamine modified;

f) comprises a phosphorylated serine or a phosphorylated tyrosine;

g) comprises a phosphorylated serine or a phosphorylated tyrosine, wherein the phosphorylated serine or phosphorylated tyrosine is within a stretch of consecutive amino acids that is identical to a stretch of consecutive amino acids comprising the serine at position 193, 202, 2X4, 262, 356, or 422 of Tau or the tyrosine at position 181, 205, 212, 231, or 262 of Tau.

h) is or comprises part of a compound that is produced by neurons in subjects afflicted with the ci-synucieinopathy, PD, ALS , LBD cr AD, wherein the neurons are in the ventral midbrain, the substantia nigra, the locus coeruieus, or the ventral tegmental area;

i) is or comprises part of a compound that is produced by neurons in subjects af licted Kith the o-synucieinopathy, Pi), ALS , LBD or Al)_f wherein the neurons are catecholami e neurons; j) comprises consecutive amino acids that are identical to a stretch of consecutive .amino acids in an o>~syn mutant;

k) comprises consecutive amino acids that are identical to a st etch of consecutive amine acids in a o:~syn utant, wherein the a~syn mutant is an of-syn A53T or A3OP mutant;

1) comprises a phosphcrylated serine or a phosphorylated tyrosine, wherein the phosphorylated serine or phosphorylated tyrosine is within a stretch of consecutive amino acids that is identical to a stretch of consecutive amino acids comprising the serine at position 129 of o:~syn or the tyrosine at position 33 of ζί-syn; ) is or com ises part of a compound that is produced by neurons in subjects afflicted with the ALS, wherein the neurons are in the motor area;

n) is or coriprises part of a compound that is produced by neurons in subjects afflicted with ALS, -wherein the neurons are motor neurons ;

o) comprises consecutive amino acids that are identical to a stretch of consecutive amino acids in DP 3, FUS, or SOD-I; ρ) comprises consecutive amino acids that are identical to a stretch of consecutive amino acids in TDP 3 mutant, PUS mutant, or SOD-l rtiutant; q) comprises a deajuidated asparagine, an oxidized threonine, or a phosphoryl ted tyrosine.

The raethcd of claim 31, wherein the epitope peptide comprises consecutive amino acids in the sequence set forth as RGVRLVEGILRAPD (SEQ ID NO; 231} , LVYVVS P D KREM (SEQ ID NO; 233} , DMTEDSLREFFSOYG ISEQ ID SO; 236), ELREEFSQYGDVMDV (SSQ ID HO; 237), EOL∑ I GISVKISKA (SEQ ID NO: 74} _f EDDG VLLSTVTAQF (SEQ ID HO: 229) , AGWG LVYVVNYP D (SEQ ID ®Q: 232}, DVMDVFIFKPFEAFA {SEQ ID NO: 238},· r F∑PKPFRAFAFYTFA (SEQ ID NO: 239} .

The method of any one of claims 1-21, wherein in step iii) the leukocytes are determined to have increased activation after contact with the epitope peptide,

a} if the leukocytes express or release more of at least one cytokine compared to corresponding leukocytes not contacted with the epitope peptide;

b) if the leukocytes release at least one cytokine;

c) if the leukocytes release at least one cytokine, wherein in step Hi) the leukocytes are determined to have released the at least one cytokine if there are over 20 spot-forraing ceils {SEC} per million cells as measured by an ELISpot assay comprising the coloriaetric detection of the at least one cytokine .

The isiethod of any one of claims 1-22, wherein

a} the leukocytes are τ cells;

fo) the at least one cytokine is at least interferon-gaama (IFM- γ> or XL-5?

c) the at least one cytokine is at least TNFa, IL~4, XL-17, IL~ 10, or IL-21;

d) the at least one cytokine is two or jsore cytokines, wherein the two or more cytokines are at least I FN~y a d IL-5; e the leukocytes are T cells are CD4÷ T cells, CD8÷ T cells, and/or CD4- CD6÷ τ cells; or

f) the leukocytes are IL~4 -producing CD4+ T cells, IFN-y- producing C 4+ T cells, or IFN-y-prodiscing CBS-f cells.

