Long non-coding RNA polymorphisms on 8q24 are associated with the prognosis of gastric cancer in a Chinese population

Background Gastric cancer (GC) remains the third leading cause of cancer death in China. Although genome-wide association studies have identified the association between several single nucleotide polymorphisms (SNPs) on 8q24 and the risk of GC, the role of these SNPs in the prognosis of GC in Chinese populations has not yet been fully evaluated. Therefore, this study was conducted to explore the association between long non-coding RNA (lncRNA) polymorphisms on 8q24 and the prognosis of GC. Methods We genotyped 726 surgically resected GC patients to explore the association between eight SNPs in the lncRNAs CCAT1 (rs10087719, rs7816475), PCAT1 (rs1026411), PRNCR1 (rs12682421, rs13252298), and CASC8 (rs1562430, rs4871789, rs6983267) transcribed from the 8q24 locus and the prognosis of GC in a Chinese population. Results We found that the patients carrying rs12682421 AA genotypes survived for a shorter time than those with the GG/GA genotype (HR = 1.39, 95% confidence interval (CI) [1.09–1.78]). Compared with the CC/CT genotype, the TT genotype of rs1562430 was associated with an increased risk of death (HR = 1.38, 95% CI [1.06–1.80]). Furthermore, the results also identified the rs1026411 SNP as an independent prognostic factor for poor survival in GC patients. Patients carrying AA/AG variant genotypes had a 36% increased risk of death compared to those carrying the GG genotype (HR = 1.36, 95% CI [1.06–1.74]). These findings suggested that the rs12682421, rs1026411 and rs1562430 SNPs may contribute to the survival of GC and be prognostic markers for GC.

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Pharmacogenomics of Lithium Response in Bipolar Disorder

Pharmaceuticals ◽

10.3390/ph14040287 ◽

2021 ◽

Vol 14 (4) ◽

pp. 287

Author(s):

Courtney M. Vecera ◽

Gabriel R. Fries ◽

Lokesh R. Shahani ◽

Jair C. Soares ◽

Rodrigo Machado-Vieira

Keyword(s):

Bipolar Disorder ◽

Association Studies ◽

Mood Stabilizer ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Non Coding Rna ◽

Genome Wide ◽

Lithium Response ◽

Genetic Loading ◽

Long Non Coding Rna

Despite being the most widely studied mood stabilizer, researchers have not confirmed a mechanism for lithium’s therapeutic efficacy in Bipolar Disorder (BD). Pharmacogenomic applications may be clinically useful in the future for identifying lithium-responsive patients and facilitating personalized treatment. Six genome-wide association studies (GWAS) reviewed here present evidence of genetic variations related to lithium responsivity and side effect expression. Variants were found on genes regulating the glutamate system, including GAD-like gene 1 (GADL1) and GRIA2 gene, a mutually-regulated target of lithium. In addition, single nucleotide polymorphisms (SNPs) discovered on SESTD1 may account for lithium’s exceptional ability to permeate cell membranes and mediate autoimmune and renal effects. Studies also corroborated the importance of epigenetics and stress regulation on lithium response, finding variants on long, non-coding RNA genes and associations between response and genetic loading for psychiatric comorbidities. Overall, the precision medicine model of stratifying patients based on phenotype seems to derive genotypic support of a separate clinical subtype of lithium-responsive BD. Results have yet to be expounded upon and should therefore be interpreted with caution.

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LINC00673 rs11655237 Polymorphism Is Associated With Increased Risk of Cervical Cancer in a Chinese Population

Cancer Control ◽

10.1177/1073274818803942 ◽

2018 ◽

Vol 25 (1) ◽

pp. 107327481880394 ◽

Cited By ~ 10

Author(s):

Yanhua Wang ◽

Tianyou Luo

Keyword(s):

Cervical Cancer ◽

Chinese Population ◽

Noncoding Rna ◽

Association Studies ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Normal Tissues ◽

