Ensembl 2018

Genomic Prediction and Genome-Wide Association Studies for Productivity, Conformation and Heat Tolerance Traits in Tropical Smallholder Dairy Cows

Genomic selection (GS) and genome-wide association studies (GWAS) have not been investigated in Vietnamese dairy cattle, even for basic milk production traits, largely due to the scarcity of individual phenotype recording in smallholder dairy farms (SDFs). This study aimed to estimate heritability (h 2) and test the applicability of GS and GWAS for milk production, body conformation and novel heat tolerance traits using single test day phenotypic data. Thirty-two SDFs located in either the north (a lowland vs. a highland) or the south (a lowland vs. a highland) of Vietnam were each visited for an afternoon and the next morning to collect phenotype data of all lactating cows (n = 345). Tail hair from each cow was sampled for subsequent genotyping with a 50K SNP chip at that same visit. Milk production traits (single-test day) were milk yield (MILK, kg/cow/day), energy corrected milk yield adjusted for body weight (ECMbw, kg/100 kg BW/day), fat (mFA, %), protein (mPR, %) and dry matter (mDM, %). Conformation traits were body weight (BW, kg) and body condition score (BCS, 1 = thin to 5 = obese). Heat tolerance traits were panting score (PS, 0 = normal to 4.5 = extremely heat-stressed) and infrared temperatures (IRTs, °C) at 11 areas on the external body surface of the cow (inner vulval lip, outer vulval surface, inner tail base surface, ocular area, muzzle, armpit area, paralumbar fossa area, fore udder, rear udder, forehoof and hind hoof), assessed by an Infrared Camera. Univariate linear mixed models and a 10-fold cross-validation approach were applied for GS. Univariate single SNP mixed linear models were applied for the GWAS. Estimated h 2 (using the genotype information to build relationships among animals) were moderate (0.20-0.37) for ECMbw, mFA, mPR, mRE, BW, BCS and IRT at rear udder; low (0.08-0.19) for PS and other IRTs; and very low (≤ 0.07) for MILK, ECM and mDM. Accuracy of genomic estimated breeding values (GEBVs) was low (≤ 0.12) for MILK, ECM, mDM and IRT at hind hoof; and moderate to high (0.32-0.46) for all other traits. The most significant regions on chromosomes (BTA) associated with milk production traits were 0.47-1.18 Mb on BTA14. Moderate to high h 2 and moderate accuracies of GEBVs for mFA, mPR, ECMbw, BCS, BW, PS and IRTs at rear udder and outer vulval surface suggested that GS using single test day phenotypic data could be applied for these traits. However, a greater sample size is required to decrease the bias of GEBVs by GS and increase the power of detecting significant quantitative trait loci (QTLs) by GWAS.

A patient-derived T cell lymphoma biorepository uncovers pathogenetic mechanisms and host-related therapeutic vulnerabilities

Peripheral T cell lymphomas (PTCLs) comprise heterogeneous malignancies with limited therapeutic options. To uncover targetable vulnerabilities, we generate a collection of PTCL patient-derived tumor xenografts (PDXs) retaining histomorphology and molecular donor-tumor features over serial xenografting. PDX demonstrates remarkable heterogeneity, complex intratumor architecture, and stepwise trajectories mimicking primary evolutions. Combining functional transcriptional stratification and multiparametric imaging, we identify four distinct PTCL microenvironment subtypes with prognostic value. Mechanistically, we discover a subset of PTCLs expressing Epstein-Barr virus-specific T cell receptors and uncover the capacity of cancer-associated fibroblasts of counteracting treatments. PDXs' pre-clinical testing captures individual vulnerabilities, mirrors donor patients' clinical responses, and defines effective patient-tailored treatments. Ultimately, we assess the efficacy of CD5KO- and CD30- Chimeric Antigen Receptor T Cells (CD5KO-CART and CD30_CART, respectively), demonstrating their therapeutic potential and the synergistic role of immune checkpoint inhibitors for PTCL treatment. This repository represents a resource for discovering and validating intrinsic and extrinsic factors and improving the selection of drugs/combinations and immune-based therapies.