The met od of any one of claims 1-23, wherein the at least one cytokine is at least interteron-garaiaa sIFN-y) , or XL- 5, w erein the at least one cytokine that is expressed, or released from the leukocytes is assayed through a process comprising an enzyme- linked iinmunosorbent assa (ELISA), enz me-lined intntunospot (ELISPOX) , intracellular cytokine staining (ICS) , or quantitative RT-PCR.

The method of any one of claims 1-24, wherein the leukocytes are CD4- cells.

The method of any one of claims 1-25, wherein determining whether the leukocytes have increased activation comprises

a) contacting the leukocytes with compound comprising a major histocompatibility complex (MHC) etranter having four MHC molecules, wherein each MHC raolecule is associated with an epitope peptide;

ta) identifying leukocytes that become bound to the compound as activated.

A method for assessing whether a test compound comprises an epitope peptide to which leukocytes of a subject suffering fro a neurological disorder are responsive comprising

1} obtaining leukocytes front the subject;

iij contacting the leukocytes with the test compound;

iii) determining whether the leukocytes has increased activation after contact with the test compound; and iv) identifying the test compound as comprising an epitope peptide to which the leukocytes are responsive if in step iii) the leukocytes are determined to have increased activation after contact wit the test com ound, and identifying the test compound as not comprising an epitope to which the leukocytes are responsive if in step iii) the leukocytes are etermine to not have increased activation after oontact with the test compound, wherein a. the epitope peptides is represented by an amino acid sequence selected from the group of au derived sequences represented by SEQ ID HO : 1-55 or 240-376,

b. wherein the epitope peptide is represented by the amino acid sequence selected froro the group of a-s n clein derived sequences GK KEGVLYVGS TK {SEQ ID NO: 48?), KTKEGVLYVGSKTKE (SEQ ID NO: 488), PVDPDNSAYEMPSS (SEQ ID ®0: 489} , DNBAYEMPSEEGYQD (SEQ ID HO: 490},· SMPSEEGYQDYEIEA (SEQ ID HO : 491), SEEGYQBYEPEA (ESQ ID NO: 492), GVLYVGSKTK (SEQ ID SO: 493},· VltWGSKTK (SEQ ID MO: 494}, or VLYVGS TKK (SEQ ID ®Qi 495} , or,

c. wherein the epitope peptide is represented by the amino acid sequence selected f om the group of TOP 3 derived sequences represented by SEQ ID NO: 56-239.

The method of claim 27, wherein the test compound is or comprises part of a com ound tha is produced by neurons in subjects afflicted with art -syuucleinepathy, a Tauopathy, Parkinson' s disease (PD) , amyotrophic lateral sclerosis (&.LS) , Le y Body dementia (LSD) , or disease (AD),

The method of any of claims 1-28, wherein the amino acid sequence is selected from the group of sequences consisting of SEQ ID NO; 136-165.

The method of claim 29, wherein the amino acid sequence is selected from the group of sequences consisting of SEQ ID NO; 136-138, SEQ ID HO; 140-143, SEQ ID NO: 145-146, SEQ ID HO: 148-152, SEQ ID KQi 154, and SEQ ID NO: 158-159, , A kit comprising an epitope peptide as in any one of claims 1-30, , A compound, for treating an ci-syoucleincpathy, a Tauopathy, Parkinson' s disease (P ) , amyotrophic lateral sclerosis (ALS) , Lewy Body dementia (LBD) _f or Alzhe mer' s disease (AD), comprising i) a major h stoco p tibi1ity c mplex (HHC Tetramer having four HC molecules, wherein each MHC molecule is associated with an epitope peptide, and ii) a toxin, wherein a. the epitope peptides is represented by an amino acid sequence selected from the group of Tau derived sequences represented by SEQ ID MO: 1-55 or 240-376,

