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Definitions

• This disclosure relates to biomarkers for and treatment of amyotrophic lateral sclerosis.
• the soluble superoxide dismutase 1 (SOD1) enzyme (also known as Cu/Zn superoxide dismutase) is one of the superoxide dismutases that provides defense against oxidative damage of biomolecules by catalyzing the dismutation of superoxide to hydrogen peroxide (H2O2) (Fridovich ,Ahhii. Rev. Biochem., 64:97-112 (1995)).
• the superoxide anion (O 2 ) is a potentially harmful cellular by-product produced primarily by errors of oxidative phosphorylation in mitochondria (Turrens, J. Physiol., 552:335-344 (2003))
• ALS Amyotrophic Lateral Sclerosis
• Lou Gehrig's disease is a devastating progressive neurodegenerative disease affecting as many as about 17,000 Americans at any given time (Mehta, P., et al. (2016). "Prevalence of Amyotrophic Lateral Sclerosis - United States, 2015.” MMWR Morb Mortal Wkly Rep 67(46): 1285-1289).) Approximately 2% of ALS cases result from mutations in the gene encoding SOD1 (Bunton-Stasyshyn RKA, et al. Neuroscientist. 2015;21:519-29).
• mutant SOD1 The toxicity of mutant SOD1 is believed to arise from an initial misfolding (gain of function) reducing nuclear protection from the active enzyme (loss of function in the nuclei), a process that may be involved in ALS pathogenesis (Sau, Hum. Mol. Genet., 16:1604-1618 (2007)).
• the progressive degeneration of the motor neurons in ALS eventually leads to their death. When the motor neurons die, the ability of the brain to initiate and control muscle movement is lost. With voluntary muscle action progressively affected, patients in the later stages of the disease may become totally paralyzed.
• This disclosure relates, in part, to treatment of amyotrophic lateral sclerosis associated with a mutation in the SOD1 gene in subjects (e.g., adults) with clinical symptoms/signs and in presymptomatic subjects (e.g., adults) with biomarker evidence of disease (e.g., neurofilament light chain level of at least 44 pg/mL).
• subjects e.g., adults
• presymptomatic subjects e.g., adults
• biomarker evidence of disease e.g., neurofilament light chain level of at least 44 pg/mL
• T a thymine
• e a 2’-0-methoxyethylribose modified sugar
• d a 2’-deoxyribose sugar
• s a phosphorothioate intemucleoside linkage
• o a phosphodiester intemucleoside linkage; or a pharmaceutically acceptable salt thereof, wherein the human subject has a neurofilament light chain level of at least 44 pg/ml prior to initiation of the treatment.
• the human subject has undergone an increase in neurofilament light chain level of at least 10 pg/ml prior to initiation of the treatment.
• the neurofilament light chain level is a level in a biological sample from the human subject, e.g., a blood, serum, plasma, or cerebrospinal fluid sample.
• the neurofilament light chain level is a plasma level, e.g., a plasma level of at least 44 pg/ml and/or a plasma level increase of at least 10 pg/ml.
• the neurofilament light chain level is a blood, serum, or cerebrospinal fluid level equivalent to the corresponding plasma level (e.g., equivalent to a plasma level of at least 44 pg/ml or plasma level increase of at least 10 pg/ml).
• the human subject has a neurofilament light chain level of at least 44 pg/ml prior to initiation of the treatment, and wherein the human subject has undergone an increase in neurofilament light chain level of at least 10 pg/ml prior to initiation of the treatment.
• the human subject has a plasma neurofilament light chain level of at least 44 pg/ml prior to initiation of the treatment, and wherein the human subject has undergone an increase in plasma neurofilament light chain level of at least 10 pg/ml prior to initiation of the treatment.
• the disclosure features a method of treating amyotrophic lateral sclerosis associated with a mutation in the SOD1 gene in a human subject in need thereof by: measuring a neurofilament light chain level of at least 44 pg/ml in a biological sample obtained from the human subject before initiation of treatment; and administering to the human subject a pharmaceutical composition comprising a therapeutically effective amount of an antisense oligonucleotide according to the following formula: mCes Aeo Ges Geo Aes Tds Ads mCds Ads Tds Tds Tds Tds mCds Tds Ads mCeo Aes Geo mCes Te (nucleobase sequence of SEQ ID NO:l), wherein,
• A an adenine
• mC a 5-methylcytosine
• G a guanine
• T a thymine
• e a 2’-0-methoxyethylribose modified sugar
• d a 2’-deoxyribose sugar
• s a phosphorothioate intemucleoside linkage
• o a phosphodiester intemucleoside linkage; or a pharmaceutically acceptable salt thereof.
• the biological sample is blood, serum, plasma, or cerebrospinal fluid.
