WO2002079503A1

WO2002079503A1 - An allele of apolipoprotein e linked to neuropsychiatric disorders

Info

Publication number: WO2002079503A1
Application number: PCT/AU2002/000424
Authority: WO
Inventors: Elizabeth Ellen Powell; Julie Ruth Jonsson
Original assignee: The University Of Queensland; The State Of Queensland Through Princess Alexandra Hospital And District Health Service
Priority date: 2001-04-02
Filing date: 2002-04-02
Publication date: 2002-10-10
Also published as: AUPR416301A0

Abstract

The invention discloses an allele of an apolipoprotein E (Apo-E) gene, or an expression product of said allele, which correlate with the development and/or progression of a neuropsychiatric disorder associated with interferon treatment. Also disclosed are methods for diagnosis of a predisposition to the development and/or progression of a neuropsychiatric disorder associated with interferon treatment by detecting the presence of an allele of an Apo-E gene, or an expression product thereof, which correlate with that predisposition. The invention also discloses a method of treatment of a disease or condition based on said diagnosis.

Description

An allele of Apolipoprotein E linked to neuropsychiatric disorders

FIELD OF THE INVENTION

THIS INVENTION relates generally to polynucleotides and polypeptides linked to neuropsychiatric disorders, including mood disorders, cognitive disorders and endocrine function. More particularly, the present invention relates to an allele of an apolipoprotein E (Apo-E) gene, or to an expression product of said allele, which correlate with the development and/or progression of a neuropsychiatric disorder associated with interferon treatment. The invention also encompasses methods for diagnosis of a predisposition to the development and/or progression of a neuropsychiatric disorder associated with interferon treatment by detecting the presence of an allele of an Apo-E gene, or an expression product thereof, which correlate with that predisposition. The invention also features a method of treatment of a disease or condition based on said diagnosis.

Bibliographic details of the publications numerically referred to in this specification are collected at the end of the description.

BACKGROUND OF THE INVENTION

Hepatitis C virus (HCV) is a major cause of chronic liver disease world-wide, affecting an estimated 170 million people, approximately 3% of the world's population.¹'²

Progression to cirrhosis may occur in up to 20% of chronically infected individuals, predisposing to the development of hepatocellular carcinoma. In many Western countries,

HCV is the leading indication for orthotopic liver transplantation.

Interferon-α (IFN-α), a cytokine with pleiotropic properties, is the recommended treatment for HCV, alone or in combination with other antivirals such as ribavirin.^3"6 However, the efficacy of IFN-α therapy is limited and treatment is associated with a number of side effects.⁵ Particularly troublesome are the neuropsychiatric complications which may be observed in more than 30% of treated patients and are largely unpredictable.⁷ These side effects include alterations of mood, cognition and neuroendocrine function. hiterferon-α induced neuropsychiatric side effects are not unique to hepatitis C, and have been reported during treatment of other diseases such as hepatitis B, metastatic melanoma and haematological malignancies with incidence rates approaching 50%.⁹ The mechanism by which interferon induces neuropsychiatric side effects remains unknown. The cognitive side effects of IFN-α such as memory loss and generalised slowing, along with depression and lack of initiative, are consistent with a mild frontal subcortical impairment.⁹ Cognitive deficits and mood disorder may occur independently, or depressive symptoms may occur secondary to cognitive impairment. The adverse effects of IFN-α therapy may be contributed to by the activation of a complex cascade of secondary cytokines both in the peripheral and central nervous system.⁸

In a variety of neurological disorders characterised by neuropsychiatric symptoms and cognitive dysfunction, inheritance of certain apolipoprotein E (Apo-E) alleles is associated with particular neuropsychiatric outcomes. Apolipoprotein E is the major protein involved in transport of cholesterol esters and lipids in the brain and is markedly increased in human astrocytes following injury.^10,11 There are three common isoforms of Apo E: E2, E3 and E4 encoded by the different alleles ε2, ε3 and ε4. Differences between the Apo-E isoforms have been noted in their ability to stimulate the branching of growing neurons and prevent neuronal death in conditions of oxidative stress.

In work leading up to the present invention, it was hypothesised that the variability in incidence, type and severity of neuropsychiatric complications observed between individuals during antiviral treatment is predicated on genetic factors that contribute to the expression of these side effects. The present inventors investigated their hypothesis by examining the inheritance of Apo-E genotypes in patients with chronic HCV and their association with neuropsychiatric side effects during antiviral therapy.

SUMMARY OF THE INVENTION

The present invention is predicated in part on the discovery that certain alleles of the Apo-E gene are linked to the development and/or progression of neuropsychiatric disorders associated with interferon treatment. It was observed that patients with an allele encoding an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E were more likely to be referred to a psychiatrist (p=0.004) and had more neuropsychiatric symptoms (p=0.002) during interferon treatment than those without that allele. Additionally, patients with that allele were more likely to experience irritability or anger (p=0.0002) and anxiety or other non-depressive mood symptoms (p=0.0004). Thus, it was concluded that knowledge of Apo-E genotypes will permit identification of patients at risk of neuropsychiatric side effects and direct practitioners toward more effective therapies. The foregoing discoveries have been reduced to practice inter alia in methods for diagnosing a predisposition to develop and/or progress a neuropsychiatric disorder, and in methods of treatment based on that diagnosis, as described hereinafter.

Accordingly, in one aspect of the present invention, there is provided a method for diagnosis in a patient of a predisposition to develop and/or progress a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E.

In another aspect, the invention contemplates a method for diagnosis in a patient of a predisposition to develop and/or progress a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E, which amino acid comprises an electropositive side chain.

In yet another aspect, the invention encompasses a method for diagnosis in a patient of a predisposition to develop and/or progress a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes arginine at codon 112 relative to the full-length open reading frame of Apo-E.

In still yet another aspect, the invention envisions a method for diagnosis in a patient of a predisposition to develop and/or progress a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele is an e4 allele of Apo-E.

According to another aspect of the invention, there is provided a method for diagnosis in a patient of a predisposition to develop and/or progress a neuropsychiatric disorder associated with the administration of an interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these, to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E. In another aspect, the invention contemplates a method for diagnosis in a patient of a predisposition to develop and/or progress a neuropsychiatric disorder associated with the administration of an interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these, to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E, which amino acid comprises an electropositive side chain.

In yet another aspect, the invention encompasses a method for diagnosis in a patient of a predisposition to develop and/or progress a neuropsychiatric disorder associated with the administration of an interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these, to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes arginine at codon 112 relative to the full- length open reading frame of Apo-E.

In still yet another aspect, the invention envisions a method for diagnosis in a patient of a predisposition to develop and/or progress a neuropsychiatric disorder associated with the administration of an interferon-c, or a biologically active fragment thereof, or a variant or derivative or analogue of these, to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele is an e4 allele of Apo-E.

In another aspect, the invention contemplates a method for diagnosis in a patient of a predisposition to develop a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E.

In yet another aspect, the invention encompasses a method for diagnosis in a patient of a predisposition to progress a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E. In still yet another aspect, the invention envisions a method for diagnosis in a patient of a higher risk of developing and or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E. hi yet another aspect, the invention encompasses a method for diagnosis in a patient of a higher risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E, which amino acid comprises an electropositive side chain.

According to another aspect of the invention, there is provided a method for diagnosis in a patient of a higher risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an arginine at codon 112 relative to the full-length open reading frame of Apo-E. In still yet another aspect, the invention envisions a method for diagnosis in a patient of a higher risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele is an e4 allele of Apo-E. In still yet another aspect, the invention envisions a method for diagnosis in a patient of a higher risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these, to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E.

In yet another aspect, the invention encompasses a method for diagnosis in a patient of a higher risk of developing and or progressing a neuropsychiatric disorder associated with the administration of an interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these, to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E, which amino acid comprises an electropositive side chain.

According to another aspect of the invention, there is provided a method for diagnosis in a patient of a higher risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these, to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an arginine at codon 112 relative to the full-length open reading frame of Apo-E.

In still yet another aspect, the invention envisions a method for diagnosis in a patient of a higher risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon-c^, or a biologically active fragment thereof, or a variant or derivative or analogue of these, to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele is an e4 allele of Apo-E. In a further aspect, the invention features a method for diagnosis in a patient of a higher risk of developing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E.

In yet a further aspect, the invention contemplates a method for diagnosis in a patient of a higher risk of progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E.

In another aspect, the invention extends to a method for diagnosis in a patient of a lower risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than an amino acid comprising an electropositive side chain at codon 112 relative to the full-length open reading frame of Apo-E.

In yet another aspect, the invention encompasses a method for diagnosis in a patient of a lower risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than arginine at codon 112 relative to the full-length open reading frame of Apo-E.

In another aspect of the invention, there is provided a method for diagnosis in a patient of a lower risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes a cysteine at codon 112 relative to the full-length open reading frame of Apo-E.

In still yet another aspect, the invention envisions a method for diagnosis in a patient of a lower risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele is other than the e4 allele of Apo-E.

In another aspect, the invention contemplates a method for diagnosis in a patient of a lower risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele is selected from the e2 allele and the e3 allele of Apo-E.

In another aspect, the invention extends to a method for diagnosis in a patient of a lower risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon- , or a biologically active fragment thereof, or a variant or derivative or analogue of these, to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than an amino acid comprising an electropositive side chain at codon 112 relative to the full-length open reading frame of Apo-E.

In yet another aspect, the invention encompasses a method for diagnosis in a patient of a lower risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these, to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than arginine at codon 112 relative to the full-length open reading frame of Apo-E. In another aspect of the invention, there is provided a method for diagnosis in a patient of a lower risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these, to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes a cysteine at codon 112 relative to the full-length open reading frame of Apo-E.

In still yet another aspect, the invention envisions a method for diagnosis in a patient of a lower risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these, to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele is other than the e4 allele of Apo-E.

In another aspect, the invention contemplates a method for diagnosis in a patient of a lower risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these, to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele is selected from the e2 allele and the e3 allele of Apo-E. hi a further aspect, the invention features a method for diagnosis in a patient of a lower risk of developing a neuropsychiatric disorder associated with the admimsfration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than an amino acid comprising an electropositive side chain at codon 112 relative to the full-length open reading frame of Apo-E.

In yet a further aspect, the invention contemplates a method for diagnosis in a patient of a lower risk of progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than an amino acid comprising an electropositive side chain at codon 112 relative to the full-length open reading frame of Apo-E. According to another aspect, the invention provides a method for diagnosis in a patient of a higher risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient at least two alleles of Apo-E, or expression products thereof, wherein each of said alleles encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E. In a preferred embodiment, the method comprises detecting a pair of alleles, each encoding an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo- E. In an especially preferred embodiment, the method comprises detecting at least two e4 alleles of Apo-E. hi a more preferred embodiment, the method comprises detecting a pair of e4 alleles of Apo-E.

