Variants in DENND1A and LHCGR are associated with endometrioid adenocarcinoma

Exploration of Alternative Splicing (AS) Events in MDV-Infected Chicken Spleens

Marek’s disease (MD) was an immunosuppression disease induced by Marek’s disease virus (MDV). MD caused huge economic loss to the global poultry industry, but it also provided an ideal model for studying diseases induced by the oncogenic virus. Alternative splicing (AS) simultaneously produced different isoform transcripts, which are involved in various diseases and individual development. To investigate AS events in MD, RNA-Seq was performed in tumorous spleens (TS), spleens from the survivors (SS) without any lesion after MDV infection, and non-infected chicken spleens (NS). In this study, 32,703 and 25,217 AS events were identified in TS and SS groups with NS group as the control group, and 1198, 1204, and 348 differently expressed (DE) AS events (p-value < 0.05 and FDR < 0.05) were identified in TS vs. NS, TS vs. SS, SS vs. NS, respectively. Additionally, Function enrichment analysis showed that ubiquitin-mediated proteolysis, p53 signaling pathway, and phosphatidylinositol signaling system were significantly enriched (p-value < 0.05). Small structural variations including SNP and indel were analyzed based on RNA-Seq data, and it showed that the TS group possessed more variants on the splice site region than those in SS and NS groups, which might cause more AS events in the TS group. Combined with previous circRNA data, we found that 287 genes could produce both circular and linear RNAs, which suggested these genes were more active in MD lymphoma transformation. This study has expanded the understanding of the MDV infection process and provided new insights for further analysis of resistance/susceptibility mechanisms.

Genetic variations of bovine PCOS-related DENND1A gene identified in GWAS significantly affect female reproductive traits

Genome-wide association studies (GWAS) have identified DENND1A as a potential candidate gene linked to the fertility-related phenotypes in dairy cows. However, to date, no studies have examined the association of the DENND1A insertion/deletions (indels) to bovine fertility on a large scale. Herein, two indel sites, including P4-del-26-bp and P8-ins-15-bp were identified in 1064 Holstein cows. The values of the minor allelic frequency (MAF) ranged between 0.471 (deletion) and 0.230 (deletion), respectively, and combined four different haplotypes by analyzing the haplotype combination. It is noteworthy that P4-del-26-bp is associated with the ovarian width (P = 0.0004) and corpus luteum diameter (P = 0.004). Meanwhile, P8-ins-15-bp was found to have a significant association with the ovarian width (P = 0.020), ovarian weight (P = 0.004), the number of mature follicles (P = 0.020), and diameter of the mature follicles (P = 0.016). Furthermore, the combinatorial analysis showed that the two indel combined-genotypes were significantly related to several reproductive traits (ovarian width, ovarian weight, etc.). Collectively, our findings indicated that these two novel indels and their combinations are correlated with the reproductive traits, and hence, they can serve in the marker-assisted selection (MAS) in cattle breeding. Nevertheless, further functional experiments are needed for understanding the mechanisms of these indels in cattle reproduction in a better way.

A Comprehensive Overview of Common Polymorphic Variants in Genes Related to Polycystic Ovary Syndrome

Polycystic ovary syndrome (PCOS) is one of the most common endocrine-metabolic disorders in women of reproductive age. It is characterized by an increase in the biosynthesis of androgens, anovulation, and infertility. PCOS has been reported as a polygenic entity in which multiple single nucleotide polymorphisms (SNPs) are associated with the clinical features of the pathology. Herein, we describe the common polymorphic variants in genes related to PCOS, their role in its pathogenesis, and etiology. Whole-genome association studies have been focused on women from Asian and European populations. The most common genes associated with PCOS are DENND1A, THADA, FSHR, and LHCGR. However, other genes have been associated with PCOS such as AMH, AMHR2, ADIPOQ, FTO, HNF1A, CYP19, YAP1, HMGA2, RAB5B, SUOX, INSR, and TOX3. Nevertheless, the relationship between the biological functions of these genes and the development of the pathology is unclear. Studies in each gene in different populations do not always comply with a general pattern, so researching these variants is essential for better understanding of this polygenic syndrome. Future population studies should be carried out to evaluate biological processes, incidence rates, allelic and genotypic frequencies, and genetic susceptibility factors that predispose PCOS.

