Non-coding Polymorphisms Research Articles

Comprehensive investigation of long non-coding RNA HOTAIR polymorphisms and cancer risk: a current meta-analysis encompassing 96,458 participants.

Cancer ranks as the second leading cause of mortality worldwide, prompting extensive investigations into factors contributing to its development. Among these factors, genetic variations, known as genotypic polymorphisms, have been identified as significant influencers in the susceptibility to various types of cancer. Recent research has focused on exploring the connection between polymorphisms in the Long Non-coding RNA HOTAIR and cancer risk. However, the results from these studies have been inconsistent, leading to ambiguity and controversy. To address this uncertainty, we conducted a systematic analysis by gathering relevant studies from PubMed, EMBASE, and Google Scholar. Specifically, we focused on three well-studied polymorphisms within the HOTAIR lncRNA (HOTAIR rs920778 C > T, HOTAIR rs1899663 G > T, HOTAIR rs4759314 A > G) and their association with cancer risk. Our meta-analysis included data from 48 case-control studies involving 42,321 cases and 54,137 controls. The results of our updated meta-analysis revealed a significant correlation between HOTAIR rs1899663 G > T and HOTAIR rs4759314 A > G polymorphisms and overall cancer risk, particularly in the homozygous and recessive genetic models. Subgroup analysis further revealed that these associations were notably pronounced in the Asian population but not observed in the Iranian population. Furthermore, our findings underscore the potential of HOTAIR polymorphisms as diagnostic markers for overall cancer risk, particularly in gynecological cancers, precisely, HOTAIR rs1899663 G > T polymorphism in breast cancer. In conclusion, our systematic analysis provides compelling evidence that Long Non-coding RNA HOTAIR polymorphisms are linked to cancer risk, particularly in certain populations and cancer types, suggesting their potential clinical relevance as diagnostic indicators.

Decoding the genetic influence of CT60 non-coding polymorphism in CTLA-4 gene and sCTLA-4 biomarker with rheumatoid arthritis in the Indian population.

Cytoplasmic T Lymphocyte Antigen - 4 (CTLA-4) gene encodes an immunoregulatory receptor expressed on surface of activated T-cells to mediate peripheral tolerance against self-antigen. It suppresses auto-reactive T-cell proliferation either by inactivation or apoptosis of T-cells. The CTLA-4 mRNA undergoes alternative splicing to synthesize a native soluble form of CTLA-4 (sCTLA-4) protein, which lacks exon 3 that encodes for transmembrane region. As a result, sCTLA-4 circulates as a soluble serum protein and acts as an immunoregulator molecule to maintain homeostasis in the blood. Techniques coupled with quantitative Polymerase Chain Reaction (qPCR) and High-Resolution Melting Analysis (HRMA) were used to screen CTLA-4 3'Untranslated Region (UTR) CT60 (A/G) rs3087243 Single Nucleotide Polymorphism (SNP) and their association with Rheumatoid Arthritis (RA) in the Indian population. In addition, we also evaluated the concentration of sCTLA-4 serum protein in RA patients carrying rs3087243 SNP with different genotypes (A/A, G/A, and G/G). Statistical analysis of Odds Ratio (OR), Confidence Interval (C.I), and Relative Risk (RR) have shown that frequency of CTLA-4 rs3087243 SNP G/G genotype was significantly associated with RA in the Indian population (OR 1.7140; CI = 1.0765 to 2.7290; RR = 1.5434; p = 0.0232). The sCTLA-4 concentration was also significantly lower in RA patients carrying rs3087243 SNP G/G genotype than control group (p < 0.001). Co-inheritance of CTLA-4 signal peptide and 3'UTR SNPs may activate RAPP pathway. Downregulation of CTLA-4 and sCTLA-4 serum protein by rs3087243 SNP can increase the hyperactivation of T-cells, which causes RA.

Semi-supervised learning with pseudo-labeling compares favorably with large language models for regulatory sequence prediction.