Genome Wide ◽

Increased Risk ◽

Cancer Tissues

Cervical cancer is the fourth most commonly diagnosed cancer and the fourth leading cause of cancer deaths in women worldwide. Few single-nucleotide polymorphisms associated with risk of cervical cancer have been identified, yet genetic predisposition contributes significantly to this malignancy. Long noncoding RNA LINC00673 has been widely explored for its role in the development and prognosis of many tumors, and 2 genome-wide association studies identified that LINC00673 rs11655237 was associated with susceptibility to pancreatic cancer. In the current study, using a case–control study design, we found rs11655237 significantly increased susceptibility of cervical cancer in a Chinese population (odds ratio = 1.27; 95% confidence interval = 1.08-1.50; P = .005). Expression of LINC00673 was significantly higher in adjacent normal tissues than in paired cancer tissues ( P < .01) and significantly lower in the cancer or paired adjacent normal tissues of patients with cervical cancer having rs11655237 allele A than in those having rs11655237 allele G ( P < .001). Our results indicate that LINC00673 rs11655237 is associated with increased risk of cervical cancer, possibly by downregulating LINC00673 expression in cervical tissues.

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GWAS Links New Variant in Long Non-Coding RNA LINC02006 with Colorectal Cancer Susceptibility

Biology ◽

10.3390/biology10060465 ◽

2021 ◽

Vol 10 (6) ◽

pp. 465

Author(s):

Ewa E. Hennig ◽

Anna Kluska ◽

Magdalena Piątkowska ◽

Maria Kulecka ◽

Aneta Bałabas ◽

...

Keyword(s):

Colorectal Cancer ◽

Cancer Susceptibility ◽

Association Studies ◽

Bioinformatic Analysis ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Tumor Invasiveness ◽

Non Coding Rna ◽

New Variant ◽

Long Non Coding Rna

Despite great efforts, most of the genetic factors contributing to the risk of colorectal cancer (CRC) remain undetermined. Including small but homogenous populations in genome-wide association studies (GWAS) can help us discover new common risk variants specific to the studied population. In this study, including 465 CRC patients and 1548 controls, a pooled DNA samples-based GWAS was conducted in search of genetic variants associated with CRC in a Polish population. Combined with a new method of selecting single-nucleotide polymorphisms (SNPs) for verification in individual DNA samples, this approach allowed the detection of five new susceptibility loci not previously reported for CRC. The discovered loci were found to explain 10% of the overall risk of developing CRC. The strongest association was observed for rs10935945 in long non-coding RNA LINC02006 (3q25.2). Three other SNPs were also located within genes (rs17575184 in NEGR1, rs11060839 in PIWIL1, rs12935896 in BCAS3), while one was intergenic (rs9927668 at 16p13.2). An expression quantitative trait locus (eQTL) bioinformatic analysis suggested that these polymorphisms may affect transcription factor binding sites. In conclusion, four of the identified variants were located within genes likely involved in tumor invasiveness and metastasis. Therefore, they could possibly be markers of poor prognosis in CRC patients.

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TLR1 and PRKAA1 Gene Polymorphisms in the Development of Atrophic Gastritis and Gastric Cancer

Journal of Gastrointestinal and Liver Diseases ◽

10.15403/jgld.2014.1121.274.tlr ◽

2018 ◽

Vol 27 (4) ◽

pp. 363-369 ◽

Cited By ~ 4

Author(s):

Gintare Dargiene ◽

Greta Streleckiene ◽

Jurgita Skieceviciene ◽

Marcis Leja ◽

Alexander Link ◽

...

Keyword(s):

