Patent Application
20160201132
Throughout this application, various publications are referred to by first author and year of publication. Full citations for these publications are presented in a References section immediately before the claims. Disclosures of the publications cited in the References section in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art as of the date of the invention described herein.
Multiple Sclerosis (MS) is a neurological disease affecting more than 1 million people worldwide. It is the most common cause of neurological disability in young and middle-aged adults and has a major physical, psychological, social and financial impact on subjects and their families, friends and bodies responsible for health care (EMEA Guideline, 2006).
A clinically isolated syndrome (CIS) is a single monosymptomatic attack suggestive of MS, such as optic neuritis, brain stem symptoms, and partial myelitis. Patients with CIS that experience a second clinical attack are generally considered to have clinically definite multiple sclerosis (CDMS). Various MS disease stages and/or types are described in Multiple Sclerosis Therapeutics (Duntiz, 1999). Among them, relapsing-remitting multiple sclerosis (RRMS) is the most common form at the time of initial diagnosis. Many subjects with RRMS have an initial relapsing-remitting course for 5-15 years, which then advances into the secondary progressive MS (SPMS) disease course. There are currently a number of disease-modifying medications approved for use in relapsing MS (RMS), which includes RRMS and SPMS (The Disease Modifying Drug Brochure, 2006). These include interferon beta 1-a (Avonex® and Rebif®), interferon beta 1-b (Betaseron®), glatiramer acetate (Copaxone®), mitoxantrone (Novantrone®), natalizumab (Tysabri®) and Fingolimod (Gilenya®). Immunosuppressants or cytotoxic agents are used in some subjects after failure of conventional therapies. However, the relationship between changes of the immune response induced by these agents and the clinical efficacy in MS is far from settled (EMEA Guideline, 2006).
Other therapeutic approaches include symptomatic treatment which refers to all therapies applied to improve the symptoms caused by the disease (EMEA Guideline, 2006) and treatment of acute relapses with corticosteroids. While steroids do not affect the course of MS over time, they can reduce the duration and severity of attacks in some subjects.
Laquinimod (TV-5600) is a novel synthetic compound with high oral bioavailability which has been suggested as an oral formulation for the treatment of Multiple Sclerosis (MS) (Polman, 2005; Sandberg-Wollheim, 2005; Comi et al 2008). Laquinimod and its sodium salt form are described, for example, in U.S. Pat. No. 6,077,851. The mechanism of action of laquinimod is not fully understood.
Animal studies show it causes a Th1 (T helper 1 cell, produces pro-inflammatory cytokines) to Th2 (T helper 2 cell, produces anti-inflammatory cytokines) shift with an anti-inflammatory profile (Yang, 2004; Brück, 2011). Another study demonstrated (mainly via the NFkB pathway) that laquinimod induced suppression of genes related to antigen presentation and corresponding inflammatory pathways (Gurevich, 2010). Other suggested potential mechanisms of action include inhibition of leukocyte migration into the CNS, increase of axonal integrity, modulation of cytokine production, and increase in levels of brain-derived neurotrophic factor (BDNF) (Runström, 2002; Brück, 2011).
Laquinimod showed a favorable safety and tolerability profile in two phase III trials (Results of Phase III BRAVO Trial Reinforce Unique Profile of Laquinimod for Multiple Sclerosis Treatment; Teva Pharma, Active Biotech Post Positive Laquinimod Phase 3 ALLEGRO Results).
IUPAC: 5-chloro-N-ethyl-4-hydroxy-1-methyl-2-oxo-N-phenyl-1,2-dihydroquinoline-3-carboxamide
As MS therapeutic options grow, the ability to identify subjects who will respond more favorably to therapy and specifically to laquinimod has become increasingly significant.
The subject invention provides a method of predicting clinical responsiveness to laquinimod therapy in subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, the method comprising evaluating expression of a biomarker in the subject, so as to thereby predict clinical responsiveness to laquinimod, wherein the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
The subject invention provides a method of treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome with laquinimod, comprising the steps of: a) determining whether the subject is a laquinimod responder by evaluating expression of a biomarker in the subject, and b) administering to the subject an amount of laquinimod effective to treat the subject only if the subject is identified as a laquinimod responder, so as to thereby treat the subject, wherein the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
The subject invention also provides a method for treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome comprising the steps of: a) administering to the subject a therapeutically effective amount of laquinimod, b) determining whether the subject is a laquinimod responder by evaluating expression of a biomarker in the subject; and c) administering to the subject an amount of laquinimod effective to treat the subject only if the subject is identified as a laquinimod responder, or modifying the administration of laquinimod to the subject if the subject is not identified as a laquinimod responder, so as to thereby treat the subject, wherein the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
The subject invention also provides laquinimod for use in treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, wherein the subject has been identified as a laquinimod responder.
The subject invention also provides a pharmaceutical composition comprising an amount of laquinimod for use in treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, wherein the subject has been identified as a laquinimod responder.
The subject invention also provides laquinimod for use in treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, wherein expression of a biomarker in the subject is up-regulated and the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
The subject invention also provides a pharmaceutical composition comprising an amount of laquinimod for use in treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, wherein expression of a biomarker in the subject is up-regulated and the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
The subject invention also provides laquinimod for use in treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, wherein expression of a biomarker in the subject is suppressed and the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
The subject invention also provides a pharmaceutical composition comprising an amount of laquinimod for use in treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, wherein expression of a biomarker in the subject is suppressed and the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
The subject invention also provides a therapeutic package for dispensing to, or for use in dispensing to, a subject identified as a laquinimod responder afflicted with multiple sclerosis or presenting a clinically isolated syndrome, which comprises: a) one or more unit doses, each such unit dose comprising an amount of laquinimod, and b) a finished pharmaceutical container therefor, said container containing said unit dose or unit doses, said container further containing or comprising labeling directing the use of said package in the treatment of said subject.
The subject invention also provides a therapeutic package for dispensing to, or for use in dispensing to, a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, which comprises: a) one or more unit doses, each such unit dose comprising an amount of laquinimod, and b) a finished pharmaceutical container therefor, said container containing said unit dose or unit doses, said container further containing or comprising labeling directing the use of said package in the treatment of said subject, wherein expression of a biomarker in the subject is suppressed or up-regulated and the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
The subject invention provides a method of predicting clinical responsiveness to laquinimod therapy in a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, the method comprising evaluating expression of a biomarker in the subject, so as to thereby predict clinical responsiveness to laquinimod, wherein the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
In one embodiment of the present invention, the method further comprises predicting positive clinical responsiveness to laquinimod if the biomarker is up-regulated in the subject. In another embodiment, the subject is naïve to laquinimod.
In another embodiment of the present invention, the method further comprises predicting positive clinical responsiveness to laquinimod if the biomarker suppressed in the subject. In another embodiment, the subject has previously received periodic laquinimod administration. In another embodiment, the expression of the biomarker is suppressed in comparison to expression of said biomarker of the patient at baseline.
In one embodiment, the subject has received periodic laquinimod administration for at least one month. In another embodiment, the subject has received periodic laquinimod administration for at least 6 months. In another embodiment, the subject has received periodic laquinimod administration for at least 12 months. In another embodiment, the subject has received periodic laquinimod administration for at least 24 months.
In one embodiment, the gene associated with inflammatory response is a gene associated with or involved in TGFb signaling, IL-12 signaling, the pathway of adhesion of phagocytes, chemotaxis of neutrophils, transmigration of leukocytes, caveolar mediated endocytosis, clathrin mediated endocytosis, and/or leukocyte extravasation signaling.
In another embodiment, the gene associated with cellular movement is a gene associated with or involved in adhesion and migration of phagocytes, chemotaxis of neutrophils, transmigration of leukocytes, invasion of cells, adhesion of cells, and/or leukocyte extravasation signaling.
In another embodiment, the gene associated with cell signaling is a gene associated with or involved in the pathway of adhesion of cells and/or neurotransmission.
In another embodiment, the gene associated with cell development is a gene associated with or involved in the pathway of G protein coupled receptor signaling, arachidonic acid metabolism and/or TGFβ signaling.
In another embodiment, the gene associated with hematological system is a gene associated with or involved in the pathway of aggregation of blood platelets, activation of blood platelets, aggregation of blood cells, coagulation of blood, intrinsic prothrombin activation pathway and/or coagulation system.
In another embodiment, the gene is TNFSF4, SELP, ITFA8, ITGB1/3/5, CXCL5/7, a BMP6 gene, ITGA2/8, ITGβ1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-1/1R/5/8/13/20/22R, IL-9/11/12/36, TNFRSF11A/B, IFNA4/8/10/17, TGβ, LTBP4, MEK1/2, TGFβ type 1 receptor, type II BMPR, smad1/2/3/4/5/6/8, PAI-1, CCL19, IKKg, LTBP1 or a combination thereof.
In one embodiment of any one of the methods, uses, pharmaceutical composition or packages described herein, the gene is ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-5/20/22, IL-9/36, TNFRSF11A/B, TGβ, LTBP4, MEK1/2, Smad2/3/4, PAI-1, SELP, ITFA8, ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-5/13/20/22, IL-9/11/36, TNFRSF11A/B, TGβ, LTBP4, MEK1/2, Smad1/2/3/4/5/6/8, PAI-1, CCL19, IKKg, LTBP1, Alpha tubulin, BMP4/7, MIS, TCF2, IL5R, IL13R, IL20R, ITGB2, NKTR, TEF, CLSTN2, LUC7L2, FABP7, TPTE, FSTL1, SF3B1, LIMS1, PDE5A, XPNPEP1, C5orf4, SPANXB1, SPANXB2, SPANXF1, KRT20, TBC1D1, GRHL2, C5orf4, SEPT6, KIAA1199, SSX2IP, TPM1, CDC14B, USP47, MMRN1, CTNNAL1, SMOX, ALOX12, GLRA3, CA2, GUCY1B3, RFPL1, CLEC1B, GNG11, TSPAN32, RGS10, CALD1, PRKAR2B, CYP4F11, CLCA3P, CELSR3, CDC14B, TPM1, SEPT6, PRKG1, MAX, CCDC93, ARMCX6, LOC653354, TUBB2B, HIST1H2AJ, MFAP3L, LIMS1, GNB5, GPRASP1, SRRT, C1orf116, FBXO7, PPM1A, GUCY1B3, CTDSPL, GNAS, IGF2BP3, TPM1, HIST1H2BK, DLG4, WDR48, CALD1, LOC157627, GNB5, ZNF415, ASAP2, PSD3, GNAS, POPDC3, NRGN, ABLIM3, XYLT1, PTGIS, ARHGEF10, PDGFA, PGRMC1, HIST1H2AC, GNAS, CLDN5, MFAP3L, PGRMC1, MYST3, CAPRIN1, CALD1, FBXW7, DNM3, CD84, PRPF4B, RBM25, WASF3, GRAP2, SPARC, TAL1, NENF, XK, GP1BA, HLA-E, CA5A, LYVE1, MARCH6, NAT8B, TRIM58, RET, SDPR, TBXA2R, TMED10, APBA2, MYL9, POU1F1, H2BFS, HIST1H2BK, FAM12B, VCL, GSPT1, ALDOB, LOC150776, SMPD4, SLC37A1, SPARC, GNAS, TAS2R4, CALM3, POM121, POM121C, GRIK2, GREM1, TNNC2, EPS15L2, ENDOD1, RGS6, SF3B1, TMSB15A, ZBTB20, FUT9, ATP9A, MAX, HIST1H2AI, BAT2D1, ABL1, SNCA, GFI1B, CTSA, SNX13, RPA1, FLNA, XPNPEP1, KIF2A, ZBTB33, PSMD11, UBE2N, FOLR1, TSC22D1, PCNP, CELSR3, ACSBG1, RNF11, SEMA3E, MARCH2, PCDH24, SUPT5H, HLA-E, EGF, HLA-C, FLNA, CDK2AP1, LEPROT, SH3TC2, TUBA4A, MTMR1, TF, PRKD1, NAPIL1, DAB2, FUCA1, HIP1, THPO, MAP1B, PARVB, GP1BB, SEPT5, GJA4, PTGS1, GUCY1A3, HIST1H2AG, GNAS, LRBA, HYAL3, GP6, IGHG1, CYP2A13, CDC14B, MAX, KDM2A, CALD1, GNAZ, C19orf22, ARHGAP6, RHOC, RBX1, GP1BB, SEPT5, PRDX6, PRB4, FLNA, HIST1H2BF, RHBDF2, NUP205, SYT1, EGFL8, PPT2, TUBB1, TMC6, FLJ11292, NAP1L1, ALDH1A3, CSNK1E, PRUNE, COL4A3, ZNF221, ILF3, CABP5, RPA1, ARF1, HIST1H2BI, PTGS1, PRKAA1, GNB5, HIST2H4A, HIST2H4B, CYB5R3, TNS1, DCT, GMPR, ABI3BP, GNAS, SASH1, AAK1, XPO6, CTSL2, QSER1, MAP1LC3B, TBX6, CABP2, MRE11A, MAPRE2, TMC6, BDKRB2, MGLL, HRASLS, WHAMML1, WHAMML2, CLU, STC1, C6orf54, PABPN1, PDLIM1, CLU, PHF20, UBL4A, RNF115, HGD, RASGRP2, PNN, SAPS3, SFI1, GOLGA2, HIST2H2BE, SGEF, HGD, DUS1L, MPP1, HLA-E, GRB14, MMD, ZFHX4, CSNK1G2, HIST1H2BE, MPDZ, B2M, TBXA2R, CTDSPL, SNCA, CD99, POLS, MPL, HIST1H3F, SFRS8, NR5A2, ZMYM2, C6orf10, TMEM40, RNF43, PRUNE, MSH6, PLCB4, PARVB, TOX3, PKNOX1, RUFY1, SNCA, C10orfB1, PDGFA, ASMT, HMGB1, CCDC90A, PROS1, hCG_1757335, RAP1B, MTSS1, GNRHR, LRRN3, MCM3AP, PLOD2, NAP1L1, PLOD2, HOXD13 