Predicting molecular processes using deep learning is a promising approach to provide biological insights for non-coding single nucleotide polymorphisms identified in genome-wide association studies. However, most deep learning methods rely on supervised learning, which requires DNA sequences associated with functional data, and whose amount is severely limited by the finite size of the human genome. Conversely, the amount of mammalian DNA sequences is growing exponentially due to ongoing large-scale sequencing projects, but in most cases without functional data. To alleviate the limitations of supervised learning, we propose a novel semi-supervised learning (SSL) based on pseudo-labeling, which allows to exploit unlabeled DNA sequences from numerous genomes during model pre-training. We further improved it incorporating principles from the Noisy Student algorithm to predict the confidence in pseudo-labeled data used for pre-training, which showed improvements for transcription factor with very few binding (very small training data). The approach is very flexible and can be used to train any neural architecture including state-of-the-art models, and shows in most cases strong predictive performance improvements compared to standard supervised learning. Moreover, small models trained by SSL showed similar or better performance than large language model DNABERT2.

Zibotentan in Microvascular Angina: A Randomized, Placebo-Controlled, Crossover Trial.

Background: Microvascular angina is associated with dysregulation of the endothelin system and impairments in myocardial blood flow, exercise capacity, and health-related quality of life. The G allele of the noncoding single nucleotide polymorphism RS9349379 enhances expression of the endothelin-1 gene (EDN1) in human vascular cells, potentially increasing circulating concentrations of Endothelin-1 (ET-1). Whether zibotentan, an oral ET-A receptor selective antagonist, is efficacious and safe for the treatment of microvascular angina is unknown. Methods: Patients with microvascular angina were enrolled in this double-blind, placebo-controlled, sequential crossover trial of zibotentan (10 mg daily for 12 weeks). The trial population was enriched to ensure a G allele frequency of 50% for the RS9349379 single nucleotide polymorphism. Participants and investigators were blinded to genotype. The primary outcome was treadmill exercise duration (seconds) using the Bruce protocol. The primary analysis estimated the mean within-participant difference in exercise duration after treatment with zibotentan versus placebo. Results: A total of 118 participants (mean ±SD; years of age 63.5 [9.2 ]; 71 [60.2% ] females; 25 [21.2% ] with diabetes) were randomized. Among 103 participants with complete data, the mean exercise duration with zibotentan treatment compared with placebo was not different (between-treatment difference, -4.26 seconds [95 ] CI, -19.60 to 11.06] P=0.5871). Secondary outcomes showed no improvement with zibotentan. Zibotentan reduced blood pressure and increased plasma concentrations of ET-1. Adverse events were more common with zibotentan (60.2%) compared with placebo (14.4%; P<0.001). Conclusions: Among patients with microvascular angina, short-term treatment with a relatively high dose (10 mg daily) of zibotentan was not beneficial. Target-related adverse effects were common.

Genetic association of diabetic retinopathy with long noncoding RNA CDKN2B-AS1 gene polymorphism.

We attempted to test the influences of cyclin dependent kinase inhibitor 2B antisense RNA 1 (CDKN2B-AS1) gene polymorphisms on the susceptibility to Diabetic retinopathy (DR). Five single-nucleotide polymorphisms (SNPs) of the CDKN2B-AS1 gene, rs564398, rs1333048, rs1537373, rs2151280, and rs8181047 were examined in 280 DR cases and 455 DR-free diabetic controls. Among these loci tested, we demonstrated that diabetic carriers of at least one polymorphic allele (G) of rs2151280 (AG and GG; AOR, 1.613; 95% CI, 1.040-2.501; p = 0.033) are more susceptible to proliferative DR but not non-proliferative DR. This genetic association with the risk of developing proliferative DR was further strengthened in homozygotes for the polymorphic allele (G) of rs2151280 (GG; AOR, 2.194; 95% CI, 1.117-4.308; p = 0.023). We detected a significant association of the polymorphic allele (G) of rs2151280 with proliferative DR patients (OR, 1.503; 95% CI, 1.112-2.033; p = 0.008) but not with the entire DR or non-proliferative DR group. Moreover, as compared to those who do not possess the polymorphic allele of rs2151280 (AA), DR patients carrying at least one polymorphic allele of rs2151280 (AG + GG) exhibited a lower glomerular filtration rate and HDL cholesterol level, revealing a promotive role of rs2151280 in renal and cardiovascular complications of diabetes. Taken together, our findings implicate an impact of CDKN2B-AS1 gene polymorphisms on the progression of DR.