PCOS-GWAS Susceptibility Variants in THADA, INSR, TOX3, and DENND1A Are Associated With Metabolic Syndrome or Insulin Resistance in Women With PCOS

Polycystic ovary syndrome is characterized by reproductive and metabolic disturbances throughout the female lifespan. Therefore, this study aimed to determine whether genome-wide association studies (GWAS)-identified risk variants for PCOS could confer risk of metabolic syndrome (MS) or insulin resistance (IR). Fifteen independent SNPs mapping to 11 GWAS loci genotyped in a total of 2,082 Han Chinese women independent of previous GWAS and phenotype-genotype correlations were assessed. The CC group for rs12478601 in THADA was associated with decreased rate of MS after adjustment for age (23.2 vs. 27%, P = 0.042, OR = 0.81). Using a dominant model, the GG+AG group for rs2059807 in INSR was associated with increased risk of MS after adjustment for age (26.8 vs. 22.5%, P = 0.023, OR = 1.27). The GG + GT group for rs4784165 in TOX3 was found to be associated with an increased rate of IR after adjustment for age and BMI(53.3 vs. 48.5%, P = 0.027, OR = 1.27). The GG+AG group for rs2479106 in DENND1A was associated with a decreased rate of IR (48.3 vs. 53.6%, adjusted P = 0.039, OR = 0.80). After exclusion of PCOS cases with a family history of diabetes, hypertension, or dyslipidemia, the phenotype-genotype correlations between the genes INSR and TOX3 and MS or IR were still significant (P < 0.05). Three SNPs (rs13429458 in THADA, rs10818854 in DENND1A, and rs2059807 in INSR) were significantly associated with IR; however, their association was not significant after adjustment for age and BMI. This genotype-phenotype study thus provides clues that THADA, INSR, TOX3, and DENND1A play a role in PCOS possibly through a metabolic disorder-related pathway.

Polymorphisms in IL-1A are associated with endometrial cancer susceptibility among Chinese Han population: A case-control study

Endometrial cancer (EC) is one of the most common malignant tumours of the female genital tract, and it has become a serious malignant disease of the female genital tract in China. Existing researches have revealed the association between polymorphisms of IL-1A and several gynaecological diseases. In this research, we analysed the association between IL-1A gene polymorphisms and endometrial cancer susceptibility in Chinese female population. A total of 81 patients and 198 healthy people were selected. Odds ratio (OR) and 95% confidence intervals (CIs) were calculated using unconditional logistic regression. Genetic models and analyses showed that IL-1A rs3783550 TT and rs3783546 CC increased the risk of endometrial cancer under the recessive model, respectively (rs3783550: OR = 2.80, 95%CI: 1.32-5.92, p = .008; rs3783546: OR = 2.79, 95%CI: 1.32-5.89, p = .008). In the recessive model, we also found that both IL-1A rs1609682 and IL-1A rs3783521 increased the risk of endometrial cancer, respectively (rs1609682: OR = 2.79, 95%CI: 1.32-5.89, p = .0081; rs3783521: OR = 2.80, 95%CI: 1.32-5.92, p = .008). Haplotype analysis was performed that did not reveal any significant results. In summary, IL-1A rs3783550, rs3783546, rs1609682 and rs3783521 polymorphisms may be associated with an increased risk of endometrial cancer in Chinese female populations.

Association of Rs13405728, Rs12478601, and Rs2479106 single nucleotide polymorphisms and in vitro fertilization and embryo transfer efficacy in patients with polycystic ovarian syndrome: A case control genome-wide association study