In another aspect, the invention resides in a method for diagnosis in a patient of a lower risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient at least two alleles of Apo-E, or expression products thereof, wherein each of said alleles encodes an amino acid other than an amino acid comprising an electropositive side chain at codon 112 relative to the full-length open reading frame of Apo-E. In a preferred embodiment, the method comprises detecting at least two copies of an allele selected from the e2 allele and the e3 allele of Apo-E. In a more preferred embodiment, the method comprises detecting a pair of alleles selected from the e2 allele and the e3 allele of Apo-E. hi yet another aspect, the invention extends to a method for diagnosis in a patient of an intermediate risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient different alleles of Apo-E, or expression products thereof, wherein at least one of said alleles encodes cysteine at codon 112 relative to the full-length open reading frame of Apo-E and at least one other of said alleles encodes an amino acid comprising an electropositive side chain at codon 112 relative to the full- length open reading frame of Apo-E. In a preferred embodiment, the method comprises detecting at least one e4 allele of Apo-E and at least one allele selected from the e2 allele and the e3 allele of Apo-E.

According to a further aspect, the invention extends to a method for treating or preventing a disease or condition in a patient, which disease or condition is treatable or preventable by the administration of an interferon to said patient, said patient comprising an allele of Apo-E, or an expression product thereof, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo- E, said method comprising administering to a patient in need of such treatment an effective amount of an agent other than said interferon, wherein said agent is effective for said treatment or prevention.

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1: Cox's proportional hazards analysis showing, over treatment time, the proportion of patients without a neuropsychiatric event for Apo-E ε4 carrier and Apo-E ε4 non-carrier patient groups. A neuropsychiatric event was defined as a cumulative neuropsychiatric symptom score of 5 or greater, psychiatric referral or cessation of interferon treatment due to neuropsychiatric side effects. Analysis was adjusted for age, sex, response to TNF-α treatment, viral genotype, and prior psychiatric history. The difference between the 2 adjusted survival curves was statistically significant (ρ=0.008).

BRIEF DESCRIPTION OF THE SEQUENCES: SUMMARY TABLE

TABLE A

DETAILED DESCRIPTION OF THE INVENTION

1. Definitions

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by those of ordinary skill in the art to which the invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, preferred methods and materials are described. For the purposes of the present invention, the following terms are defined below.

The articles "a " and "an " are used herein to refer to one or to more than one (i.e. to at least one) of the grammatical object of the article. By way of example, "an element" means one element or more than one element.

'Allele " is used herein to refer to a variant of a gene found at the same place or locus of a chromosome.

"Amplification product" refers to a nucleic acid product generated by nucleic acid amplification techniques.

By "antigen-binding molecule" is meant a molecule that has binding affinity for a target antigen. It will be understood that this term extends to immunoglobulins, immunoglobulin fragments and non-immunoglobulin derived protein frameworks that exhibit antigen-binding activity. "Antigenic or immunogenic activity" refers to the ability of a polypeptide, fragment, variant or derivative according to the invention to produce an antigenic or immunogenic response in a mammal to which it is administered, wherein the response includes the production of elements which specifically bind the polypeptide or fragment thereof. The term "biological sample" as used herein refers to a sample that may be extracted, untreated, treated, diluted or concentrated from a patient. Suitably, the biological sample is selected from a cell or tissue sample including a cell or tissue sample obtained from skin, hair, heart, lungs, kidneys, liver, cheek, blood etc.

By "biologically active fragment" is meant a fragment of a full-length parent polypeptide which fragment retains the activity of the parent polypeptide. A biologically active fragment will therefore have, for example, the activity of an interferon, preferably an interferon-α. As used herein, the term "biologically active fragment" includes deletion variants and small peptides, for example of at least 10, preferably at least 20 and more preferably at least 30 contiguous amino acids, which comprise the above activities. Peptides of this type may be obtained through the application of standard recombinant nucleic acid techniques or synthesised using conventional liquid or solid phase synthesis techniques. For example, reference may be made to solution synthesis or solid phase synthesis as described, for example, in Chapter 9 entitled "Peptide Synthesis " by Atherton and Shephard which is included in a publication entitled "Synthetic Vaccines " edited by Nicholson and published by Blackwell Scientific Publications. Alternatively, peptides can be produced by digestion of a polypeptide of the invention with proteinases such as endoLys-C, endoArg-C, endoGlu-C and staphylococcus V8-protease. The digested fragments can be purified by, for example, high performance liquid chromatographic (HPLC) techniques.

Throughout this specification, unless the context requires otherwise, the words "comprise ", "comprises " and "comprising " will be understood to imply the inclusion of a stated step or element or group of steps or elements but not the exclusion of any other step or element or group of steps or elements.

By "corresponds to" or "corresponding to" is meant (a) a polynucleotide having a nucleotide sequence that is substantially identical or complementary to all or a portion of a reference polynucleotide sequence or encoding an amino acid sequence identical to an amino acid sequence in a peptide or protein; or (b) a peptide or polypeptide having an amino acid sequence that is substantially identical to a sequence of amino acids in a reference peptide or protein.

By "derivative" is meant a polypeptide that has been derived from the basic sequence by modification, for example by conjugation or complexing with other chemical moieties or by post-translational modification techniques as would be understood in the art. The term "derivative" also includes within its scope alterations that have been made to a parent sequence including additions or deletions that provide for functional equivalent molecules. By "effective amount", in the context of treating or preventing a condition is meant the administration of that amount of active to an individual in need of such treatment or prophylaxis, either in a single dose or as part of a series, that is effective for treatment of, or prophylaxis against, that condition. The effective amount will vary depending upon the health and physical condition of the individual to be treated, the taxonomic group of individual to be treated, the formulation of the composition, the assessment of the medical situation, and other relevant factors. It is expected that the amount will fall in a relatively broad range that can be determined through routine trials. By "gene" is meant a unit of inheritance that occupies a specific locus on a chromosome and consists of transcriptional and or translational regulatory sequences and/or a coding region and/or non-translated sequences (i.e., introns, 5' and 3' untranslated sequences).

"Homology " refers to the percentage number of amino acids that are identical or constitute conservative substitutions as defined in Table 1 below. Homology may be determined using sequence comparison programs such as GAP (Deveraux et al. 1984, Nucleic Acids Research 12, 387-395) which is incorporated herein by reference. In this way sequences of a similar or substantially different length to those cited herein could be compared by insertion of gaps into the alignment, such gaps being determined, for example, by the comparison algorithm used by GAP.

"Hybridisation" is used herein to denote the pairing of complementary nucleotide sequences to produce a DNA-DNA hybrid or a DNA-RNA hybrid. Complementary base sequences are those sequences that are related by the base-pairing rules, hi DNA, A pairs with T and C pairs with G. In RNA U pairs with A and C pairs with G. hi this regard, the terms "match" and "mismatch" as used herein refer to the hybridisation potential of paired nucleotides in complementary nucleic acid strands. Matched nucleotides hybridise efficiently, such as the classical A-T and G-C base pair mentioned above. Mismatches are other combinations of nucleotides that do not hybridise efficiently.

Reference herein to "immuno-interactive " includes reference to any interaction, reaction, or other form of association between molecules and in particular where one of the molecules is, or mimics, a component of the immune system.

By "isolated" is meant material that is substantially or essentially free from components that normally accompany it in its native state.

By "obtained from " is meant that a sample such as, for example, a polynucleotide extract or polypeptide extract is isolated from, or derived from, a particular source of the host. For example, the extract can be obtained from a tissue or a biological fluid isolated directly from the host. The term "oligonucleotide" as used herein refers to a polymer composed of a multiplicity of nucleotide residues (deoxyribonucleotides or ribonucleotides, or related structural variants or synthetic analogues thereof) linked via phosphodiester bonds (or related structural variants or synthetic analogues thereof). Thus, while the term "oligonucleotide" typically refers to a nucleotide polymer in which the nucleotide residues and linkages between them are naturally occurring, it will be understood that the term also includes within its scope various analogues including, but not restricted to, peptide nucleic acids (PNAs), phosphoramidates, phosphorothioates, methyl phosphonates, 2-O-methyl ribonucleic acids, and the like. The exact size of the molecule can vary depending on the particular application. An oligonucleotide is typically rather short in length, generally from about 10 to 30 nucleotide residues, but the term can refer to molecules of any length, although the term "polynucleotide" or "nucleic acid" is typically used for large oligonucleotides.

By "operably linked" is meant that transcriptional and translational regulatory polynucleotides are positioned relative to a polypeptide-encoding polynucleotide in such a manner that the polynucleotide is transcribed and the polypeptide is translated.

The term "patient" refers to patients of human or other mammal and includes any individual it is desired to examine or treat using the methods of the invention. However, it will be understood that "patient" does not imply that symptoms are present. Suitable mammals that fall within the scope of the invention include, but are not restricted to, primates, livestock animals (e.g. sheep, cows, horses, donkeys, pigs), laboratory test animals (e.g. rabbits, mice, rats, guinea pigs, hamsters), companion animals (e.g. cats, dogs) and captive wild animals (e.g. foxes, deer, dingoes).

By "pharmaceutically acceptable carrier" is meant a solid or liquid filler, diluent or encapsulating substance that can be safely used in topical or systemic administration to a animal, preferably a mammal including humans.

The term "polynucleotide" or "nucleic acid¹' as used herein designates mRNA, RNA, cRNA, cDNA or DNA. The term typically refers to oligonucleotides greater than 30 nucleotide residues in length. "Polypeptide", "peptide" and "protein" are used interchangeably herein to refer to a polymer of amino acid residues and to variants and synthetic analogues of the same. Thus, these terms apply to amino acid polymers in which one or more amino acid residues is a synthetic non-naturally occurring amino acid, such as a chemical analogue of a corresponding naturally occurring amino acid, as well as to naturally-occurring amino acid polymers.