Genetic association between long non-coding RNA MIAT polymorphism and ischemic stroke susceptibility in the Chinese population

ObjectivesThe genetic association of long non-coding RNAs (lncRNAs) polymorphism with ischemic stroke (IS) susceptibility is not fully understood. To explore whether lncRNA MIAT rs1894720 polymorphism can predict the susceptibility of IS in the Chinese Han population. Materials and methods200 IS cases and 200 healthy controls were enrolled. Serum MIAT levels were tested via qRT-PCR. Rs1894720 genotyping was accomplished through Sanger sequencing. ResultsMIAT rs1894720 genotypes were differentially distributed in IS and control groups. Rs1894720 TT genotype was considered to be a protective factor for IS risk in dominant model (GT + TT vs GG: OR = 0.630, 95 % CI = 0.412-0.962, P = 0.032). Further stratification results showed that individuals carrying the rs1894720 G allele in people older than 65 years, men, smokers, or those with hypertension had a higher risk of IS. MIAT rs1894720 GG genotype was positively related to the susceptibility to IS of LAA subtype compared with the healthy controls. GG genotype carriers had high serum MIAT levels compared to those with GT and TT genotypes. ConclusionsMIAT rs1894720 polymorphism was associated with the risk of IS in the Chinese Han population, especially for LAA subtype. Rs1894720 GG genotype carriers were at greater risk of developing IS.

A Study on Associations of Long Noncoding RNA HOTAIR Polymorphisms With Genetic Susceptibility to Chronic Kidney Disease.

The importance of long noncoding RNAs (lncRNAs) in various biological processes has been increasingly recognized in recent years. This study investigated how gene polymorphism in HOX transcript antisense RNA (HOTAIR) lncRNA affects the predisposition to chronic kidney disease (CKD). This study comprised 150 patients with CKD and 150 healthy controls. A PCR-RFLP and ARMS-PCR techniques were used for genotyping the five target polymorphisms. According to our findings, rs4759314 confers strong protection against CKD in allelic, dominant, and codominant heterozygote genetic patterns. Furthermore, rs3816153 decreased CKD risk by 78% when TT versus GG, 55% when GG+GT versus TT, and 74% when GT versus TT+GG. In contrast, the CC+CT genotype [odds ratio (OR) = 1.66, 95% confidence intervals (CIs) = 1.05-2.63] and the T allele (OR = 1.50, 95% CI = 1.06-2.11) of rs12826786, as well as the TT genotype (OR = 2.52, 95% CI = 1.06-5.98) of rs3816153 markedly increased the risk of CKD in the Iranian population. Although no linkage disequilibrium was found between the studied variants, the Crs12826786Trs920778Grs1899663Grs4759314Grs3816153 haplotype was associated with a decreased risk of CKD by 86% (OR = 0.14, 95% CI = 0.03-0.66). The rs920778 was not correlated with CKD risk, whereas the HOTAIR rs4759314, rs12826786, rs1899663, and rs3816153 polymorphisms affected the risk of CKD in our population. It seems essential to conduct repeated studies across various ethnic groups to explore the link between HOTAIR variants and their impact on the disease outcome.

The insulin secretory granule is a hotspot for autoantigen formation in type 1 diabetes.

In type 1 diabetes, the insulin-producing beta cells of the pancreas are destroyed through the activity of autoreactive T cells. In addition to strong and well-documented HLA class II risk haplotypes, type 1 diabetes is associated with noncoding polymorphisms within the insulin gene locus. Furthermore, autoantibody prevalence data and murine studies implicate insulin as a crucial autoantigen for the disease. Studies identify secretory granules, where proinsulin is processed into mature insulin, stored and released in response to glucose stimulation, as a source of antigenic epitopes and neoepitopes. In this review, we integrate established concepts, including the role that susceptible HLA and thymic selection of the T cell repertoire play in setting the stage for autoimmunity, with emerging insights about beta cell and insulin secretory granule biology. In particular, the acidic, peptide-rich environment of secretory granules combined with its array of enzymes generates a distinct proteome that is unique to functional beta cells. These factors converge to generate non-templated peptide sequences that are recognised by autoreactive T cells. Although unanswered questions remain, formation and presentation of these epitopes and the resulting immune responses appear to be key aspects of disease initiation. In addition, these pathways may represent important opportunities for therapeutic intervention.