b. wherein the epitope peptide is represented by the amino acid sequence selected from the group of a~synuclein derived sequences GKTKEGvLYVGSK K (SEQ ID NO: 487), T EGVLYVGS T E {SEQ ID NO: 488) , MPVDPDNSAYEMPSS {SEQ ID ®Q: 489), DNEA.YEMP3SEGYQD (SEQ ID NO: 490), EMPSEEGYQDYEPEA (SEQ ID SO: 491},· SEEGYQDi'EPEA (SEQ ID HO; 492), GVLYVGSKIK {SEQ ID NO : 493), VLYVGS T (SEQ ID NO; 494} _f or vLYVGSK K (SEQ ID NO; 495), or,

c. wherein the epitope peptide is represented by the amino acid sequence selected from the group of TDP43 derived sequences represented by SEQ ID HO: 56-239, , In a process for assessing whether a subject is at risk of developing an a-synucleinopathy, a Tauopathy, Parkinson/ s disease (PD , amyotrophic lateral sclerosis (ALS), lewy Body dementia (LBD), or Alzheimer's disease (AD), which involves an array of testing, the improvement comprising including in the array of testing the steps of:

a) 1} obtaining leukocytes f ont the subject;

ii) contacting the leukocytes with an epitope peptide;

iii) determining whether the leukocytes h v increased activation after contact with the epitope peptide; and iv) identifying the subject as at risk of developing «~ synucleinopathy, D, ALS, LBD or AD if in step iii) the leukocytes are determined to have increased activation after contact with the epitope peptide, and identifying the subject as not at risk of developing the a~synu leinop th , PD, ALS , LBD or AD if in step iii) the leukocytes arc determined to not have increased activation after contact with the epitcpe peptide, wherein

a. the epitope peptides is represented by an amino acid sequence selected from the group of Tan. derived sequences represented by SEQ ID KiO: 1.-55 or 240-376,

b. wherein the epitope peptide is represented by the amino acid sequence selected from the group of a-synnciein derived sequences GK KEGVLYVGS TK {SEQ ID NO: 487), KTEEGYLYVGS E (SEQ ID O; 48S) , PVDPDESA EMPSE (SEQ ID NO : 489} , DNSAYEMPSEEGYQD ( SEQ ID ISO; 490), E PSSSGYQDYEPEA (SEQ ID NO: 491} , SESGYQDYEPEA (SEQ ID MO: 492} , GVLYVGSK K (SEQ ID MO: 493) , VLYVGSK K (SEQ ID NO; 494), or VLYVGSKTKK { SEQ ID SO: 495) , or,

c. wherein the epitope peptide is represented by the amino acid sequence selected from the group or TDP43 derived sequences represented by SEQ ID NO: 56-239 o i) obtaining leukocytes from the subject;

ii) separating the leukocytes into 2 or more pools of leukocytes and contacting each pool with an epitope peptide, wherein each pool is contacted with a different epitope; iii) determining whether each pool has increased activation after contact with the epitope peptide; and tv) identifying the subject as at risk of developing the cf~ synucLsinopathy, D, ALS , LED or AD if in step iii) 1 or more pools is det rmined to have increased activation arter contact with the epitope peptide, wherein a. the epitope peptides is represented by an araino acid seq ence selected from the group of Tax- derived sequences represented by SEQ ID KiO: 1.-55 or 240-376,

b. wherein the epitope peptide is represented by the amino acid sequence selected from the group of a-synuclein derived sequences GKT EGVLYVGSK K (ESQ ID HO: 487), KTKEGVL GSKTEE {SEQ ID NO: 488} _f MPVDE^>DNSA¥£¾PSE (SEQ ID NO: 489) , DSIEAYEMPSESG^'fQD (SEQ ID HO: 490) , EMPSSEGYQDYEPSA (SEQ ID NO: 491) , SEEGYQDYEPEA (SEQ ID HO; 492), GVLYVGSKTK {SEQ ID NO: 493) , YLYVGSKTK (SEQ ID SO: 494} , or VLYVGSKTEK {SEQ ID NO : 495) , or.

c. wherein the epitope peptide is represented by the a.mino acid sequence selected from the group of TDP43 derived sequences represented by SEQ ID NO; 56-239,

In a process for diagnosing or confirming whether a subject is afflicted with an or-syrtucleinopathy, a Tenopathy, Parkinson' s disease (PD), amyotrophic lateral sclerosis i&LS} , Le y Body dementia {LBD} , or Alzheimer's disease (AS)} , which, involves an array ot testing, the improvement comprising including in the array of testing the steps of:

a)