By "primer" is meant an oligonucleotide which, when paired with a strand of DNA, is capable of initiating the synthesis of a primer extension product in the presence of a suitable polymerising agent. The primer is preferably single-stranded for maximum efficiency in amplification but can alternatively be double-stranded. A primer must be sufficiently long to prime the synthesis of extension products in the presence of the polymerisation agent. The length of the primer depends on many factors, including application, temperature to be employed, template reaction conditions, other reagents, and source of primers. For example, depending on the complexity of the target sequence, the oligonucleotide primer typically contains 15 to 35 or more nucleotide residues, although it can contain fewer nucleotide residues. Primers can be large polynucleotides, such as from about 200 nucleotide residues to several kilobases or more. Primers can be selected to be "substantially complementary" to the sequence on the template to which it is designed to hybridise and serve as a site for the initiation of synthesis. By "substantially complementary", it is meant that the primer is sufficiently complementary to hybridise with a target polynucleotide. Preferably, the primer contains no mismatches with the template to which it is designed to hybridise but this is not essential. For example, non- complementary nucleotide residues can be attached to the 5' end of the primer, with the remainder of the primer sequence being complementary to the template. Alternatively, non-complementary nucleotide residues or a stretch of non-complementary nucleotide residues can be interspersed into a primer, provided that the primer sequence has sufficient complementarity with the sequence of the template to hybridise therewith and thereby form a template for synthesis of the extension product of the primer. "Probe " refers to a molecule that binds to a specific sequence or sub-sequence or other moiety of another molecule. Unless otherwise indicated, the term "probe" typically refers to a polynucleotide probe that binds to another polynucleotide, often called the "target polynucleotide", through complementary base pairing. Probes can bind target polynucleotides lacking complete sequence complementarity with the probe, depending on the stringency of the hybridisation conditions. Probes can be labelled directly or indirectly.

By "recombinant polypeptide" is meant a polypeptide made using recombinant techniques, i.e. through the expression of a recombinant or synthetic polynucleotide. By "reporter molecule " as used in the present specification is meant a molecule that, by its chemical nature, provides an analytically identifiable signal that allows the detection of a complex comprising an antigen-binding molecule and its target antigen. The term "reporter molecule" also extends to use of cell agglutination or inhibition of agglutination such as red blood cells on latex beads, and the like.

Terms used to describe sequence relationships between two or more polynucleotides or polypeptides include "reference sequence", "comparison window", "sequence identity", "percentage of sequence identity" and "substantial identity". A "reference sequence" is at least 12 but frequently 15 to 18 and often at least 25 monomer units, inclusive of nucleotides and amino acid residues, in length. Because two polynucleotides may each comprise (1) a sequence (i.e. only a portion of the complete polynucleotide sequence) that is similar between the two polynucleotides, and (2) a sequence that is divergent between the two polynucleotides, sequence comparisons between two (or more) polynucleotides are typically performed by comparing sequences of the two polynucleotides over a "comparison window" to identify and compare local regions of sequence similarity. A "comparison window" refers to a conceptual segment of at least 50 contiguous positions, usually about 50 to about 100, more usually about 100 to about 150 in which a sequence is compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. The comparison window may comprise additions or deletions (i.e. gaps) of about 20% or less as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. Optimal alignment of sequences for aligning a comparison window may be conducted by computerised implementations of algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Drive Madison, WI, USA) or by inspection and the best alignment (i.e. resulting in the highest percentage homology over the comparison window) generated by any of the various methods selected. Reference also may be made to the BLAST family of programs as for example disclosed by Altschul et al, 1997, Nucl Acids Res. 25:3389. A detailed discussion of sequence analysis can be found in Unit 19.3 of Ausubel et al, "Current Protocols in Molecular Biology", Jolm Wiley & Sons Inc, 1994-1998, Chapter 15.

The term "sequence identity" as used herein refers to the extent that sequences are identical on a nucleotide-by-nucleotide basis or an amino acid-by-amino acid basis over a window of comparison. Thus, a "percentage of sequence identity" is calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g. A, T, C, G, I) or the identical amino acid residue (e.g. Ala, Pro, Ser, Thr, Gly, Val, Leu, lie, Phe, Tyr, Trp, Lys, Arg, His, Asp, Glu, Asn, Gin, Cys and Met) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e. the window size), and multiplying the result by 100 to yield the percentage of sequence identity. For the purposes of the present invention, "sequence identity" will be understood to mean the "match percentage" calculated by the DNASIS computer program (Version 2.5 for windows; available from Hitachi Software engineering Co., Ltd., South San Francisco, California, USA) using standard defaults as used in the reference manual accompanying the software.

"Stringency" as used herein, refers to the temperature and ionic strength conditions, and presence or absence of certain organic solvents, during hybridisation and washing procedures. The higher the stringency, the higher will be the degree of complementarity between immobilised target nucleotide sequences and the labelled probe polynucleotide sequences that remain hybridised to the target after washing.

"Stringent conditions" refers to temperature and ionic conditions under which only nucleotide sequences having a high frequency of complementary bases will hybridise. The stringency required is nucleotide sequence dependent and depends upon the various components present during hybridisation and subsequent washes, and the time allowed for these processes. Generally, in order to maximise the hybridisation rate, non-stringent hybridisation conditions are selected; about 20 to 25 °C lower than the thermal melting point (T_m). The T_m is the temperature at which 50% of specific target sequence hybridises to a perfectly complementary probe in solution at a defined ionic strength and pH. Generally, in order to require at least about 85% nucleotide complementarity of hybridised sequences, highly stringent washing conditions are selected to be about 5 to 15 °C lower than the T_m. In order to require at least about 70% nucleotide complementarity of hybridised sequences, moderately stringent washing conditions are selected to be about 15 to 30 °C lower than the T_m. Highly permissive (low stringency) washing conditions may be as low as 50 °C below the T_m, allowing a high level of mis-matching between hybridised sequences. Those skilled in the art will recognise that other physical and chemical parameters in the hybridisation and wash stages can also be altered to affect the outcome of a detectable hybridisation signal from a specific level of homology between target and probe sequences.

The term "variant" refers to polypeptides in which one or more amino acids have been replaced by different amino acids. It is well understood in the art that some amino acids may be changed to others with broadly similar properties without changing the nature of the activity of the polypeptide (conservative substitutions) as described hereinafter. Accordingly, polypeptide variants as used herein encompass polypeptides that have one or more, and preferably all, of the activities of the interferon, preferably interferon-α

By "vector" is meant a polynucleotide molecule, preferably a DNA molecule derived, for example, from a plasmid, bacteriophage, yeast or virus, into which a polynucleotide can be inserted or cloned. A vector preferably contains one or more unique restriction sites and can be capable of autonomous replication in a defined host cell including a target cell or tissue or a progenitor cell or tissue thereof, or be integrable with the genome of the defined host such that the cloned sequence is reproducible. Accordingly, the vector can be an autonomously replicating vector, i.e. a vector that exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g. a linear or closed circular plasmid, an extrachromosomal element, a mimchromosome, or an artificial chromosome. The vector can contain any means for assuring self-replication. Alternatively, the vector can be one which, when introduced into the host cell, is integrated into the genome and replicated together with the chromosome(s) into which it has been integrated. A vector system can comprise a single vector or plasmid, two or more vectors or plasmids, which together contain the total DNA to be introduced into the genome of the host cell, or a fransposon. The choice of the vector will typically depend on the compatibility of the vector with the host cell into which the vector is to be introduced. In the present case, the vector is preferably a viral or viral-derived vector, which is operably functional in animal and preferably mammalian cells. Such vector may be derived from a poxvirus, an adenovims or yeast. The vector can also include a selection marker such as an antibiotic resistance gene that can be used for selection of suitable transformants. Examples of such resistance genes are known to those of skill in the art and include the nptll gene that confers resistance to the antibiotics kanamycin and G418 (Geneticin®) and the hph gene which confers resistance to the antibiotic hygromycin B.

As used herein, underscoring or italicising the name of a gene shall indicate the gene, in contrast to its protein product, which is indicated in the absence of any underscoring or italicising. For example, "Apo-E" shall mean the Apo-E gene or transcript thereof, whereas "Apo E" shall indicate the protein product of the "Apo-E^'' gene.

2. Alleles linked to the development and/or progression of a neuropsychiatric disorder associated with the administration of an interferon The present invention is predicated in part on the discovery that certain alleles of the Apo-E gene are linked to the development and/or progression of neuropsychiatric disorders associated with interferon treatment. Thus, the invention contemplates a method for diagnosis in a patient of a predisposition to develop and/or progress a neuropsychiatric disorder associated with the administration of an interferon to the patient, comprising detecting in a biological sample obtained from the patient an allele of Apo-E, or an expression product thereof, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E. Preferably, the interferon is interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these. In one embodiment, the amino acid comprises an electropositive side chain. In this instance, the amino acid includes, but is not restricted to, histidine, lysine and arginine. In a preferred embodiment of this type, the amino acid is arginine. In this instance, the allele is the e4 allele of Apo-E. In a preferred embodiment of this type, the e4 allele comprises, for example, the sequence set forth in SEQ ID NO: 1, which encodes the Apo-E polypeptide comprising the sequence set forth in SEQ ID NO: 2. This sequence has been found to be associated with an increased risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon.

It will be understood that the invention contemplates detection of any allele as broadly described above or expression product thereof, which is associated with a risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon. Such alleles may be obtained from individuals affected with that disorder.

Nucleic acid isolation protocols are well known to those of skill in the art. For example, an isolated polynucleotide corresponding to gene or allele as broadly described above may be prepared according to the following procedure:

(a) creating primers which flank an allele as broadly described or transcript thereof, above, or a portion of said allele or transcript; (b) obtaining a nucleic acid extract from an individual affected with a disease or condition requiring interferon treatment; and

(c) using said primers to amplify, via nucleic acid amplification techniques, at least one amplification product from said nucleic acid extract, wherein said amplification product corresponds to allele or transcript linked to the development of said condition.

Suitable nucleic acid amplification techniques are well known to the skilled artisan, and include polymerase chain reaction (PCR) as for example described in Ausubel et al. (supra); strand displacement amplification (SDA) as for example described in U.S. Patent No 5,422,252; rolling circle replication (RCR) as for example described in Liu et al, (1996, J Am. Chem. Soc. 118:1587-1594 and International application WO 92/01813) and Lizardi et al, (International Application WO 97/19193); nucleic acid sequence-based amplification (NASBA) as for example described by Sooknanan et al, (1994, Biotechniques 17:1077-1080); and Q- 3 replicase amplification as for example described by Tyagi et al, (1996, Proc. Natl. Acad. Sci. USA 93: 5395-5400). The invention also encompasses a method for determining a patient's risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon. For example, a patient may be diagnosed as having a higher risk of developing and/or progressing said disorder by detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E. hi an alternate embodiment, a higher risk of developing and/or progressing said disorder is diagnosed by detecting in said biological sample at least two alleles of Apo-E, or expression products thereof, wherein each of said alleles encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E. In a preferred embodiment of this type, a higher risk of developing and/or progressing said disorder is diagnosed by detecting in said biological sample a pair of alleles of Apo-E, or expression products thereof, wherein each of said alleles encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E. Thus, in this embodiment, said higher risk is suggested by detecting the presence of said alleles in a homozygous state.