Blood pressure-associated non-coding single nucleotide polymorphism rs217727 modulates gene expression in human endothelial cells

Majority of Blood Pressure (BP)-associated single nucleotide polymorphisms (SNPs) are in intronic or intergenic regions. Allele G of the noncoding SNP rs217727 is associated with decreased systolic, diastolic and pulse pressure. MRPL23 is the closest protein-coding gene to rs217727, and the transcriptional start site of MRPL23 is 48.3kb away from rs217727. rs217727 is an expression quantitative trait locus for MRPL23 and TNNT3 (76.1kb away). We performed a series of studies to experimentally identify genes modulated by rs217727 and to begin to understand the mechanism. We differentiated a human induced pluripotent stem cell (iPSC) line to endothelial cells (iECs). The iECs were purified using VE-cadherin sorting. Chromatin conformation analysis using Micro-C identified several genes including MRPL23, IGF2 (141.6kb away) and TNNT3 as sharing a chromatin loop with rs217727. We used CRISPR-Cas9 to generate isogenic iPSC lines with either homozygous low BP (G) or high BP allele (A) of rs217727. The screening of several hundred clones led to the establishment of three and four clones with low BP and high BP genotypes. The edited iPSC lines were subjected to six rounds of differentiation to iECs for targeted real-time PCR analysis of genes near rs217727, including the genes mentioned above. We found significantly (p&lt;0.05) decreased expression of TNNT3 (0.44±0.04 fold), LSP1 (142.6kb away; 0.12±0.02 fold) and IGF2 (0.78±0.06 fold) and slightly increased expression of CD81 (380.5kb away; 1.09±0.03 fold) in iECs with the high BP allele (n≥43) compared to the low BP allele (n≥34) of rs217727 (p&lt;0.05). TNNT3 encodes troponin T3 fast skeletal type, LSP1 encodes lymphocyte specific protein 1 and IGF2 encodes insulin-like growth factor 2. The closest gene MRPL23, CTSD (231.8kb away), and MRPS6, a gene on a different chromosome, were not significantly differentially expressed. In summary, the results indicate that rs217727 influences the expression of several local genes in an allele-specific manner. The results provide new insights into the function of a BP-associated noncoding SNP. The work is supported by NHLBI P01 HL149620. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

MicroRNA-Mediated Suppression of Glial Cell Line-Derived Neurotrophic Factor Expression Is Modulated by a Schizophrenia-Associated Non-Coding Polymorphism.

Plasma levels of glial cell line-derived neurotrophic factor (GDNF), a pivotal regulator of differentiation and survival of dopaminergic neurons, are reportedly decreased in schizophrenia. To explore the involvement of GDNF in the pathogenesis of the disease, a case-control association analysis was performed between five non-coding single nucleotide polymorphisms (SNP) across the GDNF gene and schizophrenia. Of them, the 'G' allele of the rs11111 SNP located in the 3' untranslated region (3'-UTR) of the gene was found to associate with schizophrenia. In silico analysis revealed that the rs11111 'G' allele might create binding sites for three microRNA (miRNA) species. To explore the significance of this polymorphism, transient co-transfection assays were performed in human embryonic kidney 293T (HEK293T) cells with a luciferase reporter construct harboring either the 'A' or 'G' allele of the 3'-UTR of GDNF in combination with the hsa-miR-1185-1-3p pre-miRNA. It was demonstrated that in the presence of the rs11111 'G' (but not the 'A') allele, hsa-miR-1185-2-3p repressed luciferase activity in a dose-dependent manner. Deletion of the miRNA binding site or its substitution with the complementary sequence abrogated the modulatory effect. Our results imply that the rs11111 'G' allele occurring more frequently in patients with schizophrenia might downregulate GDNF expression in a miRNA-dependent fashion.

