Table 2 The interplay of genetics and epigenetics

Genetics affect epigenetics

DNMT1

DNA methyltransferase

mutation

CRC

[128]

DNMT3A

DNA methyltransferase

mutation

hematologic malignancies, mostly AML

[118]

DNMT3B

DNA methyltransferase

mutation, SNPs

ICF syndrome

[129]

TET1

5′ methylcytosine hydroxylase

chromosome translocation

CRC, CLL

[130]

TET2

5′ methylcytosine hydroxylase

mutation

myeloid malignancies

[131]

IDH1/2

isocitrate dehydrogenase

mutation

AML, glioma

[132, 133]

ALKBH3

DNA dealkylation repair enzyme

mutation

papillary thyroid cancer

[134]

SETD2

histone lysine methyltransferase

mutation

pleural mesothelioma, lung cancer, leukemia, renal cancers, glioma

[135,136,137,138]

CREBBP

histone acetyltransferase

mutation, amplification

ALL, CRC, GC, lymphoma

[139,140,141,142]

MLL1

H3K4 histone methyltransferase

fusion protein

ALL, AML, B cell lymphoma, prostate cancer, bladder transitional cell carcinoma

[143]

EP300

histone deacetyltransferase

mutation

myeloproliferative neoplasms, GC, lymphoma, thyroid cancer

[141, 142, 144, 145]

DOT1L

histone lysine methyltransferase

mutation, amplification

GC, ovarian cancer

[146, 147]

EZH2

H3K27 Histone methyltransferase

mutation

melanoma, hematologic malignancies, mostly B-cell lymphoma

[148,149,150,151]

NSD1

nuclear receptor binding SET domain protein 1

mutation, frame shift, translocation

CRC, GC, clear cell renal cell carcinomas, head and neck cancers, AML, HCC, malignant peritoneal mesothelioma

[152, 153]

HDAC10

histone deacetyltransferase

frame-shift deletion

thyroid cancer

[145]

JMJD1C

H3K4/H3K9 histone demethylase

mutation

clear cell renal cell carcinoma, intracranial germ cell tumors

[154]

ATRX

member of SWI/SNF family proteins

mutation

adult diffuse astrocytic tumors, glioma, pancreatic neuroendocrine tumors, myxofibrosarcoma, pediatric osteosarcoma

[155,156,157,158]

CHD5

ATPase of NURD

mutation

BC, CRC, neuroblastoma, glioma, lung, ovary, prostate cancers

[159]

HELLS

helicase involving DNA strand separation

mutation

CRC, GC, NSCLC

[160, 161]

SMARCB1

BAF subunit

mutation

malignant rhabdoid tumor, epithelioid sarcoma, ovarian small cell carcinoma

[162]

ARID1A

BAF subunit

mutation, genomic rearrangement

HCC, GC, CRC, BC, endometrial cancer, ovarian clear cell carcinomas, melanoma, bladder, lung and pancreatic cancers

[162]

SMARCA4

ATPase of BAF

mutation

rhabdoid tumors, epithelioid sarcoma, ovarian small cell carcinoma

[163, 164]

Epigenetics affect genetics

SAT2

satellite 2 repetitive element

hypomethylation

BC, GC, HCC, BC, pancreatic cancer, glioblastoma

[165,166,167,168,169]

ALU

repetitive element

hypomethylation

BC, CRC, GC, glioma

[170]

LINE-1

long interspersed nuclear element-1

hypomethylation

CRC, BC, lung cancer, prostate cancer, liver cancer, ovarian cancer, and esophageal cancer

[171]

MBD4

methyl binding protein

promoter hypermethylation

CRC, ovarian cancer

[172]

MGMT

O6-meG alkyltransferase

promoter hypermethylation

NSCLC, CRC, GC, gliomas, diffuse large B-cell lymphoma, esophageal and head and neck cancers

[173]

TDG

thymine DNA glycosylase

promoter hypermethylation

Multiple myeloma

[174]

NEIL1

removes thymine glycol

promoter hypermethylation

CRC, NSCLC, head and neck cancers

[175,176,177]

OGG1

8-oxoguanine DNA glycosylase

promoter hypermethylation

BC, CRC

[175, 178]

XPC

XPC complex subunit, binds DNA distortions

promoter hypermethylation

bladder cancer

[179]

XPG

subunit of ERCC5/XPG/Rad2 NER complex

promoter hypermethylation

CRC, ovarian cancer

[180]

MLH1

MutL homologs, MMR ATPase, forming heterodimer

promoter hypermethylation

ESCC, GC, CRC, NSCLC, ovarian, pancreatic, oral squamous, head and neck cancers, adult T-cell leukemia/lymphoma

[9, 181,182,183,184,185,186]