CASKIN2, MFAP5, PITX2, SNCA, MYLK, PBX1, PRDX6, H3F3A, H3F3B, LOC440926, TMEM158, TRIM58, FSTL1, SNCA, TNS1, ATP1B1, C5orf4, LRP12, CTNNAL1, GEM, KIAA1466, ALDH1A2, MAP4K3, SNCA, RAB6B, PSD3, RIPK2, RAMP3, CALD1, CYP2E1, PSD3, PDLIM7, COBLL1, FUT3, SMOX, TGM2, LRRC50, CST6, OR7A17, C6orf145, DLEU2, DLEU2L, CPT2, HGF, TNS1, SPRY1, PLOD2, CD80, KYNU, BCAT1, NHLH1, AHCTF1, HOXA10, MTMR3, VAC14, CLCF1, FGF5, TAL1, SAMD14, ELL2, CHN1, SLC7A1, GRK5, PARD3, VPS37B, CYP2B6, CYP2B7P1, MALL, ALX4, SOX15, KRT5, ESPL1, STARD8, PSD3, KIAA0195, MYO9B, HIP1R, LOC100294412, EFNB1, ERN1, RHD, MFAP3L, PLA1A, POFUT2, C8orf39, CRYBB2, CYP4A11, PVRL2, CLCNKB, MRAS, NFIB, FKSG2, SLC11A2, FZR1, ZNF550, GLP1R, SLC19A1, RTN2, PAPOLA, STC1, GK, EXOSC6, RAPSN, HFE, EHD2, RIOK3, UBE2I, C15orf2, DMD, PRLH, MAP2K2, TP63, DACH1, PPP5C, SLC26A1, NUDT7, KCNJ12, ENTPD7, SLC26A1, PRRG3, RGS6, ZBED2, FICD, ARHGAP1, ARHGDIA, SDHB, AMHR2, ABCA4, TCF20, BGN, CASP7, LPAR4, GNA12, CYP2W1, RAX, C4A, C4B, LOC100292046, LOC100294156, PXN, ESR2, MYL10, EFS, TFF3, SRPK1, LOC441601, BIRC5, CCT8L2, PPAP2B, CMA1, APOA2, KDELR2, ASCL3, RUNX1, BUB1, SLC6A8, HNRNPC, HNRNPCL1, LOC440563, LOC649330, RIBC2, CLIC4, RAB17, SCML2, SPINLW1, ANK1, EDA2R, HTR4, CDC42EP4, KANK2, ANK1, SYN1, DUX3, DUX4, FRG2C, HPX-2, LOC100134409, LOC652119, LOC653543, LOC653544, LOC653545, LOC728410, PKNOX2, MLLT4, APOA2, PENK, GNAT1, FURIN, SEMA6A, EGFL6, HRH1, TSPAN1, DBC1, TRPC7, GPR52, HAMP, PRSS2, GPR107, FLJ11292, FLJ20184, B4GALT1, NKX3-1, ASIP, EFCAB6, GPR20, CA5A, PLK4, TAAR5, SRPX2, CNTD2, AZGP1, TIMP3, RGS6, ADARB1, DYNC1I1, C10orf10, PDIA2, PITX3, HOXC13, LPAR3, CTRC, CTSL2, MUC8, AQP5, UGT1A1, UGT1A10, UGT1A4, UGT1A6, UGT1A8, UGT1A9, KCNQ2, CYP2A13, ZNF155, KIAA0892, ATP2A2, FGF5, FGF18, FUT2, SHROOM2, PRSS3, CREB3L1, MGAT2, PLCE1, MLXIPL, OR10H3, ABCB11, CD84, ARHGEF4, ORC1L, PCIF1, CD177, C1orf116, IFT122, C11orf20, DUSP13, C6orf208, PLA2G5, PRAMEF1, PRAMEF2, CYP4F8, KCNA1, MFAP4, SLC4A3, IL1RAPL1, SERPINE1, ZCCHC14, POLR3G, C16orf68, FLJ14100, SMCHD1, ASCL1, FOXA2, SLC23A2, KLK13, MTSS1L, DNMT3L, RREB1, DNMBP, PKLR, C1orf106, CCDC134, MTSS1, CCDC40, HOXB1, SCNN1B, SEMA4G, RAPGEFL1, MAGEL2, PLSCR2, CHD2, PLCD1, C1orf116, CHRNA2, MBP, CDC42BPA, MYF6, PI15, LOC440895, SBF1, MAST1, GLT8D2, ERBB3, LOH3CR2A, AMH, HR, RDH8, PAWR, DRD3, CCT8, PRELP, SPOCK3, EPS8L3, NXN, SEMA4G, P2RY1, AVL9, TEK, MOGAT2, KLK7, MT1E, MT1H, MT1M, CLDN18, RHBDF2, SIX1, INPP5A, KCNMB3, MAP2K5, GPD1, LPO, LOC729143, MPRIP, WNT7A, RARG, CDH7, MBNL2, RASGRP2, RBMY2FP, MASP1, CASR, EGR4, APOC2, HECW1, HOXB3, IRF5, NNMT, AOC2, ESRRG, LPIN1, ACOT11, CCDC33, MBD2, ZNF323, NTRK2, TMEM151B, GPLD1, LENEP, HNF1B, NXPH3, ALDH1A3, PHF20L1, CKM, PARD6B, CRYGB, HAB1, LARGE, RAB40C, MPL, CHIT1, METTL10, DUS4L, PNLIPRP1, ELL, ST8SIA5, GRIN2B, MC4R, RTDR1, HDAC6, KCNJ13, CPSF1, SPANXC, CNOT4, LAMA2, SLC1A6, ABCA2, KLK11, GFRA3, CYP3A4, SLC1A3, ATP2B2, APBB2, VPS45, GHRHR, HOXD4, PRPH, ADCY2, LEFTY2, CYP1B1, PCP4, C8B, RANBP3, PDE6H, TRIM1S, VGLL1, TRIM3, CRKL, ADH7, PSG3, GPR153, MFAP2, FGF13, NAPA, ALDH3A1, MCM10, TLE4, ITPR3, CCDC87, C9orf7, ACTC1, OBSL1, MAP2, CRYM, RNF122, SST, HLA-DRB6, SLC22A17, HSPG2, HIP1, GRIK2, UNKL, GPR144, KIR3DX1, NARFL, UCP3, PLXNA2, BTN1A1, ERCC4, CIITA, EGFR, KRT33A, CLTB, B3GALT5, AP3M2, GJC1, MYO3A, ARHGAP1, PPP2R3A, CLIC4, C20orf195, SIGLEC8, GPRC5A, CACNB1, MYL10, PRLR, OR2S2, NCR2, CHAF1B, EYA3, CDS1, FBXL18, ACTL6B, ZNF821, C16orf71, HBBP1, PLXNA1, CDC45L, MTCP1, PLCB4, PLVAP, PROX1, CYP3A43, IGHG1, RECQL5, IDUA, DLGAP4, PLXNB1, HSD17B14, FOXP3, C19orf26, EPB41L1, RBBP9, GJB4, UPK1B, CYP19A1, LOC55908, CLDN18, C2orf72, NTRK3, NRXN2, SPDEF, IGH@, IGHD, IGHG1, IGHM, LOC100289944, VSIG6, ACRV1, PHLDB1, SORBS1, HAPLN2, FABP3, EFS, ACVR1B, CHST3, UGT2A1, UGT2A2, TAF1, MT4, MFAP3, ETV5, UBQLN3, TBX10, GJB1, ABO, SPINK5, ATAD4, CDH11, CARD14, ALPP, ALPPL2, CBL, LRP4, CDKL2, SSX3, DSG2, SLC45A2, LAMA4, WFDC8, HTR7, EFNB3, TUBB2B, OR7E19P, PMS2L4, ASAP3, FRZB, PDLIM4, PVT1, TFR2, AHI1, TAF4, ADAMTSL2, CLDN4, KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL5A, KIR2DL5B, KIR2DS1, KIR2DS2, KIR2DS4, KIR2DS5, KIR3DL2, KIR3DL3, KIR3DP1, LOC727787, RAPGEF5, CRMP1, LDB3, F11, USP46, IBSP, SLC9A3, FLRT3, TRIM17, FGF17, CAMK1G, GLYR1, CSH1, NTF3, ABHD6, TRIM15, OR52A1, FGFR2, ORAI2, C17orf53, GLP1R, SLIT1, TP63, DDR1, CFTR, DIO2, LETM1, ACSM5, ACTA1, NPR1, KCND3, POPDC3, DNAH3, SPDEF, CLEC4M, SLC30A3, NAGLU, AAK1, DHX34, NNAT, AKAP9, ICMT, FAM189A1, C10orf81, MYOZ1, PKNOX2, MGC31957, PRDM11, RET, IGHG1, XPNPEP2, NTRK2, SLC25A10, NR1I2, GRM8, OR3A3, GIPR, PAH, PACRG, CLN8, ZNF215, TRIO, TTLL5, GRM1, PRKG1, HHLA1, LAMA3, SLC37A4, HOXC11, SLCO5A1, CA10, RRBP1, SOD3, NTRK3, CYR61, STRA6, SLC6A11, CNOT4, ATN1, BCAP29, NOVA2, RELN, LAMC2, RAD51, PRSS7, DCBLD2, TACR2, RAB11B, OR2J2, VSNL1, IFNA17, DPYSL4, MGC2889, RRBP1, POLQ, OR1A2, PURA, AIF1, CBS, NECAB2, PRKCE, NOX1, IHH, EXO1, GPRIN2, PDX1, GPR12, FAM188A, HS3ST3B1, ASCL1, ZNF484, CSH1, BCAN, DDN, DUOX2, MORN1, SLC39A2, CLCN7, RUNX2, TTYH1, ZNF280B, PAX3, LZTS1, SLC8A2, HAB1, KIF1A, ARL4D, UGT2B15, NACA2, THRB, C6orf15, GPR176, WSCD1, PLXNB3, CADM3, HAP1, CYP1A2, SPAM1, IL22RA1, CDC2L5, IRX5, PPFIA2, KDELR3, CEACAM7, KCMF1, DUOX1, CDC27, HIST2H2AA3, CAV3, APOA4, NPR3, PRG3, TBC1D22B, TUSC3, RIMS2, CYP4F12, TBXA2R, HBEGF, PSG9, PYGO1, RASGRF1, SCN2A, KLHL1, DTNB, GREM1, SNCG, C22orf24, PALM, COBLL1, DNPEP, MNS1, NFATC4, DLC1, HSPC072, MCAM, CA12, CSHL1, RPAIN, COL5A2, UGT1A8, UGT1A9, IGH@, IGHA1, IGHG1, IGHG2, IGHG3, IGHM, LOC100126583, LOC100290036, LOC100290320, LOC100293211, LOC652494, ACSM5, ALOX12P2, ERBB4, CLDN16, CIB2, GALR3, MSMB, FABP7, ATXN3, KCNJ5, TRDN, CYP3A43, BAZ2A, ACCN4, SILV, DGCR14, SEMA6C, DIO2, PTHLH, LEP, PDZRN3, RGSL1, GJA4, SLC22A6, RASGRF1, MAPRE2, PVRL1, AKAP1, POMP, SOX21, DNAH9, HOXC5, SERHL2, KIAA0485, ITSN1, B4GALT1, NEK2, NUPR1, CCDC93, EPO, CRABP2, TYRO3, GOLGA2, SEMA3F, BFSP2, NCAM1, FOLH1, SSX2, TMPRSS4, DCN, LPHN3, POU4F3, CEACAM5, BCL3, EXTL3, CCNA1, DDR2, PAX8, SOX5, POU3F1, PEX16, NUP62, SIGLEC11, ALDOB, GPC3, IGFALS, WDR25, FGF1, OSR2, ARID1A, GYPA, KLK13, PARVB, LILRB5, RIMS2, C19orf21, HOXD1, PRSS3, FLT1, ATP6V1C1, LOX, CRYBB3, CA12, PRKG2, MASP1, LOC728395, LOC728403, TSPY1, PDCD1, GGTLC1, AQP8, KRT16, AICDA, BRD8, C1orf95, OR3A2, PFKFB2, FRZB, PAK3, MEIS2, ZSCAN2, MYH7, VWA1, LSAMP, SRC, UGT1 A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, DIO1, TADA3L, NFASC, CALCRL, NBLA00301, MAB21L1, FBXO42, COL10A1, CFB, SNX7, FOXN1, SRY, HLF, CLCA3P, DAZ1, DAZ2, DAZ3, DAZ4, GPR3, TMPRSS11E, EMID1, KCNMB2, MUC5AC, SORT1, HIF3A, MAPK4, TCP11L1, ZZEF1, DCAF7, DMWD, CLCA2, VAC14, CSPG5, STMN2, MLLT4, GALNT14, FGF12, MFAP5, SUMO3, HTR3A, GDF5, TSSK1B, CYP2A7P1, MARK1, ATP1B2, TBX6, PAX8, IL1R1, RALYL, OR2B2, TAAR3, C12orf32, IGHG1, LOC642131, DICER1, GLRA3, PPARD, HSPA4L, WNT2, VIPR2, CYP2C9, SRPX2, IGSF1, ALPK3, TFPI, KCNS3, MARCH8, FRMD4B, TACR3, FIGF, PDCD6, TNN, SPANXB1, SPANXB2, SPANXF1, RHBDD3, SPP2, PDE10A, ZNF224, FGL1, PGAM2, CADM4, APOBEC2, SLC9A5, GNAT1, ARHGEF16, SMARCA2, DNAH9, RBM26, WNT2B, KCNK2, NPBWR2, SP2, TMPRSS11D, DENND2A, TNIP3, STC1, DOCK6, ADAM5P, SYDE1, TNPO2, LRTM1, USH1C, PDE12, SRCAP, OR10J1, OR2H2, KCNJ8, RP11-257K9.7, DOCK5, TPD52L1, PAEP, GGA2, PHLDA3, HES2, MLL, CHRNA6, CIB2, PTPRF, TM7SF4, DAZ1, DAZ2, DAZ3, DAZ4, ALX1, OR2F1, OR2F2, PLAT, HGC6.3, WNT11, PGK2, SNAI2, COL4A6, PRUNE2, ANKS1B, LOC81691, FERMT2, TIMP3, CST8, CAPN6, IDUA, GPR32, AKR1B10, GRHL2, FBXO24, HSF4, IGHG1, HCN2, LRP12, ARHGEF15, UGT1A1, UGT1A10, UGT1A7, UGT1A8, GUCA2A, ITIH1, EGFR, UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, MYOG, TMSB15A, TLX1, EDNRA, LOC100289791, MDFI, ZER1, MYH15, CDH20, GPR63, LOC440345, LOC440354, LOC595101, LOC641298, SMG1, HOXC10, KRTAP1-1, ARSD, CPLX3, LMAN1 L, IFNA4, ABCC1, SEMA3E, MRE11A, C1QL1, LIPF, TRIM9, BBOX1, LRRC17, WNT2B, CYP3A4, SI, ANO3, OBSL1, CHRD, MSX2, PSG1, FAM107A, LRRC37B2, ANKLE2, PAX2, UNC5B, ADCYAP1R1, HFE, SYT1, GJC2, LOC100293871, FGF8, ACRV1, NRXN1, GDPD2, RGS4, CELA2A, IFNW1, MLNR, RNF17, LAD1, GLRA2, RASL12, MAGOH2, C6orf54, ZNF214, IKBKG, AP4E1, ZNRF4, OSBPL10, C1orf175, TTC4, PCDHB3, ADRBK1, ITSN1, XAGE1A, XAGE1B, XAGE1C, XAGE1D, XAGE1E, CDH22, FARP2, MYT1, TNC, MUC5AC, SLC6A15, PP14571, SMR3A, SMR3B, RXRG, SNX1, GLP1R, C6orf155, ATP1A2, TFAP4, PNPLA2, DIRAS3, ANO2, TACSTD2, MCM3AP, IL13RA2, TRIM10, RTEL1, PRRX2, TSHB, TIMELESS, FMO1, KIF18A, KIAA1199, CALB2, MFAP3L, PTGER3, EPAS1, SQSTM1, TSPY1, CPM, DLGAP1, CYP4F11, TLX3, PCDHA10, TAOK2, ERC1, TBX2, KALRN, DICER1, PAPPA, KIF5A, DNAJC22, OTUB1, KIAA1644, SEZ6L2, PCNXL2, HMHB1, ERG, SNTB2, GJA5, AGTR2, GJA3, GCK, LRRC61, CNTF, ZFP91, ZFP91-CNTF, PDLIM4, MPPED2, IFNA10, ACTN2, VGLL1, GJA9, LDLR, ANK2, COL1A1, TIMP3, OTOF, AGXT, GLI2, TRMT61A, FOXD2, TMEM212, DENND2A, B3GALT1, SPAG11A, PRDM4, TF, ELF5, GSC2, EPB41 L4B, GYG2, LYZL6, DCHS2, OBP2A, OBP2B, ANGPTL3, MYH11, NES, SLC17A1, RBM15B, CSH1, HTR5A, CYP3A7, HTR2A, KCNV2, TOX3, CLOCK, MAGEA6, FAM12A, COL4A3, S1PR2, NAT8, ACE2, SLC22A6, SLC13A2, MYH4, APBB2, RAP1QGAP, SHOX2, SLCO1A2, ETV1, MAGEA12, PLA2G6, ADRA1A, SYT5, GPR161, SEMA3F, CYP3A43, HOMER2, KCNJ5, PPL, COL17A1, CSHL1, C9orf116, PARK2, UGT2B15, CDK6, FAM174B, CELA2A, CELA2B, SPDEF, EPB41, GAB1, SMR3A, PDE60, COL5A1, ABCA6, DMD, CYLC2, CIDEA, RAG2, HIST1H2BN, FMO6P, MAOA, ANKRD53, HAPLN1, MT1M, EHD2, GAD2, CRISP2, CSN2, SULT1C2, PCDHGA3, SSX3, FGFR2, GPR161, ATN1, CHD5, A4GALT, MYBPH, CSHL1, NCAPH2, CAPN9, CNGB1, BCAM, DRD5, NR5A2, TEF, ELAVL2, DGKB, HTR7P, RHAG, GH2, COL4A6, BMP7, SOSTDC1, SOX14, TAS2R9, LPHN2, MAP1A, OSGIN2, SLC10A2, FAM13C, EMX1, FLJ40330, CHI3L1, CDH16, SPRR1A, LOX, CALCB, GABBR2, CPB2, RASL11B, CCDC81, RUNX1, CPA1, CLCNKA, CLCNKB, FHL5, THSD7A, TFAP2C, SPAG11B, CAP2, PODNL1, SSX4, SSX4B, G6PC, RPE65, TMEM222, KDR, CHP2, GPR64, TPM2, TCEB3B, E2F5, IL5RA, AOC3, ABCF3, CPN2, ACE, NRP2, INPP5J, SMAD9, FAM155A, GART, PIR, ZNF467, ITSN2, NR1D1, THRA, RP11-35N6.1, LAMB1, EPHB3, PLA2R1, RAPGEF4, DNAJC8, ARSJ, TRIM49, GC, CDH2, ATXN3L, BTF3L1, BICC1, FAM186A, PTPRF, TRPC4, TCL6, CYP4A22, FUT6, MUC1, DKFZP434B2016, LOC643313, LDHA, LOC100131613, TRIM3, MLLT10, DZIP1, ANKRD34C, BUB1, CSPG5, FBLN1, GAD2, CLDN1, CHRNA3, SCN11A, TEX11, IL20RA, AKAP5, KBTBD10, MSTN, TLL2, NACAD, UNC93A, PTGER1, OLAH, NHLH2, SERPINA6, KRT17, KCNMA1, PRKCA, STS, LAMA1, GPR88, ACTN2, TREH, AKAP4, DKK4, PRICKLE3, IRS4, TRPV4, PCDH11Y, APBB2, SLCO2A1, DRD2, MTMR7, ZNF471, TF, NRIP2, ST6GALNAC5, COMT, PAH, LRRC19, PRKAR1B, HPR, PRDM5, NCRNA00120, LOC79999, ITSN2, CACNB2, GPR98, PREX2, FAM182B, LAMA4, ARVCF, HAS2, YOD1, PPP2R3A, COL4A1, RBM12B, GSTA3, FAM66D, OR10H2, PTHLH, ZNF674, KRT19, ACCN2, COL6A1, LOC100288442, LOC100289169, LOC728888, LOC729602, NPIPL2, NPIPL3, PDXDC2, SLC37A1, ATP6V1B1, ABI3BP, HR44, ZNF324B, ZNF584, HOXD13, ADH6, IFNA8, MYOZ2, NFATC4, ADAMTS7, FOXL1, GPR17, SLC18A3, MYH6, BOK, FGA, TEAD4, GRM1, EDNRA, C8orf79, METTL7A, FOLH1, RAD54L, SOX11, CNOT3, NTS, MAPK12, DOCK6, DNAJC6, HS3ST3A1, LOC728395, TSPY1, TSPY3, PTH, LAMB4, ALDOB, FLG, MLANA, UBE2D4, LOC100287483, KRT20, POU1F1, SLCO1B3, CLTA, MECOM, C8orf71, SULT2A1, C6orf10, SLC27A6, PRKD1, SYNPO2L, THPO, GABRR1, CFTR, PPP2R3A, DCBLD2, ANP32A, ANP32C, ANP32D, LOC723972, XYLT1, STAB1, STAB1, SASH1, PID1, FUCA1, SASH1, LRRN3, LRRN3 or a combination thereof.
In another embodiment, the gene is ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-5/20/22, IL-9/36, TNFRSF11A/B, TGβ, LTBP4, MEK1/2, Smad2/3/4, PAI-1, SELP, ITFA8, ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-5/13/20/22, IL-9/11/36, TNFRSF11A/B, TGβ, LTBP4, MEK1/2, Smad1/2/3/4/5/6/8, PAI-1, CCL19, IKKg, LTBP1 or a combination thereof. In another embodiment, the gene is SELP, ITFA8, ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-1/1R/5/8/13/20/22, IL-9/11/12/36, TNFRSF11A/B, IFNA4/8/10/17, TGβ, LTBP4, MEK1/2, Smad1/2/3/4/5/6/8, PAI-1, CCL19, IKKg, LTBP1 or a combination thereof.
