The DNA repair gene ERCC6 rs1917799 polymorphism is associated with gastric cancer risk in Chinese

Comparative proteomic analysis reveals the response mechanism of freshwater leech (Whitmania pigra) under heat-stress challenge

Temperature is an environmental parameter that remarkably affects the survival and organism health of poikilothermal animal-Whitmania pigra Whitman. Heat stress destroys the physiological homeostasis of intestine tissue. However, no studies on the intestinal mucosa response of leech exposure to heat stress have been reported so far. To identify the biomarker proteins involved in heat stress response, we performed a Tandem mass tag (TMT)-based comparative proteomic analysis on leech's intestine after exposing to 27 °C and 35 °C. The cumulative mortality in the 35 °C heat stress group increased on the third day after stress compared with the control group. Mean-while, intestinal malondialdehyde (MDA) content was significantly up-regulated whereas total antioxidant capacity (T-AOC) was significantly down-regulated. A total of 3935 proteins were identified through proteomic analysis. Heat stress resulted in 144 differential proteins; 75 were up-regulated, and 69 were down-regulated. The differential expression proteins in response to heat stress are mainly involved in calcium-binding proteins, molecular chaperones, cytoskeleton integrity, immune function and inflammation response, DNA damage and repair, ribosomal protein synthesis, stress hormones and neuro-transmitters, tumorigenesis, and apoptosis. Protein-protein network interaction analysis showed that HSP, CD8A, C3, CD63, CD81, MRPL58, MRPL15, HNRNPA1, AMBP, IGHEP1, SERPINC1, CYP3A4, ATP12A, RPS13, CaM, HSP70 binding protein, HSPA6, C4A, ANXA7, ARG1, ARG2, ATP1B, CALCA, HTR1B, and GNGT1 are the critical proteins of leeches resistance to heat stress. Our results systematically provide substantial responsive candidate proteins combating heat stress and enhance our understanding of the intrinsic response mechanisms of thermal sensitivities animal W. pigra facing heat exposure.

Case Report: Next-Generation Sequencing-Based Detection in A Patient with Three Synchronous Primary Tumors

Clinically rare, multiple primary tumors are a growth or development of two or more neoplasms in the same individual. A 57-year-old woman with two primary cancers, namely, breast and gastric cancers, and a gastrointestinal stromal tumor was admitted. Next-generation sequencing (NGS) of the three tumors and blood was performed to determine their clonal origin and identify genetic cancer susceptibility. NGS identified that germline genetic variants potentially correlated with an individual risk of developing multiple cancers and that additional mutations are required to drive the formation of different tumors.

Comparative analysis of triple-negative breast cancer transcriptomics of Kenyan, African American and Caucasian Women

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The current study determined the molecular fingerprints of TNBCs of women from kenya (KE) and compared them with those of African–American (AA) and Caucasian (CA) women.

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RNA sequencing analysis highlights the role of molecular alterations in TNBCs and the potential benefit of targeting pathways in this disease for the KE population as compared to AAs and CAs.

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The dysregulated genes and signaling pathways could contributes to the aggressive phenotypes of TNBCs of KE women.

Purpose

: Triple-negative breast cancer (TNBC) patients of various ethnic groups often have discrete clinical presentations and outcomes. Women of African descent have a disproportionately higher chance of developing TNBCs. The aim of the current study was to establish the transcriptome of TNBCs from Kenyan (KE) women of Bantu origin and compare it to those TNBCs of African-Americans (AA) and Caucasians (CA) for identifying KE TNBC-specific molecular determinants of cancer progression and potential biomarkers of clinical outcomes.

Patients and Methods

: Pathology-confirmed TNBC tissues from Kenyan women of Bantu origin (n = 15) and age and stage range matched AA (n = 19) and CA (n = 23) TNBCs of patients from Alabama were included in this study. RNA was isolated from paraffin-embedded tissues, and expression was analyzed by RNA sequencing.

