MDM2 promoter polymorphism del1518 (rs3730485) and its impact on endometrial and ovarian cancer risk

Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements

Discoveries in the field of genomics have revealed that non-coding genomic regions are not merely "junk DNA", but rather comprise critical elements involved in gene expression. These gene regulatory elements (GREs) include enhancers, insulators, silencers, and gene promoters. Notably, new evidence shows how mutations within these regions substantially influence gene expression programs, especially in the context of cancer. Advances in high-throughput sequencing technologies have accelerated the identification of somatic and germline single nucleotide mutations in non-coding genomic regions. This review provides an overview of somatic and germline non-coding single nucleotide alterations affecting transcription factor binding sites in GREs, specifically involved in cancer biology. It also summarizes the technologies available for exploring GREs and the challenges associated with studying and characterizing non-coding single nucleotide mutations. Understanding the role of GRE alterations in cancer is essential for improving diagnostic and prognostic capabilities in the precision medicine era, leading to enhanced patient-centered clinical outcomes.

Association of Murine Double Minute 2 polymorphisms with gastric cancer: A systematic review with meta-analysis

Gastric cancer (GC) is the 5th most common type of cancer, with the 3rd highest mortality rate worldwide in both sexes. Murine double minute 2 (MDM2) protein is the major negative regulator of p53, and genetic polymorphisms in this gene have shown to be associated with several types of cancer. In the present study, a literature search was performed using PubMed and Scopus with the following key word combinations 'gastric cancer AND polymorphism AND MDM2'. Studies were carefully revised according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines to identify eligible studies that matched the inclusion criteria. Statistical analysis was performed to assess the association between the different genetic polymorphisms and GC risk, by calculating the odds ratios (OR) and the confidence intervals (CI), with a 5% level of significance. A total of 11 manuscripts studied MDM2 polymorphisms in GC: rs937283 (n=1), rs3730485 (n=1) and rs2279744 (n=9). Both the rs937283 and rs3730485 reports showed an association with GC; however, there was only one study on each of these polymorphisms in the literature. A meta-analysis was performed for the rs2279744 polymorphism, of which studies showed a positive association between the G allele and risk of GC, either in the dominant model (OR=1.46; 95% CI 1.21-1.75; P<0.001) or recessive model (OR 1.65; 95% CI 1.45-1.87; P<0.001). In conclusion, genetic polymorphisms in MDM2 seemed to be associated with an increased risk of GC development, nevertheless, the number of studies were relatively low and the studied populations were primarily Chinese. The present meta-analysis emphasizes the need for additional studies in other populations to corroborate the association of these polymorphisms with GC.

Polymorphisms in the TP53-MDM2-MDM4-axis in patients with rheumatoid arthritis

BACKGROUND

In addition to being a tumour suppressor, TP53 is a suppressor of inflammation, and dysfunction of this gene has been related to autoimmune diseases. Patients with autoimmunity, such as rheumatoid arthritis (RA) have an increased risk of certain cancers, like lymphomas, indicating that some underlying mechanisms may modulate risk of both cancers and autoimmunity.

METHODS

We genotyped 5 common genetic variants in TP53 and its main regulators MDM2 and MDM4 in a sample of 942 RA patients and 3,747 healthy controls, and mined previously published GWAS-data, to assess the potential impact of these variants on risk of RA.

RESULTS

For the TP53 Arg72Pro polymorphism (rs1042522), MDM4 SNP34091 (rs4245739) and MDM2 SNP285C (rs117039649), we found no association to risk of RA. For MDM2 SNP309 (rs2279744), the minor G-allele was associated with a reduced risk of RA (OR: 0.87; CI: 0.79-0.97). This association was also seen in genotype models (OR: 0.86; CI: 0.74-0.99 and OR: 0.79; CI 0.63-0.99; dominant and recessive model, respectively), but was not validated in a large GWAS data set. For MDM2 del1518 (rs3730485), the minor del-allele was associated with an increased risk of RA in the dominant model (OR: 1.18; CI: 1.02-1.38). Stratifying RA cases and controls into phylogenetic subgroups according to the combined genotypes of all three MDM2 polymorphism, we found individuals with the del158-285-309 genotype del/ins-G/G-T/T to have an increased risk of RA as compared to those with the ins/ins-G/G-G/G genotype (OR: 1.56; CI: 1.18-2.06) indicating opposite effects of the del1518 del-allele and the SNP309 G-allele.

