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Table 1 Described oncogenic alterations in chromatin regulatory factors that are candidate drivers in at least one tissue

From: The mutational landscape of chromatin regulatory factors across 4,623 tumor samples

Gene Literature evidence
ARID1A Mutated in cc ovarian carcinoma and RCC (CGC), bladder [25], HCC [26], endometrium [27], colorectal [28], gastric adenocarcinoma [29], pancreatic cancer [30], lung adenocarcinoma [31], Burkitt lymphoma [32] and aggressive neuroblastoma [33].
Down-regulated in aggressive breast cancer [34],
KMT2C Mutated in medulloblastoma (CGC), HCC [26], bladder [25], prostate cancer [35], colorectal cancer [36], gastric adenocarcinoma [29], NSCLC [37], breast cancer [38] and pancreatic cancer [30].
Deleted in leukemia [39].
DNMT3A Mutated in AML (CGC), ALL and lung cancer [40].
Over-expressed in ovarian aggressive tumors [41].
KDM6A Mutated in kidney, esophageal squamous cell carcinoma, multiple myeloma (CGC), lung cancer [42], medulloblastoma [43], ccRCC [44], bladder [25] and prostate [35].
Over-expressed in breast tumors with poor prognosis [45].
Deleted in lung cancer [46].
PBRM1 Mutated in ccRCC, breast (CGC) and pancreatic cancer [47].
NSD1 Mutated in AML (CGC) and NMSC [10].
Gained in lung adenocarcinoma of never-smokers [48].
TET2 Mutated in MDS (CGC), CMML and AML [49].
SETD2 Mutated in ccRCC (CGC).
Down-regulated in breast tumors [50].
SMARCA4 Mutated in NSCLC (CGC), lung adenocarcinoma [31], medulloblastoma [43] and Burkitt lymphoma [32].
Over-expressed in glioma [51] and in melanoma progression [52].
Gained in lung [42].
KMT2D Mutated in medulloblastoma, bladder [25], renal cancer (CGC), DLBCL [53].
Over-expressed in breast and colon tumors [54].
CHD4 Mutated in high MSI gastric and colorectal cancers [55].
Down-regulated in gastric and colorectal cancers [55].
NCOR1 Mutated in breast [56] and bladder cancer [25].
Down-regulated in aggressive breast tumors [57].
EP300 Mutated in colorectal, breast and pancreatic cancers, ALL, AML, DLBCL (CGC), bladder [25], SCLC [58] and endometrium [27].
Up-regulated in esophageal squamous cell carcinoma [59] and advanced HCC [60].
Loss of heterozygosity in glioblastoma [61].
KDM5C Mutated in ccRCC (CGC).
ARID2 Mutated in hepatocellular carcinoma (CGC), melanoma [62], NSCLC [63] and pancreatic cancer [30].
Deleted in NSCLC [63].
ASXL1 Mutated in MDS and CMML (CGC), myeloproliferative neoplasm; [64], AML with myelodysplasia-related changes [65] and castration-resistant prostate cancer [66].
MLL Mutated in AML, ALL (CGC), bladder [25], SCLC [58], HCC [26] and gastric tumors [29].
BAZ2A Over-expressed in CLL [67].
CHD3 Mutated in high MSI gastric and colorectal cancers [55].
ATRX Mutated in pediatric glioblastoma, neuroendocrine pancreatic tumors (CGC) and high grade adult gliomas [68].
ARID1B Mutated in breast tumors [56].
MBD1 Over-expressed in pancreatic cancer [69].
BAP1 Mutated in uveal melanoma, breast, NSCLC and RCC (CGC).
Over-expressed in NSCLC with good prognosis [70].
INO80 -
CHD2 Mutated in high MSI gastric and colorectal cancers [55] and CLL [71].
Down-regulated in relapsed colon cancer [72].
ASH1L Mutated in lung cancer cell lines [42].
Gained in hepatocellular carcinoma [73].
BPTF Gained in neuroblastoma and lung cancer [74].
RTF1 -
PHC3 Mutated and lost in osteosarcoma [75].
SMARCA2 Mutated in NMSC [76] and CLL [77].
Down-regulated in lung adenocarcinoma [78] and gastric cancer [79].
Amplified in AML [80].
SETDB1 Recurrently amplified and over-expressed in melanoma [81].
  1. This is an exhaustive compilation of alterations (a) reported in CRFs showing FM bias and CLUST bias in at least one tissue (Figure 1). Gene names correspond to HUGO Gene Nomenclature Committee-approved symbols. In bold typeface, genes included in the CGC [82]. ALL, acute lymphocytic leukemia; AML, acute myeloid leukemia; cc, clear cell; CGC, Cancer Gene Census; CLL, chronic lymphocytic leukemia; RCC, renal cell carcinoma; CMML, chronic myelomonocytic leukemia; CRPC, castration-resistant prostate cancer; ESCC, esophageal squamous cell carcinoma; HCC, hepatocellular carcinoma; HL, Hodgkin lymphoma; MCL, mantle cell lymphoma; MDS, myelodysplastic syndrome; MSI, microsatellite instability; MPN, myeloproliferative neoplasm; NMSC, non-melanoma skin cancer; NSCLC, non-small cell lung carcinoma; RCC, renal cell carcinoma.
  2. aEvidence based solely on cancer cell lines is excluded from this table. Only evidence in human samples have been used. Effects of pharmacological inhibition are not included. Germline polymorphisms are also excluded.