1} obtaining leukocytes from the subject;

ii} separating the leukocytes into 1 or more pools of leukocytes and contacting each pool with an epitope peptide, wherein each pool is contacted with a different epitope peptide ;

iii) determining whether each pool has increased activation arter contact with the epitope peptide; and iv) identifying he subject as afflicted with the cf~ synucleinopathy, PD_F ALS, LBD or AD if and only if i step iii) 1 or more pools is determined to have increased activation after contact with an epitope peptide, or i) obtaining leukocytes from the subject;

iii) dete mining whether each pool has increased activation after contact with the epitope peptide; and

iv) identifying the subject as afflicted with the a- synueieinopat , PD, ALS, LBD or AD if and only if in step iii) 1 or j¾ore pools is determined to have increased activation after contact with an epitope peptide, wherein a. the epitope peptides is represented by an amino acid sequence selected from the group of Tau derived sequences represented by SEQ ID «0: 1-55 or 240-376,

b. wherein the epitope peptide is represented by the amino acid sequence selected from the group of of-synuciein derived sequences GKT EGVLYVGSK K (SSQ ID HO: 487), KfKEGVLYVGSKTEE {SEQ ID NO : 488} _f MPVDE^>DNSA¥EMPSE ( SEQ ID NO: 489) , DNEAYEMPSESG^'f QO (SEQ ID HO: 490) , EMPSSEGYQDYEPSA (SEQ ID NO : 491) , SEEGYQDYEPEA ISEQ ID HO; 492), GVLYVGSKTK {SEQ ID NO : 493) , VLYVGSKTK (SEQ ID SO: 494} , or VLYVGSKTE (SEQ ID NO; 495}, or.

c. wherein the epitope peptide is represented by the amino acid sequence selected from the group of TDP43 derived sequences represented by SEQ ID HO: 56-239, The met od of any one of claiats 1-34, wherein the leukocytes have increased activation after contact with native a.1ph.a-synuclein protein or fifcrxiizeci aip a-synuclein protein.

A pharmaceutical composition for treating an o-synuclsinopathy, a Tenopathy, Parkinson's disease (PB), amyotrophic lateral sclerosis (ALS) , Lewy Body deatentia (LBD) , or Alsheiiser' s disease (AD) , comprising i } a protein comprising an amino acid sequence selected from the group of

a, the epitope peptides is represented by an amino acid sequence selected from the group of Tan derived sequences represented by SEQ ID HO: 1-55 or 240-376, b, wherein the epitope peptide is represented by the amino acid sequence selected from the gro p of cf~ synuciein derived sequences G TKEGVLYVGSKTK (SEQ IB NO: 487} _f ETKEGVLY GS KE (SEQ ID MO: 488), MPVDPD EAYE PSE (5SQ ID NO; 489), DNEAYE P5EEGYQD (SEQ ID HO; 490), EMPSEEGYQDYEPEA (SEQ ID ®Q i 491),· SEEGYQDYEPEA (SEy ID O: 492), GvLYvGSK K (SEQ ID NO; 493), VLXVGSKTK {SEQ ID MO: 494), or VLYVGSKTKK (SEQ ID NO; 495) , or.

c, wherein the epitope peptide is represented by the amino acid sequence selected from the group of TDP43 derived sequences represented by SEQ ID HO: 56-239, and ix) a pharmaceutically acceptable carrier.