Polycystic ovary syndrome (PCOS) is a common female endocrine disorder that has a detriment impact on female health. Herein, the study used a case-control analysis to sought to explore the association of rs13405728, rs12478601, and rs2479106 single nucleotide polymorphisms (SNPs) with in vitro fertilization and embryo transfer (IVF-ET) efficacy in treating PCOS. A total of 163 PCOS patients (52 cycles) were selected as the PCOS group and 171 patients with tubal factor infertility without PCOS (68 cycles) were selected as the control group. Polymerase chain reaction was used to amplify genome DNA and direct sequencing to detect SNPs. The LHCGR rs13405728, THADA rs12478601, and DENND1A rs2479106 genotypes were subsequently tested. Logistic regression analysis was conducted to analyze the risk factors influencing the occurrence of PCOS as well as those influencing the efficacy of IVF-ET. rs13405728, rs12478601, and family history of DM were influencing factors for the occurrence of PCOS. The rate of abortion and number of oocytes retrieved of patients with the THADA rs12478601 CC genotype increased but the rate of clinical gestation decreased. Patients with AG + GG genotype of the DENND1A rs2479106 had increased number of oocytes retrieved, rate of abortion and incidence of gestational DM. rs13405728, rs12478601, serum E₂ value as well as fertility rate were influencing factors for efficacy of IVF-ET. It was suggested that the TT genotype of LHCGR rs13405728, CC genotype of THADA rs12478601 and AG + GG genotype of DENND1A rs2479106 had poor outcomes of IVF-ET in treating PCOS.

Evolution and heterogeneity of non-hereditary colorectal cancer revealed by single-cell exome sequencing

Recently single-cell whole-exome sequencing (scWES) has deeply expanded and sharpened our knowledge of cancer evolution and subclonality. Herein, with scWES and matched bulk whole-exome sequencing (bulk WES) on two colorectal cancer (CRC) patients with normal or adenomatous polyps, we found that both the adenoma and cancer were of monoclonal origin, and both shared partial mutations in the same signaling pathways, but each showed a specific spectrum of heterogeneous somatic mutations. In addition, the adenoma and cancer further developed intratumor heterogeneity with the accumulation of nonrandom somatic mutations specifically in GPCR, PI3K-Akt and FGFR signaling pathways. We identified novel driver mutations that developed during adenoma and cancer evolution, particularly in OR1B1 (GPCR signaling pathway) for adenoma evolution, and LAMA1 (PI3K-Akt signaling pathway) and ADCY3 (FGFR signaling pathway) for CRC evolution. In summary, we demonstrated that both colorectal adenoma and CRC are monoclonal in origin, and the CRCs further diversified into different subclones with heterogeneous mutation profiles accumulating in GPCR, PI3K-Akt and FGFR signaling pathways. ScWES provides evidence for the importance of mutations in certain pathways that would not be as apparent from bulk sequencing of tumors, and can potentially establish whether specific mutations are mutually exclusive or occur sequentially in the same subclone of cells.

The association of DENND1A gene polymorphisms and polycystic ovary syndrome risk: a systematic review and meta-analysis

PURPOSE

Polycystic ovary syndrome is heterogeneity disease, and the association with DEEND1A gene has been discussed incompatibly for a long time. We conducted a meta-analysis to evaluate the rs10818854, rs2479106, and rs10986105 polymorphism in DENND1A gene with PCOS susceptibility.

METHODS

Meta-analysis was performed for common allele versus rare allele using random effect model on published papers from January 1, 1980 to October 1, 2015. Subgroup analysis, sensitivity analysis and publication bias were also carried out ultimately. The combined odds ratio (OR) with 95 % confidence interval (95 % CI) was calculated to estimate the strength of the association.

RESULTS

The results showed that rs10818854 (OR = 1.36, 95 % CI 1.12-1.61) and rs10986105 (OR = 1.39, 95 % CI 1.20-1.58) polymorphism increased the risk of PCOS probably. A significant association was also found between rs2479106 mutation and Asian PCOS patients but not Europeans (OR = 1.32, 95 % CI 1.25-1.39; OR = 1.01, 95 % CI 0.97-1.05, respectively).

CONCLUSIONS

In conclusion, the DENND1A gene variant is likely to have influence on PCOS risk. Further studies are warranted to assess these associations in greater detail, especially in different populations and different subtype of PCOS patients.