• the biological sample is blood.
• the biological sample is serum. In some embodiments, the biological sample is plasma.
• the method further includes measuring in the human subject an increase in blood, serum, plasma, or cerebrospinal fluid neurofilament light chain level of at least 10 pg/ml prior to administering the antisense oligonucleotide or pharmaceutically acceptable salt thereof.
• the method further includes measuring in the human subject an increase in plasma neurofilament light chain level of at least 10 pg/ml prior to administering the antisense oligonucleotide or pharmaceutically acceptable salt thereof. In some embodiments, the method further includes measuring in the human subject an increase in blood, serum, or cerebrospinal fluid level neurofilament light chain level equivalent to a plasma level increase of at least 10 pg/ml prior to administering the antisense oligonucleotide or pharmaceutically acceptable salt thereof. In some embodiments of any of the methods described herein, the pharmaceutical composition is administered by intrathecal administration.
• the pharmaceutical composition delivers a fixed dose of about 100 mg of the antisense oligonucleotide.
• the mutation in the SOD1 gene is A4V.
• the mutation in the SOD1 gene is A4V, H46R, G93S, A4T, G141X, D133A, V148G, N139K, G85R, G93A, V14G, C6S, I113T, D49K, G37R, A89V, E100G, D90A, T137A, E100K, G41A, G41D, G41S, G13R, G72S, L8V, F20C, Q22L, H48R, T54R, S591,
• the human subject is clinically presymptomatic of amyotrophic lateral sclerosis.
• the human subject is administered loading doses of the pharmaceutical composition followed by maintenance doses of the pharmaceutical composition.
• the human subject is administered loading doses of the pharmaceutical composition followed by maintenance doses of the pharmaceutical composition
• the human subject is administered three loading doses, wherein the loading doses are administered 14 days apart.
• the maintenance doses are administered every 28 days beginning 28 days after the third loading dose.
• the loading doses and maintenance doses of the pharmaceutical composition are administered to the human subject as follows:
• a first maintenance dose of the pharmaceutical composition administered 28 days or 1 month after the third loading dose.
• the loading doses and maintenance doses of the pharmaceutical composition are administered to the human subject as follows: (i) a first loading dose in an amount sufficient to deliver a fixed dose of about 100 mg of the antisense oligonucleotide;
• a second loading dose in an amount sufficient to deliver a fixed dose of about 100 mg of the antisense oligonucleotide, wherein the second loading dose is administered 14 days after the first loading dose;
• a third loading dose in an amount sufficient to deliver a fixed dose of about 100 mg of the antisense oligonucleotide, wherein the third loading dose is administered 28 days after the first loading dose;
• a first maintenance dose in an amount sufficient to deliver a fixed dose of about 100 mg of the antisense oligonucleotide, wherein the first maintenance dose is administered 28 days after the third loading dose.
• the human subject is an adult, e.g., the human subject is at least 18 years of age, e.g., at least 18, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65 years of age or older.
• Fig. 1 is a graph depicting a model-based estimate of geometric mean NfL level for participants with clinically manifested ALS 30 years or older at baseline with fast progressing mutations.
• This disclosure features the use of an antisense oligonucleotide, or salt thereof, for the treatment of amyotrophic lateral sclerosis associated with a mutation in the SOD1 gene in subjects (e.g., adults) with clinical symptoms/signs and in presymptomatic subjects (e.g., adults) with biomarker evidence of disease (e.g., neurofilament light chain level of at least 44 pg/ml).
• subjects e.g., adults
• presymptomatic subjects e.g., adults
• biomarker evidence of disease e.g., neurofilament light chain level of at least 44 pg/ml
• ALS Amyotrophic lateral sclerosis
• SOD1 superoxide dismutase 1
• Approved treatments for ALS are riluzole (Rilutek®) and edaravone
• Riluzole provides a modest increase in survival (2 to 3 months) without demonstrable improvement in strength or disability. Edaravone lessens functional decline as measured by the Revised Amyotrophic Lateral Sclerosis Functional Rating Scale (ALSFRS-R). The effect of edaravone on survival is unknown. No SOD1- specific ALS treatments are available. Superoxide Dismutase 1
• Superoxide dismutase [Cu-Zn] also known as superoxide dismutase 1 (SOD1) is an enzyme that in humans is encoded by the SOD1 gene, located on chromosome 21
• SOD1 is a 32 kDa homodimer that forms a b-barrel and contains an intramolecular disulfide bond and a binuclear Cu/Zn site in each subunit. This Cu/Zn site holds the copper and a zinc ion and is responsible for catalyzing the disproportionation of superoxide to hydrogen peroxide and dioxygen.