In one embodiment of any one of the methods, uses, pharmaceutical composition or packages described herein, the gene is TNFSF4, ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-1/5/8/20/22, IL-9/12/36, TNFRSF11A/B, IFNA4/8/10/17, TGβ, LTBP4, MEK1/2, TGFβ type 1 receptor, Smad2/3/4, PAI-1, TNFSF4, SELP, ITFA8, ITGB1/3/5, CXCL5/7, a BMP6 gene, ITGA2/8, ITGβ1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-1/1R/5/8/13/20/22R, IL-9/11/12/36, TNFRSF11A/B, IFNA4/8/10/17, TGβ, LTBP4, MEK1/2, TGFβ type 1 receptor, type II BMPR, smad1/2/3/4/5/6/8, PAI-1, CCL19, IKKg, LTBP1, IL8R (CXCR1/2), Alpha tubulin, BMP2/4/7, MIS, TCF2, LFA-1, VLA-4, IL5R, IL13R, IL20R, ITGB2, IFN gamma, TNF alpha, NKTR, TEF, CLSTN2, LUC7L2, FABP7, TPTE, FSTL1, SF31B1, LIMS1, PDE5A, XPNPEP1, C5orf4, SPANXB1, SPANXB2, SPANXF1, KRT20, TBC1D1, GRHL2, C5orf4, SEPT6, KIAA1199, SSX2IP, TPM1, CDC14B, USP47, MMRN1, CTNNAL1, SMOX, ALOX12, GLRA3, CA2, GUCY1B3, RFPL1, CLEC1B, GNG11, TSPAN32, RGS10, CALD1, PRKAR2B, CYP4F11, CLCA3P, CELSR3, CDC14B, TPM1, SEPT6, PRKG1, MAX, CCDC93, ARMCX6, LOC653354, TUBB2B, HIST1H2AJ, MFAP3L, LIMS1, GNB5, GPRASP1, SRRT, C1orf116, FBXO7, PPM1A, GUCY1B3, CTDSPL, GNAS, IGF2BP3, TPM1, HIST1H2BK, DLG4, WDR48, CALD1, LOC157627, GNB5, ZNF415, ASAP2, PSD3, GNAS, POPDC3, NRGN, ABLIM3, XYLT1, PTGIS, ARHGEF10, PDGFA, PGRMC1, HIST1H2AC, GNAS, CLDN5, MFAP3L, PGRMC1, MYST3, CAPRIN1, CALD1, FBXW7, DNM3, CD84, PRPF4B, RBM25, WASF3, GRAP2, SPARC, TAL1, NENF, XK, GP1BA, HLA-E, CA5A, LYVE1, MARCH6, NAT8B, TRIM58, RET, SDPR, TBXA2R, TMED10, APBA2, MYL9, POU1F1, H2BFS, HIST1H2BK, FAM12B, VCL, GSPT1, ALDOB, LOC150776, SMPD4, SLC37A1, SPARC, GNAS, TAS2R4, CALM3, POM121, POM121C, GRIK2, GREM1, TNNC2, EPS15L2, ENDOD1, RGS6, SF3B1, TMSB15A, ZBTB20, FUT9, ATP9A, MAX, HIST1H2AI, BAT2D1, ABL1, SNCA, GFI1B, CTSA, SNX13, RPA1, FLNA, XPNPEP1, KIF2A, ZBTB33, PSMD11, UBE2N, FOLR1, TSC22D1, PCNP, CELSR3, ACSBG1, RNF11, SEMA3E, MARCH2, PCDH24, SUPT5H, HLA-E, EGF, HLA-C, FLNA, CDK2AP1, LEPROT, SH3TC2, TUBA4A, MTMR1, TF, PRKD1, NAP1L1, DAB2, FUCA1, HIP1, THPO, MAP1B, PARVB, GP1BB, SEPT5, GJA4, PTGS1, GUCY1A3, HIST1H2AG, GNAS, LRBA, HYAL3, GP6, IGHG1, CYP2A13, CDC14B, MAX, KDM2A, CALD1, GNAZ, C19orf22, ARHGAP6, RHOC, RBX1, GP1BB, SEPT5, PRDX6, PRB4, FLNA, HIST1H2BF, RHBDF2, NUP205, SYT1, EGFL8, PPT2, TUBB1, TMC6, FLJ11292, NAP1L1, ALDH1A3, CSNK1E, PRUNE, COL4A3, ZNF221, ILF3, CABP5, RPA1, ARF1, HIST1H2BI, PTGS1, PRKAA1, GNB5, HIST2H4A, HIST2H4B, CYB5R3, TNS1, DCT, GMPR, ABI3BP, GNAS, SASH1, AAK1, XPO6, CTSL2, QSER1, MAP1LC3B, TBX6, CABP2, MRE11A, MAPRE2, TMC6, BDKRB2, MGLL, HRASLS, WHAMML1, WHAMML2, CLU, STC1, C6orf54, PABPN1, PDLIM1, CLU, PHF20, UBL4A, RNF115, HGD, RASGRP2, PNN, SAPS3, SFI1, GOLGA2, HIST2H2BE, SGEF, HGD, DUS1L, MPP1, HLA-E, GRB14, MMD, ZFHX4, CSNK1G2, HIST1H2BE, MPDZ, B2M, TBXA2R, NGFRAP1, CTDSPL, SNCA, CD99, POLS, MPL, HIST1H3F, SFRS8, NR5A2, ZMYM2, C6orf10, TMEM40, RNF43, PRUNE, MSH6, PLCB4, PARVB, TOX3, PKNOX1, RUFY1, SNCA, C10orf81, PDGFA, ASMT, HMGB1, CCDC90A, PROS1, hCG_1757335, RAP1B, MTSS1, GNRHR, LRRN3, MCM3AP, PLOD2, NAPIL1, PLOD2, HOXD13 CASKIN2, MFAP5, PITX2, SNCA, MYLK, PBX1, PRDX6, EIF2AK1, H3F3A, H3F3B, LOC440926, TMEM158, TRIM58, FSTL1, SNCA, TNS1, ATP1B1, C5orf4, LRP12, CTNNAL1, GEM, KIAA1466, ALDH1A2, MAP4K3, SNCA, RAB6B, PSD3, RIPK2, RAMP3, CALD1, CYP2E1, PSD3, PDLIM7, COBLL1, FUT3, SMOX, TGM2, LRRC50, CST6, OR7A17, C6orf145, DLEU2, DLEU2L, CPT2, HGF, TNS1, SPRY1, PLOD2, CD80, KYNU, BCAT1, NHLH1, AHCTF1, HOXA10, MTMR3, VAC14, CLCF1, FGF5, TAL1, SAMD14, ELL2, CHN1, SLC7A1, GRK5, PARD3, VPS37B, CYP2B6, CYP2B7P1, MALL, ALX4, SOX15, KRT5, ESPL1, STARD8, PSD3, KIAA0195, MYO9B, HIP1R, LOC100294412, EFNB1, ERN1, RHD, MFAP3L, PLA1A, POFUT2, C8orf39, CRYBB2, CYP4A11, PVRL2, CLCNKB, MRAS, NFIB, FKSG2, SLC11A2, FZR1, ZNF550, GLP1R, SLC19A1, RTN2, PAPOLA, STC1, GK, EXOSC6, RAPSN, HFE, EHD2, RIOK3, UBE2I, C15orf2, DMD, PRLH, MAP2K2, TP63, DACH1, PPP5C, SLC26A1, NUDT7, KCNJ12, ENTPD7, SLC26A1, PRRG3, RGS6, ZBED2, FICD, ARHGAP1, ARHGDIA, SDHB, AMHR2, ABCA4, TCF20, BGN, CASP7, LPAR4, GNA12, CYP2W1, RAX, C4A, C4B, LOC100292046, LOC100294156, ELAVL4, PXN, ESR2, MYL10, EFS, TFF3, SRPK1, LOC441601, BIRC5, CCT8L2, PPAP2B, CMA1, APOA2, KDELR2, ASCL3, RUNX1, BUB1, SLC6A8, HNRNPC, HNRNPCL1, LOC440563, LOC649330, RIBC2, CLIC4, RAB17, SCML2, SPINLW1, ANK1, EDA2R, HTR4, CDC42EP4, KANK2, ANK1, SYN1, DUX3, DUX4, FRG2C, HPX-2, LOC100134409, LOC652119, LOC653543, LOC653544, LOC653545, LOC728410, PKNOX2, MLLT4, APOA2, PENK, GNAT1, FURIN, SEMA6A, EGFL6, HRH1, TSPAN1, DBC1, TRPC7, MDM2, GPR52, HAMP, PRSS2, GPR107, FLJ11292, FLJ20184, B4GALT1, NKX3-1, ASIP, EFCAB6, GPR20, CA5A, PLK4, TAAR5, SRPX2, CNTD2, AZGP1, TIMP3, RGS6, ADARB1, DYNC1I1, C10orf10, PDIA2, PITX3, HOXC13, LPAR3, CTRC, CTSL2, MUC8, AQP5, UGT1A1, UGT1A10, UGT1A4, UGT1A6, UGT1A8, UGT1A9, KCNQ2, CYP2A13, ZNF155, KIAA0892, ATP2A2, FGF5, FGF18, FUT2, SHROOM2, PRSS3, CREB3L1, MGAT2, PLCE1, MLXIPL, OR10H3, ABCB11, CD84, ARHGEF4, ORC1L, PCIF1, CD177, C1orf116, IFT122, C11orf20, DUSP13, C6orf208, PLA2G5, PRAMEF1, PRAMEF2, CYP4F8, KCNA1, MFAP4, C6, SLC4A3, IL1RAPL1, SERPINE1, ZCCHC14, POLR3G, C16orf8, FLJ14100, SMCHD1, ASCL1, FOXA2, SLC23A2, KLK13, MTSS1L, DNMT3L, RREB1, DNMBP, PKLR, C1orf106, CCDC134, MTSS11, CCDC40, HOXB1, SCNN1B, SEMA4G, RAPGEFL1, MAGEL2, PLSCR2, CHD2, PLCD1, C1orf116, CHRNA2, MBP, CDC42BPA, MYF6, PI15, LOC440895, SBF1, MAST1, GLT8D2, ERBB3, LOH3CR2A, AMH, HR, RDH8, PAWR, DRD3, CCT8, PRELP, SPOCK3, EPS8L3, NXN, SEMA4G, P2RY1, AVL9, TEK, MOGAT2, KLK7, MT1E, MT1H, MT1M, CLDN18, RHBDF2, SIX1, INPP5A, KCNMB3, MAP2K5, GPD1, LPO, LOC729143, MPRIP, WNT7A, RARG, CDH7, MBNL2, RASGRP2, RBMY2FP, MASP1, CASR, EGR4, APOC2, HECW1, HOXB3, IRF5, NNMT, AOC2, ESRRG, LPIN1, ACOT11, CCDC33, MBD2, ZNF323, NTRK2, TMEM151B, GPLD1, LENEP, HNF1B, NXPH3, ALDH1A3, PHF20L1, CKM, PARD6B, CRYGB, HAB1, LARGE, RAB40C, MPL, CHIT1, METTL10, DUS4L, PNLIPRP1, ELL, ST8SIA5, GRIN2B, MC4R, RTDR1, HDAC6, KCNJ13, CPSF1, SPANXC, CNOT4, LAMA2, SLC1A6, ABCA2, KLK11, GFRA3, CYP3A4, SLC1A3, ATP2B2, APBB2, VPS45, GHRHR, HOXD4, PRPH, ADCY2, LEFTY2, CYP1B1, PCP4, C8B, RANBP3, PDE6H, TRIM15, VGLL1, TRIM3, CRKL, ADH7, PSG3, GPR153, MFAP2, FGF13, NAPA, ALDH3A1, MCM10, TLE4, ITPR3, CCDC87, C9orf7, ACTC1, OBSL1, MAP2, CRYM, RNF122, SST, HLA-DRB6, SLC22A17, HSPG2, HIP1, GRIK2, UNKL, GPR144, KIR3DX1, NARFL, UCP3, PLXNA2, BTN1A1, ERCC4, CIITA, EGFR, KRT33A, CLTB, B3GALT5, AP3M2, GJC1, MYO3A, ARHGAP1, PPP2R3A, CLIC4, C20orf195, SIGLEC8, GPRC5A, CACNB1, MYL10, PRLR, OR2S2, NCR2, CHAF1B, EYA3, CDS1, FBXL18, ACTL6B, ZNF821, C16orf71, HBBP1, PLXNA1, CDC45L, MTCP1, PLCB4, PLVAP, PROX1, CYP3A43, IGHG1, RECQL5, IDUA, DLGAP4, PLXNB1, HSD17B14, FOXP3, C19orf26, EPB41L1, RBBP9, GJB4, UPK1B, CYP19A1, LOC55908, CLDN18, C2orf72, NTRK3, NRXN2, SPDEF, IGH@, IGHD, IGHG1, IGHM, LOC100289944, VSIG6, ACRV1, PHLDB1, SORBS1, HAPLN2, FABP3, EFS, ACVR1B, CHST3, UGT2A1, UGT2A2, TAF1, MT4, MFAP3, ETV5, UBQLN3, TBX10, GJB1, ABO, SPINK5, ATAD4, CDH11, CARD14, ALPP, ALPPL2, CBL, LRP4, CDKL2, SSX3, DSG2, SLC45A2, LAMA4, WFDC8, HTR7, EFNB3, TUBB2B, OR7E19P, PMS2L4, ASAP3, FRZB, PDLIM4, PVT1, TFR2, AHI1, TAF4, ADAMTSL2, CLDN4, KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL5A, KIR2DL5B, KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS4, KIR2DS5, KIR3DL2, KIR3DL3, KIR3DP1, LOC727787, RAPGEF5, CRMP1, LDB3, F11, USP46, PTN, IBSP, SLC9A3, FLRT3, TRIM17, FGF17, CAMK1G, GLYR1, CSH1, NTF3, ABHD6, TRIM15, OR52A1, FGFR2, ORAI2, C17orf53, GLP1R, SLIT1, TP63, DDR1, CFTR, DIO2, LETM1, ACSM5, ACTA1, NPR1, KCND3, POPDC3, DNAH3, SPDEF, CLEC4M, SLC30A3, NAGLU, AAK1, DHX34, NNAT, AKAP9, ICMT, FAM189A1, C10orf81, MYOZ1, PKNOX2, MGC31957, PRDM11, RET, IGHG1, XPNPEP2, NTRK2, SLC25A10, NR1I2, GRM8, OR3A3, GIPR, PAN, PACRG, CLN8, ZNF215, TRIO, TTLL5, GRM1, PRKG1, HHLA1, LAMA3, PTN, SLC37A4, HOXC11, SLCO5A1, CA10, RRBP1, SOD3, NTRK3, CYR61, STRA6, SLC6A11, CNOT4, ATN1, BCAP29, NOVA2, RELN, LAMC2, RAD51, PRSS7, DCBLD2, TACR2, RAB11B, OR2J2, VSNL1, IFNA17, DPYSL4, MGC2889, RRBP1, POLQ, OR1A2, PURA, AIF1, CBS, NECAB2, PRKCE, NOX1, INH, EXO1, GPRIN2, PDX1, GPR12, FAM188A, HS3ST3B1, ASCL1, ZNF484, CSH1, BCAN, DDN, DUOX2, MORN1, SLC39A2, CLCN7, RUNX2, TTYH1, ZNF280B, PAX3, LZTS1, SLC8A2, HAB1, KIF1A, ARL4D, UGT2B15, NACA2, THRB, C6orf15, GPR176, WSCD1, PLXNB3, CADM3, HAP1, CYP1A2, SPAM1, IL22RA1, CDC2L5, IRX5, PPFIA2, KDELR3, CEACAM7, KCMF1, DUOX1, CDC27, HIST2H2AA3, CAV3, APOA4, NPR3, PRG3, TBC1D22B, TUSC3, RIMS2, CYP4F12, TBXA2R, HBEGF. PSG9, PYGO1, RASGRF1, SCN2A, KLHL1, DTNB, GREM1, SNCG, C22orf24, PALM, COBLL1, DNPEP, MNS1, NFATC4, DLC1, HSPC072, MCAM, CA12, CSHL1, RPA1N, COL5A2. UGT1A8, UGT1A9, IGH@, IGHA1, IGHG1, IGHG2, IGHG3, IGHM, LOC100126583, LOC100290036, LOC100290320, LOC100293211, LOC652494, TGFB2, ACSM5, ALOX12P2, ERBB4, CLDN16, CIB2, GALR3, MSMB, FABP7, ATXN3, KCNJ5, TRDN, CYP3A43, BAZ2A, ACCN4, SILV, DGCR14, SEMA6C, DIO2, PTHLH, LEP, PDZRN3, RGSL1, GJA4, SLC22A6, RASGRF1, MAPRE2, PVRL1, AKAP1, POMP, SOX21, DNAH9, HOXC5, SERHL2, KIAA0485, ITSN1, B4GALT1, NEK2, NUPR1, CCDC93, EPO, CRABP2, TYRO3, GOLGA2, SEMA3F, BFSP2, NCAM1, FOLH1, SSX2, TMPRSS4, DCN, LPHN3, POU4F3, CEACAM5, BCL3, EXTL3, CCNA1, DDR2, PAX8, SOX5, POU3F1, PEX16, 1L4I1, NUP62, SIGLEC11, ALDOB, GPC3, IGFALS, WDR25, FGF1, OSR2, ARID1A, GYPA, KLK13, PARVB, LILRB5, RIMS2, C19orf21, HOXD1, PRSS3, FLT1, ATP6V1C1, LOX, CRYBB3, CA12, PRKG2, MASP1, LOC728395, LOC728403, TSPY1, PDCD1, GGTLC1, AQP8, IL1F9, KRT16, AICDA, BRD8, C1orf95, OR3A2, PFKFB2, FRZB, PAK3, MEIS2, ZSCAN2, MYH7, VWA1, LSAMP, SRC, UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, DIO1, TADA3L, NFASC, CALCRL, NBLA00301, MAB21L1, FBXO42, COL10A1, CFB, SNX7, FOXN1, SRY, HLF, CLCA3P, DAZ1, DAZ2, DAZ3, DAZ4, GPR3, TMPRSS11E, EMID1, KCNMB2, MUC5AC, SORT1, HIF3A, MAPK4, TCP11L1, ZZEF1, DCAF7, DMWD, CLCA2, VAC14, CSPG5, STMN2, MLLT4, GALNT14, FGF12, MFAP5, SUMO3, HTR3A, GDF5, TSSK1B, CYP2A7P1, MARK1, ATP1B2, TBX6, PAX8, IL1R1, RALYL, OR2B2, TAAR3, C12orf32, IGHG1, LOC642131, DICER1, GLRA3, PPARD, HSPA4L, WNT2, VIPR2, CYP2C9, SRPX2, IGSF1, ALPK3, TFPI, KCNS3, MARCH8, FRMD4B, TACR3, FIGF, PDCD6, TNN, SPANXB1, SPANXB2, SPANXF1, RHBDD3, SPP2, PDE10A, ZNF224, FGL1, PGAM2, CADM4, APOBEC2, SLC9A5, GNAT1, ARHGEF16, SMARCA2, DNAH9, RBM26, WNT2B, KCNK2, NPBWR2, SP2, TMPRSS11D, DENND2A, TNIP3, STC1, DOCK6, ADAM5P, SYDE1, TNPO2, LRTM1, USH1C, PDE12, SRCAP, OR10J1, OR2H2, KCNJ8, RP11-257K9.7, DOCK5, TPD52L1, PAEP, GGA2, PHLDA3, HES2, MLL, PTN, CHRNA6, CIB2, PTPRF, TM7SF4, DAZ1, DAZ2, DAZ3, DAZ4, ALX1, OR2F1, OR2F2, PLAT, HGC6.3, WNT11, PGK2, SNAI2, COL4A6, PRUNE2, ANKS1B, LOC81691, FERMT2, TIMP3, CST8, CAPN6, IDUA, GPR32, AKR1B10, GRHL2, FBXO24, HSF4, IGHG1, HCN2, LRP12, ARHGEF15, UGT1A1, UGT1A10, UGT1A7, UGT1A8, GUCA2A, MDK, ITIH1, EGFR, UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, MYOG, TMSB15A, TLX1, EDNRA, LOC100289791, MDFI, ZER1, MYH15, CDH20, GPR63, LOC440345, LOC440354, LOC595101, LOC641298, SMG1, HOXC10, KRTAP1, ARSD, CPLX3, LMAN1L, IFNA4, ABCC1, SEMA3E, MRE11A, C1QL1, LIPF, TRIM9, BBOX1, LRRC17, WNT2B, CYP3A4, SI, ANO3, OBSL1, CHRD, MSX2, PSG1, FAM107A, LRRC37B2, ANKLE2, PAX2, UNC5B, ADCYAP1R1, HFE, SYT1, GJC2, LOC100293871, FGF8, ACRV1, NRXN1, GDPD2, RGS4, CELA2A, IFNW1, MLNR, RNF17, LAD1, GLRA2, RASL12, MAGOH2, C6orf54, ZNF214, IKBKG, AP4E1, ZNRF4, OSBPL10, C1orf175, TTC4, PCDHB3, ADRBK1, ITSN1, XAGE1A, XAGE1B, XAGE1C, XAGE1D, XAGE1E, CDH22, FARP2, MYT1, TNC, MUC5AC, SLC6A15, PP14571, SMR3A, SMR3B, RXRG, SNX1, GLP1R, C6orf155, ATP1A2, TFAP4, PNPLA2, DIRAS3, ANO2, TACSTD2, MCM3AP, IL13RA2, TRIM10, RTEL1, PRRX2, TSHB, TIMELESS, FMO1, KIF18A, KIAA1199, CALB2, MFAP3L, PTGER3, EPAS1, SQSTM1, TSPY1, CPM, DLGAP1, CYP4F11, TLX3, PCDHA10, TAOK2, ERC1, TBX2, KALRN, DICER1, PAPPA, KIF5A, DNAJC22, OTUB1, KIAA1644, SEZ6L2, PCNXL2, HMHB1, ERG, SNTB2, GJA5, AGTR2, GJA3, GCK, LRRC61, CNTF, ZFP91, ZFP91-CNTF, PDLIM4, MPPED2, IFNA10, ACTN2, VGLL1, GJA9, LDLR, ANK2, COL1A1, TIMP3, OTOF, AGXT, GLI2, TRMT61A, FOXD2, TMEM212, DENND2A, B3GALT1, SPAG11A, PRDM4, TF, ELF5, GSC2, EPB41L4B, GYG2, LYZL6, DCHS2, OBP2A. OBP2B, ANGPTL3, MYH11, NES, SLC17A1, RBM15B, CSH1, HTR5A, CYP3A7, HTR2A, KCNV2, TOX3, CLOCK, MAGEA6, FAM12A, COL4A3, S1PR2, NAT8, ACE2, SLC22A6, SLC13A2, MYH4, APBB2, RAP1GAP, SHOX2, SLCO1A2, ETV1, MAGEA12, PLA2G6, ADRA1A, SYT5, GPR161, SEMA3F, CYP3A43, HOMER2, KCNJ5, PPL, COL17A1, CSHL1, C9orf116, PARK2, UGT2B15, CDK6, FAM174B, CELA2A, CELA2B, SPDEF, EPB41, GAB1, SMR3A, PDE6G, COL5A1, ABCA6, DMD, CYLC2, CIDEA, RAG2, HIST1H2BN, FMO6P, MAOA, ANKRD53, HAPLN1, MT1M, EHD2, GAD2, CRISP2, CSN2, SULT1C2, PCDHGA3, SSX3, FGFR2, GPR161, ATN1, CHD5, A4GALT, MYBPH, CSHL1, NCAPH2, CAPN9, CNGB1, BCAM, DRD5, NR5A2, TEF, ELAVL2, DGKB, HTR7P, RHAG, GH2, COL4A6, BMP7, SOSTDC1, SOX14, TAS2R9, LPHN2, MAP1A, OSGIN2, SLC10A2, FAM13C, EMX1, FLJ40330, CHI3L1, CDH16, SPRR1A, LOX, CALCB, GABBR2, CPB2, RASL11B, CCDC81, RUNX1, CPA1, CLCNKA, CLCNKB, FHL5, THSD7A, TFAP2C, SPAG11B, CAP2, PODNL1, SSX4, SSX4B, G6PC, RPE65, TMEM222, KDR, CHP2, GPR64, TPM2, TCEB3B, E2F5, IL5RA, AOC3, ABCF3, CPN2, ACE, NRP2, INPP5J, SMAD9, FAM155A, GART, PIR, ZNF467, ITSN2, NR1D1, THRA, RP11-35N6.1, LAMB1, EPHB3, PLA2R1, RAPGEF4, DNAJC8, ARSJ, TRIM49, GC, IL12B, CDH2, ATXN3L, BTF3L1, BICC1, FAM186A, PTPRF, TRPC4, TCL6, CYP4A22, FUT6, MUC1, DKFZP434B2016, LOC643313, LDHA, LOC100131613, TRIM3, MLLT10, DZIP1, ANKRD34C, BUB1, CSPG5, FBLN1, GAD2, CLDN1, CHRNA3, SCN11A, TEX11, IL20RA, AKAP5, KBTBD10, MSTN, TLL2, NACAD, UNC93A, PTGER1, OLAH, NHLH2, SERPINA6, KRT17, KCNMA1, PRKCA, STS, LAMA1, GPR88, ACTN2, TREH, AKAP4, DKK4, PRICKLE3, IRS4, TRPV4, PCDH11Y, APBB2, SLCO2A1, DRD2, MTMR7, ZNF471, TF, NRIP2, ST6GALNAC5, COMT, PAH, LRRC19, PRKAR1B, HPR, PRDM5, NCRNA00120, LOC79999, ITSN2, CACNB2, GPR98, PREX2, FAM182B, LAMA4, ARVCF, HAS2, YOD1, PPP2R3A, COL4A1, RBM12B, GSTA3, FAM66D, OR10H2, PTHLH, ZNF674, KRT19, ACCN2, COL6A1, LOC100288442, LOC100289169, LOC728888, LOC729602, NPIPL2, NPIPL3, PDXDC2, SLC37A1, ATP6V1B1, PTN, ABI3BP, HR44, ZNF324B, ZNF584, HOXD13, ADH6, IFNA8, MYOZ2, NFATC4, ADAMTS7, FOXL1, GPR17, SLC18A3, MYH6, BOK, FGA, TEAD4, GRM1, EDNRA, C8orf79, METTL7A, FOLH1, RAD54L, SOX11, CNOT3, NTS, MAPK12, DOCK6, DNAJC6, HS3ST3A1, LOC728395, TSPY1, TSPY3, PTH, LAMB4, ALDOB, FLG, MLANA, UBE2D4, LOC100287483, KRT20, POU1F1, SLCO1B3, CLTA, MECOM, C8orf71, SULT2A1, C6orf10, SLC27A6, PRKD1, SYNPO2L, THPO, GABRR1, CFTR, PPP2R3A, DCBLD2, ANP32A, ANP32C, ANP32D, LOC723972, XYLT1, STAB1, STAB1, SASH1, PID1, FUCA1, SASH1, LRRN3, LRRN3 or any combination thereof.
In another embodiment, the gene is TNFSF4, ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-1/5/8/20/22, IL-9/12/36, TNFRSF11A/B, IFNA4/8/10/17, TGβ, LTBP4, MEK1/2, TGFβ type 1 receptor, Smad2/3/4, PAI-1, TNFSF4, SELP, ITFA8, ITGB1/3/5, CXCL5/7, a BMP6 gene, ITGA2/8, ITGβ1/3/4/5/6, ITGBL1, MMP6/24/26/28, ADAM12/18/22, IL-1/1R/5/8/13/20/22R, IL-9/11/12/36, TNFRSF11A/B, IFNA4/8/10/17, TGβ, LTBP4, MEK1/2, TGFβ type 1 receptor, type II BMPR, smad1/2/3/4/5/6/8, PAI-1, CCL19, IKKg, LTBP1 or any combination thereof. In yet another embodiment, the gene is TNFSF4, ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-1/5/8/20/22, IL-9/12/36, TNFRSF11A/B, IFNA4/8/10/17, TGβ, LTBP4, MEK1/2, TGFβ type 1 receptor, Smad2/3/4, PAI-1 or any combination thereof.