Polycystic ovary syndrome: Endometrial markers

Women with polycystic ovarian syndrome (PCOS) present with several endometrial abnormalities possibly explaining some of the adverse endometrium-related outcomes in these women. PCOS and an increased miscarriage rate have been suggested to coincide, but the results are conflicting. Recent studies have also shown increased risks of pregnancy-induced hypertension, preeclampsia, and premature delivery that may be related to altered decidualization/placentation in affected women. In the long run, PCOS per se is associated with the occurrence of endometrial cancer (EC), with obesity aggravating the risk. Most investigated markers of the endometrial abnormalities in women with PCOS are related to steroid hormone action (ERs (estrogen receptors), PRs (progesterone receptors), ARs (androgen receptors), and steroid receptor coactivators), endometrial receptivity/decidualization (HOXA10, αvβ3 integrin, and IGFBP-1 (insulin-like growth factor-binding protein 1)), glucose metabolism (IRs (insulin receptors), glucose transporters, IGFs) and inflammation/immune cell migration ((IL-6 (interleukin 6), CCL2 (CC motif ligand), and uNK (uterine natural killer) cells). Despite several endometrial abnormalities in women with PCOS, the clinical relevance of these findings still awaits future clarification; to date, no common screening protocols/recommendations for women with PCOS have been established.

Genetics of endometrial cancer

Women who report a history of endometrial cancer in a first-degree relative are at increased risk of endometrial cancer, with a hazard ratio of 1.5 to 2.0. Only a minority of patients with familial endometrial cancer have a recognized cancer syndrome. Lynch syndrome is the most common genetic syndrome associated with endometrial cancer and a marked increased risk of colon cancer. Cowden syndrome is a rare condition resulting from a mutation in the tumor suppressor gene phosphatase and tensin homolog. The risk for endometrial cancer is about five times higher in women with Cowden syndrome than in the general population. Recently, a novel germline mutation in the POLD1 gene that encodes the catalytic subunit of DNA polymerase δ was described in several families with multiple cases of endometrial cancer. This mutation is also associated with colorectal cancer. The association between BRCA1 mutations and endometrial cancer has been investigated in several studies; it appears that the risk of endometrial cancer is restricted to women with a history of tamoxifen exposure. In recent years, research has focused on genetic polymorphisms that are associated with endometrial cancer risk. Although many polymorphisms have been identified, their clinical significance is unclear and they have not been adapted for clinical practice.

Functional genomics of PCOS: from GWAS to molecular mechanisms

Polycystic ovary syndrome (PCOS) is a common endocrinopathy characterized by increased ovarian androgen biosynthesis, anovulation, and infertility. PCOS has a strong heritable component based on familial clustering and twin studies. Genome-wide association studies (GWAS) identified several PCOS candidate loci including LHCGR, FSHR, ZNF217, YAP1, INSR, RAB5B, and C9orf3. We review the functional roles of strong PCOS candidate loci focusing on FSHR, LHCGR, INSR, and DENND1A. We propose that these candidates comprise a hierarchical signaling network by which DENND1A, LHCGR, INSR, RAB5B, adapter proteins, and associated downstream signaling cascades converge to regulate theca cell androgen biosynthesis. Future elucidation of the functional gene networks predicted by the PCOS GWAS will result in new diagnostic and therapeutic approaches for women with PCOS.

Luteinizing hormone and human chorionic gonadotropin: distinguishing unique physiologic roles

Luteinizing hormone (LH) and human chorionic gonadotropin (hCG) are integral components of the hypothalamic-pituitary-gonadal axis, which controls sexual maturation and functionality. In the absence of signaling through their shared receptor, fetal sexual differentiation and post-natal development cannot proceed normally. Although they share a high degree of homology, the physiologic roles of these hormones are unique, governed by differences in expression pattern, biopotency and regulation. Whereas LH is a key regulator of gonadal steroidogenesis and ovulation, hCG is predominantly active in pregnancy and fetal development. Emerging evidence has revealed endogenous functions not previously ascribed to hCG, including participation in ovulation and fertilization, implantation, placentation and other activities in support of successful pregnancy. Spontaneous and induced mutations in LH, hCG and their mutual receptor have contributed substantially to our understanding of reproductive development and function. The lack of naturally occurring, functionally significant mutations in the β-subunit of hCG reinforce its putative role in establishment of pregnancy. Rescue of reproductive abnormalities resulting from aberrant gonadotropin signaling is possible in certain clinical contexts, depending on the nature of the underlying defect. By understanding the physiologic roles of LH and hCG in normal and pathologic states, we may better harness their diagnostic, prognostic and therapeutic potential.