US20040191818A1 — Compositions and methods for diagnosing and treat…

Claim 1

Independent Claim 67 words

1 . A method, comprising: detecting an expression profile of at least one gene in a biological sample of a subject; and comparing said expression profile to a reference expression profile of said at least one gene to detect or monitor an autoimmune disease in said subject, wherein said at least one gene is differentially expressed in pre-symptomatic lupus-affected or -predisposed tissues as compared to disease-free tissues.

Claim 2

Dependent Claim 67 words

1 . A method, comprising: detecting an expression profile of at least one gene in a biological sample of a subject; and comparing said expression profile to a reference expression profile of said at least one gene to detect or monitor an autoimmune disease in said subject, wherein said at least one gene is differentially expressed in pre-symptomatic lupus-affected or -predisposed tissues as compared to disease-free tissues.

Claim 3

Dependent Claim 27 words

2 . The method of claim 1 , wherein said at least one gene is differentially expressed in early-stage lupus-affected tissues as compared to said disease-free tissues.

Claim 4

Dependent Claim 31 words

3 . The method of claim 2 , wherein said at least one gene is over-expressed in both said pre-symptomatic tissues and early-stage lupus-affected tissues as compared to said disease-free tissues.

Claim 5

Dependent Claim 23 words

4 . The method of claim 3 , wherein said at least one gene includes one or more genes selected from Table 1.

Claim 6

Dependent Claim 23 words

5 . The method of claim 2 , wherein said at least one gene includes one or more genes selected from Table 5b.

Claim 7

Dependent Claim 14 words

6 . The method of claim 2 , wherein said subject is a human.

Claim 8

Dependent Claim 21 words

7 . The method of claim 6 , wherein said autoimmune disease is lupus nephritis (LN) or systemic lupus erythematosus (SLE).

Claim 9

Dependent Claim 23 words

8 . The method of claim 2 , wherein said expression profile and said reference expression profile are determined by RT-PCR or immunoassays.

Claim 10

Dependent Claim 20 words

9 . The method of claim 2 , wherein said pre-symptomatic, early-stage lupus-affected, and disease-free tissues are human kidney tissues.

Claim 11

Dependent Claim 56 words

10 . A pharmaceutical composition comprising a pharmaceutically-acceptable carrier and at least one active component selected from the group consisting of: a polypeptide encoded by a gene which is differentially expressed in pre-symptomatic lupus-affected or -predisposed tissues as compared to disease-free tissues; a variant of said polypeptide; and a polynucleotide encoding said polypeptide or said variant.

Claim 12

Dependent Claim 56 words

10 . A pharmaceutical composition comprising a pharmaceutically-acceptable carrier and at least one active component selected from the group consisting of: a polypeptide encoded by a gene which is differentially expressed in pre-symptomatic lupus-affected or -predisposed tissues as compared to disease-free tissues; a variant of said polypeptide; and a polynucleotide encoding said polypeptide or said variant.

Claim 13

Dependent Claim 43 words

11 . The pharmaceutical composition of claim 10 , wherein said pharmaceutical composition is a vaccine formulation capable of eliciting an immune response against a lupus-affected or lupus-predisposed human cell or a component thereof, and wherein said gene is selected from Table 1.

Claim 14

Dependent Claim 25 words

12 . A method comprising administering a therapeutically or prophylactically effective amount of said pharmaceutical composition of claim 10 to a subject in need thereof.

Claim 15

Dependent Claim 71 words

13 . A pharmaceutical composition comprising a pharmaceutically-acceptable carrier and at least one active component selected from the group consisting of: an agent capable of modulating the expression of a gene which is differentially expressed in pre-symptomatic lupus-affected or -predisposed tissues relative to disease-free tissues; an agent capable of binding to, or modulating a biological activity of, a polypeptide encoded by said gene; and a T cell activated by said polypeptide.

Claim 16

Dependent Claim 71 words

13 . A pharmaceutical composition comprising a pharmaceutically-acceptable carrier and at least one active component selected from the group consisting of: an agent capable of modulating the expression of a gene which is differentially expressed in pre-symptomatic lupus-affected or -predisposed tissues relative to disease-free tissues; an agent capable of binding to, or modulating a biological activity of, a polypeptide encoded by said gene; and a T cell activated by said polypeptide.

Claim 17

Dependent Claim 76 words

14 . The pharmaceutical composition of claim 13 , wherein said active component is selected from the group consisting of: a polynucleotide comprising or encoding an RNA that is capable of inhibiting or decreasing the expression of said gene by RNA interference or an antisense mechanism; an antibody specific for said polypeptide; and an inhibitor of the biological activity of said polypeptide, wherein said gene is over-expressed in said pre-symptomatic tissues relative to said disease-free tissues.

Claim 18

Dependent Claim 17 words

15 . The pharmaceutical composition of claim 14 , wherein said gene is selected from Table 1.

Claim 19

Dependent Claim 31 words

16 . A method comprising administering a therapeutically or prophylactically effective amount of said pharmaceutical composition of claim 15 to a human who has or is predisposed to SLE or LN.

Claim 20

Dependent Claim 31 words

17 . The pharmaceutical composition according to claim 15 , wherein said active component is a polynucleotide comprising or encoding an siRNA directed to a target sequence selected from Table 3.

Claim 21

Dependent Claim 42 words

18 . A diagnostic kit comprising: a polynucleotide capable of hybridizing under stringent or highly stringent conditions to a sequence selected from SEQ ID NOS: 1-29, or the complement thereof; and an antibody specific for a polypeptide selected from SEQ ID NOS:30-57.

Claim 22

Dependent Claim 42 words

18 . A diagnostic kit comprising: a polynucleotide capable of hybridizing under stringent or highly stringent conditions to a sequence selected from SEQ ID NOS: 1-29, or the complement thereof; and an antibody specific for a polypeptide selected from SEQ ID NOS:30-57.

Claim 23

Dependent Claim 67 words

19 . A method comprising: contacting an agent with lupus-affected or lupus-predisposed cells; comparing expression profiles or protein activities of at least one gene in said cells before and after said contacting to determine if said agent modulates expression or protein activity of said at least one gene, wherein said at least one gene is differentially expressed in lupus-affected or lupus-predisposed cells as compared to disease-free cells.

Claim 24

Dependent Claim 67 words

19 . A method comprising: contacting an agent with lupus-affected or lupus-predisposed cells; comparing expression profiles or protein activities of at least one gene in said cells before and after said contacting to determine if said agent modulates expression or protein activity of said at least one gene, wherein said at least one gene is differentially expressed in lupus-affected or lupus-predisposed cells as compared to disease-free cells.

Claim 25

Dependent Claim 76 words

20 . A method comprising: administering an agent to a lupus-affected or lupus-predisposed subject; comparing expression profiles or protein activities of at least one gene in biological samples of the subject before and after said administering to determine if said agent modulates expression or protein activity of said at least one gene in the subject, wherein said at least one gene is differentially expressed in lupus-affected or lupus-predisposed kidney tissues as compared to disease-free kidney tissues.

Claim 26

Dependent Claim 76 words

20 . A method comprising: administering an agent to a lupus-affected or lupus-predisposed subject; comparing expression profiles or protein activities of at least one gene in biological samples of the subject before and after said administering to determine if said agent modulates expression or protein activity of said at least one gene in the subject, wherein said at least one gene is differentially expressed in lupus-affected or lupus-predisposed kidney tissues as compared to disease-free kidney tissues.

Compositions and methods for diagnosing and treating autoimmune diseases

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