The subject invention also provides a method of treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome with laquinimod, comprising the steps of: a) determining whether the subject is a laquinimod responder by evaluating expression of a biomarker in the subject, and b) administering to the subject an amount of laquinimod effective to treat the subject only if the subject is identified as a laquinimod responder, so as to thereby treat the subject, wherein the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
The subject invention also provides a method for treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome comprising the steps of: a) administering to the subject a therapeutically effective amount of laquinimod, b) determining whether the subject is a laquinimod responder by evaluating expression of a biomarker in the subject; and c) administering to the subject an amount of laquinimod effective to treat the subject only if the subject is identified as a laquinimod responder, or modifying the administration of laquinimod to the subject if the subject is not identified as a laquinimod responder, so as to thereby treat the subject, wherein the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
In one embodiment, the subject is identified as a laquinimod responder if the biomarker is up-regulated in the subject. In another embodiment, the subject is identified as a laquinimod responder if the biomarker is suppressed in the subject.
In one embodiment, the gene associated with inflammatory response is a gene associated with or involved in TGFb signaling, IL-12 signaling, the pathway of adhesion of phagocytes, chemotaxis of neutrophils, transmigration of leukocytes, caveolar mediated endocytosis, clathrin mediated endocytosis, and/or leukocyte extravasation signaling.
In another embodiment, the gene associated with cellular movement is a gene associated with or involved in adhesion and migration of phagocytes, chemotaxis of neutrophils, transmigration of leukocytes, invasion of cells, adhesion of cells, and/or leukocyte extravasation signaling.
In another embodiment, the gene associated with cell signaling is a gene associated with or involved in the pathway of adhesion of cells and/or neurotransmission.
In another embodiment, the gene associated with cell development is a gene associated with or involved in the pathway of G protein coupled receptor signaling, arachidonic acid metabolism and/or TGFβ signaling.
In another embodiment, the gene associated with hematological system is a gene associated with or involved in the pathway of aggregation of blood platelets, activation of blood platelets, aggregation of blood cells, coagulation of blood, intrinsic prothrombin activation pathway and/or coagulation system.
In another embodiment, the gene is TNFSF4, SELP, ITFA8, ITGB1/3/5, CXCL5/7, a BMP6 gene, ITGA2/8, ITGβ1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-1/1R/5/8/13/20/22R, IL-9/11/12/36, TNFRSF11A/B, IFNA4/8/10/17, TGβ, LTBP4, MEK1/2, TGFβ type 1 receptor, type II BMPR, smad1/2/3/4/5/6/8, PAI-1, CCL19, IKKg, LTBP1 or a combination thereof.
In one embodiment of any one of the methods, uses, pharmaceutical composition or packages described herein, the gene is ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-5/20/22, IL-9/36, TNFRSF11A/B, TGβ, LTBP4, MEK1/2, Smad2/3/4, PAI-1, SELP, ITFA8, ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-5/13/20/22, IL-9/11/36, TNFRSF11A/B, TGβ, LTBP4, MEK1/2, Smad1/2/3/4/5/6/8, PAI-1, CCL19, IKKg, LTBP1, Alpha tubulin, BMP4/7, MIS, TCF2, IL5R, IL13R, IL20R, ITGB2, NKTR, TEF, CLSTN2, LUC7L2, FABP7, TPTE, FSTL1, SF3B1, LIMS1, PDE5A, XPNPEP1, C5orf4, SPANXB1, SPANXB2, SPANXF1, KRT20, TBC1D1, GRHL2, C5orf4, SEPT6, KIAA1199, SSX2IP, TPM1, CDC14B, USP47, MMRN1, CTNNAL1, SMOX, ALOX12, GLRA3, CA2, GUCY1B3, RFPL1, CLEC1B, GNG11, TSPAN32, RGS10, CALD1, PRKAR2B, CYP4F11, CLCA3P, CELSR3, CDC14B, TPM1, SEPT6, PRKG1, MAX, CCDC93, ARMCX6, LOC653354, TUBB2B, HIST1H2AJ, MFAP3L, LIMS1, GNB5, GPRASP1, SRRT, C1orf116, FBXO7, PPM1A, GUCY1B3, CTDSPL, GNAS, IGF2BP3, TPM1, HIST1H2BK, DLG4, WDR48, CALD1, LOC157627, GNB5, ZNF415, ASAP2, PSD3, GNAS, POPDC3, NRGN, ABLIM3, XYLT1, PTGIS, ARHGEF10, PDGFA, PGRMC1, HIST1H2AC, GNAS, CLDN5, MFAP3L, PGRMC1, MYST3, CAPRIN1, CALD1, FBXW7, DNM3, CD84, PRPF4B, RBM25, WASF3, GRAP2, SPARC, TAL1, NENF, XK, GP1BA, HLA-E, CA5A, LYVE1, MARCH6, NAT8B, TRIM58, RET, SDPR, TBXA2R, TMED10, APBA2, MYL9, POU1F1, H2BFS, HIST1H2BK, FAM12B, VCL, GSPT1, ALDOB, LOC150776, SMPD4, SLC37A1, SPARC, GNAS, TAS2R4, CALM3, POM121, POM121C, GRIK2, GREM1, TNNC2, EPS15L2, ENDOD1, RGS6, SF3B1, TMSB15A, ZBTB20, FUT9, ATP9A, MAX, HIST1H2AI, BAT2D1, ABL1, SNCA, GFI1B, CTSA, SNX13, RPA1, FLNA, XPNPEP1, KIF2A, ZBTB33, PSMD11, UBE2N, FOLR1, TSC22D1, PCNP, CELSR3, ACSBG1, RNF11, SEMA3E, MARCH2, PCDH24, SUPT5H, HLA-E, EGF, HLA-C, FLNA, CDK2AP1, LEPROT, SH3TC2, TUBA4A, MTMR1, TF, PRKD1, NAP1L1, DAB2, FUCA1, HIP1, THPO, MAP1B, PARVB, GP1BB, SEPT5, GJA4, PTGS1, GUCY1A3, HIST1H2AG, GNAS, LRBA, HYAL3, GP6, IGHG1, CYP2A13, CDC14B, MAX, KDM2A, CALD1, GNAZ, C19orf22, ARHGAP6, RHOC, RBX1, GP1BB, SEPT5, PRDX6, PRB4, FLNA, HIST1H2BF, RHBDF2, NUP205, SYT1, EGFL8, PPT2, TUBB1, TMC6, FLJ11292, NAP1L1, ALDH1A3, CSNK1E, PRUNE, COL4A3, ZNF221, ILF3, CABP5, RPA1, ARF1, HIST1H2BI, PTGS1, PRKAA1, GNB5, HIST2H4A, HIST2H4B, CYB5R3, TNS1, DCT, GMPR, ABI3BP, GNAS, SASH1, AAK1, XPO6, CTSL2, QSER1, MAP1LC3B, TBX6, CABP2, MRE11A, MAPRE2, TMC6, BDKRB2, MGLL, HRASLS, WHAMML1, WHAMML2, CLU, STC1, C6orf54, PABPN1, PDLIM1, CLU, PHF20, UBL4A, RNF115, HGD, RASGRP2, PNN, SAPS3, SFI1, GOLGA2, HIST2H2BE, SGEF, HGD, DUS1L, MPP1, HLA-E, GRB14, MMD, ZFHX4, CSNK1G2, HIST1H2BE, MPDZ, B2M, TBXA2R, CTDSPL, SNCA, CD99, POLS, MPL, HIST1H3F, SFRS8, NR5A2, ZMYM2, C6orf10, TMEM40, RNF43, PRUNE, MSH6, PLCB4, PARVB, TOX3, PKNOX1, RUFY1, SNCA, C10orf81, PDGFA, ASMT, HMGB1, CCDC90A, PROS1, hCG_1757335, RAP1B, MTSS1, GNRHR, LRRN3, MCM3AP, PLOD2, NAPIL1, PLOD2, HOXD13 CASKIN2, MFAP5, PITX2, SNCA, MYLK, PBX1, PRDX6, H3F3A, H3F3B, LOC440926, TMEM158, TRIM58, FSTL1, SNCA, TNS1, ATP1B1, C5orf4, LRP12, CTNNAL1, GEM, KIAA1466, ALDH1A2, MAP4K3, SNCA, RAB6B, PSD3, RIPK2, RAMP3, CALD1, CYP2E1, PSD3, PDLIM7, COBLL1, FUT3, SMOX, TGM2, LRRC50, CST6, OR7A17, C6orf145, DLEU2, DLEU2L, CPT2, HGF, TNS1, SPRY1, PLOD2, CD80, KYNU, BCAT1, NHLH1, AHCTF1, HOXA10, MTMR3, VAC14, CLCF1, FGF5, TAL1, SAMD14, ELL2, CHN1, SLC7A1, GRK5, PARD3, VPS37B, CYP2B6, CYP2B7P1, MALL, ALX4, SOX15, KRT5, ESPL1, STARD8, PSD3, KIAA0195, MYO9B, HIP1R, LOC100294412, EFNB1, ERN1, RHD, MFAP3L, PLA1A, POFUT2, C8orf39, CRYBB2, CYP4A11, PVRL2, CLCNKB, MRAS, NFIB, FKSG2, SLC11A2, FZR1, ZNF550, GLP1R, SLC19A1, RTN2, PAPOLA, STC1, GK, EXOSC6, RAPSN, HFE, EHD2, RIOK3, UBE2I, C15orf2, DMD, PRLH, MAP2K2, TP63, DACH1, PPP5C, SLC26A1, NUDT7, KCNJ12, ENTPD7, SLC26A1, PRRG3, RGS6, ZBED2, FICD, ARHGAP1, ARHGDIA, SDHB, AMHR2, ABCA4, TCF20, BGN, CASP7, LPAR4, GNA12, CYP2W1, RAX, C4A, C4B, LOC100292046, LOC100294156, PXN, ESR2, MYL10, EFS, TFF3, SRPK1, LOC441601, BIRC5, CCT8L2, PPAP2B, CMA1, APOA2, KDELR2, ASCL3, RUNX1, BUB1, SLC6A8, HNRNPC, HNRNPCL1, LOC440563, LOC649330, RIBC2, CLIC4, RAB17, SCML2, SPINLW1, ANK1, EDA2R, HTR4, CDC42EP4, KANK2, ANK1, SYN1, DUX3, DUX4, FRG2C, HPX-2, LOC100134409, LOC652119, LOC653543, LOC653544, LOC653545, LOC728410, PKNOX2, MLLT4, APOA2, PENK, GNAT1, FURIN, SEMA6A, EGFL6, HRH1, TSPAN1, DBC1, TRPC7, GPR52, HAMP, PRSS2, GPR107, FLJ11292, FLJ20184, B4GALT1, NKX3-1, ASIP, EFCAB6, GPR20, CA5A, PLK4, TAAR5, SRPX2, CNTD2, AZGP1, TIMP3, RGS6, ADARB11, DYNC1I1, C10orf10, PDIA2, PITX3, HOXC13, LPAR3, CTRC, CTSL2, MUC8, AQP5, UGT1A1, UGT1A10, UGT1A4, UGT1A6, UGT1A8, UGT1A9, KCNQ2, CYP2A13, ZNF155, KIAA0892, ATP2A2, FGF5, FGF18, FUT2, SHROOM2, PRSS3, CREB3L1, MGAT2, PLCE1, MLXIPL, OR10H3, ABCB11, CD84, ARHGEF4, ORC1L, PCIF1, CD177, C1orf116, IFT122, C11orf20, DUSP13, C6orf208, PLA2G5, PRAMEF1, PRAMEF2, CYP4F8, KCNA1, MFAP4, SLC4A3, IL1RAPL1, SERPINE1, ZCCHC14, POLR3G, C16orf8, FLJ14100, SMCHD1, ASCL1, FOXA2, SLC23A2, KLK13, MTSS1L, DNMT3L, RREB1, DNMBP, PKLR, C1orf106, CCDC134, MTSS1, CCDC40, HOXB1, SCNN1B, SEMA4G, RAPGEFL1, MAGEL2, PLSCR2, CHD2, PLCD1, C1orf116, CHRNA2, MBP, CDC42BPA, MYF6, PI15, LOC440895, SBF1, MAST1, GLT8D2, ERBB3, LOH3CR2A, AMH, HR, RDH8, PAWR, DRD3, CCT8, PRELP, SPOCK3, EPS8L3, NXN, SEMA4G3, P2RY1, AVL9, TEK, MOGAT2, KLK7, MT1E, MT1H, MT1M, CLDN18, RHBDF2, SIX1, INPP5A, KCNMB3, MAP2K5, GPD1, LPO, LOC729143, MPRIP, WNT7A, RARG, CDH7, MBNL2, RASGRP2, RBMY2FP, MASP1, CASR, EGR4, APOC2, HECW1, HOXB3, IRF5, NNMT, AOC2, ESRRG, LPIN1, ACOT11, CCDC33, MBD2, ZNF323, NTRK2, TMEM151B, GPLD1, LENEP, HNF1B, NXPH3, ALDH1A3, PHF20L1, CKM, PARD6B, CRYGB, HAB1, LARGE, RAB40C, MPL, CHIT1, METTL10, DUS4L, PNLIPRP1, ELL, ST8SIA5, GRIN2B, MC4R, RTDR1, HDAC6, KCNJ13, CPSF1, SPANXC, CNOT4, LAMA2, SLC1A6, ABCA2, KLK11, GFRA3, CYP3A4, SLC1A3, ATP2B2, APBB2, VPS45, GHRHR, HOXD4, PRPH, ADCY2, LEFTY2, CYP1B1, PCP4, C8B, RANBP3, PDE6H, TRIM15, VGLL1, TRIM3, CRKL, ADH7, PSG3, GPR153, MFAP2, FGF13, NAPA, ALDH3A1, MCM10, TLE4, ITPR3, CCDC87, C9orf7, ACTC1, OBSL1, MAP2, CRYM, RNF122, SST, HLA-DRB6, SLC22A17, HSPG2, HIP1, GRIK2, UNKL, GPR144, KIR3DX1, NARFL, UCP3, PLXNA2, BTN1A1, ERCC4, CIITA, EGFR, KRT33A, CLTB, B3GALT5, AP3M2, GJC1, MYO3A, ARHGAP1, PPP2R3A, CLIC4, C20orf19S, SIGLEC8, GPRC5A, CACNB1, MYL10, PRLR, OR2S2, NCR2, CHAF1B, EYA3, CDS1, FBXL18, ACTL6B, ZNF821, C16orf71, HBBP1, PLXNA1, CDC45L, MTCP1, PLCB4, PLVAP, PROX1, CYP3A43, IGHG1, RECQL5, IDUA, DLGAP4, PLXNB1, HSD17B14, FOXP3, C19orf26, EPB41L1, RBBP9, GJB4, UPK1B, CYP19A1, LOC55908, CLDN18, C2orf72, NTRK3, NRXN2, SPDEF, IGH@, IGHD, IGHG1, IGHM, LOC100289944, VSIG6, ACRV1, PHLDB1, SORBS1, HAPLN2, FABP3, EFS, ACVR1B, CHST3, UGT2A1, UGT2A2, TAF1, MT4, MFAP3, ETV5, UBQLN3, TBX10, GJB1, ABO, SPINK5, ATAD4, CDH11, CARD14, ALPP, ALPPL2, CBL, LRP4, CDKL2, SSX3, DSG2, SLC45A2, LAMA4, WFDC8, HTR7, EFNB3, TUBB2B, OR7E19P, PMS2L4, ASAP3, FRZB, PDLIM4, PVT1, TFR2, AHI1, TAF4, ADAMTSL2, CLDN4, KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL5A, KIR2DL5B, KIR2DS1, KIR2DS2, KIR2DS4, KIR2DS5, KIR3DL2, KIR3DL3, KIR3 DP1, LOC727787, RAPGEF5, CRMP1, LDB3, F11, USP46, IBSP, SLC9A3, FLRT3, TRIM17, FGF17, CAMK1G, GLYR1, CSH1, NTF3, ABHD6, TRIM15, OR52A1, FGFR2, ORAI2, C17orf53, GLP1R, SLIT1, TP63, DDR1, CFTR, DIO2, LETM1, ACSM5, ACTA1, NPR1, KCND3, POPDC3, DNAH3, SPDEF, CLEC4M, SLC30A3, NAGLU, AAK1, DHX34, NNAT, AKAP9, ICMT, FAM189A1, C10orf81, MYOZ1, PKNOX2, MGC31957, PRDM11, RET, IGHG1, XPNPEP2, NTRK2, SLC25A10, NR1I2, GRM8, OR3A3, GIPR, PAH, PACRG, CLN8, ZNF215, TRIO, TTLL5, GRM1, PRKG1, HHLA1, LAMA3, SLC37A4, HOXC11, SLCO5A1, CA10, RRBP1, SOD3, NTRK3, CYR61, STRA6, SLC6A11, CNOT4, ATN1, BCAP29, NOVA2, RELN, LAMC2, RAD51, PRSS7, DCBLD2, TACR2, RAB11B, OR2J2, VSNL1, IFNA17, DPYSL4, MGC2889, RRBP1, POLQ, OR1A2, PURA, AIF1, CBS, NECAB2, PRKCE, NOX1, IHH, EXO1, GPRIN2, PDX1, GPR12, FAM188A, HS3ST3B1, ASCL1, ZNF484, CSH1, BCAN, DDN, DUOX2, MORN1, SLC39A2, CLCN7, RUNX2, TTYH1, ZNF280B, PAX3, LZTS1, SLC8A2, HAB1, KIF1A, ARL4D, UGT2B15, NACA2, THRB, C6orf15, GPR176, WSCD1, PLXNB3, CADM3, HAP1, CYP1A2, SPAM1, IL22RA1, CDC2L5, IRX5, PPFIA2, KDELR3, CEACAM7, KCMF1, DUOX1, CDC27, HIST2H2AA3, CAV3, APOA4, NPR3, PRG3, TBC1D22B, TUSC3, RIMS2, CYP4F12, TBXA2R, HBEGF, PSG9, PYGO1, RASGRF1, SCN2A, KLHL1, DTNB, GREM1, SNCG, C22orf24, PALM, COBLL1, DNPEP, MNS1, NFATC4, DLC1, HSPC072, MCAM, CA12, CSHL1, RPA1N, COL5A2, UGT1A8, UGT1A9, IGH@, IGHA1, IGHG1, IGHG2, IGHG3, IGHM, LOC100126583, LOC100290036, LOC100290320, LOC100293211, LOC652494, ACSM5, ALOX12P2, ERBB4, CLDN16, CIB2, GALR3, MSMB, FABP7, ATXN3, KCNJ5, TRDN, CYP3A43, BAZ2A, ACCN4, SILV, DGCR14, SEMA6C, DIO2, PTHLH, LEP, PDZRN3, RGSL1, GJA4, SLC22A6, RASGRF1, MAPRE2, PVRL1, AKAP1, POMP, SOX21, DNAH9, HOXC5, SERHL2, KIAA0485, ITSN1, B4GALT1, NEK2, NUPR1, CCDC93, EPO, CRABP2, TYRO3, GOLGA2, SEMA3F, BFSP2, NCAM1, FOLH1, SSX2, TMPRSS4, DCN, LPHN3, POU4F3, CEACAM5, BCL3, EXTL3, CCNA1, DDR2, PAX8, SOX5, POU3F1, PEX16, NUP62, SIGLEC11, ALDOB, GPC3, IGFALS, WDR25, FGF1, OSR2, ARID1A, GYPA, KLK13, PARVB, LILRB5, RIMS2, C19orf21, HOXD1, PRSS3, FLT1, ATP6V1C1, LOX, CRYBB3, CA12, PRKG2, MASP1, LOC728395, LOC728403, TSPY1, PDCD1, GGTLC1, AQP8, KRT16, AICDA, BRD8, C1orf95, OR3A2, PFKFB2, FRZB, PAK3, MEIS2, ZSCAN2, MYH7, VWA1, LSAMP, SRC, UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, DIO1, TADA3L, NFASC, CALCRL, NBLA00301, MAB21L1, FBXO42, COL10A1, CFB, SNX7, FOXN1, SRY, HLF, CLCA3P, DAZ1, DAZ2, DAZ3, DAZ4, GPR3, TMPRSS11E, EMID1, KCNMB2, MUC5AC, SORT1, HIF3A, MAPK4, TCP11L1, ZZEF1, DCAF7, DMWD, CLCA2, VAC14, CSPG5, STMN2, MLLT4, GALNT14, FGF12, MFAP5, SUMO3, HTR3A, GDF5, TSSK1B, CYP2A7P1, MARK1, ATP1B2, TBX6, PAX8, IL1R1, RALYL, OR2B2, TAAR3, C12orf32, IGHG1, LOC642131, DICER1, GLRA3, PPARD, HSPA4L, WNT2, VIPR2, CYP2C9, SRPX2, IGSF1, ALPK3, TFPI, KCNS3, MARCH8, FRMD4B, TACR3, FIGF, PDCD6, TNN, SPANXB1, SPANXB2, SPANXF1, RHBDD3, SPP2, PDE10A, ZNF224, FGL1, PGAM2, CADM4, APOBEC2, SLC9A5, GNAT1, ARHGEF16, SMARCA2, DNAH9, RBM26, WNT2B, KCNK2, NPBWR2, SP2, TMPRSS11D, DENND2A, TNIP3, STC1, DOCK6, ADAM5P, SYDE1, TNPO2, LRTM1, USH1C, PDE12, SRCAP, OR10J1, OR2H2, KCNJ8, RP11-257K9.7, DOCK5, TPD52L1, PAEP, GGA2, PHLDA3, HES2, MLL, CHRNA6, CIB2, PTPRF, TM7SF4, DAZ1, DAZ2, DAZ3, DAZ4, ALX1, OR2F1, OR2F2, PLAT, HGC6.3, WNT11, PGK2, SNAI2, COL4A6, PRUNE2, ANKS1B, LOC81691, FERMT2, TIMP3, CST8, CAPN6, IDUA, GPR32, AKR1B10, GRHL2, FBXO24, HSF4, IGHG1, HCN2, LRP12, ARHGEF115, UGT1A1, UGT1A10, UGT1A7, UGT1A8, GUCA2A, ITIH1, EGFR, UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, MYOG, TMSB15A, TLX1, EDNRA, LOC100289791, MDFI, ZER1, MYH15, CDH20, GPR63, LOC440345, LOC440354, LOC595101, LOC641298, SMG1, HOXC10, KRTAP1-1, ARSD, CPLX3, LMAN1L, IFNA4, ABCC1, SEMA3E, MRE11A, C1QL1, LIPF, TRIM9, BBOX1, LRRC17, WNT2B, CYP3A4, SI, ANO3, OBSL1, CHRD, MSX2, PSG1, FAM107A, LRRC37B2, ANKLE2, PAX2, UNC5B, ADCYAP1R1, HFE, SYT1, GJC2, LOC100293871, FGF8, ACRV1, NRXN1, GDPD2, RGS4, CELA2A, IFNW1, MLNR, RNF17, LAD1, GLRA2, RASL12, MAGOH2, C6orf5S4, ZNF214, IKBKG, AP4E1, ZNRF4, OSBPL10, C1orf175, TTC4, PCDHB3, ADRBK1, ITSN1, XAGE1A, XAGE1B, XAGE1C, XAGE1D, XAGE1E, CDH22, FARP2, MYT1, TNC, MUC5AC, SLC6A15, PP14571, SMR3A, SMR3B, RXRG, SNX1, GLP1R, C6orf155, ATP1A2, TFAP4, PNPLA2, DIRAS3, ANO2, TACSTD2, MCM3AP, IL13RA2, TRIM10, RTEL1, PRRX2, TSHB, TIMELESS, FMO1, KIF18A, KIAA1199, CALB2, MFAP3L, PTGER3, EPAS1, SQSTM1, TSPY1, CPM, DLGAP1, CYP4F11, TLX3, PCDHA10, TAOK2, ERC1, TBX2, KALRN, DICER1, PAPPA, KIF5A, DNAJC22, OTUB1, KIAA1644, SEZ6L2, PCNXL2, HMHB1, ERG, SNTB2, GJA5, AGTR2, GJA3, GCK, LRRC61, CNTF, ZFP91, ZFP91-CNTF, PDLIM4, MPPED2, IFNA10, ACTN2, VGLL1, GJA9, LDLR, ANK2, COL1A1, TIMP3, OTOF, AGXT, GLI2, TRMT61A, FOXD2, TMEM212, DENND2A, B3GALT1, SPAG11A, PRDM4, TF, ELF5, GSC2, EPB41 