FYB Methylation in Peripheral Blood as A Potential Marker for the Early-stage Lung Cancer: A Case-control Study in Chinese Population

BackgroundThe disease-associated non-coding variants identified by genome-wide association studies (GWASs) were enriched in open chromatin regions (OCRs) and implicated in gene regulation. Genetic variants in OCRs thus may exert regulatory functions and contribute to non-small cell lung cancer (NSCLC) susceptibility.ObjectiveTo fine map potential functional variants in GWAS loci that contribute to NSCLC predisposition using chromatin accessibility and histone modification data and explore their functions by population study and biochemical experimental analyses.MethodsWe mapped the chromatin accessible regions of lung tissues using data of assay for transposase-accessible chromatin using sequencing (ATAC-seq) in The Cancer Genome Atlas (TCGA) and prioritized potential regulatory variants within lung cancer GWAS loci by aligning with histone signatures using data of chromatin immunoprecipitation assays followed by sequencing (ChIP-seq) in the Encyclopedia of DNA Elements (ENCODE). A two-stage case–control study with 1,830 cases and 2,001 controls was conducted to explore the associations between candidate variants and NSCLC risk in Chinese population. Bioinformatic annotations and biochemical experiments were performed to further reveal the potential functions of significant variants.ResultsSixteen potential functional single-nucleotide polymorphisms (SNPs) were selected as candidates from bioinformatics analyses. Three variants out of the 16 candidate SNPs survived after genotyping in stage 1 case–control study, and only the results of SNP rs13064999 were successfully validated in the analyses of stage 2 case–control study. In combined analyses, rs13064999 was significantly associated with NSCLC risk [additive model; odds ratio (OR) = 1.17; 95%CI, 1.07–1.29; p = 0.001]. Functional annotations indicated its potential enhancer bioactivity, and dual-luciferase reporter assays revealed a significant increase in luciferase activity for the reconstructed plasmid with rs13064999 A allele, when compared to the one with wild-type G allele (pA549 < 0.001, pSK-MES-1 = 0.004). Further electrophoretic mobility shift assays (EMSA) and super-shift assays confirmed a stronger affinity of HP1γ for the binding motif containing SNP rs13064999 A allele.ConclusionThese findings suggested that the functional variant rs13064999, identified by the integration of ATAC-seq and ChIP-seq data, contributes to the susceptibility of NSCLC by affecting HP1γ binding, while the exact biological mechanism awaits further exploration.

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C-reactive protein gene 1846C>T polymorphism is associated with increased risk and clinical features of lung cancer: a case–control study

Bioscience Reports ◽

10.1042/bsr20181936 ◽

2019 ◽

Vol 39 (6) ◽

Cited By ~ 2

Author(s):

Chen Chen ◽

Jing-Ni Liu ◽

Jian-Qiang Zhao ◽

Bao Zang

Keyword(s):

Lung Cancer ◽

Case Control Study ◽

Case Control ◽

Lung Carcinogenesis ◽

C Reactive Protein ◽

Chinese Han ◽

Reactive Protein ◽

Potential Marker ◽

Increased Risk ◽

Control Study

AbstractChronic inflammation plays an important role in lung carcinogenesis. Recently, several studies investigated the association of C-reactive protein (CRP) gene 1846C>T polymorphism and lung cancer (LC) risk, but with conflicting findings. In the present study, we conducted this case–control study with 408 LC patients and 472 healthy controls in a Chinese Han population. Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLR) method. Our data found that CRP gene 1846C>T polymorphism increased the risk of LC. Subgroup analyses obtained significant associations among the groups of males, ≥50 years old, smoking, and non-drinkers. Bioinformatics analysis showed that the expression levels of CRP in LC tissues were significantly increased compared with normal tissues. Additionally, the present study found CRP mRNA high expression was associated with worse survival in LC patients. Furthermore, our data indicated that TT genotype of 1846C>T polymorphism was associated with a larger size of tumor and was related with lymphatic metastasis in LC patients. In conclusion, the present study suggests that CRP gene 1846C>T polymorphism is associated with increased risk of LC. CRP gene 1846C>T polymorphism may be a potential marker for the diagnosis of LC.

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