Results

: At clinical presentation, young KE TNBC patients have tumors of higher stages. Differential expression analysis identified 160 up-regulated and 178 down-regulated genes in KE TNBCs compared to AA and CA TNBCs. Validation analyses of the TCGA breast cancer data identified 45 KE TNBC-specific genes that are involved in the apoptosis (ACTC1, ERCC6 and CD14), cell proliferation (UHRF2, KDM4C, UHMK1, KCNH5, KRT18, CSF1R and S100A13), and Wnt signaling (BCL9L) pathways.

Conclusions

: In this study, we identified biomarkers that are specific for KE TNBC patients of Bantu origin. Further study with a larger sample size of matched tumors could confirm our findings. If biologically confirmed, these molecular determinants could have clinical and biological implications and serve as targets for development of personalized therapeutics for KE TNBC patients.

[Bioinformatics analysis of expression and function of EXD3 gene in gastric cancer]

OBJECTIVE

To investigate the differentially expressed genes between gastric cancer and normal gastric mucosa by bioinformatics analysis, identify the important gene participating in the occurrence and progression of gastric cancer, and predict the functions of these genes.

METHODS

The gene expression microarray data GSE100935 (including 18 gastric cancer samples and normal gastric mucosal tissues) downloaded from the GEO expression profile database were analyzed using Morpheus to obtain the differentially expressed genes in gastric cancer, and a cluster analysis heat map was constructed. The online database UALCAN was used to obtain the expression levels of these differentially expressed genes in gastric cancer and normal gastric mucosa. The prognostic value of the differentially expressed genes in gastric cancer was evaluated with Kaplan-Meier survival analysis. GO functional enrichment analysis was performed using Fun-Rich software, and the STRING database was exploited to establish a PPI network for the differentially expressed genes.

RESULTS

A total of 45119 differentially expressed genes were identified from GSE100935 microarray data. Analysis with UALCAN showed an obvious high expression of EXD3 gene in gastric cancer, and survival analysis suggested that a high expression level of EXD3 was associated with a poorer prognosis of the patients with gastric cancer. GO functional enrichment analysis found that the differentially expressed genes in gastric cancer were involved mainly in the regulation of nucleotide metabolism and the activity of transcription factors in the cancer cells.

CONCLUSIONS

EXD3 may be a potential oncogene in gastric cancer possibly in relation to DNA damage repair. The up-regulation of EXD3 plays an important role in the development and prognosis of gastric cancer, and may serve as an important indicator for prognostic evaluation of the patients.

Functional Linkage of RKIP to the Epithelial to Mesenchymal Transition and Autophagy during the Development of Prostate Cancer

Raf kinase inhibitor protein (RKIP) plays a critical role in many signaling pathways as a multi-functional adapter protein. In particular, the loss of RKIP’s function in certain types of cancer cells results in epithelial to mesenchymal transition (EMT) and the promotion of cancer metastasis. In addition, RKIP inhibits autophagy by modulating LC3-lipidation and mTORC1. How the RKIP-dependent inhibition of autophagy is linked to EMT and cancer progression is still under investigation. In this study, we investigated the ways by which RKIP interacts with key gene products in EMT and autophagy during the progression of prostate cancer. We first identified the gene products of interest using the corresponding gene ontology terms. The weighted-gene co-expression network analysis (WGCNA) was applied on a gene expression dataset from three groups of prostate tissues; benign prostate hyperplasia, primary and metastatic cancer. We found two modules of highly co-expressed genes, which were preserved in other independent datasets of prostate cancer tissues. RKIP showed potentially novel interactions with one EMT and seven autophagy gene products (TGFBR1; PIK3C3, PIK3CB, TBC1D25, TBC1D5, TOLLIP, WDR45 and WIPI1). In addition, we identified several upstream transcription modulators that could regulate the expression of these gene products. Finally, we verified some RKIP novel interactions by co-localization using the confocal microscopy analysis in a prostate cancer cell line. To summarize, RKIP interacts with EMT and autophagy as part of the same functional unit in developing prostate cancer.

