An analysis of polymorphisms within the Wnt signaling pathway in relation to ovarian cancer risk in a Polish population

Structural variant landscapes reveal convergent signatures of evolution in sheep and goats

BACKGROUND

Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution.

RESULTS

We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats.

CONCLUSIONS

Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.

Scutellaria baicalensis Georgi and Their Natural Flavonoid Compounds in the Treatment of Ovarian Cancer: A Review

Ovarian cancer (OC) is one of the most common types of cancer in women with a high mortality rate, and the treatment of OC is prone to high recurrence rates and side effects. Scutellaria baicalensis (SB) is a herbal medicine with good anti-cancer activity, and several studies have shown that SB and its flavonoids have some anti-OC properties. This paper elucidated the common pathogenesis of OC, including cell proliferation and cell cycle regulation, cell invasion and metastasis, apoptosis and autophagy, drug resistance and angiogenesis. The mechanisms of SB and its flavonoids, wogonin, baicalein, baicalin, Oroxylin A, and scutellarein, in the treatment of OC, are revealed, such as wogonin inhibits proliferation, induces apoptosis, inhibits invasion and metastasis, and increases the cytotoxicity of the drug. Baicalein also inhibits vascular endothelial growth factor (VEGF) expression etc. Analyzing their advantages and disadvantages in treating OC provides a new perspective on the role of SB and its flavonoids in OC treatment. It serves as a resource for future OC research and development.

Plant-Derived Chinese Medicine Monomers on Ovarian Cancer via the Wnt/β-Catenin Signaling Pathway: Review of Mechanisms and Prospects

Ovarian cancer (OC) is a common malignant tumor of the female reproductive system and has a high morbidity and mortality rate. The progression and metastasis of OC are complex and involve multiple signaling pathways. The Wnt/β-catenin signaling pathway is closely related to OC, and therefore blocking the activation of the Wnt/β-catenin signaling directly or inhibiting related genes, and molecular targets is of great value in treating OC. Toxicities such as myelotoxicity, cardiotoxicity, genotoxicity, and vasospasm are the major side effects for common anticancer drugs and are well documented. There is, therefore, a need to develop new, effective, safer, and more affordable anticancer drugs from alternative sources. In recent years, plant-derived Chinese medicine monomers have drawn increasing attention due to their high safety, low toxicity, minimal side effects, and antitumor effects. Plant-derived Chinese medicine monomers are effective against multiple targets and can regulate the growth, proliferation, apoptosis, invasion, and migration of OC as well as reverse drug resistance by regulating the Wnt/β-catenin signaling pathway. In this review, we summarize and provide mechanisms and prospects for the use of plant-derived Chinese medicines for the prevention and treatment of OC.

New insights of the correlation between AXIN2 polymorphism and cancer risk and susceptibility: evidence from 72 studies

Background

Numerous studies have reported the correlation between AXIN2 polymorphism and cancer risk, but the results seem not consistent. In order to get an overall, accurate and updated results about AXIN2 polymorphism and cancer risk, we conducted this study.

Methods

An updated analysis was performed to analyze the correlation between AXIN2 polymorphisms and cancer risk. Linkage disequilibrium (LD) analysis was also used to show the associations.

Results

Seventy-two case-control studies were involved in the study, including 22,087 cases and 18,846 controls. The overall results showed rs11079571 had significant association with cancer risk (allele contrast model: OR = 0.539, 95%CI = 0.478–0.609, PAdjust = 0.025; homozygote model: OR = 0.22, 95% CI = 0.164–0.295, PAdjust< 0.001; heterozygote model: OR = 0.292, 95% CI = 0.216–0.394, PAdjust< 0.001; dominant model: OR = 0.249, 95% CI = 0.189–0.33, PAdjust< 0.001). The same results were obtained with rs1133683 in homozygote and recessive models (PAdjust< 0.05), and in rs35285779 in heterozygote and dominant models (PAdjust< 0.05). LD analysis revealed significant correlation between rs7210356 and rs9915936 in the populations of CEU, CHB&CHS, ESN and JPT (CEU: r² = 0.91; CHB&CHS: r² = 0.74; ESN: r² = 0.62, JPT: r² = 0.57), and a significant correlation between rs9915936 and rs7224837 in the populations of CHB&CHS, ESN and JPT (r²>0.5), between rs7224837 and rs7210356 in the populations of CEU, CHB&CHS, JPT (r²>0.5), between rs35435678 and rs35285779 in the populations of CEU, CHB&CHS and JPT (r²>0.5).

Conclusions

AXIN2 rs11079571, rs1133683 and rs35285779 polymorphisms have significant correlations with overall cancer risk. What’s more, two or more polymorphisms such as rs7210356 and rs9915936, rs9915936 and rs7224837, rs7224837 and rs7210356, rs35435678 and rs35285779 have significant correlation with cancer susceptibility in different populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08092-0.

A 3' Untranslated Region Polymorphism of CTNNB1 (Rs2953) Alters MiR-3161 Binding and Affects the Risk of Ischemic Stroke and Coronary Artery Disease in Chinese Han Population

BACKGROUND

CTNNB1 is reported to be related to the pathological process of ischemic stroke (IS) and coronary artery disease (CAD). Polymorphism located in the 3' untranslated region (3'UTR) of a gene might affect gene expression by modifying binding sites for microRNAs (miRNAs). This study aimed to analyze the association between polymorphism rs2953, which locates in the 3'UTR of CTNNB1, and the risk of IS and CAD.

