Specific Variants Research Articles

Microbial diversity and biogeography across gastrointestinal tracts of Takifugu pufferfish revealed by full-length 16S amplicon sequencing

Fish, which are vital for both aquatic ecosystem functionality and global food supply, rely heavily on their gastrointestinal tract (GIT) microbiota for the digestion that underpins their growth and health. Takifugu pufferfish, which are an example of species evolved through adaptive radiation, possess a GIT that is specialized for antipredator defense and gluttonous feeding behaviors, offering a unique model to explore the effects of GIT compartmentalization and host genetics on gut microbial communities. Here we compiled 78 full and partial-length 16 ​S rRNA amplicon datasets across three anteroposteriorly distinct intestinal sites in a cohort of cohabitating artificial hybrid and purebred Takifugu pufferfishes. Our findings reveal a compositional and functional biogeography of pufferfish gut microbiota along the GIT and between host genetics. Additionally, the differential abundance of specific amplicon sequence variants and their correlation with host genetic backgrounds and intestinal sections highlight the role of environmental filtering in shaping microbial communities, with certain bacterial taxa exhibiting strong preferences for particular intestinal sites or genetic backgrounds, suggesting potential localized adaptation or functional specialization. This study enhances our understanding of the intricate interplay between host genetics, gut anatomy, and microbiota in fish, underscoring the importance of detailed microbial profiling in conservation efforts and aquaculture practices, and emphasizing the necessity of integrating full-length 16 ​S rRNA sequencing with partial-length datasets to comprehensively understand microbial diversity and function, paving the way for improved fish health management and sustainable aquaculture strategies.

Novel Genes of the Male Reproductive System: Potential Roles in Male Reproduction and as Non-hormonal Male Contraceptive Targets.

The development of novel non-hormonal male contraceptives represents a pivotal frontier in reproductive health, driven by the need for safe, effective, and reversible contraceptive methods. This comprehensive review explores the genetic underpinnings of male fertility, emphasizing the crucial roles of specific genes and structural variants (SVs) identified through advanced sequencing technologies such as long-read sequencing (LRS). LRS has revolutionized the detection of structural variants and complex genomic regions, offering unprecedented precision and resolution over traditional next-generation sequencing (NGS). Key genetic targets, including those implicated in spermatogenesis and sperm motility, are highlighted, showcasing their potential as non-hormonal contraceptive targets. The review delves into the systematic identification and validation of male reproductive tract-specific genes, utilizing advanced transcriptomics and genomics studies with validation using novel knockout mouse models. We discuss the innovative application of small molecule inhibitors, developed through platforms like DNA-encoded chemistry technology (DEC-Tec), which have shown significant promise in preclinical models. Notable examples include inhibitors targeting serine/threonine kinase 33 (STK33), soluble adenylyl cyclase (sAC), cyclin-dependent kinase 2 (CDK2), and bromodomain testis associated (BRDT), each demonstrating nanomolar affinity and potential for reversible and specific inhibition of male fertility. This review also honors the contributions of Dr. David L. Garbers whose foundational work has paved the way for these advancements. The integration of genomic, proteomic, and chemical biology approaches, supported by interdisciplinary collaboration, is poised to transform male contraceptive development. Future perspectives emphasize the need for continued innovation and rigorous testing to bring these novel contraceptives from the laboratory to clinical application, promising a new era of male reproductive health management.

Peculiarities of Adverb Placement in English Sentences (exemplified by the adverb "fairly")

The article deals with the problem of adverb placement in English sentences. The paper aims at studying the main tendencies and patterns which influence the choice of the syntactic position of adverbs in English. Special attention is paid to the correlation between the semantic and syntactic features of adverbs. The article also describes possible syntactic positions of adverbs belonging to different semantic classes and the factors which determine the change of the place of the adverb in the sentence. The paper also considers the peculiarities of functioning of adverbs in the sentence based on the analysis of the adverb "fairly". The material for study includes contexts of use of the adverb "fairly" taken from the British National Corpus (BNC). The research uses the following methods: descriptive and statistical methods, methods of contextual analysis and syntactic analysis. The relevance of the subject of the research is due to the fact that in modern English adverbs are characterized by a high level of variability in syntactic placement, and even adverbs belonging to the same semantic class may have different syntactic properties. The analysis showed that "fairly" can be used as an intensifying adverb, an emphasizer, an adverb of manner, an evaluation adverb; in a number of cases it can also acquire additional modal meanings or serve as a speech act-related adverb. Each meaning of the adverb is characterised by its specific variants of syntactic positioning: before the word it modifies, in medial position, in end position and as a parenthetic word detached from the rest of the sentence. The results of the research show the necessity to study the syntactic properties of adverbs in more detail and to clarify their existing dictionary definitions.