shRNA knockdown of DNA helicase ERCC6L expression inhibits human breast cancer growth

Breast cancer is a heterogeneous disease with a high degree of diversity with regards to tumor histological stage and molecular subtypes. These heterogeneous characteristics determine the risk of disease progression and therapeutic resistance. Understanding tumor heterogeneity is of primary concern to identify and develop novel and specific potential targets for diagnosis and therapy. The present study analyzed 106 paired breast cancer tissues from The Cancer Genome Atlas and demonstrated that excision repair cross‑complementation group 6 like (ERCC6L), a newly discovered DNA helicase, was overexpressed in 91.51% (97/106), unchanged in 7.54% (8/106) and decreased in 0.94% (1/106) of breast cancer samples. A short hairpin RNA ERCC6L lentivirus was constructed to investigate the role of ERCC6LR in cancer. First, a Celigo Image Cytometry system was used to detect MDA‑MB‑231 cell growth number following transfection with shERCC6L‑lentivirus or NC‑lentivirus and it was identified that the growth number of fluorescent MDA‑MB‑231 cells post‑transduction with shERCC6L‑lentivirus was decreased compared with the cells transduced with NC‑lentivirus. Then, the effect of knockdown of ERCC6L expression on the cell cycle distribution and apoptosis was to analyzed using fluorescence‑activated cell sorting (FACS). The FACS data demonstrated that knockdown of ERCC6L expression levels in MDA‑MB‑231 cells significantly increased S phase population but decreased the G1 and G2/M phase populations compared with the NC group. The apoptosis rate of MDA‑MB‑231 cells post‑transduction with shERCC6L‑lentivirus for 5 days was increased to 12.16±0.146% compared with the negative control rate (4.86±0.204%). These functional studies demonstrated that knockdown of ERCC6L expression levels in MDA‑MB‑231 cells significantly inhibited breast cancer cell proliferation, disturbed cell cycle distribution and induced apoptosis in vitro. These findings suggested that ERCC6L, which is highly expressed in breast cancer, acts as an oncogene, is involved in breast cancer development and may serve as a novel molecular target for the treatment of breast cancer.

Epistatic SNP interaction of ERCC6 with ERCC8 and their joint protein expression contribute to gastric cancer/atrophic gastritis risk

Excision repair cross-complementing group 6 and 8 (ERCC6 and ERCC8) are two indispensable genes for the initiation of transcription-coupled nucleotide excision repair pathway. This study aimed to evaluate the interactions between single nucleotide polymorphisms of ERCC6 (rs1917799) and ERCC8 (rs158572 and rs158916) in gastric cancer and its precancerous diseases. Besides, protein level analysis were performed to compare ERCC6 and ERCC8 expression in different stages of gastric diseases, and to correlate SNPs jointly with gene expression. Sequenom MassARRAY platform method was used to detect polymorphisms of ERCC6 and ERCC8 in 1916 subjects. In situ ERCC6 and ERCC8 protein expression were detected by immunohistochemistry in 109 chronic superficial gastritis, 109 chronic atrophic gastritis and 109 gastric cancer cases. Our results demonstrated pairwise epistatic interactions between ERCC6 and ERCC8 SNPs that ERCC6 rs1917799-ERCC8 rs158572 combination was associated with decreased risk of chronic atrophic gastritis and increased risk of gastric cancer. ERCC6 rs1917799 also showed a significant interaction with ERCC8 rs158916 to reduce gastric cancer risk. The expressions of ERCC6, ERCC8 and ERCC6-ERCC8 combination have similarities that higher positivity was observed in chronic superficial gastritis compared with chronic atrophic gastritis and gastric cancer. As for the effects of ERCC6 and ERCC8 SNPs on the protein expression, single SNP had no correlation with corresponding gene expression, whereas the ERCC6 rs1917799–ERCC8 rs158572 pair had significant influence on ERCC6 and ERCC6-ERCC8 expression. In conclusion, ERCC6 rs1917799, ERCC8 rs158572 and rs158916 demonstrated pairwise epistatic interactions to associate with chronic atrophic gastritis and gastric cancer risk. The ERCC6 rs1917799–ERCC8 rs158572 pair significantly influence ERCC6 and ERCC6-ERCC8 expression.

