Genetic polymorphisms and lung cancer risk: Evidence from meta-analyses and genome-wide association studies

Liu, Caiyang; Cui, Huanxian; Gu, Dongqing; Zhang, Min; Fang, Yanfei; Chen, Siyu; Tang, Mingshuang; Zhang, Ben; Chen, Huanwen

doi:10.1016/j.lungcan.2017.08.026

Cited by 40 publications

(28 citation statements)

References 136 publications

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“…These 27 genes also include the genes of THSD4, PPP4R4, SCGB1A1, and NRG1, already detected in GWA studies to determine single nucleotide polymorphisms (SNPs) specifically for COPD (Table 4 ). Furthermore, in our study, SNPs within 4 additional genes have been detected in GWAS studies carried out previously in lung-related studies including: PRDM11 and AHRR FVC, smoking 15 , 16 , CYP1A1 childhood bronchitis 17 and CYP1B1 lung cancer 18 . In this study, we have identified 17 genes which have not previously been detected in COPD studies, these include: LINC00942, REEP1, C6orf164, LINC00589, JAKMIP3, LINC00930, DNHD1, TMCC3, ADH7, PRKAR2B, GAD1, LOC338667, CYB5A, PIEZO2, SLITRK6, KCNA1 and LOC100507560 (Table 4 ).…”

Section: Resultsmentioning

confidence: 56%

Identification of Novel Genes in Human Airway Epithelial Cells associated with Chronic Obstructive Pulmonary Disease (COPD) using Machine-Based Learning Algorithms

Mostafaei

Kazemnejad

Jamalkandi

et al. 2018

Sci Rep

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The aim of this project was to identify candidate novel therapeutic targets to facilitate the treatment of COPD using machine-based learning (ML) algorithms and penalized regression models. In this study, 59 healthy smokers, 53 healthy non-smokers and 21 COPD smokers (9 GOLD stage I and 12 GOLD stage II) were included (n = 133). 20,097 probes were generated from a small airway epithelium (SAE) microarray dataset obtained from these subjects previously. Subsequently, the association between gene expression levels and smoking and COPD, respectively, was assessed using: AdaBoost Classification Trees, Decision Tree, Gradient Boosting Machines, Naive Bayes, Neural Network, Random Forest, Support Vector Machine and adaptive LASSO, Elastic-Net, and Ridge logistic regression analyses. Using this methodology, we identified 44 candidate genes, 27 of these genes had been previously been reported as important factors in the pathogenesis of COPD or regulation of lung function. Here, we also identified 17 genes, which have not been previously identified to be associated with the pathogenesis of COPD or the regulation of lung function. The most significantly regulated of these genes included: PRKAR2B, GAD1, LINC00930 and SLITRK6. These novel genes may provide the basis for the future development of novel therapeutics in COPD and its associated morbidities.

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Section: Resultsmentioning

confidence: 56%

Identification of Novel Genes in Human Airway Epithelial Cells associated with Chronic Obstructive Pulmonary Disease (COPD) using Machine-Based Learning Algorithms

Mostafaei

Kazemnejad

Jamalkandi

et al. 2018

Sci Rep

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“…The literatures which studied the connection of IL-10 polymorphisms with disease susceptibility were extensively reported. IL-10 polymorphisms were considered to be connected with multiple disease susceptibility such as ischemic stroke, pulmonary tuberculosis, HIV-1, nasopharyngeal carcinoma and multiple sclerosis, gastric cancer and inflammatory bowel disease [17][18][19][20][21][22][23]. The increased risk or reduced risk can be detected due to diverse reasons including studied races, sample size, genotyping methods and source of control population, which may lead to different conclusions.…”

Section: Discussionmentioning

confidence: 99%

Association between the IL-10-1082G/A, IL-10-819T/C and IL-10-592A/C polymorphisms and Brucellosis susceptibility: a meta-analysis