DEVELOPMENT OF A RAPID SNP PCR ASSAY TO DIFFERENTIATE BETWEEN EUROPEAN AND NORTH AMERICAN HAPLOTYPES OF ECHINOCOCCUS MULTILOCULARIS.

Herein we describe a single nucleotide polymorphism-specific polymerase chain reaction (PCR) assay to rapidly detect and differentiate variants belonging to the European and North American lineages of Echinococcus multilocularis in clinical samples. This is an extremely relevant and applicable test in North America because the range of E. multilocularis continues to expand across the continent and because of a rise in prevalence in wildlife, domestic animals, and humans. The endemic North American (NA) and introduced European (EU) variants are believed to have different pathogenic potentials, with the EU variants being more infective and pathogenic than the NA variants. The rise of the EU variants of E. multilocularis increases the risk of spillover from wildlife to humans because of its increased potential for infectivity. Current PCR-based diagnostics can detect E. multilocularis deoxyribonucleic acid (DNA), but DNA sequencing is required to identify the specific variant. Our assay provides a straightforward conventional PCR method to differentiate the NA and EU variants, and we suggest this same approach could be used for the diagnosis of other parasites or variants that are genetically very similar. As surveillance continues for E. multilocularis across North America, identifying the different genetic variants from different geographic regions will become essential to understanding the current epidemiological shift that the parasite is experiencing, as well as informing public health decisions in affected areas.

MECP2 Variants in Males: More Common than Previously Appreciated

BackgroundTo assess the age and MECP2 variants of recently identified males and set the stage for further study of clinical features in males. MethodsGenetic information on the specific MECP2 variant was acquired from the coordinator (K.F.) of the Parent Group for Males. Data were collected indicating whether these variants were de novo or transmitted from the mother and whether males who appeared to meet the diagnostic criteria for Rett syndrome had mosaicism for the MECP2 variant. ResultsFifty-nine males were identified through the parent group. Their ages ranged from 2 to 28 years, with the median age being 7.0 years and the mean age being 10.8 years. Of these variants, 46 (78.0%) were de novo, nine (15.3%) were maternally inherited, and for four (6.8%) inheritance was not known. Eleven (18.6%) were mosaic, 10 with somatic mosaicism and one with Klinefelter syndrome (47XXY). Together with males reported previously from the US Natural History Study, the total group represents 85 males, of whom 27 are deceased. ConclusionsThese data on males with MECP2 variants are important to caregivers, physicians, and researchers to begin to characterize their historical and clinical features, improve diagnostic recognition and overall care, and accelerate access to therapeutic studies including gene replacement strategies. Equal access to such therapies for males is critical.

Analysis of Total Microcystins using LC-MS/MS: Method Improvements and Sample Applications

Microcystin variants (MCs), including microcystin-LR (MC-LR) and related variants, are produced by cyanobacteria and are regulated due to their potential health risks. Current methods for MC analysis predominantly employ LC-MS/MS, limited by the availability of reference materials necessary for quantification. As an alternative method for total MC quantification, the analysis of 2-methyl-3-methoxy-4-phenylbutyric acid (MMPB), formed by oxidation of the common ADDA structure in MCs, offers economic and practical advantages by avoiding the need for multiple MC reference materials. This method allows total MC quantification across various matrices, independent of specific MC variants. In this study, we evaluated the utility of MMPB-d3 as a surrogate to assess recovery rates throughout the processes critical for MMPB quantification. Comparative analysis with 4-phenylbutyric acid (4-PB) highlighted the stability of MMPB-d3 under oxidative conditions, which is critical for its application as a surrogate or internal standard. The oxidation process was optimized to achieve consistent recovery rates, averaging 101%, ensuring reliable conversion of MCs to MMPB for subsequent analysis. The limit of quantification (LOQ) has been improved due to the large volume injection of up to 0.1 µg/L. Comparison of MMPB concentrations from field samples with conventional LC-MS/MS results showed a significant correlation (r = 0.80, p < 0.005), but with variations in the absolute concentrations. Calculations using a formulation model with MMPB concentrations allowed us to estimate total MC levels, demonstrating the potential of the proposed method to complement existing target measurement techniques.