The pharmaceutical composition of cl im 36, wherein the amino acid sequence is selected from the group of sequences SEQ ID NO; 74, 139, 144 and 230-239, or wherein the amino acid sequence is selected from the group of sequences SEQ ID NO: 231 , 233, 236, and 237, or 20? wherein the amino acid sequence is selected fr is the group ot sequences SEQ ID NO: 14, 229, 231, 232, 239, or 239. , A met od comprising:

a. providing a biological sam le from a subject;

fo„ processing the biological sample to determine presence of a T oell receptor (TCR) specific to a peptide, wherein the peptide is a fragment from a protein associated with, said neurodegenerative disease, , The method of claim 38, wherein the processing step includes contacting ϊ cells from said sample with said peptide, and detecting activation of a T ceil having said TCR, , The jnethod of claim 38, wherein the processing step includes performing gene sequencing on at least a cellular fraction of said biological sample to amplify a gene encoding the TCR specific to said peptide, and detecting presence of said gene encoding said TCR, preferably wherein said at least a cellular fraction o said biological sample includes peripheral blood mononuclear ceils (PBMC), preferably leukocytes. , The method of claim 39 or 40, wherei the peptide associated Kith a neurodegenerative disease is ta , alpha-synuciein, or transactive response DNA binding protein 43 kDa (TDP-43) , , The method of any one of claims 39-41, wherein the peptide is selected fr is any one of tables 1 to , , A method comprising:

a) providing a biological sample from a subject;

b) processing the biological sample to determine presence of a human leukocyte antigen ( HLA capable of presenting a peptide, -wherein the peptide is a fragment fro a protein associated with said neurodegenerative disease; and c processing the biological sam le to determine presence of a T cell receptor (TCR) speci ic to said peptide .

44. The method of claim 38 or 43, wherein the peptide is a fragment from a protein that forms aggregates in a patient having the neurodegenerative disease .

45. The method of claim 44, wherein step c) includes contacting T cells present in said sample with said peptide, and detecting activation of a T cell having said TCR ,

46. The method of claim 44, wherein said step fo) includes performing gene sequencing on at least a cellular fraction of said biological sample to amplify a gene encoding the HLA capable of presenting said peptide, and detecting presence of said gene encoding said HLA and c) includes performing gene sequencing on at least a cellular fraction of said biological sample to amplify a gene encoding the TCR specific to said peptide, and detecting presence of said gene encoding said TCR.

47. The method of claim 46, wherein said at least a cellular fraction of said biological sample includes peripheral blood mononuclear ceils iFBMC), preferably leukocytes,

^•I . The method of any one of claims to 47, wherein the protein that forms aggregates in a patient having a neurodegenerative disease is tan, aipha-synuciein, or transactive response DNA binding protein 43 kDa i Df- 3} .

49, The Htet od of claim 41 or 48, wherein the protein is tau, preferably wherein the peptide derived from the tau protein includes a phosphorylated serine and/or tyrosine.

50, The method of claim 41 or 48, wherein the protein is TDP~~43, preferably wherein the peptide derived from the TDP~43 protein includes a phosphorylated serine and/or tyrosine. , The method of any one of claims 43 to 50, wherein the peptide is selected from any one of tables 1 to _f preferably wherein the peptide is selected from any one of GKTKSGVBYVGSKTK <SEQ ID NO : 487} , TKEGvLYVGS KE (SEQ ID NO; 488) , MPVDPDNEAYEMPSB (SEQ ID HO: 489), DNEAYEMPSEEG QD {SEQ HO: 490), EMPSEEGYQDYEPEA {SEQ ID SO: 491), SEEGYQDYEPEA { SEQ ID NO : 492) , GvLYVGSK K (SEQ ID NO; 93 , VLYVGSKIK (SEQ ID HO: 494},· or VLW6SKTKK (SEQ ID HO: 495). , The method of any one of clairos 43 to 51, wherein the HEA is DRBS*01:01, DRB1*15:01, DQBl*03:04_r A*ll:01, D Bl*07:01, BRBl*09:01, or DQB1*03:01, , The method of any one of claims 3 to 51, wherein the method comprises detecting a peptide :HHC complex comprising any one of the peptides and any one of the HLAs listed in Table 5. , The method of any one of claims 43 to 53, wherein the presence of the TCR and the HL& is indicative that the subject is predisposed to, at risk of, or has a neurodegenerative disease, preferably wherein the presence of the TCR is indicative that the subject is predisposed to, at risk of or has a neurodegenerative disease, preferably wherein the neurodegenerative disease or disorder is alpha-synucleinopathy, a Ta opathy, Parkinson's disease (PD) , Lewy Body dementia (LED), or Alzheimer's disease (AD),