A regulatory variant impacting TBX1 expression contributes to basicranial morphology in Homo sapiens

Changes in gene regulatory elements play critical roles in human phenotypic divergence. However, identifying the base-pair changes responsible for the distinctive morphology of Homo sapiens remains challenging. Here, we report a noncoding single-nucleotide polymorphism (SNP), rs41298798, as a potential causal variant contributing to the morphology of the skull base and vertebral structures found in Homo sapiens. Screening for differentially regulated genes between Homo sapiens and extinct relatives revealed 13 candidate genes associated with basicranial development, with TBX1, implicated in DiGeorge syndrome, playing a pivotal role. Epigenetic markers and in silico analyses prioritized rs41298798 within a TBX1 intron for functional validation. CRISPR editing revealed that the 41-base-pair region surrounding rs41298798 modulates gene expression at 22q11.21. The derived allele of rs41298798 acts as an allele-specific enhancer mediated by E2F1, resulting in increased TBX1 expression levels compared to the ancestral allele. Tbx1-knockout mice exhibited skull base and vertebral abnormalities similar to those seen in DiGeorge syndrome. Phenotypic differences associated with TBX1 deficiency are observed between Homo sapiens and Neanderthals (Homo neanderthalensis). In conclusion, the regulatory divergence of TBX1 contributes to the formation of skull base and vertebral structures found in Homo sapiens.

The relationship between long non-coding gene CASC21 polymorphisms and cervical cancer

ABSTRACT Background CASC21 was reported to be a hotspot gene in cervical cancer. The relationship between CASC21 genetic polymorphisms and cervical cancer has not been reported. Genetic factors influence the occurrence of cervical cancer. Thus, we explored the correlation between CASC21 polymorphisms and cervical cancer. Methods A total of 973 participants within 494 cervical cancer cases and 479 healthy controls were recruited. Five single nucleotide polymorphisms (SNPs) in the CASC21 gene were genotyped using the Agena MassARRAY platform. Chi-squared test, logistic regression analysis, odds ratio (OR), multifactor dimensionality reduction (MDR), and 95% confidence interval (95%CI) were used for data analysis. Results In the overall analysis, rs16902094 (p = .014, OR = 1.86, 95% CI = 1.12–3.08) and rs16902104 (p = .014, OR = 1.86, 95% CI = 1.12–3.09) had the risk-increasing correlation with the occurrence of cervical cancer. Stratification analysis showed that rs16902094 and rs16902104 were still associated with cervical cancer risk in the subgroups with age > 51, BMI < 24 kg/m2, smokers, and patients with cervical squamous cell carcinoma. MDR analysis displayed that rs16902094 (.49%) and rs16902104 (.52%) were the main influential attribution factor for cervical cancer risk. Conclusion Our finding firstly determined that two CASC21 SNPs (rs16902094, rs16902104) were associated with an increased risk of cervical cancer, which adds to our knowledge regarding the effect of CASC21 on cervical carcinogenesis.

Non-coding autoimmune risk variant defines role for ICOS in T peripheral helper cell development

Fine-mapping and functional studies implicate rs117701653, a non-coding single nucleotide polymorphism in the CD28/CTLA4/ICOS locus, as a risk variant for rheumatoid arthritis and type 1 diabetes. Here, using DNA pulldown, mass spectrometry, genome editing and eQTL analysis, we establish that the disease-associated risk allele is functional, reducing affinity for the inhibitory chromosomal regulator SMCHD1 to enhance expression of inducible T-cell costimulator (ICOS) in memory CD4+ T cells from healthy donors. Higher ICOS expression is paralleled by an increase in circulating T peripheral helper (Tph) cells and, in rheumatoid arthritis patients, of blood and joint fluid Tph cells as well as circulating plasmablasts. Correspondingly, ICOS ligation and carriage of the rs117701653 risk allele accelerate T cell differentiation into CXCR5-PD-1high Tph cells producing IL-21 and CXCL13. Thus, mechanistic dissection of a functional non-coding variant in human autoimmunity discloses a previously undefined pathway through which ICOS regulates Tph development and abundance.

Upregulated GIRK2 Counteracts Ethanol-Induced Changes in Excitability and Respiration in Human Neurons.

Genome-wide association studies (GWAS) of electroencephalographic endophenotypes for alcohol use disorder (AUD) has identified noncoding polymorphisms within the KCNJ6 gene. KCNJ6 encodes GIRK2, a subunit of a G-protein-coupled inwardly rectifying potassium channel that regulates neuronal excitability. We studied the effect of upregulating KCNJ6 using an isogenic approach with human glutamatergic neurons derived from induced pluripotent stem cells (male and female donors). Using multielectrode arrays, population calcium imaging, single-cell patch-clamp electrophysiology, and mitochondrial stress tests, we find that elevated GIRK2 acts in concert with 7-21 d of ethanol exposure to inhibit neuronal activity, to counteract ethanol-induced increases in glutamate response, and to promote an increase intrinsic excitability. Furthermore, elevated GIRK2 prevented ethanol-induced changes in basal and activity-dependent mitochondrial respiration. These data support a role for GIRK2 in mitigating the effects of ethanol and a previously unknown connection to mitochondrial function in human glutamatergic neurons.