Gastric Cancer ◽

Atrophic Gastritis ◽

Genetic Polymorphisms ◽

Association Studies ◽

Control Group ◽

Similar Distribution ◽

Genome Wide Association Studies ◽

Increased Risk ◽

Infection Susceptibility ◽

H Pylori

Background & Aims: Previous genome-wide association studies showed that genetic polymorphisms in toll-like receptor 1 (TLR1) and protein kinase AMP-activated alpha 1 catalytic subunit (PRKAA1) genes were associated with gastric cancer (GC) or increased Helicobacter pylori (H. pylori) infection susceptibility. The aim of this study was to evaluate the association between TLR1 and PRKAA1 genes polymorphisms and H.pylori infection, atrophic gastritis (AG) or GC in the European population.Methods: Single-nucleotide polymorphisms (SNPs) were analysed in 511 controls, 340 AG patients and 327 GC patients. TLR1 C>T (rs4833095) and PRKAA1 C>T (rs13361707) were genotyped by the real-time polymerase chain reaction. H. pylori status was determined by testing for anti-H. pylori IgG antibodies in the serum.Results: The study included 697 (59.2%) H. pylori positive and 481 (40.8%) H. pylori negative cases. We observed similar distribution of TLR1 and PRKAA1 alleles and genotypes in H. pylori positive and negative cases. TLR1 and PRKAA1 SNPs were not linked with the risk of AG. TC genotype of TLR1 gene was more prevalent in GC patients compared to the control group (29.7% and 22.3% respectively, p=0.002). Carriers of TC genotype had a higher risk of GC (aOR=1.89, 95% CI: 1.26–2.83, p=0.002). A similar association was observed in a dominant inheritance model for TLR1 gene SNP, where comparison of CC+TC vs. TT genotypes showed an increased risk of GC (aOR=1.86, 95% CI: 1.26–2.75, p=0.002). No association between genetic polymorphism in PRKAA1 gene and GC was observed.Conclusions: TLR1 rs4833095 SNP was associated with an increased risk of GC in a European population, while PRKAA1 rs13361707 genetic variant was not linked with GC. Both genetic polymorphisms were not associated with H. pylori infection susceptibility or the risk of AG.

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Functional genomics of autoimmune diseases

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2019-216794 ◽

2021 ◽

pp. annrheumdis-2019-216794

Author(s):

Akari Suzuki ◽

Matteo Maurizio Guerrini ◽

Kazuhiko Yamamoto

Keyword(s):

Autoimmune Diseases ◽

Association Studies ◽

Linkage Disequilibrium Block ◽

Causal Variant ◽

Genome Wide Association Studies ◽

Coding Region ◽

Risk Variants ◽

Non Coding Rna ◽

Genome Wide ◽

Long Non Coding Rna

For more than a decade, genome-wide association studies have been applied to autoimmune diseases and have expanded our understanding on the pathogeneses. Genetic risk factors associated with diseases and traits are essentially causative. However, elucidation of the biological mechanism of disease from genetic factors is challenging. In fact, it is difficult to identify the causal variant among multiple variants located on the same haplotype or linkage disequilibrium block and thus the responsible biological genes remain elusive. Recently, multiple studies have revealed that the majority of risk variants locate in the non-coding region of the genome and they are the most likely to regulate gene expression such as quantitative trait loci. Enhancer, promoter and long non-coding RNA appear to be the main target mechanisms of the risk variants. In this review, we discuss functional genetics to challenge these puzzles.

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Abstract 288: Novel Mechanisms of Non-coding Genomic Regulation Identified in Cardiac Disease-in-a-dish Models

Circulation Research ◽

10.1161/res.119.suppl_1.288 ◽

2016 ◽

Vol 119 (suppl_1) ◽

Author(s):

Aditya Kumar ◽

Stephanie Thomas ◽

Kirsten Wong ◽

Kevin Tenerelli ◽

Valentina Lo Sardo ◽

...

Keyword(s):

Heart Attack ◽

Connexin 43 ◽

Disease Risk ◽

Association Studies ◽

Correlation Coefficients ◽

Induced Pluripotent Stem Cell ◽

Genome Wide Association Studies ◽

Isogenic Line ◽

Nucleotide Polymorphisms ◽

Increased Risk

Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) at gene loci that affect cardiovascular function, and while mechanisms in protein-coding loci are obvious, those in non-coding loci are difficult to determine. 9p21 is a recently identified locus associated with increased risk of coronary artery disease (CAD) and myocardial infarction. Associations have implicated SNPs in altering smooth muscle and endothelial cell properties but have not identified adverse effects in cardiomyocytes (CMs) despite enhanced disease risk. Using induced pluripotent stem cell-derived CMs from patients that are homozygous risk/risk (R/R) and non-risk/non-risk (N/N) for 9p21 SNPs and either CAD positive or negative, we assessed CM function when cultured on hydrogels capable of mimicking the fibrotic stiffening associated with disease post-heart attack, i.e. “heart attack-in-a-dish” stiffening from 11 kiloPascals (kPa) to 50 kPa. While all CMs independent of genotype and disease beat synchronously on soft matrices, R/R CMs cultured on dynamically stiffened hydrogels exhibited asynchronous contractions and had significantly lower correlation coefficients versus N/N CMs in the same conditions. Dynamic stiffening reduced connexin 43 expression and gap junction assembly in R/R CMs but not N/N CMs. To eliminate patient-to-patient variability, we created an isogenic line by deleting the 9p21 gene locus from a R/R patient using TALEN-mediated gene editing, i.e. R/R KO. Deletion of the 9p21 locus restored synchronous contractility and organized connexin 43 junctions. As a non-coding locus, 9p21 appears to repress connexin transcription, leading to the phenotypes we observe, but only when the niche is stiffened as in disease. These data are the first to demonstrate that disease-specific niche remodeling, e.g. a “heart attack-in-a-dish” model, can differentially affect CM function depending on SNPs within a non-coding locus.