METHODS

The CTNNB1 messenger RNA (mRNA) expression level in peripheral venous blood was measured. In total, 533 patients with IS, 500 patients with CAD, and 531 healthy individuals were genotyped by Sequenom Mass-Array technology. The binding of miR-3161 to CTNNB1 was determined by dual-luciferase reporter assay.

RESULTS

The CTNNB1 mRNA expression level for the IS group was significantly lower than that for the control group. Rs2953 was significantly associated with both IS risk and CAD risk. Significant association was also found between polymorphism rs2953 and many conventional factors, such as serum lipid level, blood coagulation markers, blood glucose level, and homocysteine level in patients. Rs2953 T allele introduced a binding site to miRNA-3161 and thus decreased luciferase activity.

CONCLUSION

Polymorphism rs2953 is associated with the risk of both IS and CAD. Moreover, polymorphism rs2953 (T) introduces a binding site to miRNA-3161 and thus decreases luciferase activity in cell lines.

The Association of Polymorphisms in Base Excision Repair Genes with Ovarian Cancer Susceptibility in Chinese Women: A Two-Center Case-Control Study

Base excision repair (BER) acts upon the most important mechanism of the DNA repair system, protecting DNA stability and integrity from the mutagenic and cytotoxic effects. Multiple researches have indicated that single-nucleotide polymorphisms (SNPs) in the BER-related gene may be associated with the susceptibility of ovarian cancer. However, the results are controversial. In this two-center case-control study, 19 potentially functional SNPs in six BER-related genes (hOGG1, APE1, PARP1, FEN1, LIG3 and XRCC1) was genotyped in 196 ovarian cancer cases and 272 cancer-free controls. And, their associations with ovarian cancer risk were assessed by unconditional logistic regression analyses. We found that PARP1 rs8679 and hOGG1 rs293795 polymorphisms were associated with a decreased risk of ovarian cancer under dominant model (adjusted OR=0.39, 95% CI=0.17-0.90, P=0.026; and adjusted OR=0.36, 95% CI=0.13-0.99, P=0.049, respectively). Stratification analysis demonstrated that this association was more pronounced in the subgroups of lower BMI and patients with early menarche and serous carcinoma. Moreover, LIG3 rs4796030 AA/AC variant genotypes performed an increased risk of ovarian cancer under recessive model (adjusted OR=1.54, 95% CI=1.01-2.35, P=0.046), especially in the subgroups of higher BMI, early clinic stage and the carcinoma at the left. These results suggested that PARP1, hOGG1 and LIG3 polymorphisms might impact on the risk of ovarian cancer. However, more researches with larger and different ethnic populations are warranted to support our findings.

Variations in AXIN2 predict risk and prognosis of colorectal cancer

Objective

Colorectal cancer (CRC) and hypodontia are frequent and different diseases with common genes are involved in their etiology. The objective of this study was to identify the association between AXIN2 rs2240308 with hypodontia and CRC.

Patients and methods

This study consisted of 50 individuals with hypodontia, 50 individuals with CRC, and 155 healthy individuals from Colombia. SNP genotyping assays of rs2240308 were performed and family history of cancer in individuals with hypodontia was documented. In silico analysis was implemented to define the genomic profile of the AXIN2 gene associated with CRC. Multivariate analysis, chi square, odd ratio tests, and R software were used for statistical analysis.

Results

AXIN2 rs2240308 showed association with CRC (OR = 5.4 CI: 2.7–10.4; p < 0.001) and with other familial cancer in individuals with hypodontia (p < 0.005 OR = 1.75, 95% CI: 1.22–6.91). In silico analysis showed that variations in AXIN2 found in CRC patients, were more frequently in earlier stages of tumor and patients who carry variations in the AXIN2 gene have a worse prognosis (p < 0.05). The association between AXIN2 rs2240308 with hypodontia was not significant.

Conclusions

These results suggest that AXIN2 rs2240308 polymorphism is associated with CRC and AXIN2 could be a risk marker for predisposition and prognosis of CRC.

The Association Between AXIN2 Gene Polymorphisms and the Risk of Breast Cancer in Chinese Women

Background: The protein AXIN2 is involved in the negative feedback regulation of the Wnt/β-catenin signaling pathway; it functions by promoting β-catenin degradation. AXIN2 mutations have been studied in various cancers. In this study, we genotyped three single nucleotide polymorphisms in the AXIN2 gene and investigated their association with the risk of breast cancer (BC) in the Chinese Han population. Methods: In a population of 415 BC patients and 528 controls the expression of AXIN2 was measured using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and compared with the overall survival (OS) of BC patients analyzed through Oncomine and Kaplan-Meier plotter databases. Bioinformatic analyses demonstrated that AXIN2 mRNA levels were downregulated in BC patients; this in turn correlated with a poorer survival rate for BC patients. Results: The polymorphisms rs11079571 and rs3923087, but not rs3923086, were associated with an increased risk of BC. The minor allele containing genotypes of polymorphism rs3923087 were positively associated with lymph node metastases. A haplotype analysis demonstrated that the ATA haplotype was correlated with an increased risk of BC. Conclusion: In conclusion, the downregulation of AXIN2 is related to poorer OS for BC patients. Its polymorphisms rs11079571 and rs3923087 confer susceptibility to BC. These findings should be confirmed with larger studies that include more diverse ethnic populations.

New insights into the association between AXIN2 148 C/T, 1365 C/T, and rs4791171 A/G variants and cancer risk

BACKGROUND

Many epidemiological studies have investigated association of AXIN2 variants on overall cancer risks; however, the available results remain inconsistent.