CONCLUSION

We find a potential association between the MDM2 del1518 variant and RA, and indications that combinatorial genotypes and haplotypes in the MDM2 locus may be related to RA.

Impact of MDM2 promoter SNP55 (rs2870820) on risk of endometrial and ovarian cancer

BACKGROUND

While large GWAS analyses have not found convincing associations between MDM2 promoter SNP55 and gynaecological cancers, SNP55 is in linkage disequilibrium with two other functional SNPs in the same promoter, likely to obscure associations between single SNPs and cancer risk. Here, we assessed the impact of SNP55 on risk of endometrial and ovarian cancer, including sub-analyses stratified for other functional SNPs in the region.

MATERIAL AND METHODS

Using a custom LightSNiP assay, we genotyped SNP55 in two large hospital-based cohorts of patients with ovarian (n = 1,332) and endometrial (n = 1,363) cancer and compared genotypes to healthy female controls (n = 1,858).

RESULTS

Among individuals harbouring the SNP309TT genotype, the minor SNP55T-allele was associated with a reduced risk of endometrial (dominant model: OR = 0.63; CI = 0.45-0.88; p = 0.01). Regardless of the genotype in neighbouring SNPs, the SNP55T-allele was also associated with a reduced risk of endometrial cancer before 50 years of age (dominant model: OR = 0.56; CI = 0.34-0.90; p = 0.02). No association between SNP55 status and ovarian cancer risk was observed.

CONCLUSIONS

MDM2 SNP55T-allele may correlate with reduced risk for endometrial cancer in a SNP309T-, but not SNP309G, context.

The 40bp Indel Polymorphism rs150550023 in the MDM2 Promoter is Associated with Intriguing Shifts in Gene Expression in the p53-MDM2 Regulatory Hub

Most low-penetrance genetic risk factors for cancer are located in noncoding regions, presumably altering the regulation of neighboring genes. The poorly characterized Indel polymorphism rs150550023 (rs3730485; del1518) in the promoter of MDM2 (human homolog of mouse double minute 2) is a biologically plausible candidate genetic risk factor, which might influence the expression of MDM2, a key negative regulator of the central tumor suppressor p53. Here, we genotyped rs150550023 in a Central European hospital-based case-control study of 407 breast cancer patients and 254 female controls. mRNA levels of MDM2, p53, and the p53 target genes p21, BAX, and PERP were quantified with qRT-PCR, and p53 protein was assessed with immune histochemistry in ≈100 primary breast tumors with ascertained rs150550023 genotype. We found no evidence for an association of rs150550023 with the risk, age at onset, or prognosis of breast cancer. A possible synergism was observed with SNP309 in promoter P2 of MDM2. Mean mRNA levels of MDM2, p53, p21, and BAX were ≈1.5-3 fold elevated in TP53 wildtype tumors with the minor homozygous Del/Del genotype. However, systematic shifts in p53 protein levels or mutation rates were not observed, suggesting that the elevated p53 mRNA levels are due to regulatory feedback loops that compensate for the effects of rs150550023 on MDM2 expression.

Association Analysis of TP53 rs1042522, MDM2 rs2279744, rs3730485, MDM4 rs4245739 Variants and Acute Myeloid Leukemia Susceptibility, Risk Stratification Scores, and Clinical Features: An Exploratory Study