• SOD1 is one of three superoxide dismutases responsible for destroying free superoxide radicals in the body.
• the encoded isozyme is a soluble cytoplasmic and mitochondrial intermembrane space protein, acting as a homodimer to convert naturally occurring, but harmful, superoxide radicals to molecular oxygen and hydrogen peroxide. Hydrogen peroxide can then be broken down by another enzyme called catalase.
• At least 180 mutations in the SOD1 gene have been linked to familial ALS (Conwit RA, J Neurol Sci., 251 (1-2): 1-2 (2006); Al-Chalabi A, Leigh PN,
• amino acid sequence of human SOD1 can be found at UniProt P00441 and GENBANK Accession No. NP_000445, and is provided below:
• nucleotide sequence encoding human SOD1 is provided at GENBANK Accession No. NM_000454.4, and is also provided below (the region recognized by the antisense oligonucleotide of this disclosure is underlined):
• Antisense A is a 5-10-5 MOE gapmer, having the sequence of (from 5’ to
• each of nucleosides 1- 5 and 16-20 are 2’-0-methoxyethylribose modified nucleosides
• each of nucleosides 6-15 are 2’-deoxynucleosides
• the intemucleoside linkages between nucleosides 2 to 3, 4 to 5, 16 to 17, and 18 to 19 are phosphodiester linkages
• the intemucleoside linkages between nucleosides 1 to 2, 3 to 4, 5 to 6, 6 to 7, 7 to 8, 8 to 9, 9 to 10, 10 to 11, 11 to 12, 12 to 13, 13 to 14, 14 to 15, 15 to 16, 17 to 18, and 19 to 20 are phosphorothioate linkages
• each cytosine is a 5- methylcytosine.
• Antisense A is described by the following chemical notation: mCes Aeo Ges Geo Aes Tds Ads mCds Ads Tds Tds Tds mCds Tds Ads mCeo Aes Geo mCes Te (SEQ ID NO: 1); wherein,
• A an adenine
• mC a 5-methylcytosine
• G a guanine
• T a thymine
• e a 2’-0-methoxyethylribose modified sugar
• d a 2’-deoxyribose sugar
• s a phosphorothioate intemucleoside linkage
• o a phosphodiester intemucleoside linkage.
• 2'-0-methoxyethyl also 2'-MOE and 2'-OCH2CH2-OCH3 and MOE refers to an O-methoxy-ethyl modification of the 2' position of a furanose ring.
• a 2'-0- methoxy ethyl modified sugar is a modified sugar.
• 5-methylcytosine means a cytosine modified with a methyl group attached to the 5' position.
• a 5-methylcytosine is a modified nucleobase.
• Phosphorothioate linkage or “phosphorothioate intemucleoside linkage” means a linkage between nucleosides where the phosphodiester bond is modified by replacing one of the non-bridging oxygen atoms with a sulfur atom.
• a phosphorothioate linkage is a modified intemucleoside linkage.
• the Antisense A sequence can also be written in shorthand as follows:
• the underlined residues are 2'-MOE nucleosides.
• 2'-MOE nucleoside (also 2'-0-methoxy ethyl nucleoside) means a nucleoside comprising a MOE modified sugar moiety.
• Antisense A is depicted by the following chemical structure:
• Antisense A is described in detail in U.S. Patent No. 10,385,341, the content of which is incorporated herein by reference.
• the antisense oligonucleotide in solution (e.g., in solution in a pharmaceutical composition) may exist in free acid form, in a salt form, or a mixture thereof.
• Antisense oligonucleotides of this disclosure may be covalently linked to one or more moieties or conjugates which enhance the activity, cellular distribution or cellular uptake of the resulting antisense oligonucleotides.
• Typical conjugate groups include cholesterol moieties and lipid moieties.
• Additional conjugate groups include carbohydrates, phospholipids, biotin, phenazine, folate, phenanthridine, anthraquinone, acridine, fluoresceins, rhodamines, coumarins, and dyes.
• Antisense oligonucleotides can also be modified to have one or more stabilizing groups that are generally attached to one or both termini of antisense oligonucleotides to enhance properties such as, for example, nuclease stability. Included in stabilizing groups are cap structures. These terminal modifications protect the antisense oligonucleotide having terminal nucleic acid from exonuclease degradation, and can help in delivery and/or localization within a cell. The cap can be present at the 5'-terminus (5'-cap), or at the 3'-terminus (3'-cap), or can be present on both termini. Cap structures are well known in the art and include, for example, inverted deoxy abasic caps. Further 3' and 5'stabilizing groups that can be used to cap one or both ends of an antisense oligonucleotide to impart nuclease stability include those disclosed in WO 03/004602.