METHODS

An updated analysis was conducted to ascertain a more accurate estimation of the correlation between AXIN2 148 C/T, 1365 C/T, and rs4791171 A/G polymorphisms and cancer risk. We also used in silico tools to assess the effect of AXIN2 expression on cancer susceptibility and overall survival time.

RESULTS

A total of 4281 cases and 3955 control participants were studied. The overall results indicated that AXIN2 148 C/T variant was associated with cancer risk (allelic contrast: OR = 0.88, 95% CI 0.77-0.99, P heterogeneity = 0.004; dominant model: OR = 0.82, 95% CI 0.69-0.96, P heterogeneity = 0.022), especially for lung and prostate adenocarcinoma. Similar results were observed in 1365 C/T polymorphism (OR = 0.71, 95% CI 0.61-0.98, P heterogeneity = 0.873; dominant model: OR = 0.66, 95% CI 0.47-0.94, P heterogeneity = 0.775). Moreover, in subgroup analysis by ethnicity, similar findings were obtained for Asian and Caucasian populations. Results from in silico tools suggested that AXIN2 expressions in lung adenocarcinoma were lower than that in normal group.

CONCLUSIONS

Our findings indicated that AXIN2 148 C/T and 1365 C/T variants may be associated with decreased cancer susceptibility.

The association between three AXIN2 variants and cancer risk

Plenty of epidemiological studies have assessed the effects of AXIN2 polymorphisms on the risk of developing cancer, but the available results were somewhat inconclusive. Odds ratios (ORs) with 95% confidence intervals (CIs) were utilized to investigate the relationship between three AXIN2 variants (rs2240308 C/T, rs1133683 C/T, and rs4791171 A/G) and overall cancer susceptibility. In silico tools were undertaken to investigate the correlation of AXIN2 expression with cancer risk and survival time. Furthermore, we explored the serum expression of AXIN2 by enzyme-linked immunosorbent assay. A total of 4167 cancer patients and 3515 control subjects were evaluated. The overall results demonstrated that there was no major association of these polymorphisms on cancer risk. However, stratified analysis by cancer type showed evidence that rs2240308 C/T polymorphism had a lower risk in lung cancer (OR, 0.76; 95% CI, 0.63-0.92; P_{heterogeneity}  = 0.865) and prostate cancer (OR, 0.54; 95% CI, 0.35-0.84; P_{heterogeneity}  = 0.088) by heterozygote comparison. Similar results were indicated in Asian descendants and population-based studies. In silico analysis showed evidence that AXIN2 expressions in lung cancer and prostate cancer were lower than that in normal counterpart. High expression of AXIN2 may have longer overall survival time than low expression group for lung cancer participants. In addition, individuals who were CC/TC carriers had a higher serum expression level than TT carriers. In conclusion, this pooled analysis suggested that AXIN2 rs2240308 C/T variant may decrease both lung and prostate cancer susceptibility, particularly in Asian descendants and population-based studies. Future large scale and well-designed research are required to validate these effects in more detail.

Influence of CTNNB1 rs2953 polymorphism on schizophrenia susceptibility in Chinese Han population through modifying miR-485 binding to CTNNB1

Schizophrenia (SCZ) and bipolar disorder (BD) are two major neuropsychiatric diseases that are the most substantial causes of disability and mortality worldwide. CTNNB1 encodes beta-catenin, an important protein in canonical Wnt signaling. We aimed to investigate the association between the rs2953 of CTNNB1 and the risk of SCZ and BD and to further explore the function of rs2953. A total of 1658 samples (548 SCZ cases, 512 BD cases, and 598 controls) were examined in terms of the genotype of CTNNB1 rs2953. The mRNA expression level of CTNNB1 significantly increased in the SCZ and BD groups compared with that in the control group. Significant association remained between CTNNB1 3'-untranslated region (UTR) variant rs2953 and SCZ susceptibility (additive and dominant model) after gender and age were adjusted. rs2953 disrupted the binding of CTNNB1 and miR-485. miR-485 significantly suppressed the luciferase activity of CTNNB1-T vector by binding to the CTNNB1 3'-UTR containing the T allele of rs2953. The mRNA expression of CTNNB1 can be used as a biomarker for the diagnosis of SCZ and BD. The 3'-UTR variant rs2953 in CTNNB1 influences the risk of SCZ in the Han Chinese population and modifies the binding of miR-485 to CTNNB1.

Polymorphisms and expression pattern of circular RNA circ-ITCH contributes to the carcinogenesis of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) ranks the sixth most common cancer and the third cause of cancer-related mortality worldwide. Recent studies identified that circ-ITCH Suppresses mutiple cancers proliferation via inhibiting the Wnt/beta-Catenin pathway. In current study, conducted a genetic association study together with epidemiological follow-up study to delineate the role of circ-ITCH in the development and progression of HCC. we found rs10485505 (adjusted OR =1.18; 95% CI=1.06-1.31; P value =3.1×10^-3) and rs4911154 (adjusted OR =1.27; 95% CI=1.14-1.43; P value =3.7×10^-5) were significantly associated with increased HCC risk. The expression level of circ-ITCH was significantly lower in HCC tissues, compared with that in adjacent tissues (P value < 0.001). Cox regression analysis indicated that high expression of circ-ITCH was associated with favorable survival of HCC (HR=0.45; 95% CI=0.29-0.68; P value < 0.001). These results indicate that circ-ITCH may have an inhibitory effect on HCC, and could serve as susceptibility and prognostic biomarkers for HCC patients.