This study aimed to explore the associations between the TP53 rs1042522 (TP53 Arg72Pro), MDM2 rs2279744 (MDM2 309T>G), rs3730485 (MDM2 del1518), MDM4 rs4245739 (MDM4 34091 C>A) variants and odds of developing acute myeloid leukemia (AML) in a cohort of 809 adult subjects, consisting of 406 healthy controls and 403 AML patients. Model-based multifactor dimensionality reduction (MB-MDR) framework was used to identify the interactions of the mentioned variants and their association with AML risk. Associations of the mentioned variants with clinical features of AML, somatic mutations, and response to treatment were also evaluated. Significant associations between TP53 rs1042522 and MDM4 rs4245739 variants and AML susceptibility were noticed. MB-MDR and logistic regression analysis revealed an interaction between MDM2 rs2279744 and TP53 rs1042522, between MDM4 rs4245739 and MDM2 rs3730485, as well as significant associations with AML susceptibility. Several associations between the mentioned variants and clinical features of AML and somatic mutations were also noticed. Individually, the variant genotypes of TP53 rs1042522 and MDM4 rs4245739 were associated with AML susceptibility, but their interaction with MDM2 rs2279744 and rs3730485 modulated the risk for AML. The variant genotypes of TP53 rs1042522 were associated with adverse molecular and cytogenetic risk and also with NPM1 mutations.

Association between genetic polymorphisms and endometrial cancer risk: a systematic review

Introduction

Endometrial cancer is one of the most commonly diagnosed cancers in women. Although there is a hereditary component to endometrial cancer, most cases are thought to be sporadic and lifestyle related. The aim of this study was to systematically review prospective and retrospective case–control studies, meta-analyses and genome-wide association studies to identify genomic variants that may be associated with endometrial cancer risk.

Methods

We searched MEDLINE, Embase and CINAHL from 2007 to 2019 without restrictions. We followed PRISMA 2009 guidelines. The search yielded 3015 hits in total. Following duplicate exclusion, 2674 abstracts were screened and 453 full-texts evaluated based on our pre-defined screening criteria. 149 articles were eligible for inclusion.

Results

We found that single nucleotide polymorphisms (SNPs) in HNF1B, KLF, EIF2AK, CYP19A1, SOX4 and MYC were strongly associated with incident endometrial cancer. Nineteen variants were reported with genome-wide significance and a further five with suggestive significance. No convincing evidence was found for the widely studied MDM2 variant rs2279744. Publication bias and false discovery rates were noted throughout the literature.

Conclusion

Endometrial cancer risk may be influenced by SNPs in genes involved in cell survival, oestrogen metabolism and transcriptional control. Larger cohorts are needed to identify more variants with genome-wide significance.

Long noncoding RNA TUG1 facilitates cell ovarian cancer progression through targeting MiR-29b-3p/MDM2 axis

Ovarian cancer (OC) is one of the most aggressive female cancers in the world. OC trends to be diagnosed at an advanced stage with abdominal metastasis. Our study explored the biological function and underlying mechanism of lncRNA on OC cell proliferation and migration. The expression of turine up-regulated gene 1 (TUG1) in human OC tissues and cell lines was measured by qRT-PCR. OC cell proliferation, viability, migration, and invasion were measured by MTT assays, colony formation assays, and transwell assays in vitro. Furthermore, the nude mice xenograft model was established to determine the effects of TUG1 in vivo. The relationship between TUG1 and miR-29b-3p, as well as miR-29b-3p and MDM2 were identified using the luciferase reporter assays. We showed that the expression of TUG1 and MDM2 were significantly increased, but the expression of miR-29b-3p was remarkably decreased in OC tissues and cell lines. Knockdown of TUG1 strongly inhibited the ability of cell proliferation, colony formation, migration, and invasion in vitro. The relationship between TUG1 and miR-29b-3p, or miR-29b-3p and MDM2 were predicted by StarBase and miRanda online software. Besides, miR-29b-3p reversed the positive effect of TUG1 on the OC cell proliferation, migration, and invasion through inhibiting MDM2 expression and increasing p53 phosphorylation level. Moreover, knockdown of TUG1 suppressed tumor growth in vivo. Taken all together, this study shows that TUG1 plays a crucial oncogenic role and facilitates cell proliferation, migration, and invasion in OC through regulating miR-29b-3p/MDM2 axis.