Genomic and Transcriptomic Profile of HNF1A-Mutated Liver Adenomas Highlights Molecular Signature and Potential Therapeutic Implications.

Hepatocellular adenomas (HAs) are tumors that can develop under different conditions, including in patients harboring a germline mutation in HNF1A. However, little is known about the pathogenesis of such disease. This work aims to better define what mechanisms lie under the development of this condition. Six HAs were sampled from the liver of a 17-year-old male affected by diabetes and multiple hepatic adenomatosis harboring the heterozygous pathogenic germline variant c.815G>A, p.(Arg272His) in HNF1A, which has a dominant negative effect. All HAs were molecularly characterized. Four of them were shown to harbor a second somatic HNF1A variant and one had a mutation in the ARID1A gene, while no additional somatic changes were found in the remaining HA and normal parenchyma. A transcriptomic profile of the same HA samples was also performed. HNF1A biallelic mutations were associated with the up-regulation of several pathways including the tricarboxylic acid cycle, the metabolism of fatty acids, and mTOR signaling while angiogenesis, endothelial and vascular proliferation, cell migration/adhesion, and immune response were down-regulated. Contrariwise, in the tumor harboring the ARID1A variant, angiogenesis was up-modulated while fatty acid metabolism was down-modulated. Histological analyses confirmed the molecular data. Independently of the second mutation, energetic processes and cholesterol metabolism were up-modulated, while the immune response was down-modulated. This work provides a complete molecular signature of HNF1A-associated HAs, analyzing the association between specific HNF1A variants and the development of HA while identifying potential new therapeutic targets for non-surgical treatment.

Review of p.(Val429Met), a Variant of LDLR That Is Associated with Familial Hypercholesterolemia

Patients affected by familial hypercholesterolemia possess elevated low-density lipoprotein cholesterol and therefore have greater risk for cardiovascular disease. About 90% of familial hypercholesterolemia cases are associated with aberrant LDLR. Over 3500 LDLR variants have been identified, 15% of which are considered “pathogenic.” Given the genetic diversity of LDLR variants, specific variants rarely receive attention. However, investigators have proposed the critical evaluation of individual variants as a method to clarify knowledge and to resolve discrepancies in the literature. This article reviews p.(Val429Met) (rs28942078) in the areas of pathology, epidemiology, lipid-lowering therapy, and genetic testing. The p.(Val429Met) variant is associated with a missense point substitution in exon 9 of chromosome 19. Biochemical studies have found severely reduced low-density lipoprotein receptor protein in autologous and heterologous expression systems. Additionally, there are inconsistencies regarding the functional classification of p.(Val429Met). Considered to be of European origin, p.(Val429Met) is found in extant populations due to founder effects. Evidence from clinical trials have also demonstrated variable responses to newer lipid-lowering therapies in patients with a p.(Val429Met) variant. Proper clinical detection and adequate genetic testing have been shown to greatly improve outcomes. Future research may be aimed at resolving discrepancies to better comprehend the implications of familial hypercholesterolemia.

Handrim Reaction Force and Moment Assessment Using a Minimal IMU Configuration and Non-Linear Modeling Approach during Manual Wheelchair Propulsion.