High-order gene interactions between the genetic polymorphisms in Wnt and AhR pathway in modulating lung cancer susceptibility

AIM

Genetic variations present within Wnt and AhR pathway might be related to the lung cancer susceptibility.

METHODS

A total of 555 subjects were genotyped using PCR-RFLP technique for polymorphic sites in DKK4, DKK3, DKK2, sFRP3, sFRP4, Axin2 and AhR. Multifactor dimensionality reduction method and classification and regression tree analysis was used.

RESULTS

Overall sFRP4_rs1802073 which has a cross validation consistency of 10/10, prediction error = 0.43 (p > 0.0001) is the best factor model. The second best model was sFRP4_rs1802073 and DKK2_rs419558 with cross validation consistency of 9/10 and prediction error = 0.40. In classification and regression tree analysis, DKK2 _rs419558 came out to be a significant factor; DKK2_rs17037102 (M)/DKK2_rs419558 (M) showed a tenfold risk of acquiring lung cancer, p = 0.0001. DKK2_rs17037102 (M)/AhR_rs2066853 (W)/AhR_rs10250822 (M) showed an 11-fold risk of developing lung cancer, p = 0.00001.

CONCLUSION

Both DKK2 and sFRP4 polymorphisms are found to play a crucial role; especially for smokers towards modulating risk for lung cancer. AhR variants are contributing maximally toward lung cancer risk.

Comprehensive assessment and meta-analysis of the association between CTNNB1 polymorphisms and cancer risk

CTNNB1, encoding β-catenin, is a well-known tumor-related gene in the wnt signaling pathway. It has been reported that CTNNB1 polymorphisms are associated with cancer risk. However, the data were inconsistent. In this article, we conducted a systematic review for the researches related to the association of single nucleotide polymorphisms (SNPs) in CTNNB1 with overall cancer risk. Meanwhile, a series of inclusion and exclusion criteria were set to select articles for quantitative analysis. Consequently, eight case-control studies containing 4388 cases and 4477 controls were included in a meta-analysis of four highly studied CTNNB1 SNPs (rs1798802 A/G, rs4135385 A/G, rs11564475 A/G, and rs2293303 C/T). The association between each SNP and cancer risk was estimated by calculating odds ratios (ORs) and their 95% confidence intervals (95%CIs). The results showed rs1798802 (AA compared with GG: P=0.044, OR=0.72) and rs2293303 (TT compared with CC: P=0.002, OR=2.86; recessive model: P=0.006, OR=2.91; T compared with C: P=0.004, OR=1.19) polymorphisms were associated with overall cancer risk. In stratified analysis, rs4135385 polymorphism was found to elevate the risk in Caucasian or in gastrointestinal cancer subgroup. Additionally, rs2293303 conferred to an increased cancer risk when the source of control groups was hospital-based (HB). In conclusion, the three CTNNB1 SNPs were suggested to have the potential to be novel biomarkers for risk prediction of cancer in overall population or some specific subgroups. Our study could provide research clues for further related investigations.

Informed walks: whispering hints to gene hunters inside networks' jungle

Background

Systemic approaches offer a different point of view on the analysis of several types of molecular associations as well as on the identification of specific gene communities in several cancer types. However, due to lack of sufficient data needed to construct networks based on experimental evidence, statistical gene co-expression networks are widely used instead. Many efforts have been made to exploit the information hidden in these networks. However, these approaches still need to capitalize comprehensively the prior knowledge encrypted into molecular pathway associations and improve their efficiency regarding the discovery of both exclusive subnetworks as candidate biomarkers and conserved subnetworks that may uncover common origins of several cancer types.

Methods

In this study we present the development of the Informed Walks model based on random walks that incorporate information from molecular pathways to mine candidate genes and gene-gene links. The proposed model has been applied to TCGA (The Cancer Genome Atlas) datasets from seven different cancer types, exploring the reconstructed co-expression networks of the whole set of genes and driving to highlighted sub-networks for each cancer type. In the sequel, we elucidated the impact of each subnetwork on the indication of underlying exclusive and common molecular mechanisms as well as on the short-listing of drugs that have the potential to suppress the corresponding cancer type through a drug-repurposing pipeline.

Conclusions

We have developed a method of gene subnetwork highlighting based on prior knowledge, capable to give fruitful insights regarding the underlying molecular mechanisms and valuable input to drug-repurposing pipelines for a variety of cancer types.

Electronic supplementary material

The online version of this article (10.1186/s12918-017-0473-6) contains supplementary material, which is available to authorized users.

Effect of integrin‑linked kinase gene silencing on microRNA expression in ovarian cancer

Integrin‑linked kinase (ILK) is overexpressed in ovarian cancer (OC), and ILK gene silencing results in apoptosis in OC cells. In the present study, the mechanism by which ILK induces apoptosis was explored from the perspective of microRNA (miRNA) expression. Alterations in the global miRNA expression profile were detected using a miRNA microarray after OC cells were transduced with an ILK small hairpin RNA lentivirus. ILK silencing led to a significant upregulation of 14 miRNAs by at least 1.5‑fold. These findings were validated by reverse transcription‑quantitative polymerase chain reaction. A pathway analysis of experimentally validated target genes revealed the inhibition of multiple cancer‑associated signaling pathways and the wnt signaling pathway. Compared with cells transfected with scrambled RNA, the ILK‑silenced cells had remarkably lower expression of wnt ligands (wnt3a, wnt4 and wnt5a) and downstream β‑catenin. ILK silencing led to apoptosis of OC cells and impaired the migratory ability. Taken together, the present results suggested that miRNA‑mediated wnt pathway alterations are involved in the anti‑apoptotic role of ILK in OC. It was also indicated that ILK silencing reduced the ability of OC cells to adhere to fibronectin, which may lead to unstable focal contact. Consistently, the phosphorylation levels of focal adhesion kinase and RAC‑α serine/threonine protein kinase were downregulated. The present work demonstrated the first global miRNA expression profile of OC cells when ILK was inhibited, and this expression profile may provide a basis for the development of biomarkers and therapeutic targets for OC.