L4B, GYG2, LYZL6, DCHS2, OBP2A, OBP2B, ANGPTL3, MYH11, NES, SLC17A1, RBM15B, CSH1, HTR5A, CYP3A7, HTR2A, KCNV2, TOX3, CLOCK, MAGEA6, FAM12A, COL4A3, S1PR2, NAT8, ACE2, SLC22A6, SLC13A2, MYH4, APBB2, RAP1GAP, SHOX2, SLCO1A2, ETV1, MAGEA12, PLA2G6, ADRA1A, SYT5, GPR161, SEMA3F, CYP3A43, HOMER2, KCNJ5, PPL, COL17A1, CSHL1, C9orf116, PARK2, UGT2B15, CDK6, FAM174B, CELA2A, CELA2B, SPDEF, EPB41, GAB1, SMR3A, PDE60, COL5A1, ABCA6, DMD, CYLC2, CIDEA, RAG2, HIST1H2BN, FMO6P, MAOA, ANKRD53, HAPLN1, MT1M, EHD2, GAD2, CRISP2, CSN2, SULT1C2, PCDHGA3, SSX3, FGFR2, GPR161, ATN1, CHD5, A4GALT, MYBPH, CSHL1, NCAPH2, CAPN9, CNGB1, BCAM, DRD5, NR5A2, TEF, ELAVL2, DGKB, HTR7P, RHAG, GH2, COL4A6, BMP7, SOSTDC1, SOX14, TAS2R9, LPHN2, MAP1A, OSGIN2, SLC10A2, FAM13C, EMX1, FLJ140330, CHI3L1, CDH16, SPRR1A, LOX, CALCB, GABBR2, CPB2, RASL11B, CCDC81, RUNX1, CPA1, CLCNKA, CLCNKB, FHL5, THSD7A, TFAP2C, SPAG11B, CAP2, PODNL1, SSX4, SSX4B, G6PC, RPE65, TMEM222, KDR, CHP2, GPR64, TPM2, TCEB3B, E2F5, IL5RA, AOC3, ABCF3, CPN2, ACE, NRP2, INPP5J, SMAD9, FAM155A, GART, PIR, ZNF467, ITSN2, NR1D1, THRA, RP11-35N6.1, LAMB1, EPHB3, PLA2R1, RAPGEF4, DNAJC8, ARSJ, TRIM49, GC, CDH2, ATXN3L, BTF3L1, BICC1, FAM186A, PTPRF, TRPC4, TCL6, CYP4A22, FUT6, MUC1, DKFZP434B2016, LOC643313, LDHA, LOC100131613, TRIM3, MLLT10, DZIP1, ANKRD34C, BUB1, CSPG5, FBLN1, GAD2, CLDN1, CHRNA3, SCN11A, TEX11, IL20RA, AKAP5, KBTBD10, MSTN, TLL2, NACAD, UNC93A, PTGER1, OLAH, NHLH2, SERPINA6, KRT17, KCNMA1, PRKCA, STS, LAMA1, GPR88, ACTN2, TREH, AKAP4, DKK4, PRICKLE3, IRS4, TRPV4, PCDH11Y, APBB2, SLCO2A1, DRD2, MTMR7, ZNF471, TF, NRIP2, ST6GALNAC5, COMT, PAH, LRRC19, PRKAR1B, HPR, PRDM5, NCRNA00120, LOC79999, ITSN2, CACNB2, GPR98, PREX2, FAM182B, LAMA4, ARVCF, HAS2, YOD1, PPP2R3A, COL4A1, RBM12B, GSTA3, FAM66D, OR10H2, PTHLH, ZNF674, KRT19, ACCN2, COL6A1, LOC100288442, LOC100289169, LOC728888, LOC729602, NPIPL2, NPIPL3, PDXDC2, SLC37A1, ATP6V1B1, ABI3BP, HR44, ZNF324B, ZNF584, HOXD13, ADH6, IFNA8, MYOZ2, NFATC4, ADAMTS7, FOXL1, GPR17, SLC18A3, MYH6, BOK, FGA, TEAD4, GRM1, EDNRA, C8orf79, METTL7A, FOLH1, RAD54L, SOX11, CNOT3, NTS, MAPK12, DOCK6, DNAJC6, HS3ST3A1, LOC728395, TSPY1, TSPY3, PTH, LAMB4, ALDOB, FLG, MLANA, UBE2D4, LOC100287483, KRT20, POU1F1, SLCO1B3, CLTA, MECOM, C8orf71, SULT2A1, C6orf1, SLC27A6, PRKD1, SYNPO2L, THPO, GABRR1, CFTR, PPP2R3A, DCBLD2, ANP32A, ANP32C, ANP32D, LOC723972, XYLT1, STAB1, STAB1, SASH1, PID1, FUCA1, SASH1, LRRN3, LRRN3 or a combination thereof.
In another embodiment, the gene is ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-5/20/22, IL-9/36, TNFRSF11A/B, TGβ, LTBP4, MEK1/2, Smad2/3/4, PAI-1, SELP, ITFA8, ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-5/13/20/22, IL-9/11/36, TNFRSF11A/B, TGβ, LTBP4, MEK1/2, Smad1/2/3/4/5/6/8, PAI-1, CCL19, IKKg, LTBP1 or a combination thereof. In another embodiment, the gene is SELP, ITFA8, ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-1/1R/5/8/13/20/22, IL-9/11/12/36, TNFRSF11A/B, IFNA4/8/10/17, TGβ, LTBP4, MEK1/2, Smad1/2/3/4/5/6/8, PAI-1, CCL19, IKKg, LTBP1 or a combination thereof.
In one embodiment of any one of the methods, uses, pharmaceutical composition or packages described herein, the gene is TNFSF4, ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-1/5/8/20/22, IL-9/12/36, TNFRSF11A/B, IFNA4/8/10/17, TGβ, LTBP4, MEK1/2, TGFβ type 1 receptor, Smad2/3/4, PAI-1, TNFSF4, SELP, ITFA8, ITGB1/3/5, CXCL5/7, a BMP6 gene, ITGA2/8, ITGβ1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-1/1R/5/8/13/20/22R, IL-9/11/12/36, TNFRSF11A/B, IFNA4/8/10/17, TGβ, LTBP4, MEK1/2, TGFβ type 1 receptor, type II BMPR, smad1/2/3/4/5/6/8, PAI-1, CCL19, IKKg, LTBP1, IL8R (CXCR1/2), Alpha tubulin, BMP2/4/7, MIS, TCF2, LFA-1, VLA-4, IL5R, IL13R, IL2OR, ITGB2, IFN gamma, TNF alpha, NKTR, TEF, CLSTN2, LUC7L2, FABP7, TPTE, FSTL1, SF3B1, LIMS1, PDE5A, XPNPEP1, C5orf4, SPANXB1, SPANXB2, SPANXF1, KRT20, TBC1D1, GRHL2, C5orf4, SEPT6, KIAA1199, SSX2IP, TPM1, CDC14B, USP47, MMRN1, CTNNAL1, SMOX, ALOX12, GLRA3, CA2, GUCY1B3, RFPL1, CLEC1B, GNG11, TSPAN32, RGS10, CALD1, PRKAR2B, CYP4F11, CLCA3P, CELSR3, CDC114B, TPM1, SEPT6, PRKG1, MAX, CCDC93, ARMCX6, LOC653354, TUBB2B, HIST1H2AJ, MFAP3L, LIMS1, GNB5, GPRASP1, SRRT, C1orf116, FBXO7, PPM1A, GUCY1B3, CTDSPL, GNAS, IGF2BP3, TPM1, HIST1H2BK, DLG4, WDR48, CALD1, LOC157627, GNB5, ZNF415, ASAP2, PSD3, GNAS, POPDC3, NRGN, ABLIM3, XYLT1, PTGIS, ARHGEF10, PDGFA, PGRMC1, HIST1H2AC, GNAS, CLDN5, MFAP3L, PGRMC1, MYST3, CAPRIN1, CALD1, FBXW7, DNM3, CD84, PRPF4B, RBM25, WASF3, GRAP2, SPARC, TAL1, NENF, XK, GP1BA, HLA-E, CA5A, LYVE1, MARCH6, NAT8B, TRIM58, RET. SDPR, TBXA2R, TMED10, APBA2, MYL9, POU1F1, H2BFS, HIST1H2BK, FAM12B, VCL, GSPT1, ALDOB, LOC150776, SMPD4, SLC37A1, SPARC, GNAS, TAS2R4, CALM3, POM121, POM121C, GRIK2, GREM1, TNNC2, EPS15L2, ENDOD1, RGS6, SF3B1, TMSB15A, ZBTB20, FUT9, ATP9A, MAX, HIST1H2AI, BAT2D1, ABL1, SNCA, GFI1B, CTSA, SNX13, RPA1, FLNA, XPNPEP1, KIF2A, ZBTB33, PSMD11, UBE2N, FOLR1, TSC22D1, PCNP, CELSR3, ACSBG1, RNF11, SEMA3E, MARCH2, PCDH24, SUPT5H, HLA-E, EGF, HLA-C, FLNA, CDK2AP1, LEPROT, SH3TC2, TUBA4A, MTMR1, TF, PRKD1, NAP1L1, DAB2, FUCA1, HIP1, THPO, MAP1B, PARVB, GP1BB, SEPT5, GJA4, PTGS1, GUCY1A3, HIST1H2AG, GNAS, LRBA, HYAL3, GP6, IGHG1, CYP2A13, CDC14B, MAX, KDM2A, CALD1, GNAZ, C19orf22, ARHGAP6, RHOC, RBX1, GP1BB, SEPT5, PRDX6, PRB4, FLNA, HIST1H2BF, RHBDF2, NUP205, SYT1, EGFL8, PPT2, TUBB1, TMC6, FLJ11292, NAP1L1, ALDH1A3, CSNK1E, PRUNE, COL4A3, ZNF221, ILF3, CABP5, RPA1, ARF1, HIST1H2BI, PTGS1, PRKAA1, GNB5, HIST2H4A, HIST2H4B, CYB5R3, TNS1, DCT, GMPR, ABI3BP, GNAS, SASH1, AAK1, XPO6, CTSL2, QSER1, MAP1LC3B, TBX6, CABP2, MRE11A, MAPRE2, TMC6, BDKRB2, MGLL, HRASLS, WHAMML1, WHAMML2, CLU, STC1, C6orf54, PABPN1, PDLIM1, CLU, PHF20, UBL4A, RNF115, HGD, RASGRP2, PNN, SAPS3, SFI1, GOLGA2, HIST2H2BE, SGEF, HGD, DUS1L, MPP1, HLA-E, GRB14, MMD, ZFHX4, CSNK1G2, HIST1H2BE, MPDZ, B2M, TBXA2R, NGFRAP1, CTDSPL, SNCA, CD99, POLS, MPL, HIST1H3F, SFRS8, NR5A2, ZMYM2, C6orf10, TMEM40, RNF43, PRUNE, MSH6, PLCB4, PARVB, TOX3, PKNOX1, RUFY1, SNCA, C10orf81, PDGFA, ASMT, HMGB1, CCDC90A, PROS1, hCG_1757335, RAP1B, MTSS1, GNRHR, LRRN3, MCM3AP, PLOD2, NAP1L1, PLOD2, HOXD13 CASKIN2, MFAP5, PITX2, SNCA, MYLK, PBX1, PRDX6, EIF2AK1, H3F3A, H3F3B, LOC440926, TMEM158, TRIM58, FSTL1, SNCA, TNS1, ATP1B1, C5orf4, LRP12, CTNNAL1, GEM, KIAA1466, ALDH1A2, MAP4K3, SNCA, RAB6B, PSD3, RIPK2, RAMP3, CALD1, CYP2E1, PSD3, PDLIM7, COBLL1, FUT3, SMOX, TGM2, LRRC50, CST6, OR7A17, C6orf145, DLEU2, DLEU2L, CPT2, HGF, TNS1, SPRY1, PLOD2, CD80, KYNU, BCAT1, NHLH1, AHCTF1, HOXA10, MTMR3, VAC14, CLCF1, FGF5, TAL1, SAMD14, ELL2, CHN1, SLC7A1, GRK5, PARD3, VPS37B, CYP2B6, CYP2B7P1, MALL, ALX4, SOX15, KRT5, ESPL1, STARD8, PSD3, KIAA0195, MYO9B, HIP1R, LOC100294412, EFNB1, ERN1, RHD, MFAP3L, PLA1A, POFUT2, C8orf39, CRYBB2, CYP4A11, PVRL2, CLCNKB, MRAS, NFIB, FKSG2, SLC11A2, FZR1, ZNF550, GLP1R, SLC19A1, RTN2, PAPOLA, STC1, GK, EXOSC6, RAPSN, HFE, EHD2, RIOK3, UBE2I, C15orf2, DMD, PRLH, MAP2K2, TP63, DACH1, PPP5C, SLC26A1, NUDT7, KCNJ12, ENTPD7, SLC26A1, PRRG3, RGS6, ZBED2, FICD, ARHGAP1, ARHGDIA, SDHB, AMHR2, ABCA4, TCF20, BGN, CASP7, LPAR4, GNA12, CYP2W1, RAX, C4A, C4B, LOC100292046, LOC100294156, ELAVL4, PXN, ESR2, MYL10, EFS, TFF3, SRPK1, LOC441601, BIRC5, CCT8L2, PPAP2B, CMA1, APOA2, KDELR2, ASCL3, RUNX1, BUB1, SLC6A8, HNRNPC, HNRNPCL1, LOC440563, LOC649330, RIBC2, CLIC4, RAB17, SCML2, SPINLW1, ANK1, EDA2R, HTR4, CDC42EP4, KANK2, ANK1, SYN1, DUX3, DUX4, FRG2C, HPX-2, LOC100134409, LOC652119, LOC653543, LOC653544, LOC653545, LOC728410, PKNOX2, MLLT4, APOA2, PENK, GNAT1, FURIN, SEMA6A, EGFL6, HRH1, TSPAN1, DBC1, TRPC7, MDM2, GPR52, HAMP, PRSS2, GPR107, FLJ11292, FLJ20184, B40ALT1, NKX3-1, ASIP, EFCAB6, GPR20, CA5A, PLK4, TAAR5, SRPX2, CNTD2, AZGP1, TIMP3, RGS6, ADARB1, DYNC1I1, C10orf10, PDIA2, PITX3, HOXC13, LPAR3, CTRC, CTSL2, MUC8, AQP5, UGT1A1, UGT1A10, UGT1A4, UGT1A6, UGT1A8, UGT1A9, KCNQ2, CYP2A13, ZNF155, KIAA0892, ATP2A2, FGF5, FGF18, FUT2, SHROOM2, PRSS3, CREB3L1, MGAT2, PLCE1, MLXIPL, OR10H3, ABCB11, CD84, ARHGEF4, ORC1L, PCIF1, CD177, C1orf116, IFT122, C11orf20, DUSP13, C6orf208, PLA2G5, PRAMEF1, PRAMEF2, CYP4F8, KCNA1, MFAP4, C6, SLC4A3, IL1RAPL1, SERPINE1, ZCCHC14, POLR3G, C16orf8, FLJ14100, SMCHD1, ASCL1, FOXA2, SLC23A2, KLK13, MTSS1L, DNMT3L, RREB1, DNMBP, PKLR, C1orf106, CCDC134, MTSS1, CCDC40, HOXB1, SCNN1B, SEMA4G, RAPGEFL1, MAGEL2, PLSCR2, CHD2, PLCD1, C1orf116, CHRNA2, MBP, CDC42BPA, MYF6, PI15, LOC440895, SBF1, MAST1, GLT8D2, ERBB3, LOH3CR2A, AMH, HR, RDH8, PAWR, DRD3, CCT8, PRELP, SPOCK3, EPS8L3, NXN, SEMA4G, P2RY1, AVL9, TEK, MOGAT2, KLK7, MT1E, MT1H, MT1M, CLDN18, RHBDF2, SIX1, INPP5A, KCNMB3, MAP2K5, GPD1, LPO, LOC729143, MPRIP, WNT7A, RARG, CDH7, MBNL2, RASGRP2, RBMY2FP, MASP1, CASR, EGR4, APOC2, HECW1, HOXB3, IRF5, NNMT, AOC2, ESRRG, LPIN1, ACOT11, CCDC33, MBD2, ZNF323, NTRK2, TMEM151B, GPLD1, LENEP, HNF1B, NXPH3, ALDH1A3, PHF20L1, CKM, PARD6B, CRYGB, HAB1, LARGE, RAB40C, MPL, CHIT1, METTL10, DUS4L, PNLIPRP1, ELL, ST8SIA5, GRIN2B, MC4R, RTDR1, HDAC6, KCNJ13, CPSF1, SPANXC, CNOT4, LAMA2, SLC1A6, ABCA2, KLK11, GFRA3, CYP3A4, SLC1A3, ATP2B2, APBB2, VPS45, GHRHR, HOXD4, PRPH, ADCY2, LEFTY2, CYP1B1, PCP4, C8B, RANBP3, PDE6H, TRIM15, VGLL1, TRIM3, CRKL, ADH7, PSG3, GPR153, MFAP2, FGF13, NAPA, ALDH3A1, MCM10, TLE4, ITPR3, CCDC87, C9orf7, ACTC1, OBSL1, MAP2, CRYM, RNF122, SST, HLA-DRB6, SLC22A17, HSPG2, HIP1, GRIK2, UNKL, GPR144, KIR3DX1, NARFL, UCP3, PLXNA2, BTN1A1, ERCC4, CIITA, EGFR, KRT33A, CLTB, B3GALT5, AP3M2, GJC1, MYO3A, ARHGAP1, PPP2R3A, CLIC4, C20orf195, SIGLEC8, GPRC5A, CACNB1, MYL10, PRLR, OR2S2, NCR2, CHAF1B, EYA3, CDS1, FBXL18, ACTL6B, ZNF821, C16orf71, HBBP1, PLXNA1, CDC45L, MTCP1, PLCB4, PLVAP, PROX1, CYP3A43, IGHG1, RECQL5, IDUA, DLGAP4, PLXNB1, HSD17B14, FOXP3, C19orf26, EPB41L1, RBBP9, GJB4, UPK1B, CYP19A1, LOC55908, CLDN18, C2orf72, NTRK3. NRXN2, SPDEF, IGH@IGHD, IGHG1, IGHM, LOC100289944, VSIG6, ACRV1, PHLDB1, SORBS1, HAPLN2, FABP3, EFS, ACVR1B, CHST3, UGT2A1, UGT2A2, TAF1, MT4, MFAP3, ETV5, UBQLN3, TBX10, GJB1, ABO, SPINK5, ATAD4, CDH11, CARD14, ALPP, ALPPL2, CBL, LRP4, CDKL2, SSX3, DSG2, SLC45A2, LAMA4, WFDC8, HTR7, EFNB3, TUBB2B, OR7E19P, PMS2L4, ASAP3, FRZB, PDLIM4, PVT1, TFR2, AHI1, TAF4, ADAMTSL2, CLDN4, KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL5A, KIR2DL5B, KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS4, KIR2DS5, KIR3DL2, KIR3DL3, KIR3 DP1, LOC727787, RAPGEF5, CRMP1, LDB3, F11, USP46, PTN, IBSP, SLC9A3, FLRT3, TRIM17, FGF17, CAMK1G, GLYR1, CSH1, NTF3, ABHD6, TRIM15, OR52A1, FGFR2, ORAI2, C17orf53, GLP1R, SLIT1, TP63, DDR1, CFTR, DIO2, LETM1, ACSM5, ACTA1, NPR1, KCND3, POPDC3, DNAH3, SPDEF, CLEC4M, SLC30A3, NAGLU, AAK1, DHX34, NNAT, AKAP9, ICMT, FAM189A1, C10orf81, MYOZ1, PKNOX2, MGC31957, PRDM11, RET, IGHG1, XPNPEP2, NTRK2, SLC25A10, NR1I2, GRM8, OR3A3, GIPR, PAH, PACRG, CLN8, ZNF215, TRIO, TTLL5, GRM1, PRKG1, HHLA1, LAMA3, PTN, SLC37A4, HOXC11, SLCO5A1, CA10, RRBP1, SOD3, NTRK3, CYR61, STRA6, SLC6A11, CNOT4, ATN1, BCAP29, NOVA2, RELN, LAMC2, RAD51, PRSS7, DCBLD2, TACR2, RAB11B, OR2J2, VSNL1, IFNA17, DPYSL4, MGC2889, RRBP1, POLQ, OR1A2, PURA, AIF1, CBS, NECAB2, PRKCE, NOX1, IHH, EXO1, GPRIN2, PDX1, GPR12, FAM188A, HS3ST3B1, ASCL1, ZNF484, CSH1, BCAN, DDN, DUOX2, MORN11, SLC39A2, CLCN7, RUNX2, TTYH1, ZNF280B, PAX3, LZTS1, SLC8A2, HAB1, KIF1A, ARL4D, UGT2B15, NACA2, THRB, C6orf15, GPR176, WSCD1, PLXNB3, CADM3, HAP1, CYP1A2, SPAM1, IL22RA1, CDC2L5, IRX5, PPFIA2, KDELR3, CEACAM7, KCMF1, DUOX1, CDC27, HIST2H2AA3, CAV3, APOA4, NPR3, PRG3, TBC1D22B, TUSC3, RIMS2, CYP4F12, TBXA2R, HBEGF, PSG9, PYGO1, RASGRF1, SCN2A, KLHL1, DTNB, GREM1, SNCG, C22orf24, PALM, COBLL1, DNPEP, MNS1, NFATC4, DLC1, HSPC072, MCAM, CA12, CSHL1, RPAIN, COL5A2, UGT1A8, UGT1A9, IGH@, IGHA1, IGHG1, IGHG2, IGHG3, IGHM, LOC100126583, LOC100290036, LOC100290320, LOC100293211, LOC652494, TGFB2, ACSM5, ALOX12P2, ERBB4, CLDN16, CIB2, GALR3, MSMB, FABP7, ATXN3, KCNJ5, TRDN, CYP3A43, BAZ2A, ACCN4, SILV, DGCR14, SEMA6C, DIO2, PTHLH, LEP, PDZRN3, RGSL1, GJA4, SLC22A6, RASGRF1, MAPRE2, PVRL1, AKAP1, POMP, SOX21, DNAH9, HOXC5, SERHL2, KIAA0485, ITSN1, B4GALT1, NEK2, NUPR1, CCDC93, EPO, CRABP2, TYRO3, GOLGA2, SEMA3F, BFSP2, NCAM1, FOLH1, SSX2, TMPRSS4, DCN, LPHN3, POU4F3, CEACAM5, BCL3, EXTL3, CCNA1, DDR2, PAX8, SOX5, POU3F1, PEX16, IL4I1, NUP62, SIGLEC11, ALDOB, GPC3, IGFALS, WDR25, FGF1, OSR2, ARID1A, GYPA, KLK13, PARVB, LILRB5, RIMS2, C19orf21, HOXD1, PRSS3, FLT1, ATP6V1C1, LOX, CRYBB3, CA12, PRKG2, MASP1, LOC728395, LOC728403, TSPY1, PDCD1, GGTLC1, AQP8, IL1F9, KRT16, AICDA, BRD8, C1orf95, OR3A2, PFKFB2, FRZB, PAK3, MEIS2, ZSCAN2, MYH7, VWA1, LSAMP, SRC, UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, DIO1, TADA3L, NFASC, CALCRL, NBLA00301, MAB21L1, FBXO42, COL10A1, CFB, SNX7, FOXN1, SRY, HLF, CLCA3P, DAZ1, DAZ2, DAZ3, DAZ4, GPR3, TMPRSS11E, EMID1, KCNMB2, MUC5AC, SORT1, HIF3A, MAPK4, TCP11L1, ZZEF1, DCAF7, DMWD, CLCA2, VAC14, CSPG5, STMN2, MLLT4, GALNT14, FGF12, MFAP5, SUMO3, HTR3A, GDF5, TSSK1B, CYP2A7P1, MARK1, ATP1B2, TBX6, PAX8, IL1R1, RALYL, OR2B2, TAAR3, C12orf32, IGHG1, LOC642131, DICER1, GLRA3, PPARD, HSPA4L, WNT2, VIPR2, CYP2C9, SRPX2, IGSF1, ALPK3, TFPI, KCNS3, MARCH8, FRMD4B, TACR3, FIGF, PDCD6, TNN, SPANXB1, SPANXB2, SPANXF1, RHBDD3, SPP2, PDE10A, ZNF224, FGL1, PGAM2, CADM4, APOBEC2, SLC9A5, GNAT1, ARHGEF16, SMARCA2, DNAH9, RBM26, WNT2B, KCNK2, NPBWR2, SP2, TMPRSS11D, DENND2A, TNIP3, STC1, DOCK6, ADAM5P, SYDE1, TNPO2, LRTM1, USH1C, PDE12, SRCAP, OR10J1, OR2H2, KCNJ8, RP11-257K9.7, DOCK5, TPD52L1, PAEP, GGA2, PHLDA3, HES2, MLL, PTN, CHRNA6, CIB2, PTPRF, TM7SF4, DAZ1, DAZ2, DAZ3, DAZ4, ALX1, OR2F1, OR2F2, PLAT, HGC6.3, WNT11, PGK2, SNAI2, COL4A6, PRUNE2, ANKS1B, LOC81691, FERMT2, TIMP3, CST8, CAPN6, IDUA, GPR32, AKR1B10, GRHL2, FBXO24, HSF4, IGHG1, HCN2, LRP12, ARHGEF15, UGT1A1, UGT1A10, UGT1A7, UGT1A8, GUCA2A, MDK, ITIH1, EGFR, UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, MYOG, TMSB15A, TLX1, EDNRA, LOC100289791, MDFI, ZER1, MYH15, CDH20, GPR63, LOC440345, LOC440354, LOC595101, LOC641298, SMG1, HOXC10, KRTAP1-1, ARSD, CPLX3, LMAN1L, IFNA4, ABCC1, SEMA3E, MRE11A, C1QL1, LIPF, TRIM9, BBOX1, LRRC17, WNT2B, CYP3A4, SI, ANO3, OBSL1, CHRD, MSX2, PSG1, FAM107A, LRRC37B2, ANKLE2, PAX2, UNC5B, ADCYAP1R1, HFE, SYT1, GJC2, LOC100293871, FGF8, ACRV1, NRXN1, GDPD2, RGS4, CELA2A, IFNW1, MLNR, RNF17, LAD1, GLRA2, RASL12, MAGOH2, C6orf54, ZNF214, IKBKG, AP4E1, ZNRF4, OSBPL10, C1orf175, TTC4, PCDHB3, ADRBK1, ITSN1, XAGE1A, XAGE1B, XAGE1C, XAGE1D, XAGE1E, CDH22, FARP2, MYT1, TNC, MUC5AC, SLC6A15, PP14571, SMR3A, SMR3B, RXRG, SNX1, GLP1R, C6orf155, ATP1A2, TFAP4, PNPLA2, DIRAS3, ANO2, TACSTD2, MCM3AP, IL13RA2, TRIM10, RTEL1, PRRX2, TSHB, TIMELESS, FMO1, KIF18A, KIAA1199, CALB2, MFAP3L, PTGER3, EPAS1, SQSTM1, TSPY1, CPM, DLGAP1, CYP4F11, TLX3, PCDHA10, TAOK2, ERC1, TBX2, KALRN, DICER1, PAPPA, KIF5A, DNAJC22, OTUB1, KIAA1644, SEZ6L2, PCNXL2, HMHB1, ERG, SNTB2, GJA5, AGTR2, GJA3, GCK, LRRC61, CNTF, ZFP91, ZFP91-CNTF, PDLIM4, MPPED2, IFNA10, ACTN2, VGLL1, GJA9, LDLR, ANK2, COL1A1, TIMP3, OTOF, AGXT, GLI2, TRMT61A, FOXD2, TMEM2I2, DENND2A, B3GALT1, SPAG11A, PRDM4, TF, ELF5, GSC2, EPB41L4B, GYG2, LYZL6, DCHS2, OBP2A, OBP2B, ANGPTL3, MYH11, NES, SLC17A1, RBM15B, CSH1, HTR5A, CYP3A7, HTR2A, KCNV2, TOX3, CLOCK, MAGEA6, FAM12A, COL4A3, S1PR2, NAT8, ACE2, SLC22A6, SLC13A2, MYH4, APBB2, RAP1GAP, SHOX2, SLCO1A2, ETV1, MAGEA12, PLA2G6, ADRA1A, SYT5, GPR161, SEMA3F, CYP3A43, HOMER2, KCNJ5, PPL, COL17A1, CSHL1, C9orf116, PARK2, UGT2B15, CDK6, FAM174B, CELA2A, CELA2B, SPDEF, EPB41, GAB1, SMR3A, PDE6G, COL5A1, ABCA6, DMD, CYLC2, CIDEA, RAG2, HIST1H2BN, FMO6P, MAOA, ANKRD53, HAPLN1, MT1M, EHD2, GAD2, CRISP2, CSN2, SULT1C2, PCDHGA3, SSX3, FGFR2, GPR161, ATN1, CHD5, A4GALT, MYBPH, CSHL1, NCAPH2, CAPN9, CNGB1, BCAM, DRD5, NR5A2, TEF, ELAVL2, DGKB, HTR7P, RHAG, GH2, COL4A6, BMP7, SOSTDC1, SOX14, TAS2R9, LPHN2, MAP1A, OSGIN2, SLC10A2, FAM13C, EMX1, FLJ40330, CHI3L1, CDH16, SPRR1A, LOX, CALCB, GABBR2, CPB2, RASL11B, CCDC81, RUNX1, CPA1, CLCNKA, CLCNKB, FHL5, THSD7A, TFAP2C, SPAG11B, CAP2, PODNL1, SSX4, SSX4B, G6PC, RPE65, TMEM222, KDR, CHP2, GPR64, TPM2, TCEB3B, E2F5, IL5RA, AOC3, ABCF3, CPN2, ACE, NRP2, INPP5J, SMAD9, FAM155A, GART, PIR, ZNF467, ITSN2, NRID1, THRA, RP11-35N6.1, LAMB1, EPHB3, PLA2R1, RAPGEF4, DNAJC8, ARSJ, TRIM49, GC, IL12B, CDH2, ATXN3L, BTF3L1, BICC1, FAM186A, PTPRF, TRPC4, TCL6, CYP4A22, FUT6, MUC1, DKFZP434B2016, LOC643313, LDHA, LOC100131613, TRIM3, MLLT10, DZIP1, ANKRD34C, BUB1, CSPG5. FBLN1, GAD2, CLDN1, CHRNA3, SCN11A, TEX11, IL20RA, AKAP5, KBTBD10, MSTN, TLL2, NACAD, UNC93A, PTGER1, OLAH, NHLH2, SERPINA6, KRT17, KCNMA1, PRKCA, STS, LAMA1, GPR88, ACTN2, TREH, AKAP4, DKK4, PRICKLE3, IRS4, TRPV4, PCDH11Y, APBB2, SLCO2A1, DRD2, MTMR7, ZNF471, TF, NRIP2, ST6GALNAC5, COMT, PAH, LRRC19, PRKAR1B, HPR, PRDM5, NCRNA00120, LOC79999, ITSN2, CACNB2, GPR98, PREX2, FAM182B, LAMA4, ARVCF, HAS2, YOD1, PPP2R3A, COL4A1, RBM12B, GSTA3, FAM66D, OR10H2, PTHLH, ZNF674, KRT19, ACCN2, COL6A1, LOC100288442, LOC100289169, LOC728888, LOC729602, NPIPL2, NPIPL3, PDXDC2, SLC37A1, ATP6V1B1, PTN, ABI3BP, HR44, ZNF324B, ZNF584, HOXD13, ADH6, IFNA8, MYOZ2, NFATC4, ADAMTS7, FOXL1, GPR17, SLC18A3, MYH6, BOK, FGA, TEAD4, GRM1, EDNRA, C8orf79, METTL7A, FOLH1, RAD54L, SOX11, CNOT3, NTS, MAPK12, DOCK6, DNAJC6, HS3ST3A1, LOC728395, TSPY1, TSPY3, PTH, LAMB4, ALDOB, FLG, MLANA, UBE2D4, LOC100287483, KRT20, POU1F1, SLCO1B3, CLTA, MECOM, C8orf71, SULT2A1, C6orf10, SLC27A6, PRKD1, SYNPO2L, THPO, GABRR1, CFTR, PPP2R3A, DCBLD2, ANP32A, ANP32C, ANP32D, LOC723972, XYLT1, STAB1, STAB1, SASH1, PID1, FUCA1, SASH1, LRRN3, LRRN3 or any combination thereof.
In another embodiment, the gene is TNFSF4, ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGβB/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-1/5/8/20/22, IL-9/12/36, TNFRSF11A/B, IFNA4/8/10/17, TGβ, LTBP4, MEK1/2, TGFβ type 1 receptor, Smad2/3/4, PAI-1, TNFSF4, SELP, ITFA8, ITGB1/3/5, CXCL5/7, a BMP6 gene, ITGA2/8, ITGβ1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-1/1R/5/8/13/20/22R, IL-9/11/12/36, TNFRSF11A/B, IFNA4/8/10/17, TGβ, LTBP4, MEK1/2, TGFβ type 1 receptor, type 11 BMPR, smad1/2/3/4/5/6/8, PAI-1, CCL19, IKKg, LTBP1 or any combination thereof. In yet another embodiment, the gene is TNFSF4, ITGB1/3/5, CXCL5/7, BMP6, ITGA2/8, ITGB1/3/4/5/6, ITGBL1, MMP16/24/26/28, ADAM12/18/22, IL-1/5/8/20/22, IL-9/12/36, TNFRSF11A/B, IFNA4/8/10/17, TGβ, LTBP4, MEK1/2, TGFβ type 1 receptor, Smad2/3/4, PAI-1 or any combination thereof.
In one embodiment, laquinimod is administered orally. In another embodiment, laquinimod is administered daily.
In one embodiment, laquinimod is administered at a dose of less than 0.6 mg/day. In another embodiment, laquinimod is administered at a dose of 0.1-40.0 mg/day. In another embodiment, laquinimod is administered at a dose of 0.1-2.5 mg/day. In another embodiment, laquinimod is administered at a dose of 0.25-2.0 mg/day. In another embodiment, laquinimod is administered at a dose of 0.5-1.2 mg/day. In another embodiment, laquinimod is administered at a dose of 0.25 mg/day. In another embodiment, laquinimod is administered at a dose of 0.3 mg/day. In another embodiment, laquinimod is administered at a dose of 0.5 mg/day. In another embodiment, laquinimod is administered at a dose of 0.6 mg/day. In another embodiment, laquinimod is administered at a dose of 1.0 mg/day. In another embodiment, laquinimod is administered at a dose of 1.2 mg/day. In another embodiment, laquinimod is administered at a dose of 1.5 mg/day. In yet another embodiment, laquinimod is administered at a dose of 2.0 mg/day.
In one embodiment, the subject is a naïve subject. In another embodiment, the subject is naïve to laquinimod. In another embodiment, the subject has been previously administered laquinimod.
In another embodiment, the subject has been previously administered a multiple sclerosis drug other than laquinimod.
In an embodiment, the step of evaluating expression of the biomarker comprises normalization of the subject's gene expression. In another embodiment, the step of evaluating expression of the biomarker comprises comparing expression level in the subject relative to a reference value. In another embodiment, the reference value is based on the level of expression of the biomarker in a laquinimod Non-Responder population. In another embodiment, the reference value is based on the level of expression of the biomarker in a healthy control population. In yet another embodiment, the reference value is based on the level of expression of the subject at baseline.
In one embodiment, the subject is identified as a laquinimod responder if expression of the biomarker is higher than a reference value. In yet another embodiment, the subject is identified as a laquinimod responder if expression level of the biomarker is lower than a reference value.
In one embodiment, expression of the biomarker is evaluated in the blood of the subject. In another embodiment, expression of the biomarker is evaluated in the peripheral blood mononuclear cells (PBMCs) of the subject. In another embodiment, expression of the biomarker is evaluated prior to treatment with laquinimod.
In one embodiment, expression of the biomarker is evaluated after beginning treatment with laquinimod. In another embodiment, expression of the biomarker is evaluated one month after beginning treatment with laquinimod. In another embodiment, expression of the biomarker is evaluated 6 months after beginning treatment with laquinimod. In another embodiment, expression of the biomarker is evaluated 12 months after beginning treatment with laquinimod. In another embodiment, expression of the biomarker is evaluated 24 months after beginning treatment with laquinimod.
In one embodiment, if the subject is identified as a laquinimod responder, the subject is thereafter administered a pharmaceutical composition comprising laquinimod and a pharmaceutically acceptable carrier as monotherapy. In another embodiment, if the subject is identified as a laquinimod responder, the subject is thereafter administered a pharmaceutical composition comprising laquinimod and a pharmaceutically acceptable carrier in combination with another multiple sclerosis drug. In another embodiment, if the subject is identified as a laquinimod non-responder, the subject is thereafter administered a multiple sclerosis drug which is not laquinimod.
In one embodiment, the subject is a human patient.
The subject invention also provides laquinimod for use in treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, wherein the subject has been identified as a laquinimod responder.
The subject invention also provides a pharmaceutical composition comprising an amount of laquinimod for use in treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, wherein the subject has been identified as a laquinimod responder
The subject invention also provides laquinimod for use in treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, wherein expression of a biomarker in the subject is up-regulated and the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
The subject invention also provides a pharmaceutical composition comprising an amount of laquinimod for use in treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, wherein expression of a biomarker in the subject is up-regulated and the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
The subject invention also provides laquinimod for use in treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, wherein expression of a biomarker in the subject is suppressed and the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
The subject invention also provides a pharmaceutical composition comprising an amount of laquinimod for use in treating a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, wherein expression of a biomarker in the subject is suppressed and the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
The subject invention also provides a therapeutic package for dispensing to, or for use in dispensing to, a subject identified as a laquinimod responder afflicted with multiple sclerosis or presenting a clinically isolated syndrome, which comprises: a) one or more unit doses, each such unit dose comprising an amount of laquinimod, and b) a finished pharmaceutical container therefor, said container containing said unit dose or unit doses, said container further containing or comprising labeling directing the use of said package in the treatment of said subject.
The subject invention also provides a therapeutic package for dispensing to, or for use in dispensing to, a subject afflicted with multiple sclerosis or presenting a clinically isolated syndrome, which comprises: a) one or more unit doses, each such unit dose comprising an amount of laquinimod, and b) a finished pharmaceutical container therefor, said container containing said unit dose or unit doses, said container further containing or comprising labeling directing the use of said package in the treatment of said subject, wherein expression of a biomarker in the subject is suppressed or up-regulated and the biomarker is a gene associated with inflammatory response, a gene associated with cellular movement, a gene associated with cell signaling, a gene associated with cell development, a gene associated with hematological system, or a combination thereof.
For the foregoing embodiments, each embodiment disclosed herein is contemplated as being applicable to each of the other disclosed embodiment. For example, the elements recited in the method embodiments can be used in the use and package embodiments described herein and vice versa.
A pharmaceutically acceptable salt of laquinimod as used in this application includes lithium, sodium, potassium, magnesium, calcium, manganese, copper, zinc, aluminum and iron. Salt formulations of laquinimod and the process for preparing the same are described, e.g., in U.S. Patent Application Publication No. 2005/0192315 and PCT International Application Publication No. WO 2005/074899, which are hereby incorporated by reference into this application.
A dosage unit may comprise a single compound or mixtures of compounds thereof. A dosage unit can be prepared for oral dosage forms, such as tablets, capsules, pills, powders, and granules.