A patient may be diagnosed as having a lower risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than an amino acid comprising an electropositive side chain at codon 112 relative to the full-length open reading frame of Apo-E. In one embodiment, the allele encodes an amino acid other than arginine at said codon 112. hi a preferred embodiment, the allele encodes a cysteine at said codon 112. In an especially preferred embodiment of this type, said allele is selected from the el allele or the e3 allele of Apo-E. In a one embodiment, the el allele comprises, for example, the sequence set forth in SEQ ID NO: 5, which encodes a polypeptide comprising the sequence set forth in SEQ ID NO: 6. In another embodiment, the e3 allele comprises, for example, the sequence set forth in SEQ ID NO: 3, which encodes a polypeptide comprising the sequence set forth in SEQ ID NO: 4. hi another embodiment, a lower risk of developing and/or progressing said disorder is diagnosed by detecting in said biological sample at least two alleles of Apo-E, or expression products thereof, wherein each of said alleles encodes an amino acid other than an amino acid comprising an electropositive side chain at codon 112 relative to the full-length open reading frame of Apo-E. In a preferred embodiment of this type, a lower risk of developing and/or progressing said disorder is diagnosed by detecting in said biological sample a pair of alleles of Apo-E, or expression products thereof, wherein each of said alleles encodes an amino acid other than an amino acid comprising an electropositive side chain at said codon 112. Thus, in this embodiment, said lower risk is suggested by detecting the presence of said alleles in a homozygous state.

A patient may be diagnosed as having an intermediate risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient different alleles of Apo-E, or expression products thereof, wherein at least one of said alleles encodes cysteine at codon 112 relative to the full-length open reading frame of Apo- E and at least one other of said alleles encodes an amino acid comprising an electropositive side chain at codon 112 relative to the full-length open reading frame of Apo-E. In a preferred embodiment, the method comprises detecting at least one e4 allele of Apo-E and at least one allele selected from the group consisting of the el allele and the e3 allele of Apo-E. In an especially preferred embodiment, the method comprises detecting a single e4 allele of Apo-E and a single allele selected from the el allele and the e3 allele of Apo-E. Accordingly, detection of a pair of such alleles would suggest that the patient has an intermediate risk.

The neuropsychiatric disorder includes, but is not restricted to, a mood disorder

(e.g., depression, anxiety, irritability, manic symptoms, suicidal behaviour) or a cognition dysfunction (e.g., reduced or abrogated concentration, decreased attention span, impaired short term memory, indecisiveness, confusion, delirium, vacant staring mid-sentence, prolonged silence and progression to a demented state).

Suitably, the administration of said interferon, preferably interferon-α, is used for treating or preventing a disease or condition selected from a pathogenic infection, an autoimmune disease and a cancer. The pathogenic infection is suitably a viral, bacterial or parasitic infection. Viral infections contemplated by the present invention include, but are not restricted to, infections caused by human immunodeficiency virus (HIV), hepatitis virus, influenza virus, Japanese encephalitis virus, Epstein-Barr virus and respiratory syncytial virus. In a preferred embodiment, the viral infections are caused by hepatitis B virus, hepatitis C virus, hepatitis D virus and papilloma virus. Accordingly, suitable interferon, preferably interferon-α, treatable conditions include, but are not limited to, herpetic keratitis and papillomas.

Bacterial infections include, but are not restricted to, those caused by Neisseria species, Meningococcal species, Haemophilus species Salmonella species, Streptococcal species, Legionella species and Mycobacterium species. Parasitic infections encompassed by the invention include, but are not restricted to, those caused by Plasmodium species, Schistosoma species, Leishmania species, Trypanosoma species, Toxoplasma species and Giardia species.

The autoimmune disease includes, but is not restricted to, multiple sclerosis, myasthenia gravis, atopic dermatitis, chronic granulomatous disease, psoriasis and ankylosing spondylitis. In a preferred embodiment, the interferon, especially interferon-α, treatable autoimmune disease is selected from multiple sclerosis and chronic granulomatous disease.

The cancer includes, but is not restricted to, melanoma, lung cancer, breast cancer, cervical cancer, prostate cancer, colon cancer, pancreatic cancer, stomach cancer, bladder cancer, kidney cancer, liver cancer, PTLD, Hodgkin's Lymphoma. Preferred interferon, particularly interferon-α, treatable cancers include hairy cell leukemia, chronic myelogenous leukemia, myeloma, renal cell carcinoma, Kaposi's sarcoma and melanoma. In an especially preferred embodiment, the administration of said interferon, preferably interferon-α, is used for treating or preventing hepatitis C virus infection, more preferably chronic hepatitis C virus infection.

3. Vectors The invention also envisions a vector comprising a polynucleotide corresponding to an allele of the invention, or part thereof. Such a vector may be utilised as a control for nucleic acid detection techniques as described hereinafter, or as a means to produce an expression product, including a polypeptide, from said polynucleotide. A polynucleotide can be rendered expressible in a host cell by operably linking the polynucleotide with a regulatory polynucleotide. The synthetic construct or vector thus produced may be introduced firstly into an organism or part thereof before subsequent expression of the construct in a particular cell or tissue type. Any suitable organism is contemplated by the invention, which may include unicellular as well as multi-cellular organisms. Suitable unicellular organisms include bacteria. Exemplary multi-cellular organisms include yeast, mammals and plants.

The construction of the vector may be effected by any suitable technique as for example described in the relevant sections of Ausubel et al. (supra) and Sambrook et al (supra). However, it should be noted that the present invention is not dependent on and not directed to any one particular technique for constructing the vector. Regulatory polynucleotides which may be utilised to regulate expression of the polynucleotide include, but are not limited to, a promoter, an enhancer, and a transcriptional terminator. Such regulatory sequences are well known to those of skill in the art. Suitable promoters that may be utilised to induce expression of the polynucleotides of the invention include constitutive promoters and inducible promoters.

4. Antigen-binding molecules

The invention also contemplates antigen-binding molecules that bind specifically to a polypeptide encoded by an allele linked to a neuropsychiatric disorder associated with interferon administration, or that bind specifically to a fragment of said polypeptide. For example, the antigen-binding molecules may comprise whole polyclonal antibodies. Such antibodies may be prepared, for example, by injecting a polypeptide of the invention or fragment thereof into a production species, which may include mice or rabbits, to obtain polyclonal antisera. Methods of producing polyclonal antibodies are well known to those skilled in the art. Exemplary protocols which may be used are described for example in Coligan et al, CURRENT PROTOCOLS IN IMMUNOLOGY, (John Wiley & Sons, Inc, 1991), and Ausubel et al, (1994-1998, supra), in particular Section III of Chapter 11.

In lieu of the polyclonal antisera obtained in the production species, monoclonal antibodies may be produced using the standard method as described, for example, by Kδhler and Milstein (1975, Nature 256, 495-497), or by more recent modifications thereof as described, for example, in Coligan et al, (1991, supra) by immortalising spleen or other antibody producing cells derived from a production species which has been inoculated with a polypeptide of the invention or a fragment thereof. The invention also contemplates as antigen-binding molecules Fv, Fab, Fab' and

F(ab')₂ immunoglobulin fragments. Alternatively, the antigen-binding molecule may comprise a synthetic stabilised Fv fragment. Exemplary fragments of this type include single chain Fv fragments (sFv, frequently termed scFv) in which a peptide linker is used to bridge the N terminus or C terminus of a V_# domain with the C terminus or N-terminus, respectively, of a V_L domain. ScFv lack all constant parts of whole antibodies and are not able to activate complement. Suitable peptide linkers for joining the V_# and domains are those which allow the V_# and V_L domains to fold into a single polypeptide chain having an antigen binding site with a three dimensional structure similar to that of the antigen binding site of a whole antibody from which the Fv fragment is derived. Linkers having the desired properties may be obtained by the method disclosed in U.S. Patent No 4,946,778. However, in some cases a linker is absent. ScFvs may be prepared, for example, in accordance with methods outlined in Kreber et al (Kreber et al. 1997, J. Immunol. Methods; 201(1): 35-55). Alternatively, they may be prepared by methods described in U.S. Patent No 5,091,513, European Patent No 239,400 or the articles by Winter and Milstein (1991, Nature 349:293) and Plϋnckthun et al (1996, In Antibody engineering: A practical approach. 203-252).

Alternatively, the synthetic stabilised Fv fragment comprises a disulphide stabilised Fv (dsFv) in which cysteine residues are introduced into the V_# and _L domains such that in the fully folded Fv molecule the two residues will form a disulphide bond therebetween. Suitable methods of producing dsFv are described for example in (Glockscuther et al. Biochem. 29: 1363-1367; Reiter et al. 1994, J. Biol. Chem. 269: 18327-18331; Reiter et al. 1994, Biochem. 33: 5451-5459; Reiter et al. 1994. Cancer Res. 54: 2714-2718; Webber et al. 1995, Mol. Immunol. 32: 249-258). Also contemplated as antigen-binding molecules are single variable region domains (termed dAbs) as for example disclosed in (Ward et al. 1989, Nature 341: 544- 546; Hamers-Casterman et al. 1993, Nature. 363: 446-448; Davies & Riechmann, 1994, FEBSLett. 339: 285-290). Alternatively, the antigen-binding molecule may comprise a "minibody". In this regard, minibodies are small versions of whole antibodies, which encode in a single chain the essential elements of a whole antibody. Suitably, the minibody is comprised of the V_H and _L domains of a native antibody fused to the hinge region and CH3 domain of the immunoglobulin molecule as, for example, disclosed in U.S. Patent No 5,837,821. In an alternate embodiment, the antigen binding molecule may comprise non- immunoglobulin derived, protein frameworks. For example, reference may be made to (Ku & Schultz, 1995, Proc. Natl. Acad. Sci. USA, 92: 652-6556) which discloses a four-helix bundle protein cytochrome b562 having two loops randomised to create complementarity determining regions (CDRs), which have been selected for antigen binding. The antigen-binding molecule may be multivalent (i.e., having more than one antigen-binding site). Such multivalent molecules may be specific for one or more antigens. Multivalent molecules of this type may be prepared by dimerisation of two antibody fragments through a cysteinyl-containing peptide as, for example disclosed by (Adams et al, 1993, Cancer Res. 53: 4026-4034; Cumber et al, 1992, J Immunol. 149: 120-126). Alternatively, dimerisation may be facilitated by fusion of the antibody fragments to amphiphilic helices that naturally dimerise (Pack P. Plϋnckthun, 1992, Biochem. 31: 1579-1584), or by use of domains (such as the leucine zippers jun and fos) that preferentially heterodimerise (Kostelny et al, 1992, J Immunol. 148: 1547-1553). In an alternate embodiment, the multivalent molecule may comprise a multivalent single chain antibody (multi-scFv) comprising at least two scFvs linked together by a peptide linker, hi this regard, non-covalently or covalently linked scFv dimers termed "diabodies" may be used. Multi-scFvs may be bispecific or greater depending on the number of scFvs employed having different antigen binding specificities. Multi-scFvs may be prepared for example by methods disclosed in U.S. Patent No. 5,892,020. The antigen-binding molecules of the invention may be used for affinity chromatography in isolating a natural or recombinant polypeptide or biologically active fragment of the invention. For example reference may be made to immunoaffinity chromatographic procedures described in Chapter 9.5 of Coligan et al, (1995-1997, supra).