Single nucleotide polymorphisms and cancer susceptibility

A large number of genes associated with various cancer types contain single nucleotide polymorphisms (SNPs). SNPs are located in gene promoters, exons, introns as well as 5'- and 3'- untranslated regions (UTRs) and affect gene expression by different mechanisms. These mechanisms depend on the role of the genetic elements in which the individual SNPs are located. Moreover, alterations in epigenetic regulation due to gene polymorphisms add to the complexity underlying cancer susceptibility related to SNPs. In this systematic review, we discuss the various genetic and epigenetic mechanisms involved in determining cancer susceptibility related to various SNPs located in different genetic elements. We also discuss the diagnostic potential of these SNPs and the focus for future studies.

Meta-analysis reveals no significant association between ERCC6 polymorphisms and bladder cancer risk

BACKGROUND

Numerous studies have been conducted to evaluate the association between excision repair cross-complementing group 6 (ERCC6) gene polymorphisms and bladder cancer risk, but their findings have been inconsistent. Here we performed a meta-analysis to attempt to clarify this association.

METHODS

Studies were retrieved from the PubMed and China National Knowledge Infrastructure databases up to October 1, 2015, with strict selection and exclusion criteria. A total of 5,032 samples, comprising samples from 2,475 bladder cancer patients and 2,557 controls from 5 studies, were included in the meta-analysis. The odds ratio (OR) with 95% confidence interval (CI) was used to evaluate the strength of the associations.

RESULTS

Regarding the Met1097Val polymorphism, no significant association with bladder cancer risk was found in any of the genetic models evaluated (Val vs. Met: OR = 1.10, 95% CI, 0.97-1.25; Val/Val vs. Met/Met: OR = 1.23, 95% CI, 0.86-1.75; Val/Val + Val/Met vs. Met/Met: OR = 1.12, 95% CI, 0.96-1.30; Val/Val vs. Met/Met + Val/Met: OR = 0.81, 95% CI, 0.57-1.14). Similarly, as regards the Arg1230Pro polymorphism, we also found no positive results.

CONCLUSIONS

According to the results of our meta-analysis, there is no evidence of a link between the ERCC6 gene polymorphisms and bladder cancer risk. Well-designed further studies, with larger sample sizes and adjustment for confounders such as smoking status, are needed to confirm these conclusions.

Polymorphisms of multiple genes involved in NER pathway predict prognosis of gastric cancer