• Antisense oligonucleotides or salts thereof of this disclosure may be admixed with pharmaceutically acceptable active or inert substances for the preparation of pharmaceutical compositions or formulations.
• Compositions and methods for the formulation of pharmaceutical compositions are dependent upon a number of criteria, including, but not limited to, route of administration, extent of disease, or dose to be administered.
• An antisense oligonucleotide, or salt thereof, targeted to a SOD1 nucleic acid can be used in pharmaceutical compositions by combining the antisense oligonucleotide, or salt thereof, with a suitable pharmaceutically acceptable diluent or carrier.
• a pharmaceutically acceptable diluent includes phosphate-buffered saline (PBS).
• PBS is a diluent suitable for use in compositions to be delivered parenterally.
• employed in the methods described herein is a pharmaceutical composition comprising an antisense oligonucleotide, or salt thereof, targeted to a SOD1 nucleic acid and a pharmaceutically acceptable diluent.
• An antisense oligonucleotide, or salt thereof, described herein may be formulated as a pharmaceutical composition for intrathecal administration to a subject.
• compositions comprising antisense oligonucleotides of this disclosure encompass any pharmaceutically acceptable salts, esters, or salts of such esters, or any other oligonucleotide which, upon administration to an animal, including a human, is capable of providing (directly or indirectly) the biologically active metabolite or residue thereof. Accordingly, for example, the disclosure is also drawn to pharmaceutically acceptable salts of antisense oligonucleotides and other bioequivalents. Suitable pharmaceutically acceptable salts include, but are not limited to, sodium and potassium salts.
• the disclosure features methods of treating amyotrophic lateral sclerosis (e.g., clinically presymptomatic amyotrophic lateral sclerosis) associated with a mutation in the human SOD1 gene in a human subject in need thereof.
• the method involves administering to the human subject (e.g., by intrathecal administration) an antisense oligonucleotide, wherein the nucleobase sequence of the antisense oligonucleotide consists of CAGGATACATTTCTACAGCT (SEQ ID NO:l), wherein each of nucleosides 1-5 and 16-20 are 2’-0-methoxyethylribose modified nucleosides, and each of nucleosides 6-15 are 2’-deoxynucleosides, wherein the intemucleoside linkages between nucleosides 2 to 3, 4 to 5, 16 to 17, and 18 to 19 are phosphodiester linkages and the intemucleoside linkages between nucleosides 1 to 2, 3 to
• “About” in the context of the amount of a substance means +/- 10% of the indicated value. “About” 100 mg of an antisense oligonucleotide includes 90 mg to 110 mg of the antisense oligonucleotide. In the context of temporal units, e.g., about 10 days or about 1 week, “about” means +/- 3 days.
• “Intrathecal or IT” means administration into the cerebrospinal fluid under the arachnoid membrane which covers the brain and spinal cord.
• the method involves administering to the human subject (e.g., by intrathecal administration) an antisense oligonucleotide, wherein the nucleobase sequence of the antisense oligonucleotide consists of CAGGATACATTTCTACAGCT (SEQ ID NO: 1), wherein each of nucleosides 1-5 and 16-20 are 2’-0-methoxyethylribose modified nucleosides, and each of nucleosides 6-15 are 2’-deoxynucleosides, wherein the intemucleoside linkages between nucleosides 2 to 3, 4 to 5, 16 to 17, and 18 to 19 are phosphodiester linkages and the intemucleoside linkages between nucleosides 1 to 2, 3 to 4, 5 to 6, 6 to 7, 7 to 8, 8 to 9, 9 to 10, 10 to 11,
• the method involves administering to the human subject (e.g., by intrathecal administration) an antisense oligonucleotide, wherein the nucleobase sequence of the antisense oligonucleotide consists of CAGGATACATTTCTACAGCT (SEQ ID NO: 1), wherein each of nucleosides 1-5 and 16-20 are 2’-0-methoxyethylribose modified nucleosides, and each of nucleosides 6-15 are 2’-deoxynucleosides, wherein the intemucleoside linkages between nucleosides 2 to 3, 4 to 5, 16 to 17, and 18 to 19 are phosphodiester linkages and the intemucleoside linkages between nucleosides 1 to 2, 3 to 4, 5 to 6, 6 to 7, 7 to 8, 8 to 9, 9 to 10, 10 to
• amyotrophic lateral sclerosis e.g., clinically presymptomatic amyotrophic lateral sclerosis
• the method entails administering to the human subject (e.g., by intrathecal administration) a pharmaceutical composition comprising an antisense oligonucleotide or a salt thereof, wherein the antisense oligonucleotide has the following structure:
• the antisense oligonucleotide or the salt thereof is administered at a dose equivalent to about 100 mg or 100 mg of the antisense oligonucleotide.