The antigen-binding molecules can be used to screen expression libraries for variant mutant polypeptides of the invention as described herein. They can also be used to detect polypeptide mutants, polypeptide mutant fragments, variants and derivatives of the invention as described hereinafter.

5. Methods of detecting modulation of the level of an expression product of a gene or allele linked to afibrotic condition

5.1 Detection of specific polypeptides encoded by an allele linked to a neuropsychiatric disorder associated with interferon treatment

It is to be understood that although the following discussion is specifically directed to human patients, the teachings are also applicable to any animal that expresses a polypeptide encoded by an allele or transcript thereof in accordance with the present invention, such that clinical manifestations such as those seen in patients with a neuropsychiatric disorder associated with interferon treatment are found. It will be appreciated that the methods described herein are applicable to any patient suspected of developing, or having, said disorder, whether such disorder is manifest at a young age or at a more advanced age in a patient's life.

The diagnostic and screening methods of the invention are especially useful for a patient suspected of being at risk of developing said disorder based on family history, or a patient in which it is desired to diagnose or eliminate the presence of that disorder as a causative agent underlying a patient's symptoms.

Screening or diagnosis of predisposition to develop or progress a neuropsychiatric disorder associated with interferon treatment in a patient is now possible by detecting a polypeptide linked to that condition. For example, the presence or absence of a polypeptide linked to a said condition in a patient may determined by isolating a biological sample from a patient, contacting the sample with an antigen-binding molecule as described in Section 4 and detecting the presence of a complex comprising the said antigen-binding molecule and the said polypeptide in said contacted sample. Any suitable technique for determining formation of the complex may be used.

For example, an antigen-binding molecule according to the invention, having a reporter molecule associated therewith may be utilised in immunoassays. Such immunoassays include, but are not limited to, radioimmunoassays (RIAs), enzyme-linked immunosorbent assays (ELISAs) and immunochromatographic techniques (ICTs), Western blotting which are well known those of skill in the art. For example, reference may be made to "CURRENT PROTOCOLS IN IMMUNOLOGY" (1994, supra) which discloses a variety of immunoassays that may be used in accordance with the present invention. Immunoassays may include competitive assays as understood in the art or as for example described infra. It will be understood that the present invention encompasses qualitative and quantitative immunoassays.

Suitable immunoassay techniques are described for example in US Patent Nos. 4,016,043, 4, 424,279 and 4,018,653. These include both single-site and two-site assays of the non-competitive types, as well as the traditional competitive binding assays. These assays also include direct binding of a labelled antigen-binding molecule to a target antigen.

Two site assays are particularly favoured for use in the present invention. A number of variations of these assays exist, all of which are intended to be encompassed by the present invention. Briefly, in a typical forward assay, an unlabelled antigen-binding molecule such as an unlabelled antibody is immobilised on a solid substrate and the sample to be tested brought into contact with the bound molecule. After a suitable period of incubation, for a period of time sufficient to allow formation of an antibody-antigen complex, another antigen-binding molecule, suitably a second antibody specific to the antigen, labelled with a reporter molecule capable of producing a detectable signal is then added and incubated, allowing time sufficient for the formation of another complex of antibody-antigen-labelled antibody. Any unreacted material is washed away and the presence of the antigen is determined by observation of a signal produced by the reporter molecule. The results may be either qualitative, by simple observation of the visible signal, or may be quantitated by comparing with a control sample containing known amounts of antigen. Variations on the forward assay include a simultaneous assay, in which both sample and labelled antibody are added simultaneously to the bound antibody. These techniques are well known to those skilled in the art, including minor variations as will be readily apparent. In accordance with the present invention, the sample is one that might contain an antigen including tissue biopsies, serum, whole blood, plasma or lymph fluid.

In the typical forward assay, a first antibody having specificity for the antigen or antigenic parts thereof is either covalently or passively bound to a solid surface. The solid surface is typically glass or a polymer, the most commonly used polymers being cellulose, polyacrylamide, nylon, polystyrene, polyvinyl chloride or polypropylene. The solid supports may be in the form of tubes, beads, discs of microplates, or any other surface suitable for conducting an immunoassay. The binding processes are well known in the art and generally consist of cross-linking covalently binding or physically adsorbing, the polymer-antibody complex is washed in preparation for the test sample. An aliquot of the sample to be tested is then added to the solid phase complex and incubated for a period of time sufficient and under suitable conditions to allow binding of any antigen present to the antibody. Following the incubation period, the antigen-antibody complex is washed and dried and incubated with a second antibody specific for a portion of the antigen. The second antibody has generally a reporter molecule associated therewith that is used to indicate the binding of the second antibody to the antigen. The amount of labelled antibody that binds, as determined by the associated reporter molecule, is proportional to the amount of antigen bound to the immobilised first antibody. An alternative assay involves immobilising the antigen in the biological sample and then exposing the immobilised antigen to specific antibody that may or may not be labelled with a reporter molecule. Depending on the amount of target and the strength of the reporter molecule signal, a bound antigen may be detectable by direct labelling with the antibody. Alternatively, a second labelled antibody, specific to the first antibody is exposed to the target-first antibody complex to form a target-first antibody-second antibody tertiary complex. The complex is detected by the signal emitted by the reporter molecule.

From the foregoing, it will be appreciated that the reporter molecule associated with the antigen-binding molecule may include the following:

(a) direct attachment of the reporter molecule to the antigen-binding molecule; (b) indirect attachment of the reporter molecule to the antigen-binding molecule; i.e., attachment of the reporter molecule to another assay reagent which subsequently binds to the antigen-binding molecule; and

(c) attachment to a subsequent reaction product of the antigen-binding molecule.

The reporter molecule may be selected from a group including a chromogen, a catalyst, an enzyme, a fluorochrome, a chemiluminescent molecule, a lanthanide ion such ^' as Europium (Eu³⁴), a radioisotope and a direct visual label. In the case of a direct visual label, use may be made of a colloidal metallic or non- metallic particle, a dye particle, an enzyme or a substrate, an organic polymer, a latex particle, a liposome, or other vesicle containing a signal producing substance and the like.

A large number of enzymes suitable for use as reporter molecules is disclosed in United States Patent Specifications U.S. 4,366,241, U.S. 4,843,000, and U.S. 4,849,338. Suitable enzymes useful in the present invention include alkaline phosphatase, horseradish peroxidase, luciferase, /3-galactosidase, glucose oxidase, lysozyme, malate dehydrogenase and the like. The enzymes may be used alone or in combination with a second enzyme that is in solution. Suitable fluorochromes include, but are not limited to, fluorescein isothiocyanate

(FITC), tetramethyhhodamine isothiocyanate (TRITC), R-Phycoerythrin (RPE), and Texas Red. Other exemplary fluorochromes include those discussed by Dower et al. (International Publication WO 93/06121). Reference also may be made to the fluorochromes described in U.S. Patents 5,573,909 (Singer et al), 5,326,692 (Brinkley et al). Alternatively, reference may be made to the fluorochromes described in U.S. Patent Nos. 5,227,487, 5,274,113, 5,405,975, 5,433,896, 5,442,045, 5,451,663, 5,453,517, 5,459,276, 5,516,864, 5,648,270 and 5,723,218. hi the case of an enzyme immunoassay, an enzyme is conjugated to the second antibody, generally by means of glutaraldehyde or periodate. As will be readily recognised, however, a wide variety of different conjugation techniques exist which are readily available to the skilled artisan. The substrates to be used with the specific enzymes are generally chosen for the production of, upon hydrolysis by the corresponding enzyme, a detectable colour change. Examples of suitable enzymes include those described supra. It is also possible to employ fluorogenic substrates, which yield a fluorescent product rather than the chromogenic substrates noted above, hi all cases, the enzyme-labelled antibody is added to the first antibody-antigen complex. It is then allowed to bind, and excess reagent is washed away. A solution containing the appropriate substrate is then added to the complex of antibody-antigen-antibody. The substrate will react with the enzyme linked to the second antibody, giving a qualitative visual signal, which may be further quantitated, usually specfrophotometrically, to give an indication of the amount of antigen which was present in the sample.

Alternately, fluorescent compounds, such as fluorescein, rhodamine and the lanthanide, europium (EU), may be chemically coupled to antibodies without altering their binding capacity. When activated by illumination with light of a particular wavelength, the fluorochrome-labelled antibody adsorbs the light energy, inducing a state to excitability in the molecule, followed by emission of the light at a characteristic colour visually detectable with a light microscope. The fluorescent-labelled antibody is allowed to bind to the first antibody-antigen complex. After washing off the unbound reagent, the remaining tertiary complex is then exposed to light of an appropriate wavelength. The fluorescence observed indicates the presence of the antigen of interest. Immunofluorometric assays (JJFMA) are well established in the art. However, other reporter molecules, such as radioisotope, chemiluminescent or bioluminescent molecules may also be employed.

5.2 Screening for polynucleotide corresponding to an allele linked to a neuropsychiatric disorder associated with interferon treatment

In another embodiment, the invention provides a method of screening a patient for a polynucleotide linked to a neuropsychiatric disorder associated with interferon treatment, comprising providing a biological sample from the patient, and detecting said polynucleotide by a suitable nucleic acid detection technique.

According to the invention, presymptomatic screening of a patient for their likelihood of developing said disorder is now possible by detecting an allele as broadly described above linked to that disorder. The screening method of the invention allows a presymptomatic diagnosis, including prenatal diagnosis, for the presence of an allele or transcript thereof in such a patient and thus the basis for an opinion concerning the likelihood that such patient would develop or has developed said disorder or symptoms associated therewith.