Association of MDM2 gene SNP 309 polymorphism and human non-small cell lung cancer susceptibility: A meta-analysis

This updated meta-analysis was performed to evaluate the relationship of a common polymorphism (T309 G, rs2279744 T > G) in the murine double minute 2 (MDM2) gene with susceptibility and prognosis of non-small cell lung cancer (NSCLC). The Cochrane Library, PubMed, Embase, CNKI, WanFang and CNKI databases were searched comprehensively for related study. Odds ratios (ORs) with their 95% confidence intervals (95% CI) were calculated. 11 articles with a total 6470 NSCLC patients and 8027 controls met the inclusion criteria were included. MDM2 T309 G polymorphism might be strongly correlated with an increased risk of NSCLC. The overall pooled analysis indicated that MDM2 309 T/G polymorphism was significantly associated with NSCLC susceptibility in the whole population under allelic (OR: 1.22, 95% CI: 1.08-1.38), recessive (OR: 1.37, 95% CI: 1.15-1.63), dominant (OR: 1.23, 95% CI: 1.04-1.45), and homozygous genetic models (OR: 1.49, 95% CI: 1.20-1.86). The subgroup analysis showed a significant association of MDM2 309 T/G polymorphism with NSCLC susceptibility in Asian population, but not in Caucasian population. Besides, a significant association was found again in the female population. The meta-analysis provides convincing evidence that the MDM2 T309 G polymorphism may contribute to NSCLC susceptibility, especially for Asians and women.

Goat PDGFRB: unique mRNA expression profile in gonad and significant association between genetic variation and litter size

β-Type platelet-derived growth factor receptor (PDGFRB) is a typical tyrosine kinase, as a candidate gene associated with reproduction. Its main roles include regulation of gonocytes (migration and proliferation) and of the cell cycle. The objectives of this study were to identify mRNA expression of the goat PDGFRB gene, as well as insertion/deletion (indel) variants and their association with litter size in 1122 healthy Shaanbei white cashmere goats. The results revealed that PDGFRB was widely expressed in all tested tissues, and the expression levels in testes at different developmental stages indicated a potential association with the mitosis-to-meiosis transition. Furthermore, the expression of PDGFRB was relatively higher in the ovary tissue of mothers of two lambs compared with mothers of single lamb. These results implied that PDGFRB was related to goat fertility. Meanwhile, two intronic indels, 5 bp (n = 501) and 10 bp (n = 1122), were identified. Statistical analysis revealed that only the 10 bp indel was associated with first-born litter size (n = 1122, p = 6.030 × 10^-5), and that individuals of the genotype insertion/deletion had larger litter sizes than those of genotype insertion/insertion. Overall, these results indicated that the 10 bp indel of PDGFRB could be used in marker-assisted selection during goat genetic breeding.

Association between MDM2 SNP309 and endometrial cancer risk: A PRISMA-compliant meta-analysis

BACKGROUND

Murine double minute 2 homolog (MDM2) plays an important role in the downregulation of P53 tumor suppressor gene. MDM2 inhibits P53 transcriptional activity and thereby results in accelerated tumor formation. Overexpression of MDM2 has been found in several cancer types including endometrial cancer. SNP309 is located in the promoter region of MDM2 and contributes to the overexpression of MDM2. The association between MDM2 SNP309 polymorphism and endometrial cancer risk has been investigated in several studies; however, the conclusion remains controversial.

OBJECTIVES

We performed the present meta-analysis to give a comprehensive conclusion of the association between MDM2 SNP309 polymorphism and endometrial cancer susceptibility.

METHODS

We conducted a literature research on PubMed, Embase, Cochrane Library, OVID, Web of Science, Wan Fang, CNKI, and CQVIP databases up to July 31, 2018. Newcastle-Ottawa scale was used to assess the quality of studies. We evaluated the strength of association by combining odds ratios (ORs) and 95% confidence intervals (CIs) in 5 different genetic models under a fixed-effect model or random-effect model. We further conducted subgroup analysis by ethnicity, source of control, histological type, clinical type, grade, and stage of tumor. Sensitivity analysis and publication bias were also performed.