Evaluating the regulatory function of non-coding autism-associated single nucleotide polymorphisms on gene expression in human brain tissue.

Common variants account for most of the estimated heritability associated with autism spectrum disorder (autism). Although several replicable single nucleotide polymorphisms (SNPs) for the condition have been detected using genome-wide association study (GWAS) methodologies, their pathophysiological relevance remains elusive. Examining this is complicated, however, as all detected loci are situated within non-coding regions of the genome. It is therefore likely that they possess roles of regulatory function as opposed to directly affecting gene coding sequences. To bridge the gap between SNP discovery and mechanistic insight, we applied a comprehensive bioinformatic pipeline to functionally annotate autism-associated polymorphisms and their non-coding linkage disequilibrium (i.e., non-randomly associated) partners. We identified 82 DNA variants of probable regulatory function that may contribute to autism pathogenesis. To validate these predictions, we measured the impact of 11 high-confidence candidates and their GWAS linkage disequilibrium partners on gene expression in human brain tissue from Autistic and non-Autistic donors. Although a small number of the surveyed variants exhibited measurable influence on gene expression as determined via quantitative polymerase chain reaction, these did not survive correction for multiple comparisons. Additionally, no significant genotype-by-diagnosis effects were observed for any of the SNP-gene associations. We contend that this may reflect an inability to effectively capture the modest, neurodevelopmental-specific impact of individual variants on biological dysregulation in available post-mortem tissue samples, as well as limitations in the existing autism GWAS data.

Associations of long non-coding RNAs HOTAIR, LINC00951, POLR2E and HULC polymorphisms with the risk of esophageal and esophagogastric junction cancer in a western population: a case-control study

BackgroundThe incidence of single-nucleotide-polymorphisms with malignant potential in esophageal cancer tissues has only been sparsely investigated in the west. Hence, we explored the contribution of four long non-coding RNAs’ polymorphisms HOTAIR rs920778, LINC00951 rs11752942, POLR2E rs3787016 and HULC rs7763881 in esophageal cancer susceptibility.Methods and resultsFormalin-fixed paraffin-embedded tissue specimens from 95 consecutive patients operated for esophageal/esophagogastric junction carcinoma during 25/03/2014-25/09/2018 were processed. Demographic data, histopathological parameters, surgical and oncological outcomes were collected. DNA findings of the abovementioned population were compared with 121 healthy community controls. Both populations were of European/Greek ancestry. Sixty-seven patients underwent Ivor Lewis/McKeown esophagectomy for either squamous cell esophageal carcinoma (N = 6) or esophageal/esophagogastric junction Siewert I or II adenocarcinoma (N = 61). Twenty-eight patients were subjected to extended total gastrectomy for esophagogastric junction Siewert III adenocarcinoma. Neither LINC00951 rs11752942 nor HULC rs7763881 polymorphisms were detected more frequently in esophageal cancer patients compared with healthy community subjects. A significantly higher presence of HOTAIR rs920778 TT genotype in esophagogastric junction Siewert I/II adenocarcinoma was identified. POLR2E rs3787016 C allele and CC genotypes were overrepresented in the control group, and when found in esophageal cancer carriers were associated with earlier disease stages, as well as with minor lymph node involvement and lesser metastatic potential.ConclusionsHOTAIR rs920778 may serve as a potential therapeutic suppression target, while POLR2E rs3787016 may represent a valuable biomarker to evaluate esophageal cancer predisposition and predict treatment response and prognosis. Clinical implications of these findings need to be verified with further prospective studies with larger sample-size.