For example, in the method of screening, a tissue sample can be taken from a patient, and screened for the presence of one or more alleles associated with a low risk or a high risk of developing a neuropsychiatric disorder associated with interferon treatment. Such genes or alleles can be characterised based upon, for example, detection of restriction digestion patterns in 'normal' versus the patient's DNA, including Restriction Fragment Length Polymorphism (RFLP) analysis, using nucleic acid probes prepared against those gene or alleles (or fragments thereof). Similarly, mRNA may be characterised and compared to a reference mRNA level and/or size as found in human population not at risk of developing said disorder using similar probes. Alternatively, a nucleic acid extract from the patient may be utilised in concert with oligonucleotide primers corresponding to sense and antisense sequences of a polynucleotide sequence under test, or flanking sequences thereof, in a nucleic acid amplification reaction such as PCR, or the ligase chain reaction (LCR) as for example described in International Application WO89/09385. A variety of automated solid-phase detection techniques are also appropriate. For example, very large scale immobilised primer arrays (VLSIPS™) are used for the detection of nucleic acids as for example described by Fodor et al, (1991, Science 251:767-777) and Kazal et al, (1996, Nature Medicine 2:753-759). The above generic techniques are well known to persons skilled in the art. Preferably, at least one of said primers is an allele-specific primer specific for the polynucleotide under test. Alternatively, the presence or absence of a restriction endonuclease cleavage site resulting from a mutation in a gene of the present invention may be taken advantage by subjecting a polynucleotide corresponding thereto to digestion with the restriction endonuclease. Accordingly, the present invention encompasses detecting an allele as described herein by RFLP analysis.

Alternatively, the nucleic acid polymorphism in a gene linked to a neuropsychiatric disorder associated with interferon treatment may be detected using first- nucleotide change technology described by Dale et al. in U.S. Pat. No. 5,856,092.

The presence in the biological sample of a size pattern (e.g., generated by RFLP), and or mRNA sizes or levels and/or a gene or allele linked to a fibrotic condition would indicate that the patient has developed or is at risk of developing a symptom associated with said disorder.

Prenatal diagnosis can be performed when desired, using any known method to obtain foetal cells, including amniocentesis, chorionic villous sampling (CVS), and foetoscopy. Prenatal chromosome analysis can be used to determine if the portion of the respective chromosomes possessing one or more gene or alleles described herein are, present in a heterozygous state.

6. Detection kits

The present invention also provides kits for the detection in a biological sample of an allele linked to a neuropsychiatric disorder associated with interferon treatment, or a polypeptide encoded by said allele. These will contain one or more particular agents described above depending upon the nature of the test method employed. In this regard, the kits may include one or more of a polypeptide, antigen-binding molecule and polynucleotide according to the invention. The kits may also optionally include appropriate reagents for detection of labels, positive and negative controls, washing solutions, dilution buffers and the like. For example, a nucleic acid-based detection kit may include (i) a polynucleotide according to the invention (which may be used as a positive control), (ii) an oligonucleotide primer according to the invention, and optionally a DNA polymerase, DNA ligase etc depending on the nucleic acid amplification technique employed.

In order that the invention may be readily understood and put into practical effect, particular preferred embodiments will now be described by way of the following non- limiting examples.

EXAMPLE

Methods

Patients

One hundred and seventy three patients with chronic HCV commenced antiviral treatment with IFN-α at the Princess Alexandra Hospital, Brisbane, Australia between February 1995 and August 2000. Genomic DNA was available for 110 patients and this group comprised the study population. Informed consent was obtained from each patient and the Princess Alexandra Hospital Research Ethics Committee approved the study protocol. Diagnosis of chronic HCV was based on standard serological assays and abnormal serum aminofransferase levels (greater than or equal to 1.5x upper limit of normal) for at least 6 months. All patients were positive for HCV antibody by the second generation ELISA (Abbott Labs, North Chicago, IL, USA) with infection confirmed by detection of circulating HCV RNA by polymerase chain reaction using the Amplicor HCV assay (Roche, New Jersey, USA) and were negative for HBsAg or antibodies to human immunodeficiency virus. Viral genotyping was performed using the Inno-Lipa HCV II assay (frrnogenetics, Zwijnaarde, Belgium). Patients with chronic liver diseases due to other causes were excluded from the analysis.

Details about average alcohol intake (g/day) during the 12 months preceding antiviral therapy were obtained from all patients (current alcohol intake). Information regarding average alcohol intake (g/day) before the last 12 months (past alcohol intake) and source of HCV infection were obtained at initial assessment. Alcohol consumption during antiviral treatment was assessed by interview and recorded at each patient encounter. The alcohol intake over a weekly period was averaged and recorded in grams per day. Liver biopsies were performed before treatment with antiviral therapy. Specimens were fixed in buffered formalin, embedded in paraffin and the degree of inflammation and fibrosis was assessed and graded according to the method of Scheuer.¹³

Antiviral treatment

Patients received treatment with TFN-α at a dose of 3 million units, 3 times weekly or an elevated induction dose of 3 - 10 million units, daily for the first month of treatment, followed by 3 or 5 million units, 3 times weekly. Differences in induction doses were due to ongoing clinical trials performed during the study period to test response to increased IFN-α. Patients were seen weekly for the first month and monthly thereafter. Patients were classified as IFN-α "non-responders" if they had recurrent viremia and elevated LFTs after 12 weeks of therapy. IFN-α "responders" had normal serum ALT levels and loss of HCV RNA after 12 weeks of therapy. For statistical purposes IFN-α "responders" were not subdivided into "sustained responders" or "relapsers" due to the small numbers within each category. Patients were seen in the Hepatitis Management Clinic by the Hepatitis Nurse Manager (CS) and one of three hepatologists at each visit. All patients were followed serially during therapy by the same clinician.

Psychological data collection

All data were abstracted from patients' medical records by an independent observer, blinded to patients' clinical details and Apo-E genotypes. Psychiatric history, psychotropic medications and contributing medical conditions, both prior to and after commencing treatment, were noted starting with the initial referral for assessment of hepatitis and ending with most current visit. Patient-reported psychological and somatic symptoms of depression, irritability and other mood symptoms that occurred after commencement of IFN-α treatment were noted along with the date of occurrence (Table 1). Continuing ethanol or illicit drug use, ongoing distress and work or family related difficulties were detailed. Only symptoms that occurred for the first time or increased in severity after initiation of antiviral therapy, but within 6 months of its cessation, were considered interferon-induced and included in the analysis. Psychiatric referral during antiviral treatment was initiated by the hepatologist if the neuropsychiatric side effects required treatment in their own right, or were impacting on the patient's ability to complete antiviral therapy. Neither the clinicians nor patients were aware of Apo-E genotypes during treatment or subsequent follow-up.

Polymorphism genotyping Genomic DNA was extracted from peripheral blood mononuclear cells using the

DNAzol Reagent (Life Technologies, Melbourne, Australia). Genomic Apo-E sequences were amplified by polymerase chain reaction using a MJ Research PTC- 100 Thermal Cycler, Qiagen HotStar Taq polymerase (Qiagen Pty Ltd, Clifton Hill, Australia) and the oligonucleotide primers, 5'-TCCAAGGAGCTGCAGGCGGCGCA-3' and 5'- ACAGAATTCGCCCCGGCCTGGTACACTGCCA-3' as described by Wenham et al.^u Once amplification was complete, 4U of endonuclease cfoϊ (Roche Molecular Biochemicals, Castle Hill, Australia) was added to each reaction mixture followed by incubation for 3 hours at 37° C.¹⁵ The resulting restriction fragments were resolved by electrophoresis using a 15% non-denaturing polyacrylamide gel. The DNA was stained with ethidium bromide prior to UV visualisation and photography.

Statistical Analysis The prevalence of neuropsychiatric symptoms, and of subjects with certain neuropsychiatric outcomes, was compared between patient groups using chi-square tests. The degree of association between various patient characteristics and neuropsychiatric outcomes was measured using the odds ratio, along with a 95% confidence interval. Mean age of patients and time on IFN-α (which were both approximately normally distributed) were compared between groups using a Student's t-test. Multiple logistic regression analysis was used to calculate odds ratios (and 95% confidence intervals) between patient characteristics and neuropsychiatric outcomes, after adjustment for potential confounding factors. A significance level of p<0.05 was used for all analyses.

As follow-up was limited for some patients, a survival analysis was conducted to compare the time to a treatment related neuropsychiatric event (defined as a neuropsychiatric symptom score of 5 or more, psychiatric referral during treatment, or cessation of IFN-α treatment due to neuropsychiatric side-effects) between Apo-E allele patient groups. A Cox's Proportional Hazards Model approach was used to obtain adjusted survival curves for each group. The characteristics of the patients with and without treatment-related neuropsychiatric events were compared, and any variables on which differences were found, and could thus be considered as potential confounders (as well as age and sex), were adjusted for in the Cox regression analysis.

Results

Characteristics of the patients studied The age of the patients (68.2% male) ranged from 22 to 64 yrs, with a mean age of 39.2 yrs (SD 6.85). The source of hepatitis was previous intravenous drug use (IVDU) in 63 (57.3%), post transfusion in 13 (11.8%) and other risk factors or unknown in 34 (30.9%). Alcohol intake in the past and in the 12 months preceding antiviral treatment ranged from none to very heavy (>360 g/day). No patients were identified as using intravenous drugs during antiviral therapy. Two patients were drinking >10 g alcohol/day during antiviral therapy and three patients were smoking marijuana on a daily or weekly basis. The stage of liver fibrosis was 0 in 16, 1 in 44, 2 in 25, 3 in 12, 4 in 9 and unavailable in 4. No patients had decompensated liver disease.

Antiviral treatment

The majority of patients (75.5%) received IFN-α at a dose of 3 million units 3 times weekly. The remaining patients (24.5 %) received a higher dose of interferon (3, 5 or 10 million units daily) for the first month of treatment. The mean duration of treatment was 35.4 weeks (range 4 to 104).

Sixty-one patients completed antiviral treatment and at least 6 months of follow- up. Forty-five patients remained on treatment or had not completed 6 months follow-up. Four patients stopped antiviral treatment prematurely due to side-effects (3 due to neuropsychiatric side-effects). Forty-six patients (43%) were non-responders.

Neuropsychiatric symptoms

Psychiatric history prior to antiviral therapy

Twenty-four patients (21.8 %) had a history of prior psychiatric disorders and/or prior referral to a psychiatrist. All pre-treatment psychiatric referrals indicated no contraindication to interferon treatment. A history of prior antidepressant use was noted in 1 (6.4 %) patients.

Interferon-induced neuropsychiatric symptoms

Individual neuropsychiatric symptoms occurring during TFN-α therapy and the number of patients in which they occurred are listed in Table 1. Symptoms were not grouped into specific syndromes (i.e. major depression, cognitive disorder) as this may be artificial and potentially misleading. Instead, the incidence of neuropsychiatric events experienced by each patient during treatment was summated to provide a "neuropsychiatric symptom score". The relationship between clinical variables and the neuropsychiatric symptom score is detailed in Table 2. A score of > 5 was significantly associated with psychiatric referral during antiviral therapy (p < 0.0001). Twelve of 14 patients with a neuropsychiatric symptom score of > 5 required a psychiatric referral compared with only 6 of 96 with a neuropsychiatric symptom score of < 5.