Different effection of p.1125Val>Ala and rs11954856 in APC on Wnt signaling pathway

Colorectal cancer (CRC) is among the most common and fatal forms of solid tumors worldwide and more than two thirds of CRC and adenomas patients have APC gene mutations. APC is a key regulator in the Wnt/β-catenin signaling pathway but its roles in CRC remains to be elucidated. In this study, we compared APC genes between CRC patients and controls to determine possible associations of nucleotide changes in the APC gene with the pathways involved in CRC pathogenesis. All participants received physical and enteroscopic examinations. The APC gene was sequenced for 300 Chinese Han CRC patients and 411 normal controls, and the expression levels of genes in the signaling pathway were analyzed using Western Blotting. Statistical analyses were conducted using SPSS (version 19.0) software. We found that rs11954856 in the APC gene was associated with colorectal cancer and could increase the expression levels of APC, β-catenin, TCF7L1, TCF7L2 and LEF1 genes in the pathway in the CRC patients, demonstrating the involvement of APC in the pathological processes leading to CRC.

RNA-based ovarian cancer research from 'a gene to systems biomedicine' perspective

Ovarian cancer remains the leading cause of death from a gynecologic malignancy, and treatment of this disease is harder than any other type of female reproductive cancer. Improvements in the diagnosis and development of novel and effective treatment strategies for complex pathophysiologies, such as ovarian cancer, require a better understanding of disease emergence and mechanisms of progression through systems medicine approaches. RNA-level analyses generate new information that can help in understanding the mechanisms behind disease pathogenesis, to identify new biomarkers and therapeutic targets and in new drug discovery. Whole RNA sequencing and coding and non-coding RNA expression array datasets have shed light on the mechanisms underlying disease progression and have identified mRNAs, miRNAs, and lncRNAs involved in ovarian cancer progression. In addition, the results from these analyses indicate that various signalling pathways and biological processes are associated with ovarian cancer. Here, we present a comprehensive literature review on RNA-based ovarian cancer research and highlight the benefits of integrative approaches within the systems biomedicine concept for future ovarian cancer research. We invite the ovarian cancer and systems biomedicine research fields to join forces to achieve the interdisciplinary caliber and rigor required to find real-life solutions to common, devastating, and complex diseases such as ovarian cancer.

ABBREVIATIONS

CAF: cancer-associated fibroblasts; COG: Cluster of Orthologous Groups; DEA: disease enrichment analysis; EOC: epithelial ovarian carcinoma; ESCC: oesophageal squamous cell carcinoma; GSI: gamma secretase inhibitor; GO: Gene Ontology; GSEA: gene set enrichment analyzes; HAS: Hungarian Academy of Sciences; lncRNAs: long non-coding RNAs; MAPK/ERK: mitogen-activated protein kinase/extracellular signal-regulated kinases; NGS: next-generation sequencing; ncRNAs: non-coding RNAs; OvC: ovarian cancer; PI3K/Akt/mTOR: phosphatidylinositol-3-kinase/protein kinase B/mammalian target of rapamycin; RT-PCR: real-time polymerase chain reaction; SNP: single nucleotide polymorphism; TF: transcription factor; TGF-β: transforming growth factor-β.

Association study between genetic variations in Axin2 gene and lung cancer risk in North Indian population: A multiple interaction analysis

Wnt pathway has been implicated in the process of human carcinogenesis. Axis inhibition protein2 ( Axin2), a major scaffold protein is an antagonist of Wnt pathway and is potent to act as a tumor suppressor gene in various human cancers. Therefore, the seven polymorphic sites of Axin2 gene were analyzed, in relation to lung cancer susceptibility in North Indians. A total of 608 subjects were genotyped using PCR-RFLP technique for each polymorphic site including 303 cases and 305 controls. Further association analysis was carried out using logistic regression approach to obtain adjusted odds ratio and statistical significance. MDR and CART analysis were applied to evaluate high order interactions between the SNP's. Three out of seven studied polymorphic sites showed a strong protective effect in subjects having mutant genotype for Axin2 148 C >T and heterozygous genotype for 1365 G > A and 1712 + 19 G > T towards lung cancer risk. The other important finding was the significant association of Axin2 148 C >T in SQCC patients having variant (TT) genotype. Axin2 1712 + 19 G >T showed a decreased risk for all the histological subtypes in patients with heterozygous (GT) genotype. MDR analysis predicted a best interaction model ( Axin2 148, Axin2 2062 and Axin2 1712 +19) with maximum CVC (10/10) and minimum prediction error (0.38) along with significant permutation p-value. CART analysis gave a wide spectrum of interactive combinations which exhibited a major contribution in modulating lung cancer susceptibility. Axin2 148 and Axin2 1712 + 19 were found to play a major role in modulating lung cancer risk.