RESULTS

Nine eligible studies were finally included in our meta-analysis. We found MDM2 SNP309 polymorphism increased the risk of endometrial cancer under allele model (OR: 1.23, 95% CI: 1.06-1.41, P = .005), homozygote model (OR: 1.43, 95% CI: 1.13-1.81, P = .003) and recessive model (OR: 1.55, 95% CI: 1.17-2.04, P = .002). Subgroup analysis suggested a similar elevated risk in both Asians and Caucasians. We identified a strong association of enhanced susceptibility to endometrial cancer in endometrioid group (OR: 2.13, 95% CI: 1.28-3.54, P = .004) and Type I group (OR: 1.89, 95% CI: 1.25-2.86, P = .002) under dominant model. We identified no significant publication bias according to Egger's test.

CONCLUSIONS

Our meta-analysis suggested that MDM2 SNP309 polymorphism increased the risk of endometrial cancer significantly, especially in endometrioid and Type I endometrial cancer, indicating MDM2 could serve as a potential diagnostic factor marker for endometrial cancer.

Polymorphisms of the Ras-Association Domain Family 1 Isoform A (RASSF1A) Gene are Associated with Ovarian Cancer, and with the Prognostic Factors of Grade and Stage, in Women in Southern China

BACKGROUND The aim of this study was to determine whether polymorphisms of the Ras-association domain family 1 isoform A (RASSF1A) gene were associated with ovarian cancer and with tumor grade and stage, which affect the prognosis of ovarian cancer, in women in Southern China. MATERIAL AND METHODS Women from Southern China with histologically confirmed, graded and staged ovarian cancer (n=1,375), and cancer-free controls (n=1,227), provided samples of peripheral blood. DNA was extracted from the blood samples, and five tagging single nucleotide polymorphisms (SNPs) (rs4688728G>T, rs72932987C>T, rs1989839C>T, rs2073497A>C, and rs2236947A>C) were evaluated using an online assay-by-design platform. Polymerase chain reaction (PCR) DNA amplification was performed and computational haplotyping analysis of genetic associations between the five tagging SNPs was performed to identify frequent haplotypes in women with ovarian cancer, and the associations with tumor grade and stage. RESULTS In women in Southern China, the CT genotype of rs1989839 was associated with the patients with ovarian cancer (P=0.001), and was significantly correlated with tumor grade and stage (P=0.008). One of the remaining four SNPs studied, rs2073497A>C showed an association with the prognostic factors of grade and stage, but this association did not reach statistical significance. CONCLUSIONS Polymorphisms of the RASSF1A gene, most significantly the CT genotype of rs1989839, might play a role in the development and prognosis of ovarian cancer in women in Southern China. To our knowledge, this is the first study to demonstrate an association between polymorphisms in the RASSF1A gene in ovarian cancer.

MDM2 promoter del1518 polymorphism and cancer risk: evidence from 22,931 subjects

Studies have shown that single-nucleotide polymorphisms in MDM2 gene may play important roles in the development of malignant tumor. The association of del1518 polymorphism (rs3730485) in the MDM2 promoter with cancer susceptibility has been extensively studied; however, the results are contradictory. To quantify the association between this polymorphism and overall cancer risk, we conducted a meta-analysis with 12,905 cases and 10,026 controls from 16 eligible studies retrieved from PubMed, Embase, and Chinese Biomedical (CBM) databases. We assessed the strength of the connection using odds ratios (ORs) and 95% confidence intervals (CIs). In summary, no significant associations were discovered between the del1518 polymorphism and overall cancer risk (Del/Del vs Ins/Ins: OR =1.01, 95% CI =0.90-1.14; Ins/Del vs Ins/Ins: OR =1.03, 95% CI =0.96-1.12; recessive model: OR =0.98, 95% CI =0.90-1.07; dominant model: OR =1.03, 95% CI =0.94-1.12; and Del vs Ins: OR =1.01, 95% CI =0.94-1.07). In the stratified analysis by source of control, quality score, cancer type, and ethnicity, no significant associations were found. Despite some limitations, the current meta-analysis provides solid statistical evidence of lacking association between the MDM2 del1518 polymorphism and cancer risk.