There was no significant relationship between the neuropsychiatric symptom score and mode of acquisition of HCV, alcohol consumption, response to freatment or prior psychiatric history. There was no difference between treating clinicians and the number of patients referred to a psychiatrist or the mean number of neuropsychiatric events experienced among patients (data not shown).

Apolipoprotein E genotypes in patients with chronic HCV

The frequencies of the Apo-E genotypes in this patient cohort are summarised in Table 3. The genotype frequencies are similar to previously published studies. There was no significant association between number or proportion of patients with specific Apo-E alleles and treating hepatologist.

A statistically significant association was seen between the Apo-E alleles and TFN-α induced neuropsychiatric symptoms. Patients with an ε4 allele were more likely to be referred to a psychiatrist during IFN-α treatment than those without an ε4 allele (p=0.004) (Table 4). A statistically significant difference between Apo-E genotypes was seen with a neuropsychiatric symptom score of > 4 (p=0.010), with the greatest significance observed with a neuropsychiatric symptom score of > 5 (p=0.002) (Table 4). The specific neuropsychiatric symptoms significantly associated with the Apo-E ε4 allele were anger, irritability or short temper (p=0.0002) and anxiety, emotional lability or other non-depressive mood symptoms (p=0.0004). No association was found between Apo-E ε4 and a previous history of psychiatric disorders or psychiatric referral prior to treatment, though a positive association was observed.

A Cox's regression analysis was conducted to compare time till neuropsychiatric symptoms, psychiatric referral or cessation of antiviral therapy due to side effects between individuals with and without an Apo-E ε4 allele (Figure 1). This analysis shows that patients with an Apo-E ε4 allele are more likely to experience a neuropsychiatric event sooner than those patients without an Apo-E ε4 allele (p=0.008). This trend was observed early, and was consistent throughout treatment. From the foregoing, it would be apparent that a highly significant association has been found between referral to a psychiatrist during IFN-α treatment, neuropsychiatric side-effects and common genetic variation in the Apo-E gene. Accordingly, knowledge of a patient's Apo-E genotype may have important therapeutic implications in the management of a disease or condition afflicting that patient, which is treatable or preventable by the administration of an interferon (e.g. , IFN-α). The disclosure of every patent, patent application, and publication cited herein is hereby incorporated herein by reference in its entirety.

The citation of any reference herein should not be construed as an admission that such reference is available as "Prior Art" to the instant application Throughout the specification the aim has been to describe the preferred embodiments of the invention without limiting the invention to any one embodiment or specific collection of features. Those of skill in the art will therefore appreciate that, in light of the instant disclosure, various modifications and changes can be made in the particular embodiments exemplified without departing from the scope of the present invention. All such modifications and changes are intended to be included within the scope of the appended claims.

TABLES

TABLE 1

Neuropsychiatric symptoms observed during treatment with interferon-

SUMMATED TO PROVIDE A "NEUROPSYCHIATRIC SYMPTOM SCORE"

TABLE 2

Relationship between clinical variables and neuropsychiatric score

¹ Reported for patients who have completed at least 3 months treatment

TABLE 3

Apolipoprotein E genotype frequencies in patients with HCV

TABLE 4

Association of apolipoprotein E ε4 with neuropsychiatric outcomes

¹ Odds ratios adjusted for age, sex, response to INF-α treatment, viral genotype, and prior psychiatric history BIBLIOGRAPHY

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Claims

1. A method for diagnosis in a patient of a predisposition to develop and/or progress a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E.

I. The method of claim 1, wherein said amino acid comprises an electropositive side chain.

3. The method of claim 1, wherein said amino acid is selected from the group consisting of histidine, lysine and arginine.

4. The method of claim 1, wherein said amino acid is arginine.

5. The method of claim 4, wherein said allele is the e4 allele of Apo-E.

6. The method of claim 1, wherein said interferon is interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these.

7. The method of claim 1, wherein said neuropsychiatric disorder is selected from a mood disorder or a cognition dysfunction.

8. The method of claim 7, wherein said mood disorder is selected from the group consisting of depression, anxiety, irritability, manic symptoms and suicidal behaviour.

9. The method of claim 7, wherein said cognition dysfunction is selected from the group consisting of reduced or abrogated concenfration, decreased attention span, impaired short term memory, indecisiveness, confusion, delirium, vacant staring mid-sentence, prolonged silence and progression to a demented state.

10. The method of claim 1, wherein the administration of said interferon is used for treating or preventing a disease or condition selected from the group consisting of a pathogenic infection, an autoimmune disease and a cancer.

II. The method of claim 10, wherein said pathogenic infection is a viral infection which is caused by a virus selected from the group consisting of HIV, hepatitis virus, influenza virus, Japanese encephalitis virus, Epstein-Barr virus and respiratory syncytial virus.

12. The method of claim 10, wherein said pathogenic infection is a viral infection which is caused by a virus selected from the group consisting hepatitis B virus, hepatitis C virus, hepatitis D virus and papilloma virus.

13. The method of claim 10, wherein said pathogenic infection is a bacterial infection which is caused by a bacterium selected from the group consisting of Neisseria species, Meningococcal species, Haemophilus species Salmonella species, Streptococcal species, Legionella species and Mycobacterium species.

14. The method of claim 10, wherein said pathogenic infection is a parasitic infection which is caused by a parasite selected from the group consisting of Plasmodium species, Schistosoma species, Leishmania species, Trypanosoma species, Toxoplasma species and Giardia species.

15. The method of claim 10, wherein said autoimmune disease is selected from the group consisting of multiple sclerosis, myasthenia gravis, atopic dermatitis, chronic granulomatous disease, psoriasis and ankylosing spondylitis.

16. The method of claim 10, wherein said autoimmune disease is selected from the group consisting of multiple sclerosis and chronic granulomatous disease.

17. The method of claim 10, wherein said cancer is selected from the group consisting of melanoma, lung cancer, breast cancer, cervical cancer, prostate cancer, colon cancer, pancreatic cancer, stomach cancer, bladder cancer, kidney cancer, liver cancer, hairy cell leukemia, chronic myelogenous leukemia, myeloma, PTLD, Hodgkin's Lymphomarenal cell carcinoma and Kaposi's sarcoma.

18. The method of claim 10, wherein said cancer is selected from the group consisting of hairy cell leukemia, chronic myelogenous leukemia, myeloma, renal cell carcinoma, Kaposi's sarcoma and melanoma.

19. The method of claim 10, wherein said condition is selected from herpetic keratitis or papillomas.

20. The method of claim 1, wherein the said interferon is used for treating or preventing hepatitis C virus infection.

21. The method of claim 1, wherein the said interferon is used for treating or preventing chronic hepatitis C virus infection.

22. A method for diagnosis in a patient of a higher risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E.

23. A method for diagnosis in a patient of a higher risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient at least two alleles of Apo-E, or expression products thereof, wherein each of said alleles encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E.

24. The method of claim 22 or claim 23, wherein said amino acid comprises an electropositive side chain.

25. The method of claim 24, wherein said amino acid is selected from the group consisting of histidine, lysine and arginine.

26. The method of claim 24, wherein said amino acid is arginine.

27. The method of claim 24, wherein said allele is the e4 allele of Apo-E.

28. The method of claim 22 or claim 23, wherein said interferon is interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these.

29. The method of claim 22 or claim 23, wherein said neuropsychiatric disorder is selected from a mood disorder or a cognition dysfunction.

30. The method of claim 29, wherein said mood disorder is selected from the group consisting of depression, anxiety, irritability, manic symptoms and suicidal behaviour.

31. The method of claim 29, wherein said cognition dysfunction is selected from the group consisting of reduced or abrogated concentration, decreased attention span, impaired short term memory, indecisiveness, confusion, delirium, vacant staring mid-sentence, prolonged silence and progression to a demented state.

32. The method of claim 22 or claim 23, wherein the administration of said interferon is used for treating or preventing a disease or condition selected from the group consisting of a pathogenic infection, an autoimmune disease and a cancer.

33. The method of claim 32, wherein said pathogenic infection is a viral infection which is caused by a virus selected from the group consisting of HIV, hepatitis virus, influenza virus, Japanese encephalitis virus, Epstein-Barr virus and respiratory syncytial virus.

34. The method of claim 32, wherein said pathogenic infection is a viral infection which is caused by a virus selected from the group consisting hepatitis B virus, hepatitis C virus, hepatitis D virus and papilloma virus.

35. The method of claim 32, wherein said pathogenic infection is a bacterial infection which is caused by a bacterium selected from the group consisting of Neisseria species, Meningococcal species, Haemophilus species Salmonella species, Streptococcal species, Legionella species and Mycobacterium species.

36. The method of claim 32, wherein said pathogenic infection is a parasitic infection which is caused by a parasite selected from the group consisting of Plasmodium species, Schistosoma species, Leishmania species, Trypanosoma species, Toxoplasma species and Giardia species.

37. The method of claim 32, wherein said autoimmune disease is selected from the group consisting of multiple sclerosis, myasthenia gravis, atopic dermatitis, chronic granulomatous disease, psoriasis and ankylosing spondylitis.

38. The method of claim 32, wherein said autoimmune disease is selected from the group consisting of multiple sclerosis and chronic granulomatous disease.

39. The method of claim 32, wherein said cancer is selected from the group consisting of melanoma, lung cancer, breast cancer, cervical cancer, prostate cancer, colon cancer, pancreatic cancer, stomach cancer, bladder cancer, kidney cancer, liver cancer, hairy cell leukemia, chronic myelogenous leukemia, myeloma, PTLD, Hodgkin's Lymphomarenal cell carcinoma and Kaposi's sarcoma.

40. The method of claim 32, wherein said cancer is selected from the group consisting of hairy cell leukemia, chronic myelogenous leukemia, myeloma, renal cell carcinoma, Kaposi's sarcoma and melanoma.

41. The method of claim 32, wherein said condition is selected from herpetic keratitis or papillomas.

42. The method of claim 22 or claim 23, wherein the said interferon is used for treating or preventing hepatitis C virus infection.

43. The method of claim 22 or claim 23, wherein the said interferon is used for treating or preventing chronic hepatitis C virus infection.

44. A method for diagnosis in a patient of a lower risk of developing and or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient an allele of Apo-E, or an expression product of said allele, wherein said allele encodes an amino acid other than an amino acid comprising an electropositive side chain at codon 112 relative to the full-length open reading frame of Apo-E.

45. A method for diagnosis in a patient of a lower risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient at least two alleles of Apo-E, or expression products thereof, wherein each of said alleles encodes an amino acid other than an amino acid comprising an electropositive side chain at codon 112 relative to the full-length open reading frame of Apo-E.

46. The method of claim 44 or claim 45, wherein said allele or alleles encode(s) an amino acid other than arginine at said codon 112.