Abstract IA18: Genetic susceptibility to breast cancer: Recent advances and application to personalised prevention

Abstract The past two decades have seen dramatic progress in our understanding of the inherited basis of breast cancer, driven by large international collaborative epidemiological studies. Genetic factors identified include rare coding variants in susceptibility genes, and more than 200 common polymorphisms, identified through genome-wide association studies (GWAS) and largely in non-coding regions, that confer more moderate risks. The majority of the common variants are more strongly associated with ER-positive disease, but a subset is specifically associated with ER-negative disease. Variants are strongly enriched for regulatory regions and transcription factor binding sites, and the putative target genes are strongly enriched for known breast cancer drivers: however, the underlying target genes and mechanisms remain largely obscure. The associations for common variants appear to be largely independent of each other and can be summarised by a polygenic risk score (PRS) that is strongly predictive of risk. The most extensively validated PRS, comprising 313 SNPs, is associated with a relative risk of approximately 1.6 per standard deviation; women in the top 1% of the risk distribution have an approximately 4-fold risk of ER-positive disease and 3-fold risk of ER-negative disease. The PRS was developed in women of European ancestry but is also predictive of risk in Asian ancestry women, though less so in African ancestry women. In contrast, despite their widespread use, the evidence for association with cancer for coding variants in genes on genetic testing panels is often weak. Recent very large-scale targeted sequencing studies, however, have clarified the position, providing strong evidence for an association between protein truncating or missense variants and breast cancer risk for nine genes: BRCA1, BRCA2, ATM, CHEK2, PALB2, BARD1, RAD51C, RAD51D and TP53. Recent large-scale exome-wide sequencing analysis has shown that rare variants in several additional genes are also risk associated, with the majority being tumour suppressor genes: these include MAP3K1, ATRIP and SAMHD1. These analyses also demonstrate, however, that the contribution of coding variation, beyond the known genes, is likely to be small. The currently identified variants explain about half of the familial risk of breast cancer. Part of the “missing” heritability is due to weaker common variants, many of which should be identified in ongoing larger GWAS. The causes of the remainder are obscure and may include rare non-coding variants, repeat polymorphisms, and epistatic interactions. Risk discrimination is most powerful when all risk factors are considered. The BOADICEA model, implemented in the CanRisk tool, provides a well validated model that incorporates the effects of gene variants, polygenic risk scores, lifestyle factors and breast density to predict breast and ovarian cancer risk. Multiple translational studies are ongoing to evaluate the feasibility and utility of such personalised risk prediction for stratifying screening and prevention. Citation Format: Douglas F Easton. Genetic susceptibility to breast cancer: Recent advances and application to personalised prevention [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr IA18.

Association between non-coding transcript variant polymorphisms (rs3135499, rs3135500) of the NOD2 gene and the propensity to rheumatoid arthritis in the Iraqi population

AimThe objective of this study was to explore how the existence of two particular SNPs located in potential binding sites for microRNAs in the 3′- UTR region of the NOD2 gene could impact the susceptibility to rheumatoid arthritis (RA) among the Iraqi population. BackgroundRheumatoid arthritis (RA) is a chronic autoimmune condition that predominantly affects the joints. In RA, the immune system erroneously attacks the tissue surrounding the joints, resulting in stiffness, inflammation, pain, and mobility restrictions, particularly in areas such as the wrists, spine, knees, ankles, and feet. While numerous genes in the human genome play a part in the development of RA, specific genetic regions within these genes may have a noteworthy influence on both the initiation and progression of RA and this influence may extend to other inflammatory conditions as well. MethodIn a case-control study, genomic DNA (gDNA) was isolated from the peripheral blood of 200 individuals. These participants were categorized into two groups: one comprising 100 individuals diagnosed with rheumatoid arthritis, and the other composed of 100 healthy individuals who served as the control group. Various laboratory parameters and anthropometric data, such as age, gender, body mass index (BMI), levels of anti-cyclic citrullinated peptide (anti-CCP), and rheumatoid factor (RF), were assessed. Subsequently, all samples were genotyped for two specific polymorphisms located within the NOD2 gene (rs3135499 and rs3135500) using rhAmp-polymerase chain reaction technology. Finally, the collected data underwent analysis using a range of statistical methods. ResultsThe results indicated a substantial correlation between the risk of developing rheumatoid arthritis (RA) and the allele frequencies of the rs3135500G > A polymorphism, specifically [G vs A; Odds Ratio (OR) = 1.76; 95% Confidence Interval (CI) (1.8 – –2.6); p < 0.005], as well as the genotypes [GG vs GA + AA; OR = 2.4; 95% CI (1.15–2.2), p < 0.001], [GA vs GG; OR = 0.1; 95% CI (0.33–0.4), p < 0.001], and [AA vs GG; OR = 0.08; 95% CI (0.02–0.37), p < 0.001]. Conversely, the rs3135499 A > C polymorphism did not exhibit significant variations, except for [CC vs AA+AC; OR = 2.7; 95% CI (1.3–5.73), p < 0.009], and [AC vs AA; OR = 2.95; 95% CI (0.87–10.02), p < 0.03] after adjusting for factors like gender, age, BMI, smoking status, and family history. It's worth noting that markers such as anti-CCP, RF, and CRP produced positive results exclusively among RA patients. Additionally, parameters like BMI, ESR, WBCs, and Urea exhibited significant differences between the RA group and the healthy control group (p < 0.02, p < 0.0001, p < 0.002, and p < 0.01, respectively). Furthermore, there was a strong linkage observed between the rs3135500G > A and rs3135499A > C polymorphism of the NOD2 gene in patients (D′ = 0.85). ConclusionOur findings indicate an association between rheumatoid arthritis (RA) and the rs3135500 G/A polymorphism situated in the 3′-UTR of the NOD2 gene, particularly in the presence of the A allele. Additionally, the AA haplotype model was associated with an increased susceptibility to RA within the genetic region of NOD2.

