PMID- 31641374
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20220410
IS  - 1756-0381 (Print)
IS  - 1756-0381 (Electronic)
IS  - 1756-0381 (Linking)
VI  - 12
DP  - 2019
TI  - Integrative analysis of genetic and epigenetic profiling of lung squamous cell 
      carcinoma (LSCC) patients to identify smoking level relevant biomarkers.
PG  - 18
LID - 10.1186/s13040-019-0207-y [doi]
LID - 18
AB  - BACKGROUND: Incidence and mortality of lung cancer have dramatically decreased 
      during the last decades, yet still approximately 160,000 deaths per year occurred 
      in United States. Smoking intensity, duration, starting age, as well as 
      environmental cofactors including air-pollution, showed strong association with 
      major types of lung cancer. Lung squamous cell carcinoma is a subtype of 
      non-small cell lung cancer, which represents 25% of the cases. Thus, exploring 
      the molecular pathogenic mechanisms of lung squamous cell carcinoma plays crucial 
      roles in lung cancer clinical diagnosis and therapy. RESULTS: In this study, we 
      performed integrative analyses on 299 comparative datasets of RNA-seq and 
      methylation data, collected from 513 lung squamous cell carcinoma cases in The 
      Cancer Genome Atlas. The data were divided into high and low smoking groups based 
      on smoking intensity (Numbers of packs per year). We identified 1002 
      significantly up-regulated genes and 534 significantly down-regulated genes, and 
      explored their cellular functions and signaling pathways by bioconductor packages 
      GOseq and KEGG. Global methylation status was analyzed and visualized in circular 
      plot by CIRCOS. RNA-and methylation data were correlatively analyzed, and 24 
      unique genes were identified, for further investigation of regional CpG sites' 
      interactive patterns by bioconductor package coMET. AIRE, PENK, and SLC6A3 were 
      the top 3 genes in the high and low smoking groups with significant differences. 
      CONCLUSIONS: Gene functions and DNA methylation patterns of these 24 genes are 
      important and useful in disclosing the differences of gene expression and 
      methylation profiling caused by different smoking levels.
CI  - (c) The Author(s). 2019.
FAU - Ma, Bidong
AU  - Ma B
AD  - Department of Medical Oncology, Zhe Jiang Chinese Medicine University affiliated 
      Chinese Medicine Hospital, Wen Zhou, Zhe Jiang province People's Republic of 
      China.
FAU - Huang, Zhiyou
AU  - Huang Z
AD  - Department of Medical Oncology, Zhe Jiang Chinese Medicine University affiliated 
      Chinese Medicine Hospital, Wen Zhou, Zhe Jiang province People's Republic of 
      China.
FAU - Wang, Qian
AU  - Wang Q
AD  - Tianjia Genomes Tech CO., LTD., No. 6 Longquan Road, Anhui Chaohu economic 
      develop zone, Hefei, 238014 People's Republic of China.
FAU - Zhang, Jizhou
AU  - Zhang J
AD  - Department of Medical Oncology, Zhe Jiang Chinese Medicine University affiliated 
      Chinese Medicine Hospital, Wen Zhou, Zhe Jiang province People's Republic of 
      China.
FAU - Zhou, Bin
AU  - Zhou B
AD  - Department of Medical Oncology, Zhe Jiang Chinese Medicine University affiliated 
      Chinese Medicine Hospital, Wen Zhou, Zhe Jiang province People's Republic of 
      China.
FAU - Wu, Jiaohong
AU  - Wu J
AD  - 3Department of Gynecology and Oncology, Wen Zhou Medical University affiliated 
      People's Hospital, Wen Zhou, Zhe Jiang province People's Republic of China. ISNI: 
      0000 0001 0348 3990. GRID: grid.268099.c
LA  - eng
PT  - Journal Article
DEP - 20191021
PL  - England
TA  - BioData Min
JT  - BioData mining
JID - 101319161
PMC - PMC6802182
OTO - NOTNLM
OT  - Data mining
OT  - Lung squamous cell carcinoma
OT  - Methylation
OT  - RNA-seq
OT  - Smoking intensity
OT  - The Cancer genome atlas
COIS- Competing interestsThe authors declare that they have no competing interests.
EDAT- 2019/10/24 06:00
MHDA- 2019/10/24 06:01
PMCR- 2019/10/21
CRDT- 2019/10/24 06:00
PHST- 2019/06/06 00:00 [received]
PHST- 2019/09/12 00:00 [accepted]
PHST- 2019/10/24 06:00 [entrez]
PHST- 2019/10/24 06:00 [pubmed]
PHST- 2019/10/24 06:01 [medline]
PHST- 2019/10/21 00:00 [pmc-release]
AID - 207 [pii]
AID - 10.1186/s13040-019-0207-y [doi]
PST - epublish
SO  - BioData Min. 2019 Oct 21;12:18. doi: 10.1186/s13040-019-0207-y. eCollection 2019.