47. The method of claim 44 or claim 45, wherein said allele or allele(s) is/are other than the e4 allele of Apo-E.

48. The method of claim 44 or claim 45, wherein said allele or alleles encode(s) cysteine at said codon 112.

49. The method of claim 44or claim 45, wherein said allele or alleles is/are selected from the el allele or the e3 allele of Apo-E.

50. The method of claim 44 or claim 45, wherein said interferon is interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these.

51. The method of claim 44 or claim 45, wherein said neuropsychiatric disorder is selected from a mood disorder or a cognition dysfunction.

52. The method of claim 51, wherein said mood disorder is selected from the group consisting of depression, anxiety, irritability, manic symptoms and suicidal behaviour.

53. The method of claim 51, wherein said cognition dysfunction is selected from the group consisting of reduced or abrogated concentration, decreased attention span, impaired short term memory, indecisiveness, confusion, delirium, vacant staring mid-sentence, prolonged silence and progression to a demented state.

54. The method of claim 43 or claim 44, wherein the administration of said interferon is used for treating or preventing a disease or condition selected from the group consisting of a pathogenic infection, an autoimmune disease and a cancer.

55. The method of claim 54, wherein said pathogenic infection is a viral infection which is caused by a virus selected from the group consisting of HTV, hepatitis virus, influenza virus, Japanese encephalitis virus, Epstein-Barr virus and respiratory syncytial virus.

56. The method of claim 54, wherein said pathogenic infection is a viral infection which is caused by a virus selected from the group consisting hepatitis B virus, hepatitis C virus, hepatitis D virus and papilloma virus.

57. The method of claim 54, wherein said pathogenic infection is a bacterial infection which is caused by a bacterium selected from the group consisting of Neisseria species, Meningococcal species, Haemophilus species Salmonella species, Streptococcal species, Legionella species and Mycobacterium species.

58. The method of claim 54, wherein said pathogenic infection is a parasitic infection which is caused by a parasite selected from the group consisting of Plasmodium species, Schistosoma species, Leishmania species, Trypanosoma species, Toxoplasma species and Giardia species.

59. The method of claim 54, wherein said autoimmune disease is selected from the group consisting of multiple sclerosis, myasthenia gravis, atopic dermatitis, chronic granulomatous disease, psoriasis and ankylosing spondylitis.

60. The method of claim 54, wherein said autoimmune disease is selected from the group consisting of multiple sclerosis and chronic granulomatous disease.

61. The method of claim 54, wherein said cancer is selected from the group consisting of melanoma, lung cancer, breast cancer, cervical cancer, prostate cancer, colon cancer, pancreatic cancer, stomach cancer, bladder cancer, kidney cancer, liver cancer, hairy cell leukemia, chronic myelogenous leukemia, myeloma, PTLD, Hodgkin's Lymphomarenal cell carcinoma and Kaposi's sarcoma.

62. The method of claim 54, wherein said cancer is selected from the group consisting of hairy cell leukemia, chronic myelogenous leukemia, myeloma, renal cell carcinoma, Kaposi's sarcoma and melanoma.

63. The method of claim 54, wherein said condition is selected from herpetic keratitis or papillomas.

64. The method of claim 43 or claim 44, wherein the said interferon is used for treating or preventing hepatitis C virus infection.

65. The method of claim 43 or claim 44, wherein the said interferon is used for treating or preventing chronic hepatitis C virus infection.

66. A method for diagnosis in a patient of an intermediate risk of developing and/or progressing a neuropsychiatric disorder associated with the administration of an interferon to said patient, comprising detecting in a biological sample obtained from said patient different alleles of Apo-E, or expression products thereof, wherein at least one of said alleles encodes cysteine at codon 112 relative to the full-length open reading frame of Apo- E and at least one other of said alleles encodes an amino acid comprising an electropositive side chain at said codon 112.

67. The method of claim 66, wherein said amino acid comprising said electropositive side chain is arginine.

68. The method of claim 66, comprising detecting at least one e4 allele of Apo-E and at least one allele selected from the el allele and the e3 allele of Apo-E.

69. The method of claim 66, comprising detecting a single e4 allele of Apo-E and a single allele selected from the el allele and the e3 allele of Apo-E.

70. The method of claim 66, wherein said interferon is interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these.

71. The method of claim 66, wherein said neuropsychiatric disorder is selected from a mood disorder or a cognition dysfunction.

72. The method of claim 71, wherein said mood disorder is selected from the group consisting of depression, anxiety, irritability, manic symptoms and suicidal behaviour.

73. The method of claim 71, wherein said cognition dysfunction is selected from the group consisting of reduced or abrogated concentration, decreased attention span, impaired short term memory, indecisiveness, confusion, delirium, vacant staring mid-sentence, prolonged silence and progression to a demented state.

74. The method of claim 66, wherein the administration of said interferon is used for treating or preventing a disease or condition selected from the group consisting of a pathogenic infection, an autoimmune disease and a cancer.

75. The method of claim 74, wherein said pathogenic infection is a viral infection which is caused by a virus selected from the group consisting of HIV, hepatitis virus, influenza virus, Japanese encephalitis virus, Epstein-Barr virus and respiratory syncytial virus.

76. The method of claim 74, wherein said pathogenic infection is a viral infection which is caused by a virus selected from the group consisting hepatitis B virus, hepatitis C virus, hepatitis D virus and papilloma virus.

77. The method of claim 74, wherein said pathogenic infection is a bacterial infection which is caused by a bacterium selected from the group consisting of Neisseria species, Meningococcal species, Haemophilus species Salmonella species, Streptococcal species, Legionella species and Mycobacterium species.

78. The method of claim 74, wherein said pathogenic infection is a parasitic infection which is caused by a parasite selected from the group consisting of Plasmodium species, Schistosoma species, Leishmania species, Trypanosoma species, Toxoplasma species and Giardia species.

79. The method of claim 74, wherein said autoimmune disease is selected from the group consisting of multiple sclerosis, myasthenia gravis, atopic dermatitis, chronic granulomatous disease, psoriasis and ankylosing spondylitis.

80. The method of claim 74, wherein said autoimmune disease is selected from the group consisting of multiple sclerosis and chronic granulomatous disease.

81. The method of claim 74, wherein said cancer is selected from the group consisting of melanoma, lung cancer, breast cancer, cervical cancer, prostate cancer, colon cancer, pancreatic cancer, stomach cancer, bladder cancer, kidney cancer, liver cancer, hairy cell leukemia, chronic myelogenous leukemia, myeloma, PTLD, Hodgkin's Lymphomarenal cell carcinoma and Kaposi's sarcoma.

82. The method of claim 74, wherein said cancer is selected from the group consisting of hairy cell leukemia, chronic myelogenous leukemia, myeloma, renal cell carcinoma, Kaposi's sarcoma and melanoma.

83. The method of claim 74, wherein said condition is selected from herpetic keratitis or papillomas.

84. The method of claim 66, wherein the said interferon is used for treating or preventing hepatitis C virus infection.

85. The method of claim 66, wherein the said interferon is used for treating or preventing chronic hepatitis C virus infection.

86. A method for treating or preventing a disease or condition in a patient, which disease or condition is treatable or preventable by the admimsfration of an interferon to said patient, said patient comprising an allele of Apo-E, or an expression product thereof, wherein said allele encodes an amino acid other than cysteine at codon 112 relative to the full-length open reading frame of Apo-E, said method comprising administering to a patient in need of such treatment an effective amount of an agent other than said interferon, wherein said agent is effective for said treatment or prevention.

87. The method of claim 86, wherein said amino acid comprises an electropositive side chain.

88. The method of claim 86, wherein said amino acid is selected from the group consisting of histidine, lysine and arginine.

89. The method of claim 86, wherein said amino acid is arginine.

90. The method of claim 89, wherein said allele is the e4 allele of Apo-E.

91. The method of claim 86, wherein said interferon is interferon-α, or a biologically active fragment thereof, or a variant or derivative or analogue of these.

92. The method of claim 86, wherein said neuropsychiatric disorder is selected from a mood disorder or a cognition dysfunction.

93. The method of claim 92, wherein said mood disorder is selected from the group consisting of depression, anxiety, irritability, manic symptoms and suicidal behaviour.

94. The method of claim 92, wherein said cognition dysfunction is selected from the group consisting of reduced or abrogated concentration, decreased attention span, impaired short term memory, indecisiveness, confusion, delirium, vacant staring mid-sentence, prolonged silence and progression to a demented state.

95. The method of claim 86, wherein the administration of said interferon is used for treating or preventing a disease or condition selected from the group consisting of a pathogenic infection, an autoimmune disease and a cancer.

96. The method of claim 95, wherein said pathogenic infection is a viral infection which is caused by a virus selected from the group consisting of HIV, hepatitis virus, influenza virus, Japanese encephalitis virus, Epstein-Barr virus and respiratory syncytial virus.

97. The method of claim 95, wherein said pathogenic infection is a viral infection which is caused by a virus selected from the group consisting hepatitis B virus, hepatitis C virus, hepatitis D virus and papilloma virus.

98. The method of claim 95, wherein said pathogenic infection is a bacterial infection which is caused by a bacterium selected from the group consisting of Neisseria species, Meningococcal species, Haemophilus species Salmonella species, Streptococcal species, Legionella species and Mycobacterium species.

99. The method of claim 95, wherein said pathogenic infection is a parasitic infection which is caused by a parasite selected from the group consisting of Plasmodium species, Schistosoma species, Leishmania species, Trypanosoma species, Toxoplasma species and Giardia species.

100. The method of claim 95, wherein said autoimmune disease is selected from the group consisting of multiple sclerosis, myasthenia gravis, atopic dermatitis, chronic granulomatous disease, psoriasis and ankylosing spondylitis.

101. The method of claim 95, wherein said autoimmune disease is selected from the group consisting of multiple sclerosis and chronic granulomatous disease.

102. The method of claim 95, wherein said cancer is selected from the group consisting of melanoma, lung cancer, breast cancer, cervical cancer, prostate cancer, colon cancer, pancreatic cancer, stomach cancer, bladder cancer, kidney cancer, liver cancer, hairy cell leukemia, chronic myelogenous leukemia, myeloma, PTLD, Hodgkin's Lymphomarenal cell carcinoma and Kaposi's sarcoma.

103. The method of claim 95, wherein said cancer is selected from the group consisting of hairy cell leukemia, chronic myelogenous leukemia, myeloma, renal cell carcinoma, Kaposi's sarcoma and melanoma.

104. The method of claim 95, wherein said condition is selected from herpetic keratitis or papillomas.

105. The method of claim 86, wherein the said interferon is used for treating or preventing hepatitis C virus infection.

106. The method of claim 86, wherein the said interferon is used for treating or preventing chronic hepatitis C virus infection.