Methods and compositions for treating liver cancer and liver disease

A method of determining if an HCC specific methylation signature is detected in a subject suspected of having liver cancer, comprising:

• (a) obtaining a tissue sample comprising a nucleic acid from the subject;
• (b) isolating the nucleic acid from the tissue sample;
• (c) determining a concentration of the HCC-specific methylation signature in the tissue sample by contacting the nucleic acid with at least one HCC-specific methylation signature detection molecule, wherein the HCC-specific methylation signature detection molecule is a probe comprising at least 5 nucleotides of a nucleotide sequence of any one of SEQ ID NOs:1-100;
• and
• (d) determining if the HCC-specific methylation signature is detected in the tissue sample.

A method of detecting at least one HCC-specific methylation signature in a tissue sample of a subject, comprising:

• contacting a HCC-specific methylation signature detection molecule with a nucleic acid obtained from the tissue sample;
• wherein the HCC-specific methylation signature detection molecule is capable of binding to one or more methylation patterns associated with POM121L12, CSMD3, AJAP1, COTL1, TRIL, SLC25A36, TMEM51-AS1, TACC2, NUDT16L1, NLRP2, MIR7160, MYL1, LOC391322, EGR3, PCDHGA12, GAS1, CCDC177, SIX2, BASP1P1, ANKRD30A, TMEM132D, LINC02500, SMOC2, MIR4689, THEGS, MROHS, MRPL36, LINC00602, MEGF6, MIR4456, MIR6072, LINC02667, MIR4472-1, EFNAS, LONRF3, TBC1D28, NLGN4Y, USP3, UTP14A, FOXD1, SLC22A31, PRRX1, LINC01381, ACTG1, HOXA11-AS, FOXC1, DUSP10, LOC101929268, ENGASE, DPP10, LSAMP-AS1, DLGAP2-AS1, PXDN, LINC01103, WWOX, PBX1, LINC02645, LINC00200, VCX3A, ZFPM2, COL14A1, LINC01587, MIR561, AJAP1, RIMS1, OCA2, PBX1, MIR4251, RASA3, GRIA1, LOC102725193, HLA-DPA1, MMP17, AFAP1-AS1, DTX2P1-UPK3BP1-PMS2P11, MIR5739, PRRX1, TBX15, PTPRN2, TNR, SCUBE3, SEPTIN9, TM2D3, LOC105374620, PIGBOS1, UNKL, LBX2-AS1, TIMP1, PSCA, PNMA3, RPF2, ADCY1, TFAP2A, HOXA10-AS, SEPTIN9, SEPTIN9, EFNB2, SDK1, MMP24OS, and EVX1;
• and
• wherein the HCC-specific methylation signature detection molecule is a probe comprising at least 5 nucleotides of a nucleotide sequence of any one of SEQ ID NOs:1-100.