Genetic polymorphisms of Wnt/β-catenin pathway genes are associated with the efficacy and toxicities of radiotherapy in patients with nasopharyngeal carcinoma

Radiotherapy (RT) is the normative therapeutic treatment for primary nasopharyngeal carcinoma (NPC). Single nucleotide polymorphisms (SNPs) of genes in Wnt/β-catenin pathway are correlated to the development, prognosis, and treatment benefit of various cancers. However, it has not been established whether SNPs of Wnt/β-catenin pathway are associated with nasopharyngeal tumorigenesis and the efficacy of RT in NPC patients. Therefore, in this study, we aimed to investigate the nine potentially functional SNPs of four genes in the Wnt/β-catenin pathway and genotyped these in 188 NPC patients treated with RT. To achieve this goal, associations between these SNPs and the RT's curative efficacy, as well as acute radiation-induced toxic reaction were determined by multifactorial logistic regression. We observed that catenin beta 1 gene (CTNNB1) rs1880481 and rs3864004, and glycogen synthase kinase 3 beta gene (GSK3β) rs3755557 polymorphisms were significantly associated with poorer efficacy of RT in NPC patients. Moreover, GSK3β rs375557 and adenomatous polyposis coli gene (APC) rs454886 polymorphisms were correlated with acute grade 3-4 radiation-induced dermatitis and oral mucositis, respectively. In conclusion, this study suggests that gene polymorphisms of Wnt/β-catenin may be novel prognostic factors for NPC patients treated with RT.

AXIN2 Polymorphisms, the β-Catenin Destruction Complex Expression Profile and Breast Cancer Susceptibility

BACKGROUND

The Wnt/β-catenin signaling pathway is an important regulator of cellular functions such as proliferation, survival and cell adhesion. Wnt/β-catenin signaling is associated with tumor initiation and progression; β-catenin mutations explain only 30% of aberrant signaling found in breast cancer, indicating that other components and/or regulation of the Wnt/β-catenin pathway may be involved.

OBJECTIVE

We evaluated AXIN2 rs2240308 and rs151279728 polymorphisms, and expression profiles of β-catenin destruction complex genes in breast cancer patients.

MATERIALS AND METHODS

We collected peripheral blood samples from 102 breast cancer and 102 healthy subjects. The identification of the genetic variation was performed using PCR-RFLPs and DNA sequencing. RT-qPCR was used to determine expression profiles.

RESULTS

We found significant association of AXIN2 rs151279728 and rs2240308 polymorphisms with breast cancer risk. Significant increase was observed in AXIN2 level expression in breast cancer patients. Further analyses showed APC, β-catenin, CK1α, GSK3β and PP2A gene expression to be associated to clinic-pathological characteristics.

CONCLUSIONS

The present study demonstrated, for the first time, that AXIN2 genetic defects and disturbance of β-catenin destruction complex expression may be found in breast cancer patients, providing additional support for roles of Wnt/β-catenin pathway dysfunction in breast cancer tumorigenesis. However, the functional consequences of the genetic alterations remain to be determined.

AXIN2 Polymorphisms and Their Association with Colorectal Cancer in Mexican Patients

AIM

The aim of this study was to investigate the association of the rs2240308 and rs1133683 polymorphisms in the AXIN2 gene with colorectal cancer (CRC) in Mexican patients.

MATERIALS AND METHODS

Genomic DNAs from 201 CRC patients and 100 healthy blood donors were analyzed for AXIN2 gene polymorphisms by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methodology. Statistical associations were calculated using the odds ratio (OR) test.

RESULTS

The genotype distribution of the rs1133683 polymorphism C > T showed a statistical difference between the two study groups (p = 0.0019). Moreover, OR analyses demonstrated that individuals with either the C/T or T/T genotype have a decreased risk for CRC compared with individuals with the C/C genotype (OR = 0.47, 95% confidence interval [CI] = 0.25-0.86, p = 0.0134 and OR = 0.24, 95% CI = 0.10-0.57, p = 0.005, respectively). This association was also evident in a stratified analysis based on tumor-node-metastasis (TNM) stage. For the rs2240308 polymorphism C > T, the OR analysis showed a significantly increased risk for carriers of the T/T genotype (OR = 2.64, 95% CI = 1.12-6.24, p = 0.0236) and this association was also evident in the stratified analysis by TNM stage.

CONCLUSION

Our results indicate the possibility that variations in the AXIN2 gene may play a significant role in promoting or preventing CRC development.

Cyclin Y regulates the proliferation, migration, and invasion of ovarian cancer cells via Wnt signaling pathway

This study is designated to investigate the roles of cyclin Y (CCNY) and Wnt signaling pathway in regulating ovarian cancer (OC) cell proliferation, migration, and invasion. Quantitative real-time PCR (qRT-PCR), Western blot, MTT assay, cell scratch, and transwell test were used in our study, and transplanted tumor model was constructed on nude mice. C-Myc, cyclin D1, PFTK1, ki67, OGT, and β-catenin protein expressions in tumor tissues were detected. CCNY was significantly upregulated in OC cell lines and tissues (both P < 0.05); significant association was observed between CCNY expression and clinicopathological stage, lymph node metastasis (LNM) (P < 0.05); and the CCNY expression in stages III to IV was higher than that in stages I to II, and patients with LNM had higher CCNY expression when compared with those in patients without LNM (P < 0.05); expressions of c-Myc, cyclin D, PFTK1, ki67, and OGT were upregulated in OC tissues compared with ovarian benign tissues, suggesting that these expressions were significantly different between the two groups (P < 0.05); CCNY significantly exacerbated proliferation, migration, and invasion of A2780 cells; c-Myc and cyclin D1 protein expressions increased as the expression of CCNY increased (P < 0.001); β-catenin expressions in A2780 cells with over-expression of CCNY were significantly increased in the nucleus, but significantly decreased in the cytoplasm (both P < 0.05); high expressions of CCNY exacerbated the proliferation of A2780 cells in nude mice and significantly increased c-Myc, cyclin D1, PFTK1, ki67, and OGT protein expressions in tumor tissues which were transplanted into nude mice (P < 0.01). CCNY might exacerbate the proliferation, migration, and invasion of OC cells via activating the Wnt signaling pathway. Thus, this study provides a theoretical foundation for the development of therapeutic drugs that are able to cure OC by targeting CCNY.