Laquinimod can be administered in admixture with suitable pharmaceutical diluents, extenders, excipients, or carriers (collectively referred to herein as a pharmaceutically acceptable carrier) suitably selected with respect to the intended form of administration and as consistent with conventional pharmaceutical practices. The unit will be in a form suitable for oral administration. Laquinimod can be administered alone but is generally mixed with a pharmaceutically acceptable carrier, and co-administered in the form of a tablet or capsule, liposome, or as an agglomerated powder. Examples of suitable solid carriers include lactose, sucrose, gelatin and agar. Capsule or tablets can be easily formulated and can be made easy to swallow or chew; other solid forms include granules, and bulk powders. Tablets may contain suitable binders, lubricants, diluents, disintegrating agents, coloring agents, flavoring agents flow-inducing agents, and melting agents.
Specific examples of the techniques, pharmaceutically acceptable carriers and excipients that may be used to formulate oral dosage forms of the present invention are described, e.g., in U.S. Patent Application Publication No. 2005/0192315, PCT International Application Publication Nos. WO 2005/074899, WO 2007/047863, and 2007/146248.
General techniques and compositions for making dosage forms useful in the present invention are described-in the following references: 7 Modern Pharmaceutics, Chapters 9 and 10 (Banker & Rhodes, Editors, 1979); Pharmaceutical Dosage Forms: Tablets (Lieberman et al., 1981); Ansel, Introduction to Pharmaceutical Dosage Forms 2nd Edition (1976); Remington's Pharmaceutical Sciences, 17th ed. (Mack Publishing Company, Easton, Pa., 1985); Advances in Pharmaceutical Sciences (David Ganderton, Trevor Jones, Eds., 1992); Advances in Pharmaceutical Sciences Vol 7. (David Ganderton, Trevor Jones, James McGinity, Eds., 1995); Aqueous Polymeric Coatings for Pharmaceutical Dosage Forms (Drugs and the Pharmaceutical Sciences, Series 36 (James McGinity, Ed., 1989); Pharmaceutical Particulate Carriers: Therapeutic Applications: Drugs and the Pharmaceutical Sciences, Vol 61 (Alain Rolland, Ed., 1993); Drug Delivery to the Gastrointestinal Tract (Ellis Horwood Books in the Biological Sciences. Series in Pharmaceutical Technology; J. G. Hardy, S. S. Davis, Clive G. Wilson, Eds.); Modern Pharmaceutics Drugs and the Pharmaceutical Sciences, Vol. 40 (Gilbert S. Banker, Christopher T. Rhodes, Eds.). These references in their entireties are hereby incorporated by reference into this application.
Tablets may contain suitable binders, lubricants, disintegrating agents, coloring agents, flavoring agents, flow-inducing agents, and melting agents. For instance, for oral administration in the dosage unit form of a tablet or capsule, the active drug component can be combined with an oral, non-toxic, pharmaceutically acceptable, inert carrier such as lactose, gelatin, agar, starch, sucrose, glucose, methyl cellulose, dicalcium phosphate, calcium sulfate, mannitol, sorbitol, microcrystalline cellulose and the like. Suitable binders include starch, gelatin, natural sugars such as glucose or beta-lactose, corn starch, natural and synthetic gums such as acacia, tragacanth, or sodium alginate, povidone, carboxymethylcellulose, polyethylene glycol, waxes, and the like. Lubricants used in these dosage forms include sodium oleate, sodium stearate, sodium benzoate, sodium acetate, sodium chloride, stearic acid, sodium stearyl fumarate, talc and the like. Disintegrators include, without limitation, starch, methyl cellulose, agar, bentonite, xanthan gum, croscarmellose sodium, sodium starch glycolate and the like.
As used herein, and unless stated otherwise, each of the following terms shall have the definition set forth below.
As used herein, “laquinimod” means laquinimod acid or a pharmaceutically acceptable salt thereof.
As used herein, an “amount” or “dose” of an agent, e.g., laquinimod as measured in milligrams refers to the milligrams of the agent, e.g., laquinimod acid present in a preparation, regardless of the form of the preparation. A “dose of 0.6 mg laquinimod” means the amount of laquinimod acid in a preparation is 0.6 mg, regardless of the form of the preparation. Thus, when in the form of a salt, e.g. a laquinimod sodium salt, the weight of the salt form necessary to provide a dose of 0.6 mg laquinimod would be greater than 0.6 mg (e.g., 0.64 mg) due to the presence of the additional salt ion.
As used herein, a “unit dose”, “unit doses” and “unit dosage form(s)” mean a single drug administration entity/entities.
As used herein, “about” in the context of a numerical value or range means±10% of the numerical value or range recited or claimed.
As used herein, “effective” or “therapeutically effective” when referring to an amount of laquinimod or a therapy regimen using laquinimod refers to the quantity or regimen of laquinimod that is sufficient to yield a desired therapeutic response. Efficacy can be measured by an improvement of a symptom of multiple sclerosis. Such symptoms can include a MRI-monitored multiple sclerosis disease activity, relapse rate, accumulation of physical disability, frequency of relapses, time to confirmed disease progression, time to confirmed relapse, frequency of clinical exacerbation, brain atrophy, neuronal dysfunction, neuronal injury, neuronal degeneration, neuronal apoptosis, risk for confirmed progression, visual function, fatigue, impaired mobility, cognitive impairment, brain volume, abnormalities observed in whole Brain MTR histogram, general health status, functional status, quality of life, and/or symptom severity on work.
As used herein, “clinical responsiveness” is a measure of the degree of a patients' response to an agent, e.g., laquinimod. Positive clinical responsiveness corresponds to a patient who responds favorably to and/or benefits from receiving laquinimod (a laquinimod responder) while negative clinical responsiveness corresponds a patient who responds unfavorably to and/or does not benefit from receiving laquinimod (a laquinimod non-responder).
As used herein, “a gene associated with” a process or a system, e.g., a gene associated with inflammatory response or a gene associated with hematological system, is a gene which plays a role in that process or system. As an example, a gene associated with inflammatory response can be IL-1R, IL-8R, IL-22R, IL-9, TNFRSF4 or RORC.
Administering to the subject” or “administering to the (human) patient” means the giving of, dispensing of, or application of medicines, drugs, or remedies to a subject/patient to relieve, cure, or reduce the symptoms associated with a condition, e.g., a pathological condition. The administration can be periodic administration. As used herein, “periodic administration” means repeated/recurrent administration separated by a period of time. The period of time between administrations is preferably consistent from time to time. Periodic administration can include administration, e.g., once daily, twice daily, three times daily, four times daily, weekly, twice weekly, three times weekly, four times weekly and so on, etc.
“Treating” as used herein encompasses, e.g., inducing inhibition, regression, or stasis of a disease or disorder, e.g., Relapsing MS (RMS), or alleviating, lessening, suppressing, inhibiting, reducing the severity of, eliminating or substantially eliminating, or ameliorating a symptom of the disease or disorder. “Treating” as applied to patients presenting CIS can mean delaying the onset of clinically definite multiple sclerosis (CDMS), delaying the progression to CDMS, reducing the risk of conversion to CDMS, or reducing the frequency of relapse in a patient who experienced a first clinical episode consistent with multiple sclerosis and who has a high risk of developing CDMS.
“Inhibition” of disease progression or disease complication in a subject means preventing or reducing the disease progression and/or disease complication in the subject.
A “symptom” associated with MS or RMS includes any clinical or laboratory manifestation associated with MS or RMS and is not limited to what the subject can feel or observe.
As used herein, “a subject afflicted with multiple sclerosis” or “a subject afflicted with relapsing multiple sclerosis” means a subject who has been clinically diagnosed to have multiple sclerosis or relapsing multiple sclerosis (RMS), which includes relapsing-remitting multiple sclerosis (RRMS) and Secondary Progressive multiple sclerosis (SPMS).
As used herein, a subject at “baseline” is as subject prior to administration of laquinimod.
A “patient at risk of developing MS” (i.e. clinically definite MS) as used herein is a patient presenting any of the known risk factors for MS. The known risk factors for MS include any one of a clinically isolated syndrome (CIS), a single attack suggestive of MS without a lesion, the presence of a lesion (in any of the CNS, PNS, or myelin sheath) without a clinical attack, environmental factors (geographical location, climate, diet, toxins, sunlight), genetics (variation of genes encoding HLA-DRB1, IL7R-alpha and IL2R-alpha), and immunological components (viral infection such as by Epstein-Barr virus, high avidity CD4+ T cells, CD8+ T cells, anti-NF-L, anti-CSF 114(Glc)).
“Clinically isolated syndrome (CIS)” as used herein refers to 1) a single clinical attack (used interchangeably herein with “first clinical event” and “first demyelinating event”) suggestive of MS, which, for example, presents as an episode of optic neuritis, blurring of vision, diplopia, involuntary rapid eye movement, blindness, loss of balance, tremors, ataxia, vertigo, clumsiness of a limb, lack of co-ordination, weakness of one or more extremity, altered muscle tone, muscle stiffness, spasms, tingling, paraesthesia, burning sensations, muscle pains, facial pain, trigeminal neuralgia, stabbing sharp pains, burning tingling pain, slowing of speech, slurring of words, changes in rhythm of speech, dysphagia, fatigue, bladder problems (including urgency, frequency, incomplete emptying and incontinence), bowel problems (including constipation and loss of bowel control), impotence, diminished sexual arousal, loss of sensation, sensitivity to heat, loss of short term memory, loss of concentration, or loss of judgment or reasoning, and 2) at least one lesion suggestive of MS. In a specific example, CIS diagnosis would be based on a single clinical attack and at least 2 lesions suggestive of MS measuring 6 mm or more in diameter.
As used herein, a “multiple sclerosis drug” is a drug or an agent intended to treat clinically defined MS, CIS, any form of neurodegenerative or demyelinating diseases, or symptoms of any of the above mentioned diseases. “Multiple sclerosis drugs” may include but are not limited to antibodies, immunosuppressants, anti-inflammatory agents, immunomodulators, cytokines, cytotoxic agents and steroids and may include approved drugs, drugs in clinical trial, or alternative treatments, intended to treat clinically defined MS, CIS or any form of neurodegenerative or demyelinating diseases. “Multiple sclerosis drugs” include but are not limited to Interferon and its derivatives (including BETASERON®, AVONEX® and REBIF®), Mitoxantrone and Natalizumab. Agents approved or in-trial for the treatment of other autoimmune diseases, but used in a MS or CIS patient to treat MS or CIS are also included.
As used herein, a “naïve patient” is a subject that has not been treated with a multiple sclerosis drug as defined herein. Similarly, a patient or subject who is “naïve” to an agent, e.g., laquinimod, is a patient or subject that has not been treated with said agent.
As used herein, “in the blood of the subject” is represented by PBMCs, lymphocytes, monocytes, macrophages, basophils, dendritic cells or other cells derived from the subject's blood.
As used herein a “reference value” is a value or range of values that characterizes a specified population in a defined state of health.
A “pharmaceutically acceptable carrier” refers to a carrier or excipient that is suitable for use with humans and/or animals without undue adverse side effects (such as toxicity, irritation, and allergic response) commensurate with a reasonable benefit/risk ratio. It can be a pharmaceutically acceptable solvent, suspending agent or vehicle, for delivering the instant compounds to the subject.
It is understood that where a parameter range is provided, all integers within that range, and tenths thereof, are also provided by the invention. For example, “0.1-2.5 mg/day” includes 0.1 mg/day, 0.2 mg/day, 0.3 mg/day, 0.4 mg/day, 0.5 mg/day etc. up to 2.5 mg/day.
This invention will be better understood by reference to the Experimental Details which follow, but those skilled in the art will readily appreciate that the specific experiments detailed are only illustrative of the invention as described more fully in the claims which follow thereafter.
In a previous study by Gurevich et al. (Gurevich et al. 2010), in vitro molecular effects of laquinimod (LAQ) in peripheral blood mononuclear cells (PBMC) of healthy subjects and relapsing-remitting multiple sclerosis (RRMS) patients were characterized by gene expression microarrays. Gurevich et al. demonstrated that LAQ induced suppression of genes related to antigen presentation and corresponding inflammatory pathways. To further elucidate the molecular mechanism/s underlying the therapeutic effect of LAQ following treatment of patients displaying RRMS, the inventors performed gene expression microarray analysis of PBMCs from RRMS patients treated with LAQ as ancillary study to ALLEGRO clinical trial.
ALLEGRO was a multinational (24 countries), multicenter (approximately 139 sites), randomized, double-blinded, parallel-group, placebo-controlled clinical trial conducted to evaluate the efficacy, safety and tolerability of daily oral administration of laquinimod 0.6 mg in subjects with relapsing remitting multiple sclerosis (RRMS) for a 24 months duration.
One thousand one hundred and six (1106) patients were equally randomized to either laquinimod 0.6 mg or placebo and treated in a double-blind manner and baseline characteristics were balanced between groups. The primary endpoint of the study was the number of confirmed relapses during the double-blind treatment period, which corresponds to the annualized relapse rate (ARR—number of relapses divided by total exposure of all patients). Secondary endpoints included disability as measured by Expanded Disability Status Scale (EDSS) changes confirmed at 3 months, and cumulative number of gadolinium enhancing (GdE) and new/enlarging T2 MRI lesions.
Screening phase: 1 month.
Double blind treatment phase: 24 months of once-daily oral administration of daily dose of 0.6 mg laquinimod or matching placebo.
Upon blinded variance and power reassessment of the population progression (planned prior to first subject completes the 20 months of treatment), the double blind study duration may be extended to 30 months. This is planned in order to enhance the statistical power to detect the effect of laquinimod on disability accumulation. The recommendation to extend the study duration is based on a pre-defined rule.
Eligible subjects were equally randomized 1:1 into one of the following treatment arms:
Subjects were evaluated at study sites for 12 scheduled visits of the double blind phase at months: −1 (screening), 0 (baseline), 1, 2, 3, 6, 9, 12, 15, 18, 21 and 24 (termination/early discontinuation). In case of the 6 months extended study, subjects were evaluated at study sites at months 27 and 30 (termination/early discontinuation of extended study), in this case month 24 was a regular scheduled visit.
EDSS was assessed every 3 months, MSFC every 6 months, and MRI was performed annually in all patients. A subgroup of patients (n=189) underwent additional MRI scans at months 3 and 6. Subjects successfully completing the study were offered the opportunity to enter into a 1-year open label extension. Patients who discontinued the study underwent a final termination visit and were not further evaluated, except for those who discontinued due to adverse events.
The following assessments were performed at specified time points:
The goal of this ancillary study was to characterize gene expression changes and corresponding biological mechanisms induced in PBMC of RRMS patients by LAQ treatment. According to ALLEGRO clinical trial inclusion criteria, 25 patients were randomly assigned to receive LAQ (n=13, age 38.8±2.3 years, female/male ratio: 8/5) or placebo (n=12, age 37.2±3.4 years, female/male ratio: 8/4).
Peripheral blood samples were obtained from RRMS patients at baseline before start of LAQ treatment or placebo, after 0, 1, 6 and 24 month of treatment (visit 0, 1, 6 and 7 according to ALLEGRO clinical trial protocol correspondently) for gene microarray analysis.
Briefly, 1) Peripheral blood mononuclear cells (PBMC) were obtained from RRMS patients that participated in ALLEGRO and were treated daily with 0.6 mg LAQ or placebo. PBMC were subjected for gene expression analysis (HU-133A-2-Affymatrix arrays) at baseline and at 1 and 6 months of LAQ treatment; 2) Data was analyzed by Partek Genomics Solution software. Most informative genes (MIGs) were defined as those that differentiated between groups with p<0.01. Gene functional annotation, enrichment and pathway analysis were performed by Ingenuity software. For each time point, genes that changed in placebo group were excluded from further analysis; and 3) Verification of LAQ related mechanism was performed by Western blot.
LAQ was found to induce a differential gene expression of 354 MIGs at 1 month and 1562 MIGs at 6 months of treatment.
This study shows that LAQ down-regulates genes associated with adhesion, migration and chemotaxis of PBMC either directly or via TGFb suppression. These effects were observed after 1 and strengthened after 6 month of LAQ treatment. LAQ also down-regulates PAI-1 suggesting activation of fibrinolysis and possibly subsequent neuroprotection. Both effects can contribute to amelioration of MS clinical symptoms.
PBMC were extracted from 15 ml peripheral blood, separated by Ficoll-Hypaque gradient. Total RNA was extracted using both Trizol (Invitrogen, USA) and Phase-Lock-Gel columns (Eppendorf, Germany) including a DNase digestion step. RNA integrity was assessed by RNA Experion automated electrophoresis system (Bio-Rad Laboratories, Hercules, Calif.).
Probe synthesis using 3 μg total RNA, hybridization, detection, and scanning was performed according to the standard Affymetrix, Inc. USA protocols; cDNA was synthesized using the Two-Cycle cDNA Synthesis Kit (Affymetrix, Inc., USA), and in-vitro transcription performed with the GeneChip IVT Labeling Kit (Affymetrix, Inc., USA). The biotin-labeled IVT-RNA was hybridized to HG-U133A-2 arrays containing 18,400 gene transcripts, each corresponding to 14,500 well-annotated human genes, washed in a GeneChip Fluidics Station 450 (Hewlett Packard, USA, GeneArray-™ scanner G2500A) and scanned according to the manufacturer's protocol (Affymetrix, Inc., USA).
Data analysis was performed on Partek Genomics Solution software (www.partek.com; Partek Incorporated, St. Louis, Mo.). Expression values were computed from raw CEL files by applying the Robust Multi-Chip Average (RMA) background correction algorithm. RMA correction included: 1) values background correction; 2) quintile normalization; 3) log 2 transformation; and 4) median polish summarization. The ANOVA, Repeated Measures and correlation analysis implicated in Partek software ware applied to evaluate LAQ effects. Most informative genes MIGs were defined as those that differentiated between experimental groups with p<0.01. All p-values were calculated for False Discovery Rate (FDR) multiple test correction at p=0.05.
Additionally, significance of individual genes was tested by parametric T-test and non parametric Mann-Whitney test using Bootstrapping approach based on repeated permutations of the data with 5% FDR for multiple testing.
Gene functional annotation, enrichment, and pathway analyses to identify the leading biological pathways that operated under LAQ treatment were performed by Ingenuity Pathways Analysis software (www.ingenuity.com). Enrichment was defined as significantly (p<0.05) higher proportion of genes than expected by chance in a given gene set.
For verification of key genes on protein level Western blot analysis was performed. Supernatant was collected and protein concentration was determined using a Bradford assay (Pierce, Rockford, Ill., USA) according the manufacturer's guidelines. Equal amounts of protein were suspended in sample buffer and boiled for 5 min. Cell lysates were resolved on 10% SDS-polyacrylamide gel electrophoresis (PAGE). Gels were transferred to a Nitrocellulose membrane (Amersham, Buckinghamshire, UK), blocked with 1% BSA in Tris-buffered saline Tween (TBST) buffer (20 mM Tris, 137 mM NaCl and 0.1% Tween 20) and incubated with primary antibody overnight at 4° C. After washing three times with TBST buffer, blots were incubated with alkaline peroxidase-conjugated secondary antibody. Antibodies were diluted in the blocking solution. The blots were then washed three times with TBST buffer and analyzed by standard chemiluminescence (Supersignal Kit, Pierce, Rockford, Ill., USA) according to the company's protocol.
According to ancillary study aims, 72 blood samples were collected. The number of samples and corresponding demographical data is presented in Table 1.
ANOVA analysis was used to compare PBMC gene expression after 1, 6 or 24 month of LAQ treatment with baseline gene expression.
For each time point inventors performed analysis source of variation in dataset. (
Table 2 below shows number of genes significantly changed by ANOVA test in each time point as compared with baseline.
Table 3 and Table 4 below shows the main biological pathways and functions affected by LAQ.
3.5*10−10
4*10−3
The majority of genes that showed significant changes at each time points were down regulated. The functional enrichment analysis of 354 genes affected after 1 month of treatment showed suppression of 50 molecules associated with different mechanisms of inflammatory response (p value from 3.4*10−10 to 1.1*10−2). This included for example suppression of adhesion of phagocytes (p=1.2*10−3) and chemotaxis of neutrophils (p=6.0*10−3) based on suppression of TGFB1, ITGB1, ITGB3, ITGB5 and CXCL5, ITGB1, MMP1, TGFB1 correspondently. The most significant canonical pathways are suppression of Caveolar and Clatrin mediated Endocytosis Signaling (p=1.8*10−4 and 2.1*10−4). The interesting findings are suppression of PTCR and CD84 that function in adhesion interaction between T lymphocytes and accessory cells.
As shown in Table 2 the number of genes significantly affected by LAQ (p<0.01) changed from 354 to 1562 between 1 and 6 months of treatment, and 43 genes passed stringent FDR criteria for 6 months of treatment (
The number of patients involved in analysis at 24 months of treatment was relatively low, thus in order to improve statistical power, the inventors combined data from 6 and 24 months which resulted in evaluation of 2922 genes with p<0.01 and 1564 genes that passed FDR criteria (
Functional analysis of 1564 genes that passed FDR criteria after more than 6 months of treatment showed significant enrichment of down-regulated genes (n=305) related to different kind of cellular movement mechanisms with p values from 1.5*10−3 to 4.5*10−14. This included for example suppression of cell migration function (n=233, p=4.5*10−14) and chemotaxis (n=78, p=4.3*10−5).