Nucleotide excision repair (NER) is a versatile system that repairs various DNA damage. Polymorphisms of core NER genes could change NER ability and affect gastric cancer (GC) prognosis. We systematically analyzed the association between 43 SNPs of ten key NER pathway genes (ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, ERCC6, ERCC8, XPA, XPC, and DDB2) and overall survival (OS) of 373 GC patients in Chinese. Genotyping was performed by Sequenom MassARRAY platform. We found for the first time that carriers of ERCC2 rs50871 GG genotype demonstrated significantly increased hazards of death than GT/TT individuals (HR=2.55, P=0.002); ERCC6 rs1917799 heterozygote GT were associated with significantly shorter OS than wild-type TT (adjusted HR=1.68, P=0.048); patients with DDB2 rs3781619 GG genotype suffered higher hazards of death compared with AG/AA carriers (adjusted HR=2.30, P=0.003). Patients with ERCC1 rs3212961 AA/AC genotype exhibited longer OS than CC genotype (adjusted HR=0.63, P=0.028); ERCC5 rs2094258 AA/AG genotype revealed significantly favorable OS compared with GG genotype (adjusted HR=0.65, P=0.033); DDB2 rs830083 CG genotype could increase OS compared with GG genotype (adjusted HR=0.61, P=0.042). Furthermore, patients simultaneously carrying two "hazard" genotypes exhibited even significantly worse survival with HR of 3.75, 3.76 and 6.30, respectively. Similarly, combination of "favorable" genotypes predicted better prognosis with HR of 0.56, 0.49 and 0.33, respectively. In conclusion, ERCC2 rs50871 G/T, ERCC6 rs1917799 G/T, DDB2 rs3781619 A/G polymorphisms could predict shorter OS while ERCC1 rs3212961 A/C, ERCC5 rs2094258 A/G, DDB2 rs830083 C/G polymorphisms could predict longer OS of GC, which might serve as promising biomarkers for GC prognosis.

Impact of a Eukaryotic Translation Initiation Factor 3a Polymorphism on Susceptibility to Gastric Cancer

OBJECTIVE

To investigate single nucleotide polymorphisms in the eukaryotic translation initiation factor 3a (eIF3a) gene and the risk for gastric cancer within the Chinese population.

SUBJECTS AND METHODS

A total of 322 patients with gastric cancer were selected as the patient group and 340 non-gastric cancer patients were selected as the control group using the case-control method. Polymerase chain reaction-sequence-specific primer technology was leveraged to genotype the rs77382849 single nucleotide polymorphism in the eIF3a gene. The demographic characteristics of the study population and other exposures to risk factors were collected. Unconditional logistic regression analysis was performed to determine the association between the risk factors and gastric cancer.

RESULTS

A higher frequency of the eIF3a rs77382849 GG homozygote genotype was observed in the gastric cancer patients compared with the controls (63.98 vs. 54.41%, p < 0.05). After adjustment of exposure risks, such as age, gender, smoking, and drinking, the rs77382849 single nucleotide polymorphism was still associated with susceptibility to gastric cancer. When the eIF3a rs77382849 GG homozygote genotype was used as the reference group, the GA genotype (GA vs. GG: OR = 0.545, 95% CI: 0.386-0.769, p = 0.001) and AA genotype (AA vs. GG: OR = 0.245, 95% CI: 0.072-0.836, p = 0.025) were both correlated with a significantly decreased risk for gastric cancer development.

CONCLUSION

An association between eIF3a rs77382849 polymorphism and susceptibility to gastric cancer was observed in these Chinese patients.

Genetic Variation in the 3'-Untranslated Region of NBN Gene Is Associated with Gastric Cancer Risk in a Chinese Population

NBN plays a crucial role in carcinogenesis as a core component for both homologous recombination (HR) and non-homologous end-joining (NHEJ) DNA double-strand breaks (DSBs) repair pathways. Genetic variants in the NBN gene have been associated with multiple cancers risk, suggesting pleiotropic effect on cancer. We hypothesized that genetic variants in the NBN gene may modify the risk of gastric cancer. To test this hypothesis, we evaluated the association between four potentially functional single nucleotide polymorphisms in NBN and gastric cancer risk in a case-control study of 1,140 gastric cancer cases and 1,547 controls in a Chinese population. We found that the A allele of rs10464867 (G>A) was significantly associated with a decreased risk of gastric cancer (odds ratio [OR] = 0.81, 95% confidence interval [95% CI] = 0.71-0.94; P = 4.71×10-3). Furthermore, the association between A allele of rs10464867 and decreased risk of gastric cancer was more significantly in elder individuals (per-allele OR = 0.72[0.59-0.88], P = 1.07×10-3), and male individuals (per-allele OR = 0.73[0.62-0.87], P = 3.68×10-4). We further conducted a haplotype analysis and identified that the NBN Ars10464867Grs14448Grs1063053 haplotype conferred stronger protective effect on gastric cancer (OR = 0.76[0.65-0.89], P = 6.39×10-4). In summary, these findings indicate that genetic variants at NBN gene may contribute to gastric cancer susceptibility and may further advance our understanding of NBN gene in cancer development.