Retinoic acid signaling regulates spatiotemporal specification of human green and red cones.

Trichromacy is unique to primates among placental mammals, enabled by blue (short/S), green (medium/M), and red (long/L) cones. In humans, great apes, and Old World monkeys, cones make a poorly understood choice between M and L cone subtype fates. To determine mechanisms specifying M and L cones, we developed an approach to visualize expression of the highly similar M- and L-opsin mRNAs. M-opsin was observed before L-opsin expression during early human eye development, suggesting that M cones are generated before L cones. In adult human tissue, the early-developing central retina contained a mix of M and L cones compared to the late-developing peripheral region, which contained a high proportion of L cones. Retinoic acid (RA)-synthesizing enzymes are highly expressed early in retinal development. High RA signaling early was sufficient to promote M cone fate and suppress L cone fate in retinal organoids. Across a human population sample, natural variation in the ratios of M and L cone subtypes was associated with a noncoding polymorphism in the NR2F2 gene, a mediator of RA signaling. Our data suggest that RA promotes M cone fate early in development to generate the pattern of M and L cones across the human retina.

Comprehensive characterization of coding and non-coding single nucleotide polymorphisms of the Myoneurin (MYNN) gene using molecular dynamics simulation and docking approaches.

Genome-wide association studies (GWAS) identified a coding single nucleotide polymorphism, MYNN rs10936599, at chromosome 3q. MYNN gene encodes myoneurin protein, which has been associated with several cancer pathogenesis and disease development processes. However, there needed to be a more detailed characterization of this polymorphism's (and other coding and non-coding polymorphisms) structural, functional, and molecular impact. The current study addressed this gap and analyzed different properties of rs10936599 and non-coding SNPs of MYNN via a thorough computational method. The variant, rs10936599, was predicted functionally deleterious by nine functionality prediction approaches, like SIFT, PolyPhen-2, and REVEL, etc. Following that, structural modifications were estimated through the HOPE server and Mutation3D. Moreover, the mutation was found in a conserved and active residue, according to ConSurf and CPORT. Further, the secondary structures were predicted, followed by tertiary structures, and there was a significant deviation between the native and variant models. Similarly, molecular simulation also showed considerable differences in the dynamic pattern of the wildtype and mutant structures. Molecular docking revealed that the variant binds with better docking scores with ligand NOTCH2. In addition to that, non-coding SNPs located at the MYNN locus were retrieved from the ENSEMBL database. These were found to disrupt the transcription factor binding regulatory regions; nonetheless, only two affect miRNA target sites. Again, eight non-coding variants were detected in the testes with normalized expression, whereas HaploReg v4.1 unveiled annotations for non-coding variants. In summary, in silico comprehensive characterization of coding and non-coding single nucleotide polymorphisms of MYNN gene will assist researchers to work on MYNN gene and establish their association with certain types of cancers.