Manual wheelchair propulsion represents a repetitive and constraining task, which leads mainly to the development of joint injury in spinal cord-injured people. One of the main reasons is the load sustained by the shoulder joint during the propulsion cycle. Moreover, the load at the shoulder joint is highly correlated with the force and moment acting at the handrim level. The main objective of this study is related to the estimation of handrim reactions forces and moments during wheelchair propulsion using only a single inertial measurement unit per hand. Two approaches are proposed here: Firstly, a method of identification of a non-linear transfer function based on the Hammerstein-Wiener (HW) modeling approach was used. The latter represents a typical multi-input single output in a system engineering modeling approach. Secondly, a specific variant of recurrent neural network called BiLSTM is proposed to predict the time-series data of force and moments at the handrim level. Eleven subjects participated in this study in a linear propulsion protocol, while the forces and moments were measured by a dynamic platform. The two input signals were the linear acceleration as well the angular velocity of the wrist joint. The horizontal, vertical and sagittal moments were estimated by the two approaches. The mean average error (MAE) shows a value of 6.10 N and 4.30 N for the horizontal force for BiLSTM and HW, respectively. The results for the vertical direction show a MAE of 5.91 N and 7.59 N for BiLSTM and HW, respectively. Finally, the MAE for the sagittal moment varies from 0.96 Nm (BiLSTM) to 1.09 Nm for the HW model. The approaches seem similar with respect to the MAE and can be considered accurate knowing that the order of magnitude of the uncertainties of the dynamic platform was reported to be 2.2 N for the horizontal and vertical forces and 2.24 Nm for the sagittal moments. However, it should be noted that HW necessitates the knowledge of the average force and patterns of each subject, whereas the BiLSTM method do not involve the average patterns, which shows its superiority for time-series data prediction. The results provided in this study show the possibility of measuring dynamic forces acting at the handrim level during wheelchair manual propulsion in ecological environments.

Unraveling the shared genetics of common epilepsies and general cognitive ability

PurposeCognitive impairment is prevalent among individuals with epilepsy, and increasing evidence indicates that genetic factors can underlie this relationship. However, the extent to which epilepsy subtypes differ in their genetic relationship with cognitive function, and information about the specific genetic variants involved remain largely unknown. MethodsWe investigated the genetic relationship between epilepsies and general cognitive ability (COG) using complementary statistical tools, including linkage disequilibrium score (LDSC) regression, MiXeR and conjunctional false discovery rate (conjFDR). We analyzed genome-wide association study data on COG (n = 269,867) and common epilepsies (n = 27,559 cases, 42,436 controls), including the broad phenotypes ‘all epilepsy’, focal epilepsies and genetic generalized epilepsies (GGE), as well as specific subtypes. We functionally annotated the identified loci using several biological resources and validated the results in independent samples. ResultsUsing MiXeR, COG (11.2k variants) was estimated to be almost four times more polygenic than ‘all epilepsy’, GGE, juvenile myoclonic epilepsy (JME), and childhood absence epilepsy (CAE) (2.5k – 2.9k variants). The other epilepsy phenotypes were insufficiently powered for MiXeR analysis. We quantified extensive genetic overlap between COG and epilepsy types, but with varying negative genetic correlations (-0.23 to -0.04). COG was estimated to share 2.9k variants with both GGE and ‘all epilepsy’, and 2.3k variants with both JME and CAE. Using conjFDR, we identified 66 distinct loci shared between COG and epilepsies, including novel associations for GGE (27), ‘all epilepsy’ (5), JME (5) and CAE (5). The implicated genes were significantly expressed in multiple brain regions. The results were validated in independent samples (COG: p = 3.62 × 10–7; ‘all epilepsy’: p = 2.58 × 10–3). ConclusionOur study further dissects the substantial genetic basis shared between epilepsies and COG and identifies novel shared loci. An improved understanding of the genetic relationship between epilepsies and COG may lead to the development of novel comorbidity-targeted epilepsy treatments.

Characterisation of Ovine KRTAP19-3 and Its Impact on Wool Traits in Chinese Tan Sheep.

Wool, a natural fibre derived from sheep, can present a challenge to wool processing and manufacturing industries because of the variation in fibre traits. Genetic improvement offers one solution to this challenge, and having a better understanding of the genes that affect wool fibre traits is therefore important. Here, we describe ovine KRTAP19-3, a new member of the KAP19 gene family. Phylogenetic analysis revealed its relationship to other known KRTAP19 gene sequences, and an analysis of the nucleotide sequence variation in KRTAP19-3 from 288 sheep of a variety of breeds revealed six unique variant sequences. Among these variants, eleven single nucleotide polymorphisms (SNPs) were detected, with six located in the coding region. Three of these coding region SNPs were non-synonymous and would result in amino acid changes. Associations were observed between the presence of specific sequence variants in Chinese Tan sheep and wool trait variation, particularly an increase in fibre diameter variability in the heterotypic hair fibres. These findings enhance our understanding of the genes that encode sheep wool proteins.