2019

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Brucellosis is a widespread zoonosis caused by small bacteria of the genus Brucella. The promoter polymorphisms of IL-10 (-1082 loci, -819 loci and -590 loci) are closely related to the production of IL-10, leading to the alteration of development and pathogenesis of Brucellosis. However, the previous results were controversial. In the present study, we conduct the meta-analysis to get a more precise result of IL-10 polymorphisms with Brucellosis risk. The quality of the studies was assessed according to a predefined scale. The odds ratio (OR) and 95% confidence interval (CI) were counted to evaluate the association strength. No significant association was found between position -1082 loci or -590 loci polymorphism and Brucellosis risk. The significant association was found in Asian population of position -819 (T vs. C: OR 0.60, 95% CI 0.44–0.82, P = 0.001), homozygote comparison (TT vs. CC: OR 0.24, 95% CI 0.09–0.62, P = 0.003) and recessive genetic model (TT vs. TC/CC: OR 0.22, 95% CI 0.05–0.91, P = 0.036). The present meta-analysis demonstrates that IL-10-819 loci polymorphism is not associated with Brucellosis risk of Caucasian population but may contribute a decreased risk to Asian population. And neither IL-10-1082 loci nor -592 loci polymorphism is associated with Brucellosis risk.

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“…18; and/or !10% frequency in DogSD, ref. 19) in 81 genes potentially associated with susceptibility to human lung cancer (20). We identified nine rare putatively pathogenic SNPs in five dogs in the genes CHRNA3, CYP1B1, DNAH11, and HER2 (Supplementary Table S10).…”

Section: The Genomic Landscape Of Naturally Occurring Primary Canine mentioning

confidence: 99%

Identification of Recurrent ActivatingHER2Mutations in Primary Canine Pulmonary Adenocarcinoma

Lorch

Sivaprakasam

Zismann

et al. 2019

Clinical Cancer Research

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Purpose: Naturally occurring primary canine lung cancers share clinicopathologic features with human lung cancers in never-smokers, but the genetic underpinnings of canine lung cancer are unknown. We have charted the genomic landscape of canine lung cancer and performed functional characterization of novel, recurrent HER2 (ERBB2) mutations occurring in canine pulmonary adenocarcinoma (cPAC). Experimental Design: We performed multiplatform genomic sequencing of 88 primary canine lung tumors or cell lines. Additionally, in cPAC cell lines, we performed functional characterization of HER2 signaling and evaluated mutationdependent HER2 inhibitor drug dose-response. Results: We discovered somatic, coding HER2 point mutations in 38% of cPACs (28/74), but none in adenosquamous (cPASC, 0/11) or squamous cell (cPSCC, 0/3) carcinomas. The majority (93%) of HER2 mutations were hotspot V659E transmembrane domain (TMD) mutations comparable to activating mutations at this same site in human cancer. Other HER2 mutations were located in the extracellular domain and TMD. HER2 V659E was detected in the plasma of 33% (2/6) of dogs with localized HER2 V659E tumors. HER2 V659E cPAC cell lines displayed constitutive phosphorylation of AKT and significantly higher sensitivity to the HER2 inhibitors lapatinib and neratinib relative to HER2-wild-type cell lines (IC 50 < 200 nmol/L in HER2 V659E vs. IC 50 > 2,500 nmol/L in HER2 WT). Conclusions: This study creates a foundation for molecular understanding of and drug development for canine lung cancer. These data also establish molecular contexts for comparative studies in dogs and humans of low mutation burden, never-smoker lung cancer, and mutant HER2 function and inhibition.

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Genetic polymorphisms and lung cancer risk: Evidence from meta-analyses and genome-wide association studies

Cited by 40 publications

References 136 publications

Identification of Novel Genes in Human Airway Epithelial Cells associated with Chronic Obstructive Pulmonary Disease (COPD) using Machine-Based Learning Algorithms

Identification of Novel Genes in Human Airway Epithelial Cells associated with Chronic Obstructive Pulmonary Disease (COPD) using Machine-Based Learning Algorithms

Association between the IL-10-1082G/A, IL-10-819T/C and IL-10-592A/C polymorphisms and Brucellosis susceptibility: a meta-analysis

Identification of Recurrent ActivatingHER2Mutations in Primary Canine Pulmonary Adenocarcinoma

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