Method for detecting a panel of biomarkers
The present invention relates to development, validation and application of new sets of biomarkers for diagnosis of Alzheimer's disease (AD) and related disorders including early diagnosis of MCI and early prodrome of AD, identification of disease sub types, prediction of their response to disease management procedures, drugs and their combinations and for monitoring response for these treatments, including validation of biomarkers for clinical trials.
1. A method for detecting the amount of each biomarker in a set of biomarkers in a sample from a mammal and optionally, in a control sample, said method comprising contacting said set of biomarkers with antibody specific to said each biomarker in said set of biomarkers and detecting the binding of antibodies specific to each biomarker in said set of biomarkers, wherein said set of biomarkers comprises 24 proteins encoded by the following 24 genes: APBA1, ATG7, BECN1, CD44, CDH2, COL18A1, ERBB4, F3, FLNA, FYN, GRIN2B, IL20, ITPR1, LRP8, MTOR, NPPC, NRP1, PDGFC, ROBO1, SEMA3E, TGFB1, THBS1, VEGFR1 and WWOX.
2. The method of claim 1 , wherein the set of biomarkers further comprises at least one protein encoded by a gene selected from: A2M, ACHE, ALDH2, ANXA1, APOA1, ATP2A3, CASK, CASP8, CDH1, CDH5, CDKN1A, CHAT, CTNND2, DOCK3, EDN1, F13A1, FGF2, FLNB, GABRB2, ITGA1, LAMA1, LAMA3, LEPR, LRP1, MAP2, MMP9, NFATC2, NOS3, NOTCH3, NPPB, PDGFA, PDGFB, PIK3CB, PLAU, PLXDC2, PLXNA2, PRKG1, PRNP, PTK2, RYR2, SEMA5A, SERPINA6, SERPINB2, SERPIND1, STAT3, THBS2, TNF, TP53, TRPC4, TSC1 or VEGFA.
3. The method of claim 2 , wherein at least one further biomarker is selected from disease associated SNP, a protein, RNA, metabolite, lipid or glucid.
4. The method of claim 3 , wherein the at least one further biomarker is selected from metabolites of the:
cholesterol metabolic pathway; and/or
folate metabolic pathway; and/or
phosphatidic acid metabolic pathway; and/or
sphingosine metabolic pathway; and/or
terpenoid metabolic pathway.
5. The method of claim 3 , wherein the at least one further biomarker is a SNP or a combination of SNPs for the genes selected from: APBA1, ATG7, BECN1, CD44, CDH2, COL18A1, ERBB4, F3, FLNA, FYN, GRIN2B, 1L20, ITPR1, LRP8, MTOR, NPPC, NRP1, PDGFC, ROBO1, SEMA3E, TGFB1, THBS1, VEGFR1 or WWOX, or for other genes involved in synapse biology, angiogenesis or cellular stress response.
6. The method of claim 1 , wherein the set of biomarkers further comprises at least one protein encoded by a gene selected from: ABCC4, ACC2, ACTN1, ADAM12, ADRA1A, AKAP13, ALCAM, ANXA3, ARHGEF11, ARHGEF12, ATF3, ATM, ATP6V1C1, ATR, BAP1, BGLAP, BIN1, BRIP1, BSN, CACNA1D, CALCB, CDC42BPB, CDH12, CDH13, CHEK1, CHL1, CLTC, COL3A1, COPS7B, CSF1, CSH1, CSNK1A1, CTNNA2, CUL1, CYP11A1, DAAM1, DGKZ, DLG3, DOCK2, EGF, EGFR, EPB41L2, ERC1, F2, FAS, FER1L3, FES, FKBP1A, FSTL5, GFRA3, GFRA4, GH1, GRIP1, GUCY2D, HGF, HIPK1, HMBOX1, HRG, HSP90B1, HSPA5, HYOU1, IGF2, IL16, IL6ST, IL8, INS, IPPK, IQGAP1, IQGAP2, ITGA9, JAK1, LEP, LETMD1, LIFR, LRP2, LRP6, LTBP1, MAD1L1, MAML3, MMP2, MMP3, MSR1, MUC1, MYO10, NCAM1, NCK1, NGF, NISCH, NOS1, NOTCH2, NPPA, NRIP1, NTF3, OPRM1, PCAF, PCLO, PDE3A, PDE5A, PFKP, PIK3CA, PLA2G2A, PLAT, PLG, PRL, PRLR, PSAP, PSD3, PTGS2, PTK2B, PTPRF, PTPRG, PTPRM, RELN, RET, RIMS2, ROCK1, RPS6KA1, RPS6KA2, RPS6KB1, SCN9A, SERPINA5, SERPINC1, SERPINE1, SERPINE2, SNAP25, SPP1, SREBF2, STAT5B, SV2B, TIMP2, TNFSF11, TRIO, TSC2, UBE3A, VCL, VIL2, WASPIP, XDH or ZFHX1B.
7. The method of claim 1 , wherein the sample is selected from blood, serum and plasma.
8. The method of claim 1 , wherein the quantification of the amount of said proteins is carried out using a protein biochip.
9. The method of claim 8 , wherein said method comprises contacting a plasma sample from the mammal and optionally, the control sample, with the protein biochip, said protein biochip comprising antibodies specific for APBA1, ATG7, BECN1, CD44, CDH2, COL18A1, ERBB4, F3, FLNA, FYN, GRIN2B, IL20, ITPR1, LRP8, MTOR, NPPC, NRP1, PDGFC, ROBO1, SEMA3E, TGFB1, THBS1, VEGFR1 and WWOX and the binding of said target biomarker to its specific antibody to form an antibody-biomarker complex and detecting antibody-biomarker complexes formed during said contacting with labelled secondary antibodies specific for APBA1, ATG7, BECN1, CD44, CDH2, COL18A1, ERBB4, F3, FLNA, FYN, GRIN2B, 1L20, ITPR1, LRP8, MTOR, NPPC, NRP1, PDGFC, ROBO1, SEMA3E, TGFB1, THBS1, VEGFR1 and WWOX.
10. A method of detecting a combination of biomarkers, the method comprising contacting a plasma sample from a subject, and optionally, a control sample, with a protein biochip comprising antibodies specific for APBA1, ATG7, BECN1, CD44, CDH2, COL18A1, ERBB4, F3, FLNA, FYN, GRIN2B, IL20, ITPR1, LRP8, MTOR, NPPC, NRP1, PDGFC, ROBO1, SEMA3E, TGFB1, THBS1, VEGFR1 and WWOX and detecting antibody-biomarker complexes formed during said contacting with labelled secondary antibodies specific for APBA1, ATG7, BECN1, CD44, CDH2, COL18A1, ERBB4, F3, FLNA, FYN, GRIN2B, 1L20, ITPR1, LRP8, MTOR, NPPC, NRP1, PDGFC, ROBO1, SEMA3E, TGFB1, THBS1, VEGFR1 and WWOX.