• the antisense oligonucleotide or the salt thereof is administered at a dose equivalent to about 100 mg or 100 mg of the antisense oligonucleotide.
• the antisense oligonucleotide or the salt thereof is administered at a dose equivalent to about 100 mg or 100 mg of the antisense oligonucleotide.
• an above-noted fixed dose of the antisense oligonucleotide, or salt thereof is administered to the human subject once every week, once every two weeks, once every three weeks, or once every four weeks.
• the antisense oligonucleotide described herein is administered to the human subject as part of a pharmaceutical composition.
• the pharmaceutical composition is administered to the human subject in an amount sufficient to deliver a fixed dose of about 100 mg of the antisense oligonucleotide.
• the antisense oligonucleotide, or salt thereof is administered as a loading dose(s). In some embodiments, the antisense oligonucleotide is administered as a maintenance dose(s). In certain instances, the antisense oligonucleotide is administered as a loading dose(s) and followed by a maintenance dose(s).
• the loading dose(s) can be administered, e.g., every week, every two weeks, every three weeks, or every four weeks.
• the maintenance dose(s) can be administered, e.g., every week, every two weeks, every three weeks, or every four weeks after the last loading dose. In some instances, the maintenance dose(s) is administered every month.
• “Loading Dose” means a dose administered during a dosing phase during which administration is initiated and steady state concentration of the drug (e.g., antisense oligonucleotide) achieved.
• drug e.g., antisense oligonucleotide
• “Maintenance Dose” means a dose administered during a dosing phase after steady state concentration of the drug (e.g., antisense oligonucleotide) has been achieved.
• the drug e.g., antisense oligonucleotide
• the human subject is administered three loading doses of the antisense oligonucleotide, or salt thereof, followed by at least one (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more) maintenance dose.
• the three loading doses are administered two weeks apart. In some instances, the three loading doses are administered 14 days apart.
• the maintenance dose/doses are administered beginning 4 weeks after the third loading dose. In some instances, the maintenance dose/doses are administered every month beginning after the third loading dose. In some instances, the maintenance dose/doses are administered every 28 days beginning after the third loading dose.
• the mutation in SOD1 may be any mutation in the human SOD1 gene that is associated with ALS. In some instances, the mutation is a slow-progressing ALS disease mutation. In other instances, the mutation is a fast-progressing ALS disease mutation. In certain instances, the mutation in the human SOD1 gene is one or more of A4V, H46R, G93S, A4T, G141X, D133A, V148G, N139K, G85R, G93A, V14G, C6S, I113T, D49K, G37R, A89V, E100G, D90A, T137A, E100K, G41A, G41D, G41S, G13R, G72S, L8V, F20C, Q22L, H48R, T54R, S591, V87A, T88deltaTAD, A89T, V97M, S105deltaSL, V118L, D124G, L114F, D90A, G12R, G147R, C6
• the human subject has an A4V mutation in the human SOD1 gene. In another particular embodiment, the human subject has a LI 06V mutation in the human SOD1 gene. In another particular embodiment, the human subject has an H46R mutation in the human SOD1 gene. In yet another particular embodiment, the human subject has a G93S mutation in the human SOD1 gene.
• the mutation in the SOD1 gene is identified by a genetic test. Accordingly, identification of a subject suffering from or susceptible to ALS can be performed by genetic testing of the subject’s SOD1 gene using assays known in the art, such as e.g., genetic sequencing.
• Analysis of a subject’s susceptibility to ALS can also be performed by analyzing the family history of the subject for ALS. Analysis of the family history may include a three-generation pedigree documenting ALS, a review of medical records and autopsy studies of family members, and identification of an autosomal dominant pattern of SOD1 mutation.
• administration of a therapeutically effective amount of an antisense oligonucleotide, or a salt thereof, to a human subject is accompanied by monitoring of SOD1 levels in the human subject, to determine the human subject’s response to administration of the antisense oligonucleotide, or salt thereof.
• a human subject’s response to administration of the antisense oligonucleotide, or a salt thereof, may be used by a physician to determine the amount and duration of therapeutic intervention.
• the human SOD1 levels are monitored in CSF.
• the human SOD1 levels are monitored in plasma.
• the human SOD1 levels are monitored in blood.
• the human SOD1 levels are monitored in serum.
• administration of an antisense oligonucleotide, or a salt thereof results in reduction of SOD1 protein expression. In certain embodiments, administration of an antisense oligonucleotide, or a salt thereof, results in reduction of SOD1 protein expression by at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 99%, or a range defined by any two of these values. In certain embodiments, the reduction of SOD1 protein expression is a reduction in the CSF. In certain embodiments, the reduction of SOD1 protein expression is a reduction in the plasma. In certain embodiments, the reduction of SOD1 protein expression is a reduction in blood.
