PMID- 29760565
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20220317
IS  - 1179-1322 (Print)
IS  - 1179-1322 (Electronic)
IS  - 1179-1322 (Linking)
VI  - 10
DP  - 2018
TI  - Genome-wide association pathway analysis to identify candidate single nucleotide 
      polymorphisms and molecular pathways associated with TP53 expression status in 
      HBV-related hepatocellular carcinoma.
PG  - 953-967
LID - 10.2147/CMAR.S163209 [doi]
AB  - BACKGROUND: The aim of this investigation was to identify candidate single 
      nucleotide polymorphisms (SNPs) and molecular pathways associated with tumor 
      protein p53 (TP53) expression status in hepatitis B virus (HBV)-related 
      hepatocellular carcinoma (HCC), clarify their potential mechanisms, and generate 
      SNP-to-gene to pathway hypothesis. MATERIALS AND METHODS: Identify candidate 
      Causal SNPs and Pathways (ICSNPathway) was used to perform pathway analysis based 
      on the results of our previous genome-wide association study of TP53 expression 
      status in 387 HBV-related HCC patients. RESULTS: Through the ICSNPathway 
      analysis, we identified 18 candidate SNPs and 10 candidate pathways that are 
      associated with TP53 expression status in HBV-related HCC. The strongest 
      mechanism involved the modulation of major histocompatibility complex, class II, 
      DP beta 1 (human leukocyte antigen [HLA]-DPB1-rs1042153), major 
      histocompatibility complex, class II, DQ beta 1 (HLA-DQB1-rs1130399, 
      HLA-DQB1-rs1049056, HLA-DQB1-rs1049059, and HLA-DQB1-rs1049060), and major 
      histocompatibility complex, class II, DR beta 1 (HLA-DRB1-rs35445101). SNPs 
      consequently affected regulatory roles in all the candidate pathways except 
      hematopoietic cell lineage pathways. Association analysis using the GSE14520 data 
      set, Gene Multiple Association Network Integration Algorithm, and Search Tool for 
      the Retrieval of Interacting Genes/Proteins suggests that all genes of the 
      candidate SNPs were associated with TP53. Survival analysis showed that the 
      collagen type VI alpha 3 chain (COL6A3) rs111231885 and COL6A3-rs113155945 and 
      COL6A3 block 4 CC haplotypes with TP53 negative status may have protective 
      effects in HBV-related HCC patients after hepatectomy. CONCLUSION: Our pathway 
      analysis identified 18 candidate SNPs and 10 candidate pathways that were 
      associated with TP53 expression status in HBV-related HCC. Among these candidate 
      SNPs, the genetic variation of COL6A3 may be a potential prognostic biomarker of 
      HBV-related HCC.
FAU - Liao, Xiwen
AU  - Liao X
AD  - Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi 
      Medical University, Nanning, People's Republic of China.
FAU - Yu, Long
AU  - Yu L
AD  - Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi 
      Medical University, Nanning, People's Republic of China.
FAU - Liu, Xiaoguang
AU  - Liu X
AD  - Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi 
      Medical University, Nanning, People's Republic of China.
AD  - Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical 
      University, Zhanjiang, People's Republic of China.
FAU - Han, Chuangye
AU  - Han C
AD  - Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi 
      Medical University, Nanning, People's Republic of China.
FAU - Yu, Tingdong
AU  - Yu T
AD  - Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi 
      Medical University, Nanning, People's Republic of China.
FAU - Qin, Wei
AU  - Qin W
AD  - Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi 
      Medical University, Nanning, People's Republic of China.
FAU - Yang, Chengkun
AU  - Yang C
AD  - Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi 
      Medical University, Nanning, People's Republic of China.
FAU - Zhu, Guangzhi
AU  - Zhu G
AD  - Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi 
      Medical University, Nanning, People's Republic of China.
FAU - Su, Hao
AU  - Su H
AD  - Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi 
      Medical University, Nanning, People's Republic of China.
FAU - Peng, Tao
AU  - Peng T
AD  - Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi 
      Medical University, Nanning, People's Republic of China.
LA  - eng
PT  - Journal Article
DEP - 20180501
PL  - New Zealand
TA  - Cancer Manag Res
JT  - Cancer management and research
JID - 101512700
PMC - PMC5937480
OTO - NOTNLM
OT  - TP53
OT  - genome-wide association study
OT  - hepatitis B virus
OT  - hepatocellular carcinoma
OT  - pathway analysis
COIS- Disclosure The authors report no conflicts of interest in this work.
EDAT- 2018/05/16 06:00
MHDA- 2018/05/16 06:01
PMCR- 2018/05/01
CRDT- 2018/05/16 06:00
PHST- 2018/05/16 06:00 [entrez]
PHST- 2018/05/16 06:00 [pubmed]
PHST- 2018/05/16 06:01 [medline]
PHST- 2018/05/01 00:00 [pmc-release]
AID - cmar-10-953 [pii]
AID - 10.2147/CMAR.S163209 [doi]
PST - epublish
SO  - Cancer Manag Res. 2018 May 1;10:953-967. doi: 10.2147/CMAR.S163209. eCollection 
      2018.