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Association of Long Non-Coding RNA Polymorphisms with Gastric Cancer and Atrophic Gastritis

Genes ◽

10.3390/genes11121505 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1505

Author(s):

Vytenis Petkevicius ◽

Greta Streleckiene ◽

Kotryna Balciute ◽

Alexander Link ◽

Marcis Leja ◽

...

Keyword(s):

Gastric Cancer ◽

Atrophic Gastritis ◽

Recessive Model ◽

Nucleotide Polymorphisms ◽

Blood Leukocytes ◽

Significance Threshold ◽

Non Coding Rna ◽

Premalignant Condition ◽

Gastric Cancer Patients ◽

Long Non Coding Rna

Long non-coding RNAs (lncRNA) play an important role in the carcinogenesis of various tumours, including gastric cancer. This study aimed to assess the associations of lncRNA ANRIL, H19, MALAT1, MEG3, HOTAIR single-nucleotide polymorphisms (SNPs) with gastric cancer and atrophic gastritis. SNPs were analyzed in 613 gastric cancer patients, 118 patients with atrophic gastritis and 476 controls from three tertiary centers in Germany, Lithuania and Latvia. Genomic DNA was extracted from peripheral blood leukocytes. SNPs were genotyped by the real-time polymerase chain reaction. Results showed that carriers of MALAT1 rs3200401 CT genotype had the significantly higher odds of atrophic gastritis than those with CC genotype (OR-1.81; 95% CI 1.17–2.80, p = 0.0066). Higher odds of AG were found in a recessive model (CC vs. TT + CT) for ANRIL rs1333045 (OR-1.88; 95% CI 1.19–2.95, p = 0.0066). Carriers of ANRIL (rs17694493) GG genotype had higher odds of gastric cancer (OR-4.93; 95% CI 1.28–19.00) and atrophic gastritis (OR-5.11; 95% CI 1.10–23.80) compared with the CC genotype, and carriers of HOTAIR rs17840857 TG genotype had higher odds of atrophic gastritis (OR-1.61 95% CI 1.04–2.50) compared with the TT genotype; however, the ORs did not reach the adjusted significance threshold (p < 0.007). In summary, our data provide novel evidence for a possible link between lncRNA SNPs and premalignant condition of gastric cancer, suggesting the involvement of lncRNAs in gastric cancer development.

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FGFR2 genotype and risk of radiation-associated breast cancer in Hodgkin lymphoma

Blood ◽

10.1182/blood-2011-10-383380 ◽

2012 ◽

Vol 119 (4) ◽

pp. 1029-1031 ◽

Cited By ~ 23

Author(s):

Yussanne P. Ma ◽

Flora E. van Leeuwen ◽

Rosie Cooke ◽

Annegien Broeks ◽

Victor Enciso-Mora ◽

...

Keyword(s):

Breast Cancer ◽

Breast Cancer Risk ◽

Cancer Risk ◽

Hodgkin Lymphoma ◽

Association Studies ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Control Series ◽

Cancer Risk Factors ◽

Increased Risk

Abstract Women treated at young ages with supradiaphragmatic radiotherapy for Hodgkin lymphoma (HL) have a highly increased risk of breast cancer. For personalized advice and follow-up regimens for patients, information is needed on how the radiotherapy-related risk is affected by other breast cancer risk factors. Genome-wide association studies have identified 14 independently replicated common single nucleotide polymorphisms that influence breast cancer risk. To examine whether these variants contribute to risk of radiation-associated breast cancer in HL, we analyzed 2 independent case-control series, from the United Kingdom and The Netherlands, totaling 693 HL patients, 232 with breast cancer and 461 without. rs1219648, which annotates the FGFR2 gene, was associated with risk in both series (combined per-allele odds ratio = 1.59, 95% confidence interval: 1.26-2.02; P = .000111). These data provide evidence that genetic variation in FGFR2 influences radiation-induced breast cancer risk.