Invention of an oral medication for cardiac Fabry disease caused by RNA mis-splicing

Pathogenic RNA splicing variants have emerged as promising therapeutic targets due to their role in disease while preserving coding sequences. In this study, we developed RECTAS-2.0, a small molecule designed to correct RNA mis-splicing caused by the GLA c.639+919G>A mutation, which leads to the inclusion of a 57-nucleotide poison exon, resulting in later-onset Fabry disease, particularly prevalent in East Asia. RECTAS-2.0 restored normal GLA mRNA splicing and α-galactosidase activity in patient-derived B-lymphoblastoid cell lines and induced pluripotent stem cell-derived cardiomyocytes. Furthermore, oral administration of RECTAS-2.0 effectively corrected splicing in a transgenic mouse model, demonstrating its substantial splice-switching activity and safety for clinical application. RECTAS-2.0 demonstrated potential applicability to other genetic disorders that involve similar exon competition. These findings underscore the therapeutic potential of RECTAS-2.0 for Fabry disease and highlight its broader implications for RNA splicing-targeted therapies in genetic disorders.

Extracellular Vesicle-Derived microRNA Crosstalk Between Equine Chondrocytes and Synoviocytes-An In Vitro Approach

This study describes a novel technique to analyze the extracellular vesicle (EV)-derived microRNA (miRNA) crosstalk between equine chondrocytes and synoviocytes. Donor cells (chondrocytes, n = 8; synoviocytes, n = 9) were labelled with 5-ethynyl uridine (5-EU); EVs were isolated from culture media and incubated with recipient cells (chondrocytes [n = 5] were incubated with synoviocyte-derived EVs, and synoviocytes [n = 4] were incubated with chondrocyte-derived EVs). Total RNA was extracted from recipient cells; the 5-EU-labelled RNA was recovered and sequenced. Differential expression analysis, pathway analysis, and miRNA target prediction were performed. Overall, 198 and 213 miRNAs were identified in recipient synoviocytes and chondrocytes, respectively. The top five most abundant miRNAs were similar for synoviocytes and chondrocytes (eca-miR-21, eca-miR-221, eca-miR-222, eca-miR-100, eca-miR-26a), and appeared to be linked to joint homeostasis. There were nine differentially expressed (p < 0.05) miRNAs (eca-miR-27b, eca-miR-23b, eca-miR-31, eca-miR-191a, eca-miR-199a-5p, eca-miR-143, eca-miR-21, eca-miR-181a, and eca-miR-181b) between chondrocytes and synoviocytes, which appeared to be linked to migration of cells, apoptosis, cell viability of connective tissue cell, and inflammation. In conclusion, the reported technique was effective in recovering and characterizing the EV-derived miRNA crosstalk between equine chondrocytes and synoviocytes and allowed for the identification of EV-communicated miRNA patterns potentially related to cell viability, inflammation, and joint homeostasis.

Exploring Human Brain Metabolism via Genome-Scale Metabolic Modeling with Highlights on Multiple Sclerosis

Cerebral dysfunctions give rise to a wide range of neurological diseases due to the structural and functional complexity of the human brain stemming from the interactive cellular metabolism of its specific cells, including neurons and glial cells. In parallel with advances in isolation and measurement technologies, genome-scale metabolic models (GEMs) have become a powerful tool in the studies of systems biology to provide critical insights into the understanding of sophisticated eukaryotic systems. In this study, brain cell-specific GEMs were reconstructed for neurons, astrocytes, microglia, oligodendrocytes, and oligodendrocyte precursor cells by integrating single-cell RNA-seq data and global Human1 via a task-driven integrative network inference for tissues (tINIT) algorithm. Then, intercellular reactions among neurons, astrocytes, microglia, and oligodendrocytes were added to generate a combined brain model, iHumanBrain2690. This brain network was used in the prediction of metabolic alterations in glucose, ketone bodies, oxygen change, and reporter metabolites. Glucose supplementation increased the subsystems' activities in glycolysis, and ketone bodies elevated those in the TCA cycle and oxidative phosphorylation. Reporter metabolite analysis identified L-carnitine and arachidonate as the top reporter metabolites in gray and white matter microglia in multiple sclerosis (MS), respectively. Carbamoyl-phosphate was found to be the top reporter metabolite in primary progressive MS. Taken together, single and integrated iHumanBrain2690 metabolic networks help us elucidate complex metabolism in brain physiology and homeostasis in health and disease.

Genetic correlation, pleiotropic loci and shared risk genes between major depressive disorder and gastrointestinal tract disorders

BACKGROUND

Major depressive disorder (MDD) is associated with gastrointestinal tract (GIT) disorders, while genetic correlation, pleiotropic loci and shared risk genes remain to be explored.

METHODS

Leveraging genome-wide association study statistics for MDD (n = 170,756), peptic ulcer disease (PUD; n = 16,666), gastroesophageal reflux disease (GORD; n = 54,854), PUD and/or GORD and/or medications (PGM; n = 90,175), irritable bowel syndrome (IBS; n = 28,518), and inflammatory bowel disease (IBD; n = 7045), we determined global and local genetic correlations, identified pleiotropic loci, performed gene-level evaluations, and inferred causal associations using bidirectional Mendelian randomization.