Association of Wnt signaling pathway genetic variants in gallbladder cancer susceptibility and survival

Gallbladder cancer (GBC) is the most common malignancy of the biliary tract with adverse prognosis and poor survival. Wnt signaling plays an important role in embryonic development and regeneration of tissues in all the species. Deregulation of expression and mutations in this pathway may lead to disease state such as cancer. In this study, we assessed the association of common germline variants of Wnt pathway genes (SFRP2, SFRP4, DKK2, DKK3, WISP3, APC, β-catenin, AXIN-2, GLI-1) to evaluate their contribution in predisposition to GBC and treatment outcomes. The study included 564 GBC patients and 250 controls. Out of 564, 200 patients were followed up for treatment response and survival. Tumor response (RECIST 1.1) was recorded in 116 patients undergoing non-adjuvant chemotherapy (NACT). Survival was assessed by Kaplan-Meier curve and Cox-proportional hazard regression. Single locus analysis showed significant association of SFRP4 rs1802073G > T [p value = 0.0001], DKK2 rs17037102C > T [p value = 0.0001], DKK3 rs3206824C > T [p value = 0.012], APC rs4595552 A/T [p value = 0.021], APC rs11954856G > T [p value = 0.047], AXIN-2 rs4791171C > T [p value = 0.001], β-catenin rs4135385A > G [p value = 0.031], and GLI-1 rs222826C > G [p value = 0.001] with increased risk of GBC. Gene-gene interaction using GMDR analysis predicted APC rs11954856 and AXIN2 rs4791171 as significant in conferring GBC susceptibility. Cox-proportional hazard model showed GLI-1 rs2228226 CG/GG and AXIN-2 rs4791171 TT genotype higher hazard ratio. In recursive partitioning, AXIN-2 rs4791171 TT genotype showed higher mortality and hazard. Most of studied genetic variants influence GBC susceptibility. APC rs11954856, GLI-1 rs2228226, and AXIN-2 rs4791171 were found to be associated with poor survival in advanced GBC patients.

The frequency of BRCA1 founder mutation c.5266dupC (5382insC) in breast cancer patients from Ukraine

Germ-line mutations in several genes, such as BRCA1 and BRCA2, are known to increase the risk of breast cancer. These heritable mutations are unequally represented among populations with different ethnic background due to founder effects and thereby contribute to differences in breast cancer rates in different populations. The BRCA1 mutation c.5266dupC (also known as 5382insC or 5385insC) was detected in a sample of 193 breast cancer patients in Ukraine by multiplex mutagenically separated PCR using published specific primers. Nine BRCA1 mutations 5382insC were detected (4.7 %). The difference in age of diagnosis (35 years in 5382insC carriers versus 45 years in non-carriers) we observed is consistent with other reports indicating that the 5382insC mutation is a factor of genetic predisposition to breast cancer, which is consistent with reports from other countries.

Association of Genetic Polymorphisms in CDH1 and CTNNB1 with Breast Cancer Susceptibility and Patients' Prognosis among Chinese Han Women

This study aims to investigate whether the germline variants in CDH1 and CTNNB1 would affect breast cancer susceptibility and patients’ prognosis among Chinese Han women using a haplotype-based association analysis. We genotyped 12 haplotype-tagging single nucleotide polymorphisms (htSNPs) in CDH1 and CTNNB1 among 1,160 BC cases and 1,336 age-matched cancer-free controls using the TaqMan^® Genotyping Assay. For association analyses of germline variants with breast cancer susceptibility, the results showed that rs7200690, rs7198799, rs17715799, rs13689 and diplotype CGC/TGC (rs7200690 + rs12185157 + rs7198799) in CDH1 as well as rs2293303 in CTNNB1 were associated with increased breast cancer risk. In addition, the Generalized Multifactor Dimensionality Reduction (GMDR) and logistic regression analysis predicted an interaction on breast cancer risk between rs17715799 and rs13689 as well as rs13689 and menarche-FFTP (First Full-Term Pregnancy) interval. For survival analyses, the results demonstrated that the minor allele homozygotes of rs13689 and haplotype TGC in CDH1 were linked with unfavorable event-free survival of breast cancer, whereas, rs4783689 of CDH1 showed the opposite effect under dominant model. Notably, the stratified analysis revealed that rs7186053 was associated with favorable event-free survival among patients with estrogen receptor (ER)-positive, progesterone receptor (PR)-positive or lymph node metastasis negative patients. Moreover, rs7200690 and rs7198799 in CDH1 as well as rs4533622 in CTNNB1 were associated with worse event-free survival among patients with clinical stage 0-I tumors. This study indicated that the genetic polymorphisms of CDH1 and CTNNB1 were associated with breast cancer susceptibility and patients’ prognosis.