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Identification of Novel Susceptible Genes of Gastric Cancer Based on Integrated Omics Data

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.712020 ◽

2021 ◽

Vol 9 ◽

Author(s):

Huang Yaoxing ◽

Yu Danchun ◽

Sun Xiaojuan ◽

Jiang Shuman ◽

Yan Qingqing ◽

...

Keyword(s):

Gene Expression ◽

Gastric Cancer ◽

Association Studies ◽

Gene Expression Level ◽

Expression Level ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Coding Region ◽

Level Data ◽

Integrated Omics

Gastric cancer (GC) is one of the most common causes of cancer-related deaths in the world. This cancer has been regarded as a biological and genetically heterogeneous disease with a poorly understood carcinogenesis at the molecular level. Thousands of biomarkers and susceptible loci have been explored via experimental and computational methods, but their effects on disease outcome are still unknown. Genome-wide association studies (GWAS) have identified multiple susceptible loci for GC, but due to the linkage disequilibrium (LD), single-nucleotide polymorphisms (SNPs) may fall within the non-coding region and exert their biological function by modulating the gene expression level. In this study, we collected 1,091 cases and 410,350 controls from the GWAS catalog database. Integrating with gene expression level data obtained from stomach tissue, we conducted a machine learning-based method to predict GC-susceptible genes. As a result, we identified 787 novel susceptible genes related to GC, which will provide new insight into the genetic and biological basis for the mechanism and pathology of GC development.

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Single nucleotide polymorphism within gene in NFKBIA is associated with the risks of nasopharyngeal carcinoma in Chinese Han population.

Journal of Global Oncology ◽

10.1200/jgo.2019.5.suppl.67 ◽

2019 ◽

Vol 5 (suppl) ◽

pp. 67-67

Author(s):

Hanyi Zhang ◽

Shun Lu ◽

Chang Sun ◽

Siyao Deng ◽

Jin Yi Lang

Keyword(s):

Nasopharyngeal Carcinoma ◽

Association Studies ◽

Sample Size Calculation ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Chinese Han ◽

Single Nucleotide ◽

Significance Level ◽

Genotype Frequencies ◽

Increased Risk

67 Background: Nasopharyngeal Carcinoma(NPC) is an Epstein-Barr virus(EBV) associated malignancy with remarkable ethnic and geographical distribution. The EBV oncoprotein latent membrane protein 1 (LMP1) is the primary oncogene of EBV infection through the its signaling cascade and its connections to other pathways including NF-κB, TGF-β and JNK signaling, which plays an important role in the pathogenesis of NPC. In GWASs (Genome-wide association studies) associations these pathways were also identified. Single nucleotide polymorphisms (SNPs) in the regulatory regions may regulate the expression of genes in these pathways, or affect the function of the coded protein. Methods: Altogether 149 SNPs were covered by the 15 SNPs in the TRAF2, TRAF3, NFKBIA, MAP2K4, and CHUK genes were genotyped in a hospital-based case-control study of 350 NPC cases and 587 healthy controls from the Chinese Han. The observed genotype frequencies in the controls were tested for Hardy–Weinberg equilibrium (HWE) using the chi-square test. Odds ratios (ORs) and 95% confidence intervals (95% CIs) for associations between genotypes and NPC risk and tumor characteristics were calculated by logistic regression, and they were adjusted for multiple testing using the SNP spectral deposition (SNPSpD) approach for multilocus analyses. Results: We found one NFKBIA SNP was associated with NPC risk after adjustment for multiple comparisons. Minor allele carriers of the NFKBIA had an increased risk of NPC (P 0.05). The analyses were adjusted for age and gender. For a polymorphism with a variant allele frequency between 10 %and 50%, the study had greater than 90% power to detect an OR of 1.50 at a significance level of 0.05 (PS—software for power and sample size calculation, http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/PowerSampleSize). The other genotyped SNPs that we found were not associated with NPC risk. Conclusions: Our data suggests that genetic variation especially in the NFKBIA maybe a useful biomarker for NPC screening and further studies are warranted.

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