METHOD OF USING GENETIC MARKERS, SINGLE NUCLEOTIDE POLYMORPHISMS AND/OR INDELS TO DETERMINE RESPONSIVENESS TO IL-10 OR IL-10 DERIVATIVE TREATMENT
The application relates to the discovery of novel gene expression profiles and/or single nucleotide polymorphisms (SNP) and/or insertions or deletions of bases (INDEL) profiles that correlate with a subject's positive receptiveness to Interleukin 10 (IL-10) or IL-10 based agent treatments. The application also relates to methods of treating patients with an IL-10 or IL-10 based agent treatment by screening, examining, or determine patients possessing a gene expression profile and/or SNP and/or INDEL profile most receptive to the treatment.
1 . A method of genotyping a single nucleotide polymorphism (SNP) or insertion or deletion of bases (INDEL) to obtain a profile indicative of patient receptiveness to treatment with IL-10 or an IL-10 based agent comprising
contacting a cellular sample from a patient with a proinflammatory stimulus to elicit IL-10 induction;
measuring the levels of TNF-α production and the levels of IL-10 induction from the cellular sample;
selecting the patient sample exhibiting a dual phenotype of
high TNF-α reduction in response to IL-10 or an IL-10 based agent stimulation and
low IL-10 induction; and
sequencing the entire genome from the patient exhibiting the dual phenotype for the presence of a SNP and/or INDEL profile.
2 . The method of claim 1 , wherein the cellular sample is obtained from peripheral blood.
3 . The method of claim 1 , wherein the cellular sample is a macrophage.
4 . The method of claim 1 , wherein the IL-10 is an IL-10 derivative.
5 . The method of claim 1 , wherein the IL-10 agent is an IL-10 fusion protein, wherein the fusion protein is an IL-10 fused to a minibody or diabody.
6 . The method of claim 1 , wherein the proinflammatory stimulus is lipopolysaccharide (LPS).
7 . The method of claim 1 , wherein the treatment is for an inflammatory disease.
8 . The method of claim 1 , wherein the inflammatory disease is inflammatory bowel disease (IBD), Crohn's disease or ulcerative colitis.
9 . The method of claim 1 , wherein patient is healthy patient or diseased patient.
10 . The method of claim 1 , further comprising selecting a patient sample exhibiting low or medium CD8+ T cell IFN-γ secretion.
11 . A method of genotyping a single nucleotide polymorphism (SNP) or insertion or deletion of bases (INDEL) to obtain a profile indicative of patient receptiveness to treatment with IL-10 or an IL-10 based agent comprising
contacting activated CD8+ T cells obtained from the patient with an amount of IL-10 or an IL-10 based agent to induce secretion of IFN-γ;
measuring the level of IFN-γ secretion;
selecting the patient sample exhibiting a phenotype of high and/or medium IFN-γ secretion by CD8+ T cells; and
sequencing the entire genome from the patient exhibiting the phenotype for the presence of a SNP and/or INDEL profile.
12 . The method of claim 11 , wherein the CD8+ T cells are purified from a peripheral blood sample.
13 . The method of claim 12 , wherein the CD8+ T cells are activated with an anti-CD3 antibody prior to stimulation by an IL-10 or IL-10 based agent.
14 . The method of claim 12 , wherein the IL-10 is an IL-10 derivative.
15 . The method of claim 12 , wherein the IL-10 agent is an IL-10 fusion protein, wherein the fusion protein is an IL-10 fused to a minibody or diabody.
16 . The method of claim 11 , wherein the treatment is for cancer or autoimmune diseases/disorders.
17 . The method of claim 11 , wherein patient is healthy patient or diseased patient.
18 . The method of claim 11 , wherein the profile is a gene and protein expression profile provided in Tables 3 and 4.
19 . A method for treating a patient suffering from an disease or disorder alleviated by IL-10 or an IL-10 based agent comprising
genetically profiling a sample obtained from a diseased patient for a SNP/INDEL profile, wherein the SNP/INDEL profile is correlated with a phenotypic trait wherein the macrophages respond to IL-10 by reducing the level of TNF-α and produces low amounts of IL-10 in response to LPS stimulation;
selecting a patient possessing the SNP/INDEL profile; and
administering to the patient a therapeutically effective amount of an IL-10 or IL-10 based agent.
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