Interplay between vertebrate adaptive immunity and bacterial infectivity genes: Bank vole MHC versus Borrelia afzelii OspC.

Coevolution of parasites with their hosts may lead to balancing selection on genes involved in determining the specificity of host-parasite interactions, but examples of such specific interactions in wild vertebrates are scarce. Here, we investigated whether the polymorphic outer surface protein C (OspC), used by the Lyme disease agent, Borrelia afzelii, to manipulate vertebrate host innate immunity, interacts with polymorphic major histocompatibility genes (MHC), while concurrently eliciting a strong antibody response, in one of its main hosts in Europe, the bank vole. We found signals of balancing selection acting on OspC, resulting in little differentiation in OspC variant frequencies between years. Neither MHC alleles nor their inferred functional groupings (supertypes) significantly predicted the specificity of infection with strains carrying different OspC variants. However, we found that MHC alleles, but not supertypes, significantly predicted the level of IgG antibodies against two common OspC variants among seropositive individuals. Our results thus indicate that MHC alleles differ in their ability to induce antibody responses against specific OspC variants, which may contribute to selection of OspC polymorphism by the vole immune system.

Exploring the role of mitochondrial uncoupling protein 4 in brain metabolism: implications for Alzheimer's disease.

The brain's high demand for energy necessitates tightly regulated metabolic pathways to sustain physiological activity. Glucose, the primary energy substrate, undergoes complex metabolic transformations, with mitochondria playing a central role in ATP production via oxidative phosphorylation. Dysregulation of this metabolic interplay is implicated in Alzheimer's disease (AD), where compromised glucose metabolism, oxidative stress, and mitochondrial dysfunction contribute to disease progression. This review explores the intricate bioenergetic crosstalk between astrocytes and neurons, highlighting the function of mitochondrial uncoupling proteins (UCPs), particularly UCP4, as important regulators of brain metabolism and neuronal function. Predominantly expressed in the brain, UCP4 reduces the membrane potential in the inner mitochondrial membrane, thereby potentially decreasing the generation of reactive oxygen species. Furthermore, UCP4 mitigates mitochondrial calcium overload and sustains cellular ATP levels through a metabolic shift from mitochondrial respiration to glycolysis. Interestingly, the levels of the neuronal UCPs, UCP2, 4 and 5 are significantly reduced in AD brain tissue and a specific UCP4 variant has been associated to an increased risk of developing AD. Few studies modulating the expression of UCP4 in astrocytes or neurons have highlighted protective effects against neurodegeneration and aging, suggesting that pharmacological strategies aimed at activating UCPs, such as protonophoric uncouplers, hold promise for therapeutic interventions in AD and other neurodegenerative diseases. Despite significant advances, our understanding of UCPs in brain metabolism remains in its early stages, emphasizing the need for further research to unravel their biological functions in the brain and their therapeutic potential.

Abstract A011: PVT1 risk variant rs127920247 for colorectal cancer is shared by African American and Hispanic colorectal cancer patients

Abstract Background: Colorectal cancer, one of the most lethal and prevalent cancers across the world, is in large part due to genetic mutations. The plasmacytoma variant translocation 1 (PVT1) gene has an established association with many cancers, including colorectal cancer. There is increasingly abundant data on the mechanisms of action of PVT1 leading to the initiation and progression of these cancers. Identifying PVT1 variants linked to cancer may lead to uncovering their utility as diagnostic or prognostic biomarkers. The All of Us Research hub contains a diverse set of data from hundreds of thousands of participants. Stratifying and comparing risk variants across racial and ethnic demographics may provide insight into disparities underlying disparate incidence of colorectal cancer amongst minoritized and medically underserved communities. The All of Us database provides a novel opportunity to study PVT1 variation in a large cohort of patients from racial backgrounds with demonstrated greater incidence, prevalence, and worse outcomes from colorectal cancer. Methods: We conducted a retrospective cohort study of patients in the All of Us Research hub. The cohort studied comprised 930 patients ranging in age from 18 to 70 years with colorectal cancer, and no additional cancer diagnosis noted. Racial and ethnic backgrounds were selected if there were at least 100 patients of identified background with colorectal cancer. These consisted of patients of: African American, non-Hispanic white, and Hispanic backgrounds. We extracted data from short-read whole genome sequencing. A filtered matrix was built comparing the genetic sequence of our cohort of cancer patients to the reference genome GRCh38. We then stratified the different variants by allelic frequency across the sample cohort to report the variants with the greatest frequencies. All analyses were conducted using Python on Jupyter Notebook in the All of Us Research platform. Results: The top 5 PVT1 variants with the greatest frequency in patients of the three chosen racial and ethnic backgrounds were identified and compared to find commonalities. Rs127920247 was a PVT1 risk variant shared by African American and Hispanic patients as the 2nd highest risk variant for both. The most frequent risk variants for each group is as follows: Rs128085054 for African Americans, Rs128139524 for Non-Hispanic White Americans, and Rs127870242 for Hispanic Americans. Conclusion: PVT1 risk variants in colorectal cancer can be uncovered from data in the All of Us Research hub. Thus, genetic risk variants for cancers can be uncovered from analysis of data available in the All of Us Research hub. Identification of specific PVT1 variants similarly prevalent in colorectal cancer amongst distinct racial and ethnic communities is a significant first step towards developing them as potential diagnostic or prognostic tools. Citation Format: Sujay Singh, Olorunseun Ogunwobi. PVT1 risk variant rs127920247 for colorectal cancer is shared by African American and Hispanic colorectal cancer patients [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr A011.