-148 C/T polymorphism of Axin2 contributes to a decreased risk of cancer: evidence from a meta-analysis

Several studies have reported an association between -148 C/T polymorphism of Axis inhibition protein 2 (Axin2) and cancer risk; however, the results are inconsistent. In this study, a meta-analysis was performed to assess the association between -148 C/T polymorphism of Axin2 and susceptibility to cancer. Published case-control and cohort-based studies from PubMed, Embase, Wanfang, and CNKI were retrieved, and data were manually extracted. The odds ratios (ORs) and 95% confidence intervals (CIs) of the included studies were pooled. Begg's and Egger's tests were used to evaluate publication bias. Cumulative and recursive cumulative meta-analyses (CMA) were performed as evidence accumulated to investigate the trends and stability of the effect size. Nine articles with 1,664 cases and 1,796 controls were included. The pooled effect size showed an association between -148 C/T polymorphism and the risk of cancer (dominant model, OR: 0.72, 95% CI: 0.63-0.83; allele model, OR: 0.81, 95% CI: 0.73-0.90). CMA showed an association trend, and the recursive CMA indicated that more evidence is needed to make conclusions about significance. In a subgroup analysis, a significant association between -148 C/T polymorphism and low cancer susceptibility was detected for lung cancer (dominant model, 0.69, 95% CI: 0.56-0.85; recessive model, OR: 0.75, 95% CI: 0.56-0.99; allele model, 0.76, 95% CI: 0.66-0.86). The -148 C/T polymorphism was also associated with low cancer susceptibility among Asians (dominant model, OR: 0.68, 95% CI: 0.57-0.81; recessive model, OR: 0.75, 95% CI: 0.56-0.99; allele model, OR: 0.76, 95% CI: 0.66-0.86). The Axin2 -148 C/T polymorphism was found to be significantly associated with a decreased risk of cancer, particularly lung cancer, in Asians and population-based controls. Thus, Axin2 should be considered as a potential therapeutic target for preventing tumor growth.

AXIN2 rs2240308 polymorphism contributes to increased cancer risk: evidence based on a meta-analysis

BACKGROUND

Variants in the axis inhibition 2 (AXIN2) gene might alter the protein's structure or function or create a multiprotein destruction complex in the Wnt signaling pathway and thus affect an individual's susceptibility to cancer. The objective of this study is to evaluate broadly the evidence available for the AXIN2 rs2240308 polymorphism and risk of cancer.

METHODS

A comprehensive literature search was undertaken for eligible studies in Embase, PubMed, and Cochrane Library up to Nov 30, 2014. Odds ratios (ORs) and the corresponding 95 % confidence intervals (CIs) were used to measure the strength of the models.

RESULTS

Eight articles (10 case-control studies with 1,502 cases and 1,590 controls) were included in this analysis. Overall, the AXIN2 rs2240308 polymorphism was associated with a significant increase in the risk of cancer (G allele vs. A allele: OR = 1.21, 95 % CI = 1.05-1.40, I (2)  = 39.5 % and P Q  = 0.094 for heterogeneity; GG vs. AA: OR = 1.30, 95 % CI = 1.04-1.63, I (2)  = 35.9 % and P Q  = 0.121 for heterogeneity; GG vs. GA + AA: OR = 1.36, 95 % CI = 1.17-1.58, I (2)  = 19.5 % and P Q  = 0.263 for heterogeneity). Asian populations showed similar results. Stratified analysis by cancer types indicated that the AXIN2 rs2240308 polymorphism increases the risk of lung cancer (G allele vs. A allele: OR = 1.36, 95 % CI = 1.17-1.59; GA vs. AA: OR = 1.43, 95 % CI = 1.01-2.02; GG vs. AA: OR = 1.93, 95 % CI = 1.36-2.75; GG + GA vs. AA: OR = 1.65, 95 % CI = 1.18-2.30; GG vs. GA + AA: OR = 1.45, 95 % CI = 1.18-1.79. All I (2)  < 50 % and P Q  > 0.100 for heterogeneity).

CONCLUSIONS

This study showed that the AXIN2 rs2240308 polymorphism contribute to increasing the risk of cancer, especially lung cancer in Asian populations.

Quantitative assessment of the association between AXIN2 rs2240308 polymorphism and cancer risk

Axin2 is involved in the regulation of Wnt/β-catenin pathway and implicated in cancer development and progression. The association between AXIN2 rs2240308 polymorphism and cancer risk has been examined in several case-control studies, but the conclusions were conflicting. Here we performed a meta-analysis to evaluate the role of rs2240308 in cancer risk. A total of 8 studies were included in this meta-analysis (1559 cancer cases and 1503 controls). The pooled odds ratios (OR) and the 95% confidence intervals (CIs) were assessed to evaluate the association of the AXIN2 rs2240308 polymorphism with a susceptibility to cancer. A significantly decreased overall cancer risk was observed in the homozygous (TT vs. CC), heterozygous (CT vs. CC), dominant (CT+TT vs. CC) and allelic (T vs. C) models (P < 0.005), rather than that in the recessive (TT vs. CT+CC) model (P = 0.092). AXIN2 polymorphism rs2240308 was also associated with decreased cancer risk under all five models in lung cancer. However, AXIN2 rs2240308 polymorphism was not associated with cancer risk under any above model in Turkish population and under homozygous, heterozygous, recessive models in Japanese population. These findings indicate that AXIN2 rs2240308 polymorphism significantly and race-specifically correlates with decreased cancer risk.