• the reduction of SOD1 protein expression is a reduction in serum.
• administration of an antisense oligonucleotide, or a salt thereof results in improved motor function and respiration in the human subject.
• administration of the antisense oligonucleotide, or salt thereof improves motor function and respiration by at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 99%, or a range defined by any two of these values.
• compositions comprising an antisense oligonucleotide, or a salt thereof, are used for the preparation of a medicament for treating a human subject suffering or susceptible to ALS (e.g., a human subject having a mutation in SOD1 associated with ALS).
• a human subject suffering or susceptible to ALS e.g., a human subject having a mutation in SOD1 associated with ALS.
• a subject is selected for treatment if the subject has a neurofilament light chain level at or above a predetermined threshold. In some instances, a subject is selected for treatment if the subject has undergone an increase in a neurofilament light chain level of a predetermined minimum amount. In some instances, a subject is selected for treatment if the subject has a neurofilament light chain level at or above a predetermined threshold and has undergone an increase in a neurofilament light chain level of a predetermined minimum amount.
• Neurofilament light chain (NfL) e.g., plasma or serum NfL
• concentrations can be measured, for example, using ready -to- use enzyme linked immunosorbent assay (ELISA) diluent (Mabtech AB, Nacka Strand, Sweden), an electrochemiluminescence (ECL) immunoassay described in Gaiottino et al., PLoS ONE 8: e75091, 2013, or a single molecule array (SIMOA) method described in Disanto et al., Ann. Neurol. 81(6): 857-870, 2017. The three assay methods have been compared in Kuhl et al., Clinical Chemistry and Laboratory Medicine 54 (10): 1655-1661, 2016.
• ELISA enzyme linked immunosorbent assay
• ECL electrochemiluminescence
• SIMOA single molecule array
• the SIMOA assay (the SimoaNF-light Advantage kit) is commercially available from Quanterix Corp. (Lexington, MA, USA).
• NfL e.g., plasma or serum NfL
• concentrations are measured using the Siemens Healthineers (SHL; Er Weg, Germany) NfL assay.
• total NfL e.g., phosphorylated and non-phosphorylated
• phosphorylated NfL is measured, and in some embodiments, non-phosphorylated NfL is measured.
• a subject e.g., a subject clinically presymptomatic of amyotrophic lateral sclerosis
• a mutation in the SOD1 gene is selected for treatment if the subject has a neurofilament light chain level at or above a predetermined minimum threshold (e.g., a neurofilament light chain level of at least 44 pg/ml, e.g., as determined using the Siemens Healthineers NfL assay or an equivalent NfL level measured using a different assay).
• a predetermined minimum threshold e.g., a neurofilament light chain level of at least 44 pg/ml, e.g., as determined using the Siemens Healthineers NfL assay or an equivalent NfL level measured using a different assay.
• a subject e.g., a subject clinically presymptomatic of amyotrophic lateral sclerosis
• a mutation in the SOD1 gene is selected for treatment if the subject has undergone an increase in a neurofilament light chain level of a predetermined minimum amount (e.g., an increase in neurofilament light chain level of at least 10 pg/ml, e.g., as determined using the Siemens Healthineers NfL assay or an equivalent NfL level measured using a different assay).
• a predetermined minimum amount e.g., an increase in neurofilament light chain level of at least 10 pg/ml, e.g., as determined using the Siemens Healthineers NfL assay or an equivalent NfL level measured using a different assay.
• a subject e.g., a subject clinically presymptomatic of amyotrophic lateral sclerosis
• a neurofilament light chain level at or above a predetermined minimum threshold e.g., a neurofilament light chain level of at least 44 pg/ml, e.g., as determined using the Siemens Healthineers NfL assay or an equivalent NfL level measured using a different assay
• a predetermined minimum threshold e.g., a neurofilament light chain level of at least 44 pg/ml, e.g., as determined using the Siemens Healthineers NfL assay or an equivalent NfL level measured using a different assay
• a predetermined minimum amount e.g., an increase in neurofilament light chain level of at least 10 pg/ml, e.g., as determined using the Siemens Healthineers NfL assay or an equivalent NfL level measured using a different assay
• a change e.g., increase
• a change e.g., increase
• a change of at least 10 pg/mL in plasma NfL level from baseline can robustly account for the potential effect of aging on NfL level.
• the amino acid sequence of human NF-L is provided in SEQ ID NO:4 and in Julien et al., Biochimica et Biohysica Acta, 909:10-20 (1987), UniProtKB - P07196, NCBI Reference Sequence: NP_006149.2, andNCBI Reference Sequence: NG_008492.1.