Genetic predisposition of suicidal behavior: variants in GRIN2B, GABRG2, and ODC1 genes in attempted and completed suicide in two Balkan populations

AbstractCompleted suicide accounts for over 700,000 deaths worldwide annually, while attempted suicide is 20 times more frequent. Genetic background is an important factor contributing to suicidal behavior, including candidate genes in glutamate, γ-aminobutyric acid (GABA), and polyamine systems. Our aim was to differentiate genetic predispositions underlying different types of suicidal behavior, attempted and completed suicide, in two Balkan populations. Analysis of variants in the genes GRIN2B (rs2268115 and rs220557), GABRG2 (rs424740), and ODC1 (rs1049500 and rs2302614) was performed on a study sample including 173 suicide attempters with comorbid psychiatric disorders, 216 non-suicidal psychiatric patients and 172 healthy controls from Serbia, and 333 suicide completers and 356 non-suicidal autopsy controls from Slovenia. CA genotype of rs220557 in GRIN2B gene increased the risk for completed suicide (P = 0.021), and violent suicide (P = 0.037), compared to controls. In ODC1 gene, CA genotype of rs2302614 decreased the risk for completed suicide compared to suicide attempt (P = 0.012). Marginally, AC haplotype for variants rs1049500-rs2302614 in ODC1 gene decreased the risk for completed suicide compared to suicide attempt (P = 0.052). Specific genetic variants of glutamate and polyamine systems are differently distributed among diverse suicidal phenotypes, providing further information on the implication of these systems in suicidality.

Detecting interest flooding attacks in NDN: A probability-based event-driven approach

The foundational concepts of the Internet were developed in the 1960s and 1970s with the goal of interconnecting hosts using the TCP/IP architecture. While this architecture has significantly impacted communication and commerce, it struggles to accommodate the Internet’s vast user base and diverse applications. Named Data Network (NDN), a next-generation Internet architecture is designed to overcome the current TCP/IP based Internet architecture’s limitations. NDN’s basic operations make it resilient against several traditional DoS/DDoS attacks. However, NDN remains vulnerable to Interest Flooding Attack (IFA), a class of DoS attacks that can exhaust the routers’ as well as the producers’ resources to disrupt network functionality. To detect these attacks, researchers came up with a few approaches. However, existing detection techniques focus on specific IFA variants but struggle to detect other variants. To address this challenge, in this paper, we propose a statistical abnormality detection scheme to identify all variants of IFA. Additionally, we generate a comprehensive NDN traffic dataset through our experiments and use it to evaluate the performance of the detection scheme. The experimental results show that our scheme can detect all variants of IFA with high accuracy. Towards the end, we also present a sensitivity analysis study that shows the impact of varying a few parameters on the detection performance of the proposed scheme.