RESULTS

We found global correlation of MDD with PUD (rg = 0.444, P = 3.135 × 10-24), GORD (rg = 0.459, P = 2.568 × 10-65), PGM (rg = 0.498, P = 6.094 × 10-114), IBS (rg = 0.621, P = 2.483 × 10-63), and IBD (rg = 0.171, P = 1.824 × 10-5). We identified 12 locally correlated regions between MDD and GIT disorders except for IBD, and one shared region (chr11:111985737-113,103,996) for PGM, GORD, and IBS. We found one pleiotropic locus for PUD, 12 for GORD, 30 for PGM, eight for IBS, and seven for IBD, and five shared loci (rs138786869, rs2284189, rs3130063, rs35789010, rs7568369) for GORD and PGM. We respectively observed 14 and 20 overlapping genes for MDD-GORD and MDD-PGM. We showed genetic liabilities to GORD, PGM, and IBS causally increase MDD risk, while all reverse causalities are significant.

CONCLUSIONS

Our work identifies genetic architectures shared between MDD and GIT disorders, contributes genetic insights to understand depression in the context of gut-brain interactions, and provides potential targets to treat gastrointestinal symptoms in depressive patients.

An early precursor CD8+ T cell that adapts to acute or chronic viral infection

This study examines the origin and differentiation of stem-like CD8+ T cells that are essential for sustained T cell immunity in chronic viral infections and cancer and also have a key role in PD-1 directed immunotherapy1-10. These PD-1+TCF-1+TOX+ stem-like CD8+ T cells (also known as precursors of exhausted T cells8,9) have a distinct program that enables them to adapt to chronic antigen stimulation. Here, using the mouse model of chronic lymphocytic choriomeningitis virus (LCMV) infection, we find that virus-specific stem-like CD8+ T cells are generated early (day 5) during chronic infection, suggesting that this crucial fate commitment occurs irrespective of the infection outcome. Indeed, we find that nearly identical populations of stem-like CD8+ T cells were generated early during acute or chronic LCMV infection, and that antigen was essential for maintaining the stem-like phenotype. We performed reciprocal adoptive transfer experiments to determine the fate of these early stem-like CD8+ T cells after viral clearance versus persistence. After transfer of day 5 stem-like CD8+ T cells from chronically infected mice into acutely infected mice, these cells downregulated canonical markers of the chronic stem-like CD8+ T cells and expressed markers (CD127 and CD62L) associated with central memory CD8+ T cells. Reciprocally, when day 5 stem-like cells from acutely infected mice were transferred into chronically infected mice, these CD8+ T cells functioned like chronic resource cells and responded effectively to PD-1 therapy. These findings highlight the ability of these early PD-1+TCF-1+TOX+ stem-like CD8+ T cells to adapt their differentiation trajectory to either an acute or a chronic viral infection. Importantly, our study shows that the host is prepared a priori to deal with a potential chronic infection.

Limosilactobacillus reuteri promotes the expression and secretion of enteroendocrine- and enterocyte-derived hormones

Intestinal microbes can beneficially impact host physiology, prompting investigations into the therapeutic usage of such microbes in a range of diseases. For example, human intestinal microbe Limosilactobacillus reuteri strains ATCC PTA 6475 and DSM 17938 are being considered for use for intestinal ailments, including colic, infection, and inflammation, as well as for non-intestinal ailments, including osteoporosis, wound healing, and autism spectrum disorder. While many of their beneficial properties are attributed to suppressing inflammatory responses, we postulated that L. reuteri may also regulate intestinal hormones to affect physiology within and outside of the gut. To determine if L. reuteri secreted factors impact the secretion of enteric hormones, we treated an engineered jejunal organoid line, NGN3-HIO, which can be induced to be enriched in enteroendocrine cells, with L. reuteri 6475 or 17938 conditioned medium and performed transcriptomics. Our data suggest that these L. reuteri strains affect the transcription of many gut hormones, including vasopressin and luteinizing hormone subunit beta, which have not been previously recognized as produced in the gut epithelium. Moreover, we find that these hormones appear to be produced in enterocytes, in contrast to canonical gut hormones produced in enteroendocrine cells. Finally, we show that L. reuteri conditioned media promote the secretion of enteric hormones, including serotonin, GIP, PYY, vasopressin, and luteinizing hormone subunit beta, and identify by metabolomics metabolites potentially mediating these effects on hormones. These results support L. reuteri affecting host physiology through intestinal hormone secretion, thereby expanding our understanding of the mechanistic actions of this microbe.