• Suitable biological samples for the methods described herein include any biological fluid, cell, tissue, or fraction thereof, which includes analyte biomolecules of interest such as NF protein or nucleic acid (e.g RNA (mRNA)).
• a biological sample can be, for example, a specimen obtained from a human subject or can be derived from such a subject.
• a sample can be a tissue section obtained by biopsy, archived biological fluid, or cells that are placed in or adapted to tissue culture.
• a biological sample is a biological fluid such as blood, serum, plasma, or cerebrospinal fluid (CSF), or such a sample absorbed onto a substrate (e.g., glass, polymer, paper).
• CSF cerebrospinal fluid
• a biological sample can be further fractionated, if desired, to a fraction containing particular cell types.
• a blood sample can be fractionated into serum or into fractions containing particular types of blood cells such as red blood cells or white blood cells (leukocytes).
• a sample can be a combination of samples from a subject such as a combination of a tissue and fluid sample.
• the biological samples can be obtained from a subject having a mutation in the SOD1 gene (e.g., a SOD1 mutation described herein).
• the subject is clinically presymptomatic of amyotrophic lateral sclerosis.
• Any suitable methods for obtaining the biological samples can be employed, although exemplary methods include, e.g., phlebotomy, fine needle aspirate biopsy procedure.
• Samples can also be collected, e.g., by microdissection (e.g., laser capture microdissection (LCM) or laser microdissection (LMD)).
• microdissection e.g., laser capture microdissection (LCM) or laser microdissection (LMD)
• a biological sample can be further contacted with one or more additional agents such as buffers and/or inhibitors, including one or more of nuclease, protease, and phosphatase inhibitors, which preserve or minimize changes in the molecules (e.g., nucleic acids or proteins) in the sample.
• additional agents such as buffers and/or inhibitors, including one or more of nuclease, protease, and phosphatase inhibitors, which preserve or minimize changes in the molecules (e.g., nucleic acids or proteins) in the sample.
• Such inhibitors include, for example, chelators such as ethylenediamine tetraacetic acid (EDTA), ethylene glycol bis(P-aminoethyl ether) N,N,NI ,N1 -tetraacetic acid (EGTA), protease inhibitors such as phenylmethylsulfonyl fluoride (PMSF), aprotinin, leupeptin, antipain, and the like, and phosphatase inhibitors such as phosphate, sodium fluoride, vanadate, and the like.
• chelators such as ethylenediamine tetraacetic acid (EDTA), ethylene glycol bis(P-aminoethyl ether) N,N,NI ,N1 -tetraacetic acid (EGTA), protease inhibitors such as phenylmethylsulfonyl fluoride (PMSF), aprotinin, leupeptin, antipain, and the like, and phosphatas
• Suitable buffers and conditions for isolating molecules are well known to those skilled in the art and can be varied depending, for example, on the type of molecule in the sample to be characterized (see, e.g., Ausubel et al. Current Protocols in Molecular Biology (Supplement 47), John Wiley & Sons, New York (1999); Harlow and Lane, Antibodies: A Laboratory Manual (Cold Spring Harbor Laboratory Press (1988); Harlow and Lane, Using Antibodies: A Laboratory Manual, Cold Spring Harbor Press (1999); Tietz Textbook of Clinical Chemistry, 3rd ed. Burtis and Ashwood, eds. W.B. Saunders, Philadelphia, (1999)).
• a sample also can be processed to eliminate or minimize the presence of interfering substances.
• a biological sample can be fractionated or purified to remove one or more materials that are not of interest.
• Methods of fractionating or purifying a biological sample include, but are not limited to, chromatographic methods such as liquid chromatography, ion-exchange chromatography, size-exclusion chromatography, or affinity chromatography.
• a sample can be in a variety of physical states.
• a sample can be a liquid or solid, can be dissolved or suspended in a liquid, can be in an emulsion or gel, or can be absorbed onto a material.
• Example 1 Use of a Neurofilament Threshold for Selection of Patients for Treatment with a SOD1 Antisense Oligonucleotide
• a Phase 3, randomized, placebo-controlled study of Antisense A (as described herein) is conducted with a longitudinal natural history run-in in clinically presymptomatic adult SOD1 mutation carriers.
• SOD1 mutations included in this study are associated with high or complete penetrance and rapid progression to disease.
• SOD1 mutation carriers are considered clinically presymptomatic of amyotrophic lateral sclerosis (ALS) if they do not have clinically manifested ALS.
• Clinically manifested ALS is defined as the emergence of clinical symptoms or signs, which may be supported by EMG findings, that definitively indicate the emergence of ALS.
• a plasma neurofilament light chain (NfL) threshold of 44 pg/mL was selected to identify study participants considered at high risk for onset of definite clinical symptoms/signs of ALS within 12 months (after reaching the NfL threshold).