High-resolution functional mapping of RAD51C by saturation genome editing

Pathogenic variants in RAD51C confer an elevated risk of breast and ovarian cancer, while individuals homozygous for specific RAD51C alleles may develop Fanconi anemia. Using saturation genome editing (SGE), we functionally assess 9,188 unique variants, including >99.5% of all possible coding sequence single-nucleotide alterations. By computing changes in variant abundance and Gaussian mixture modeling (GMM), we functionally classify 3,094 variants to be disruptive and use clinical truth sets to reveal an accuracy/concordance of variant classification >99.9%. Cell fitness was the primary assay readout allowing us to observe a phenomenon where specific missense variants exhibit distinct depletion kinetics potentially suggesting that they represent hypomorphic alleles. We further explored our exhaustive functional map, revealing critical residues on the RAD51C structure and resolving variants found in cancer-segregating kindred. Furthermore, through interrogation of UK Biobank and a large multi-center ovarian cancer cohort, we find significant associations between SGE-depleted variants and cancer diagnoses.

RNA Polymerase II coordinates histone deacetylation at active promoters.

Nucleosomes at actively transcribed promoters have specific histone post-transcriptional modifications and histone variants. These features are thought to contribute to the formation and maintenance of a permissive chromatin environment. Recent reports have drawn conflicting conclusions about whether these histone modifications depend on transcription. We used triptolide to inhibit transcription initiation and degrade RNA Polymerase II and interrogated the effect on histone modifications. Transcription initiation was dispensable for de novo and steady-state histone acetylation at transcription start sites (TSSs) and enhancers. However, at steady state, blocking transcription initiation increased the levels of histone acetylation and H2AZ incorporation at active TSSs. These results demonstrate that deposition of specific histone modifications at TSSs is not dependent on transcription and that transcription limits the maintenance of these marks.

A comprehensive guide to bioinformatics tools and databases

The interest in the functional aspects of the genome has increased eventually with the expansion of genomic databases. In this review, various genetic alterations within the genome, such as Single Nucleotide Polymorphisms (SNPs), disease-associated mutations, neutral polymorphisms, and small insertions or deletions (INDELs), have been identified and characterized. These polymorphisms, particularly SNPs, have become widely employed in genetic analyses, serving as valuable molecular markers. They are applied across diverse genetic studies, including the reconstruction of haplotypes. In addition to experimental methods for investigating specific genetic variants, there has been a significant surge in bioinformatics research over the past decade, aimed at the molecular consequences of these genetic alterations. Haplotypes, which represent various alleles of a gene, can be reconstructed not only for entire chromosomes but also for specific genes, utilizing the information derived from SNPs. The computational approach to SNP and haplotype discovery has gained prominence due to the continuous expansion of sequence data within public databases. This growth enables more precise identification of SNPs. This article aims to introduce easily accessible and practical online tools for researchers. In summary, SNP and haplotype identification tools are indispensable in bioinformatics for studying genetic variation, population genetics, disease associations, and personalized medicine. They provide valuable insights into the genetic underpinnings of various traits and diseases, helping advance our understanding of genetics and its applications in healthcare.

Housing RCS rats under specific pathogen-free conditions mildly ameliorates retinal degeneration and alters intestine microbiota

Retinitis pigmentosa (RP) is a genetic blinding disease with over 80 causative genes. Disease progression varies between patients with similar genetic backgrounds. We assessed the association between environment, gut microbiota, and retinal degeneration in the RP rat model Royal College of Surgeons (RCS). The rats were born and raised for two generations under specific pathogen-free (SPF, n = 69) or non-SPF conditions (n = 48). At the age of four weeks, SPF rats had significantly shorter dark-adapted a-wave and dark and light-adapted b-wave implicit times by electroretinogram (p = 0.014, p = 9.5*10−6, p = 0.009, respectively). The SPF rats had significantly less photoreceptor apoptosis at ages four, eight, and twelve weeks (all p < 0.022), significantly thicker debris zone at age 14 weeks, and smaller hypofluorescent lesions in SPF rats at ages 10–16 weeks, especially in the inferior retina. The non-SPF rats had significantly higher microbiota alpha diversity (p = 0.037) and failed to present the age-related maturation of Proteobacteria, Spirochaetes, Actinobacteria, and Bacteroidetes seen in SPF conditions. Specific microbial amplicon sequence variants were reduced in rats with more severe retinal degeneration. Our data suggest an environmental effect on retinal deterioration in RCS rats. These findings may lead to the development of novel microbiome-related interventions for retinal degeneration.