Circulating miRNAs are associated with successful bone regeneration

Introduction

Bone healing is a well-orchestrated process involving various bone cells and signaling pathways, where disruptions can result in delayed or incomplete healing. MicroRNAs (miRNAs) are small non-coding RNAs capable of influencing various cellular processes, including bone remodeling. Due to their biological relevance and stable presence in biofluids, miRNAs may serve as candidates for diagnosis and prognosis of delayed bone healing. The aim of the study was to investigate changes in miRNAs circulating in the blood during the healing of rat calvaria defects as biomarkers of successful bone regeneration.

Methods

Standardized calvaria defects were created in 36 Wistar rats with a trephine drill and treated with collagen hydroxyapatite (CHA) scaffolds. The treatment groups included CHA scaffolds only, CHA scaffolds containing a plasmid coding for bone morphogenetic protein 2 (BMP2) and miR-590-5p, CHA scaffolds containing mesenchymal stromal cell-derived extracellular vesicles, and empty defects as a control group. After 1, 4 and 8 weeks of healing, the animals were evaluated by microcomputed tomography (microCT), as well as subjected to histological analyses. Blood was sampled from the tail vein prior to surgeries and after 1, 4, and 8 weeks of healing. miRNAs circulating in the plasma were determined using next-generation sequencing.

Results

Variability of bone regeneration within the four groups was unexpectedly high and did not result in significant differences between the groups, as indicated by the microCT and histological analyses of the newly formed bone tissue. However, irrespective of the treatment group and regenerative activity, we identified miRNAs with distinct expression patterns of up- and downregulation at different time points. Furthermore, rats with high and low regenerative activity were characterized by distinct circulating miRNA profiles. miR-133-3p was identified as the top upregulated miRNA and miR-375-3p was identified as the top downregulated miRNA in animals exhibiting strong regeneration over all time points evaluated.

Conclusion

Our study indicates that regardless of the treatment group, success or lack of bone regeneration is associated with a distinct expression pattern of circulating microRNAs. Further research is needed to determine whether their levels in the blood can be used as predictive factors of successful bone regeneration.

Genetic analysis reveals the shared genetic architecture between breast cancer and atrial fibrillation

Background

Epidemiological studies have observed an association between atrial fibrillation (AF) and breast cancer (BC). However, the underlying mechanisms linking these two conditions remain unclear. This study aims to systematically explore the genetic association between AF and BC.

Methods

We utilized the largest available genome-wide association study (GWAS) datasets for European individuals, including summary data for AF (N = 1,030,836) and BC (N = 247,173). Multiple approaches were employed to systematically investigate the genetic relationship between AF and BC from the perspectives of pleiotropy and causality.

Results

Global genetic analysis using LDSC and HDL revealed a genetic correlation between AF and BC (rg = 0.0435, P = 0.039). Mixer predicted genetic overlap between non-MHC regions of the two conditions (n = 125, rg = 0.05). Local genetic analyses using LAVA and GWAS-PW identified 22 regions with potential genetic sharing. Cross-trait meta-analysis by CPASSOC identified one novel pleiotropic SNP and 14 pleiotropic SNPs, which were subsequently annotated. Eight of these SNPs passed Bayesian colocalization tests, including one novel pleiotropic SNP. Further fine-mapping analysis identified a set of causal SNPs for each significant SNP. TWAS analyses using JTI and FOCUS models jointly identified 10 pleiotropic genes. Phenome-wide association study (PheWAS) of novel pleiotropic SNPs identified two eQTLs (PELO, ITGA1). Gene-based PheWAS results showed strong associations with BMI, height, and educational attainment. PCGA methods combining GTEx V8 tissue data and single-cell RNA data identified 16 co-enriched tissue types (including cardiovascular, reproductive, and digestive systems) and 5 cell types (including macrophages and smooth muscle cells). Finally, univariable and multivariable bidirectional Mendelian randomization analyses excluded a causal relationship between AF and BC.

Conclusion

This study systematically investigated the shared genetic overlap between AF and BC. Several pleiotropic SNPs and genes were identified, and co-enriched tissue and cell types were revealed. The findings highlight common mechanisms from a genetic perspective rather than a causal relationship. This study provides new insights into the AF-BC association and suggests potential experimental targets and directions for future research. Additionally, the results underscore the importance of monitoring the potential risk of one disease in patients diagnosed with the other.