The 765G>C polymorphism in the cyclooxygenase-2 gene and gastric cancer risk: an update by meta-analysis

BACKGROUND

The 765G>C polymorphism in cyclooxygenase-2 (COX-2) gene has been extensively investigated for association with gastric cancer (GC). However, the results of different studies have been inconsistent. The aim of this study is to comprehensively evaluate the genetic risk of -765G>C polymorphism in the COX-2 gene for GC.

MATERIALS AND METHODS

We searched Pubmed, Embase, Medline, CNKI database, Wanfang database, Weipu database, and Chinese Biomedical database, covering all publications (last search been performed on Jan 10, 2014). Statistical analyses were performed using Revman 5.2 and STATA 10.0 software.

RESULTS

A total of 1,874 cases and 3,005 controls in 10 case-control studies were included in this meta-analysis. The results indicated that the variant C allele carriers (GC+CC) had a 69% increased risk of GC when compared with the homozygote GG (odds ratio (OR)=1.69, 95% confidence interval (CI), 1.10-2.61 for GC+CC vs GG). In the subgroup analysis by ethnicity, significant elevated risks were associated with C allele carriers in Asians (OR=1.75, 95%CI=1.40-2.18, and p<0.00001) and in Indians (OR=8.38, 95%CI=4.34-16.16, and p<0.00001) but not in Caucasians (OR=1.07, 95%CI=0.81-1.42, and p=0.62) or in Dutch (OR=0.53, 95%CI= 0.33-0.87, and p= 0.01).In the subgroup analysis by Helicobacter pylori (H. pylori) status, a significantly increased risk was identified among H. pylori (+) (OR=3.58, 95%CI=2.33-3.50, and p<0.00001) and H. pylori (-) (OR=2.32, 95%CI=1.46-3.69, and p=0.0004).

CONCLUSIONS

This meta-analysis suggested that the -765G>C polymorphism in the COX-2 gene could be a risk factor for GC in Asians and Indians.

The interaction effects of pri-let-7a-1 rs10739971 with PGC and ERCC6 gene polymorphisms in gastric cancer and atrophic gastritis

Background

The aim of this study was to investigate the interaction effects of pri-let-7a-1 rs10739971 with pepsinogen C (PGC) and excision repair cross complementing group 6 (ERCC6) gene polymorphisms and its association with the risks of gastric cancer and atrophic gastritis. We hoped to identify miRNA polymorphism or a combination of several polymorphisms that could serve as biomarkers for predicting the risk of gastric cancer and its precancerous diseases.

Methods

Sequenom MassARRAY platform method was used to detect polymorphisms of pri-let-7a-1 rs10739971 G→A, PGC rs4711690 C→G, PGC rs6458238 G→A, PGC rs9471643 G→C, and ERCC6 rs1917799 in 471 gastric cancer patients, 645 atrophic gastritis patients and 717 controls.

Results

An interaction effect of pri-let-7a-1 rs10739971 polymorphism with ERCC6 rs1917799 polymorphism was observed for the risk of gastric cancer (P_interaction = 0.026); and interaction effects of pri-let-7a-1 rs10739971 polymorphism with PGC rs6458238 polymorphism (P_interaction = 0.012) and PGC rs9471643 polymorphism (P_interaction = 0.039) were observed for the risk of atrophic gastritis.

Conclusion

The combination of pri-let-7a-1 rs10739971 polymorphism and ERCC6 and PGC polymorphisms could provide a greater prediction potential than a single polymorphism on its own. Large-scale studies and molecular mechanism research are needed to confirm our findings.