• the plasma NfL threshold of 44 pg/mL was determined based on simulations from aNF trajectory model using data from presymptomatic familial amyotrophic lateral sclerosis (Pre-fALS) samples and selected to minimize the false positive rate while allowing for adequate time for enrollment and intervention between NF elevation and clinical onset.
• Pre-fALS familial amyotrophic lateral sclerosis
• the NfL trajectory model allowed for the projection of time course from NfL elevation to emergence of clinically manifested ALS. Posterior predictive simulations from the fitted models were utilized to evaluate the performance of different NfL thresholds. Plasma NfL was analyzed herein using the Siemens Healthineers (SHL) NfL assay.
• SHL Siemens Healthineers
• a NfL threshold of 44 pg/mL was derived based on the following factors:
• the false positive rate was evaluated among presymptomatic carriers with a NfL level below the threshold at enrollment and at least 12 months of follow-up time. A participant was considered a false positive if the NfL level exceeded the threshold at a postbaseline visit and the participant remained clinically presymptomatic for at least 12 months thereafter.
• the false negative rate was evaluated among all participants with clinically manifested ALS. A participant was considered a false negative if clinically manifested ALS emerged before reaching the NfL threshold.
• the false positive rate was 0/24 (0%) and the false negative was 1/12 (8.3%).
• a threshold of 40 pg/mL was considered but rejected because of a higher false positive rate (1/24; 4.1%), while having the same false negative rate as 44 pg/mL.
• the geometric mean NfL levels prior to clinical symptom onset were estimated by month and displayed in Fig. 1.
• the expected geometric mean NfL level is approximately 44 pg/mL.
• posterior predictive probability of clinically manifested ALS for the placebo patients by 12 months is 77.66%.
• the clinical study contains four parts, Part A, Part B, Part C, and Part D.
• Part A is a natural history run-in, where participants do not receive study treatment, Antisense A or placebo. Participants in Part A are at least 18 years of age, e.g., at the time of informed consent. Participants in Part A have plasma NfL levels less than 44 pg/mL and no clinically manifested ALS during screening. Participants in Part A have one of the following SOD1 mutations confirmed during screening.
• each of the parentheticals above refers to two alternate naming conventions for each amino acid substitution.
• each of the above amino acid substitutions is referred to by the variant identifier listed first in each parenthetical (e.g., A4T).
• participants in Part A may have a S0D1 mutation other than one listed above that is adjudicated by an external Mutation Adjudication Committee for inclusion into the study. Adjudication must confirm that any additional SOD1 mutation included in the study has high or complete penetrance, and is associated with rapid disease progression.
• Part B is a randomized, double-blind, placebo-controlled period in presymptomatic participants with plasma NfL levels greater than or equal to 44 pg/mL, a change from Part A baseline in NfL that is at least 10 pg/mL, and no alternative identifiable cause for the NfL elevation per the discretion of the investigator.
• Participants from Part A whose plasma NfL levels reach a level that is greater than or equal to 44 pg/mL and exhibit a change from baseline in NfL of at least 10 pg/mL and who have not developed clinically manifested ALS may be eligible to enroll in Part B.
• Part B participants are randomized in a 1:1 (Antisense A: placebo) ratio to receive one of the treatments administered by intrathecal injection (Antisense A 100 mg or placebo). Participants in Parts B receive 3 loading doses approximately every 14 days (i.e., Days 1, 15, and 29) and maintenance doses approximately every 28 days by intrathecal injection thereafter in a blinded manner.
• the primary endpoint of the study is the proportion of participants with emergence of clinically manifested ALS within 12 months of initiating Part B. Secondary endpoints of the study include the proportion of participants with emergence of clinically manifested ALS within 24 months of initiating Part B, time to emergence of clinically manifested ALS, change in Revised Amyotrophic Lateral Sclerosis Functional Rating Scale (ALSFRS-R) total score, change in percent predicted slow vital capacity (SVC), ventilation assistance-free survival (VAFS; defined as time to the earliest occurrence of one of death or permanent ventilation), and overall survival.
• ALSFRS-R Revised Amyotrophic Lateral Sclerosis Functional Rating Scale
• SVC percent predicted slow vital capacity
• VAFS ventilation assistance-free survival
• Part C is an open-label extension study in which participants receive 100 mg of Antisense A by intrathecal injection. Participants from Part B who develop clinically manifested ALS are enrolled and monitored. Part D is a randomized, double-blind, placebo-controlled period in participants from Part A with clinically manifested ALS. Participants are randomized in a 2: 1 (Antisense A: placebo) ratio to receive via intrathecal injection either 100 mg Antisense A or placebo.

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