LAQ significantly down-regulated a range of Metalloproteinase family members such as MMP1, MMP14, MMP16, MMP24, MMP25, MMP26, MMP28, ADAM12 and ADAM22. Several Integrin and chemokine related genes were down-regulated upon treatment of LAQ: ITGB1, ITGB5, ITGB6, ITGA8, ITGB8, and GPIIB-III3 (fibrinogen receptor), CXCL4, CCL14, CCL18, CCXCR1 (XCR1), CXCL7 (PPBP).
These results are in line with previous studies reporting that LAQ interferes with the migratory capacity of T cells in mice with EAE (Wegner et al., 2010, Jadidi-Niaragh et al., 2011).
In addition to suppression of cell migration ability, treatment of LAQ demonstrated significant down-regulation of IL-1R, IL-8R and IL-22R, IL-9, TNFRSF4, and RORC (RORgamma), all of which are inflammation-related genes that are known to play a role in EAE (Jadidi-Niaragh et al., 2011). Recently, it has been shown that IL-9 is important for T-cell activation and differentiation in autoimmune inflammation of the CNS, and that IL-9−/− mice developed significantly less severe EAE than their WT counterparts (Li et al., 2011). The results show reduced expression of SOCS (suppressor of cytokine signaling), a negative regulator of immune response, which is indirectly regulated by TGFb1 and ICOSLG (inducible T-cell co-stimulator ligand). In correlation with down-regulation of the pro-inflammatory constituents, LAQ treatment significantly reduced the expression of CSF1, CSF2 and CSF3 and indirectly affected FoxP3 expression. ROR (RORgamma) can directly interact with FoxP3. However, the functional consequence of this interaction is not clear because none of the previous studies on LAQ effect described an effect on Treg. Clatrin and Caveolar-mediated Endocytosis pathways are significantly suppressed (p=5.0*10−4 and p=5.8*10−4) after 1 month of treatment.
6 months or longer treatment of LAQ induced significant suppression of genes related to the TGFB pathway (p=1.9*10−2) (
TGFB is a potent regulatory cytokine with diverse effects on hematopoietic cells. The pivotal function of TGFB in the immune system is to maintain tolerance via the regulation of lymphocyte proliferation, differentiation, and survival. Among T cells, CD4+CD25+FOXP3+ T regs contain the main source of TGFB that suppresses immune responses in inflammatory sites. Defects in TGFB1 expression or its signaling in T cells correlate with the onset of several autoimmune diseases. It has been shown previously that besides its anti-inflammatory role, TGFB paradoxically acts as a pro-inflammatory cytokine and induces IL-17-producing pathogenic T helper cells (Th IL-17 cells) during an inflammatory response in which IL-6 is produced (Mirshafiey and Mohsenzadegan, 2009) (
Western blot analyses in four out of five patients who received 6 months of LAQ treatment verified down-regulation of TGFB1 protein level by 20-50%, as shown by quantification of band intensities normalized against Tubulin (
While anti-inflammatory properties of LAQ were previously reported (Gurevich et al., 2010, Brück and Wegner, 2011), the current study demonstrated down-regulation of several members of the coagulation pathway including F2 (thrombin), F7 (factor VII), F10 (factor X), FGB (fibrinogen beta-chain), TFPI [(tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)], Serpine 1 [plasminogen activator inhibitor (PAI-1)] and also two other members of the Serpine 1 family (SerpinA3 and SerpinB3). PAI-1 inhibits the serine proteases tissue plasminogen activator (tPA) and uPA/urokinase, thus it is an inhibitor of fibrinolysis, the physiological process that degrades blood clots. Although the tPA-plasmin cascade promotes neurodegeneration in excitotoxin-induced neuronal death, it has been demonstrated to have a protective role in inflammatory conditions with BBB disruption by removing fibrin, which exacerbates axonal injury (Gveric et al., 2003). Moreover, in the mouse model of MS, EAE incidence and clinical severity were reduced in PAI-1−/− mice, where clinical relapses were absent in PAI-1−/− mice and the subsequent reduction in neuroinflammation was coupled with a higher capacity for fibrinolysis in spinal cord samples from PAI-1−/− mice, in association with increased tPA activity (East et al., 2008).
Importantly, consistent with our gene expression results, which shows significant down-regulation of PAI-1, the Western blot analysis shown in
In ANOVA model each patients has to be independent under each condition. However in repeated measures algorithm the independence requirement is removed and each patients can repeatedly tested in different condition and responses from the same patients are correlated. Repeated measures increase statistical power and thus fewer subjects are needed to have adequate power. The inventors applied repeated measures analysis to evaluated effect of LAQ in same patients across all visits (28 microarrays related to 7 patients). First, using this approach the inventors evaluated Placebo effects and excluded placebo related genes from further analysis. The effect of LAQ realized in significant changing of 174 genes that pass FDR criteria with p<0.0004. Functional analysis of this gene list confirmed ANOVA results and among other included PTCRA, ITGB3, ITGA2B, ITGB5, PF4 and TGFB1 genes. The same of those gene profiles demonstrated in
In vivo effects of LAQ on PBMC showed down-regulation of genes as shown in Tables 3 and 4, including genes involving cell motility, adhesion, chemotaxis, IL1 and IL8 mediated inflammation, and Clatrin and Caveolar-mediated Endocytosis pathways, etc.
Functional enrichment analysis of most informative genes at 1 month of LAQ treatment demonstrated down-regulation of genes associated with inflammatory response, genes associated with TGFb signaling including TGFb1, TGFb1I1 and LTBP1 (p value range=3.8*10−4 to 6.7*10−3), (see Table 4) and other genes associated with cellular movement and migration (TNFSF4, SELP, ITGA8, ITGB1/3/5, CXCL5/7 and BMP6 genes).
Suppression of inflammation was further strengthened after 6 months of LAQ treatment, where there was suppression of large number of genes associated with adhesion, migration and leukocyte extravasation signaling (ITGA2/8, ITGb1/3/4/5/6, ITGBL1, MMP16/24/26/28 and ADAM12/18/22) accompanied by suppression of IL-1/5/8/13/20/22R, IL-9/11/12/36, TNFRSF11A/B, and IFNA4/8/10/17. Notably, LAQ treatment also down-regulated TGFB expression including its downstream signaling constituents (LTBP4, MEK1/2, TGFB type I receptor and smad2/3/4). Laquinimod treatment down-regulated TGFb expression including its associated signaling constituents (LTBP4, type II BMPR and smad1/4/5/6/8) and the NFkB signaling constituents (IL-1, IL-1R and IKKg) (see,
The inventors analyzed the molecular pathways induced by LAQ treatment in patients that participated in the ALLEGRO trial using gene expression microarray analysis. Blood transcriptional changes after one and six months of treatment were compared to baseline to identify LAQ induced MIGs (p<0.01) and operating pathways.
The inventors identified 354 MIGs at one month and 1562 MIGs at six months of treatment. LAQ treatment effects were enhanced by duration of treatment and characterized by down-regulation of inflammatory responses via TGFb and NFkB signaling in combination with suppression of genes associated with cellular movement including adhesion, migration and leukocyte extravasation signaling like integrins, chemokines and metalloproteinases with further down-regulation of genes encoding pro-inflammatory cytokines.
These results demonstrate that LAQ acts via suppression of inflammation mainly through arrest of leukocytes extravasation and thereby could contribute to amelioration of disease activity in RRMS patients.
LAQ was demonstrated to inhibit the development of acute experimental autoimmune encephalomyelitis (EAE) and to reduce EAE clinical score in mice treated after disease onset (Brück and Wegner, 2011; Brunmark et al., 2002; Jolivel et al., 2013; Ruffini et al, 2013; Schulze-Topphoff et al., 2012; Wegner et al., 2010). Clinically, LAQ demonstrated about 40% reduction in the cumulative number of gadolinium enhanced lesions in brain MRI in 106 RRMS patients as compared to 102 placebo treated RRMS patients (Comi et al., 2008). Recently, the Assessment of Oral Laquinimod in Preventing Progression in Multiple Sclerosis (Filippi et al., 2014) study demonstrated that LAQ treatment modestly decreased annualized relapse rate, slowed progression of disability and prevented white and gray matter atrophy in RRMS patients treated for 24 months (Comi et al., 2008; Filippi et al., 2014).
The mechanisms by which LAQ suppresses the development of EAE involve modulation of Th1/Th2 response, interference with the migration capacity of T cells (Bruck and Vollmer, 2013; Brück and Wegner, 2011; Wegner et al., 2010; Yang et al., 2004; Zou et al., 2002), and prevention of inflammation-induced synaptic alterations occurring in EAE (Ruffini et al., 2013). In addition, in MS patients, it has been reported that LAQ modulates B cells and their regulatory effects on T cells (Toubi et al., 2012), and down-regulates immunogenicity of dendritic cell (Jolivel et al., 2013).
In a previous study (Gurevich et at, 2010), the inventors characterized the molecular effects of LAQ in-vitro in separated immune cells subtypes obtained from RRMS patients using gene expression microarrays. The inventors demonstrated that LAQ induced suppression of genes related to antigen presentation and corresponding inflammatory pathways involving NFkB signaling, pleiotrophin-induced inflammatory cytokines, chemokine and toll like receptor signaling, down-regulation of Th2 response in CD14+ macrophages and CD4+ T cells, suppression of proliferation in CD8+ T cells, and suppression of antigen presentation and adhesion in CD19+ B cells via suppression of NFkB pathway.
To further elucidate the molecular mechanisms underlying the therapeutic effects of LAQ in RRMS, the inventors performed high throughput gene expression microarray analysis of PBMCs from RRMS patients that participated in the ALLEGRO trial.
Peripheral blood samples were obtained from RRMS patients treated with LAQ 0.6 mg/day or placebo as an ancillary study to the Assessment of Oral Laquinimod in Preventing Progression in Multiple Sclerosis trial (Filippi et al., 2014). Blood samples were obtained at baseline and after one and six months of treatment.
PBMC were extracted from 15 ml peripheral blood, separated by Ficoll-Hypaque gradient. Total RNA was extracted using both Trizol including a DNase digestion step. RNA integrity was assessed by RNA Experion automated electrophoresis system. Probe synthesis using 3 μg total RNA, hybridization, detection, and scanning was performed according to the standard Affymetrix, Inc. USA protocols; cDNA was synthesized using the Two-Cycle cDNA Synthesis Kit (Affymetrix, Inc., USA), and in-vitro transcription performed with the GeneChip IVT Labeling Kit (Affymetrix, Inc., USA). The biotin-labeled IVT-RNA was hybridized to HG-U133A-2 arrays (Affymetrix, Inc., USA) containing 14,500 well-annotated human genes, washed in a GeneChip Fluidics Station 450 and scanned according to the manufacturer's protocol using GeneArray-™ scanner G2500A (Hewlett Packard, USA).
Data analysis was performed using Partek Genomics Solution software (www.partek.com). Expression values were computed from raw CEL files by applying the Robust Multi-Chip Average (RMA) background correction algorithm. RMA correction included: 1) values background correction; 2) quintile normalization; 3) log 2 transformation; and 4) median polish summarization. ANOVA analysis was applied to compare PBMC gene expression after one and six months of LAQ/placebo treatment as compared with baseline. Age, gender and batch effects were regarded as confounders in the ANOVA model. Genes that significantly changed in the placebo treated patients as compared to baseline were excluded from further analysis to yield only genes exclusively associated with LAQ effects. MIGs were defined as those that differentiated between groups with p<0.01. Gene functional annotation, enrichment and pathway analyses to identify the involved biological pathways were performed by Ingenuity Pathways Analysis software (www.ingenuity.com). All p values were applied for multiple testing corrections using False Discovery Rate (FDR) method with a cut off at p*0.05.
Protein fractions were purified from PBMC of 5 patients at baseline and after six months of LAQ treatment. Proteins were extracted from TRIZOL fractions and solubilized following the method reported by Hummon et al., 2007 (Hummon et al., 2007). Equal amounts of proteins were resolved on 10% SDS-PAGE and transferred onto nitrocellulose membranes (Invitrogen kit) for subsequent immune-blotting with antibodies specific for TGFb, ITGB1, CXCR1 and alpha Tubulin (Santa Cruz Biotechnology, Inc Santa Cruz, Calif., USA). Blots were analyzed by standard chemi-luminescence (Supersignal Kit, Pierce, Rockford, Ill., USA) and visualization was done by ChemiDoc™ XRS System (Bio-Rad).
Samples were obtained from 25 RRMS patients, age 38.0±2.0 years, female/male ratio 16/9. The LAQ treatment arm consists of 13 patients, female/male ratio 8/5, age 38.8±2.3 years and the placebo arm consists of 12 patients, female/male ratio 8/4, age 37.2±3.4 years.
LAQ induced a differential gene expression of 354 MIGs after one month of treatment and the number of MIGs increased to 1562 after six months (Table 6 and 7).
The majority of genes that significantly changed expression under LAQ treatment at one and six months of treatment were down regulated (98% and 99%, respectively).
3.1. Biological Pathways Associated with LAQ Treatment: Down-Regulation of TGFb and NFkB Signaling and Pro Inflammatory Cytokines
Functional enrichment analysis of 354 MIGs after one month of LAQ treatment disclosed the suppression of molecules associated with different mechanisms of inflammatory response and cellular movement presented in Table 5. Indeed, analysis of the 1562 MIGs after six months showed growing number of genes involved with these mechanisms. Of the significantly suppressed pathways, the TGFb superfamily signaling (Table 5, p=3.2*10−3) was suppressed after one as well as after six months of LAQ treatment (p=4.32*10−2).
Downregulation of the TGFb signaling pathway after one month of LAQ treatment was evident by suppression of TGFb and LTBP1 genes, the latter regulates secretion and activation of TGFb and thus promoting a feedback mechanism. After six months, down-regulation of additional TGFb superfamily related genes like BMP2/4/7, MIS, Type II BMP receptor, Smad14/5/6/8, TCF20, TCF2, Runx2 and the downstream ITGB1 was demonstrated (
Also, LAQ induced down-regulation of LFA-1 and VLA-4 expression that act with ITGB1 in adhesion of immune cells. The suppression of TGFb pathway after six months of LAQ treatment was accompanied by down regulation of IL-12 signaling pathway (p=6.2*10−3) and a wide range of other pro-inflammatory cytokines such as IL-9/11/12/20/36, TNFRSF11A/B, IFNA4/8/10/17, and also the receptors for IL-5/13/20/22 (p=3*10−3 to 9*10−3).
The molecular signature of LAQ after 6 months was also characterized by suppression of NFkB signaling as demonstrated by down regulation of members of the NFkB signaling that play a role in inflammation including IL-1, IL-1R and IKKg (
Altogether, these findings figure out a comprehensive suppression of pro-inflammatory cytokines and the key TGFb and NFkB pathways following six months of LAQ treatment. In view of the early down-regulation of TGFb at one month that precede the down-regulation of genes of pro-inflammatory cytokines, the inventors suggest that TGFb signaling precedes the suppression of inflammatory cytokines and that LAQ down regulates cytokine expression via suppression of TGFb.
Only five LAQ responsive MIGs were upregulated with the common three genes SASH1, FUCA1 and XYLT1 at one and six months. Although none of them integrated in firmed canonical pathway, overexpression of SASH1 and FUCA1 is associated with the inhibition of growth, proliferation, and invasion of cells (Meng et al., 2013).
Differential expression of cellular movement and migration were observed already after one month of LAQ treatment (p=3.49*10−4). These included down-regulation of genes associated with adhesion and migration of phagocytes (p=1.2*10−3), chemotaxis of neutrophils (p=6*10−3) and transmigration of leukocytes (p=1.9*10−3). Genes associated with cell movement and suppressed by LAQ were P selectin that is involved in the initial stage of adhesion and the integrin family members like ITGB1/3/5/6/8 and ITGA8 involved in later steps of adhesion and locomotion during leukocytes extravasation (p-value 1.72*10−3 to 5.5*10−3).
The suppressing effects of LAQ on cell adhesion and integrin expression were further enhanced after six months of treatment as was evident by down regulation of genes associated with cellular movement mechanisms (p value 3.15*10−6 to 3.79*10−3) including cell invasion (p=5.6*10−5), adhesion (p=2.4*10−5) and leukocyte extravasation (p=9.4*10−3), (Table 5, supra).
Similar to the observed effects of suppressed expression of the integrin family members after one month of treatment, suppression was even more evident after six months of LAQ treatment including integrin genes like ITGB/5/6/8, ITGA8, ITGB8, and ITGA2B (p value 9.84*10−4 to 1.1*10−3). In addition, suppression of inflammatory related chemokines like CCL19 and chemokine receptor CXCR1/2 was also demonstrated (p=6.79*10−3). Moreover, LAQ down-regulated a range of metalloproteinase family members such as MMP16/24/26/28, and ADAM12/18/22 that play a role during extravasation (p=4.95*10−4 to 1.26*10−3).
3.3. Verification of Key Genes Associated with LAQ Induced Molecular Pathways
The verification experiments performed by Western Blot analysis show significant down-regulation of key genes associated with most significantly affected biological mechanisms of LAQ. The TGFb protein following six months of LAQ treatment was suppressed by 69.0% (p=0.009) as could be seen from quantification of bands intensities (
The results demonstrate that the most significant effect of LAQ is induction of suppression of inflammatory response via TGFb and NFkB pathways, as well as decrease in cell movement processes including adhesion, migration and leukocyte extravasation.
The inventors observed down-regulation of signaling pathways involving integrins, chemokines and metalloproteinases accompanied by repression of pro-inflammatory cytokines. These effects were observed in RRMS patients treated over six months-period as compared with baseline. Notably, the suppressive effects of LAQ are already detected as early as one month after initiation of treatment although to a lesser extent, suggesting a time-dependent treatment effect.
The pivotal function of TGFb in the immune system is anti-inflammatory, to maintain tolerance via regulation of lymphocyte proliferation, differentiation and survival. However, in MS it has been shown that in addition to its anti-inflammatory role, TGFb paradoxically can act as pro-inflammatory factor involved in the genesis of the pathogenic EAE-inducing TH17 cells. Thus, deletion of the TGFb gene from activated T cells, is known to abrogate Th17 cell differentiation, resulting in almost complete protection from EAE, confirming TGFb proinflammatory potential (Oh and Li, 2013). In the same process of events, TGFb is involved in stimulation of inflammatory cells adhesion, migration and extravasation, and could promote penetration of auto-aggressive lymphocytes to the central nervous system (CNS) (Bartolome et al., 2003; Brill et al., 2001). TGFb is also known to regulate the expression of IL-9 (Takami et al, 2012) and IL-22 (Sanjabi et al., 2009), thereby enhancing the expression of molecules associated with inflammation. TGFb itself can be activated by IL-1 (Luo et al., 2009), however IL-1 was also found to be suppressed in LAQ gene expression signature.
In accordance with observations linking TGFb with inflammatory process, the suppression of TGFb and members of the TGFb pathway by LAQ could result in beneficial reduction of active inflammation in MS. The suppression of TGFb signaling by LAQ corroborates with previous publications in which LAQ suppresses MAP3K7 (TAK1) that is strong positive regulator of cellular proliferation mediated by TGFb activation in CD14+ cells (Gurevich et al., 2010; Wan et al., 2006).
The inventors have demonstrated the suppressed expression of large number of cell adhesion and cell movement molecules involved in different stages of leukocytes extravasation under LAQ treatment. The ability of inflammatory cells to move from the periphery to the CNS is a crucial multistep process in MS with the following components down regulated by LAQ: a) Selectin P and IL-8R (CXCR1/2), that mediate rolling and the initial leukocyte-endothelial interactions; b) VLA-4, LFA-1, ITGA2/8, and ITGB1-6 integrins that mediate leukocyte adhesion and transmigration; c) chemokines and chemokine receptors for integrin activation like CCL19 that is responsible for leukocyte arrest and transmigration, and IL-8 receptor (CXCR1/2). These genes are well fitted with the steps of rolling, activation, adhesion, locomotion protrusion and transmigration of immune cells during extravasation to the CNS (as shown in
Similarly, in MS patients, the inventors have demonstrated that LAQ down-regulates IL-1, IL-1R, IL12 and IKKg genes associated with pro-inflammatory NFkB pathway. The suppression of NFkB mechanism by LAQ was also demonstrated in an in-vitro study on PBMC obtained from MS patients (Gurevich et al., 2010) and in astrocytes following LAQ treatment in cuprizone-induced demyelination model (Bruck et al., 2012). NFkB signaling mediates IL-12 activation in macrophages (Murphy et al., 1995). The inventors have determined that LAQ may suppress both IL1 and IL2 dependent inflammation via down regulation of NFkB signaling.
These inflammation counteracting effects of LAQ could be the molecular basis of the positive imaging effect of LAQ in the ALLEGRO trial (Comi et al., 2012; Filippi et al., 2014).
Only 5 genes were up-regulated by LAQ; three of these up regulated genes were up-regulated already after one month of treatment with sustained effect at 6 months; Sash1 and FUCA1 are involved in suppression of proliferation while XYLT catalyzes the biosynthesis of glycosaminoglycan and its high activity was reported in patients with impaired BBB (Ponighaus et al., 2007). After six months of treatment, another growth inhibitor gene PID1 was overexpressed, confirming the suppression of proliferation of CD8+ cells by LAQ (Gurevich et al., 2010).
The inventors believe this to be the first study that characterizes LAQ induced transcriptional profile of RRMS patients demonstrating LAQ suppression of inflammatory cytokines and leukocytes extravasation either directly or via suppression of TGFb superfamily and NFkB signaling, thereby contributing to amelioration of the disease process of MS.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2014/055502 | 9/12/2014 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 61972782 | Mar 2014 | US | |
| 61877210 | Sep 2013 | US |