Single-cell spatial transcriptomic atlas of the whole mouse brain

A comprehensive atlas of genes, cell types, and their spatial distribution across a whole mammalian brain is fundamental for understanding the function of the brain. Here, using single-nucleus RNA sequencing (snRNA-seq) and Stereo-seq techniques, we generated a mouse brain atlas with spatial information for 308 cell clusters at single-cell resolution, involving over 4 million cells, as well as for 29,655 genes. We have identified cell clusters exhibiting preference for cortical subregions and explored their associations with brain-related diseases. Additionally, we pinpointed 155 genes with distinct regional expression patterns within the brainstem and unveiled 513 long non-coding RNAs showing region-enriched expression in the adult brain. Parcellation of brain regions based on spatial transcriptomic information revealed fine structure for several brain areas. Furthermore, we have uncovered 411 transcription factor regulons showing distinct spatiotemporal dynamics during neurodevelopment. Thus, we have constructed a single-cell-resolution spatial transcriptomic atlas of the mouse brain with genome-wide coverage.

Glucose modulates IRF6 transcription factor dimerization to enable epidermal differentiation

Non-energetic roles for glucose are largely unclear, as is the interplay between transcription factors (TFs) and ubiquitous biomolecules. Metabolomic analyses uncovered elevation of intracellular glucose during differentiation of diverse cell types. Human and mouse tissue engineered with glucose sensors detected a glucose gradient that peaked in the outermost differentiated layers of the epidermis. Free glucose accumulation was essential for epidermal differentiation and required the SGLT1 glucose transporter. Glucose affinity chromatography uncovered glucose binding to diverse regulatory proteins, including the IRF6 TF. Direct glucose binding enabled IRF6 dimerization, DNA binding, genomic localization, and induction of IRF6 target genes, including essential pro-differentiation TFs GRHL1, GRHL3, HOPX, and PRDM1. These data identify a role for glucose as a gradient morphogen that modulates protein multimerization in cellular differentiation.

Comprehensive analysis of tyrosine kinase domain mutations and imatinib resistance in chronic myeloid leukemia patients

Tyrosine kinase domain mutations (TKDMs) plays an important role in prognosis of chronic myeloid leukemia (CML). The aim of the present study was to identify the TKDMs associated with imatinib mesylate (IM) drug resistant in CML, following European leukemia Net (ELN) guidelines. Direct sequencing analysis revealed point mutations in 69.44 % (50/72), compound/ polyclonal mutations in 11.11 % (8/72) and large deletions in 4.16 % (3/72) of IM non-responder CML patients. Additionally, we have identified low level mutations in 30.55 % of warning group patients through NGS analysis, that include singly occurring point mutations (5) and polyclonal (6) mutations with mutant allele frequency ranging from 1.1 % to 14.70 %. The low-level mutations detected through NGS in warning group patients; may be responsible for suboptimal response in our study. However, follow-up studies are important to understand the mechanism of clonal evolution. We also identified 5 novel mutations that had not been reported in public databases which expands the spectrum of known mutations in BCR::ABL1 fusion gene. Our study also highlighted the impact on patient outcomes following the implementation of ELN guidelines underscores the importance of adherence to standardized protocols in clinical practice.

Individual dietary amino acid restrictions induce distinct metabolic and chromatin states

Dietary protein and essential amino acid (EAA) restriction promote favorable metabolic reprogramming, although the extent to which shared or EAA-specific mechanisms facilitate diet-associated phenotypes remains unclear. Here, we compared the physiological and molecular effects of dietary methionine, leucine, or isoleucine depletion (Met-D, Leu-D, and Ile-D) in C57BL/6J mice. Each diet elicited responses not phenocopied by mTORC1 inhibition, including reduced fat mass and hepatic amino acid catabolism. Ile-D yielded additional distinct responses, highlighted by histone H2A/H4 hypoacetylation and maintained hepatic acetyl-CoA levels despite downregulated FA β-oxidation. Multi-Omics Factor Analysis of 14,139 data points objectively affirmed Ile-D phenotypes are distinct from Met-D or Leu-D and identified several metabolic and chromatin features as primary discriminators. Metabolic and epigenetic responses to Ile-D were recapitulated in vitro , suggesting underlying mechanisms represent fundamental cellular properties. Together, these results demonstrate EAAs can stimulate unique phenotypes and highlight distinct molecular mechanisms by which EAAs may inform metabolic health.

MedKG: enabling drug discovery through a unified biomedical knowledge graph

Biomedical knowledge graphs have emerged as powerful tools for drug discovery, but existing platforms often suffer from outdated information, limited accessibility, and insufficient integration of complex data. This study presents MedKG, a comprehensive and continuously updated knowledge graph designed to address these challenges in precision medicine and drug discovery. MedKG integrates data from 35 authoritative sources, encompassing 34 node types and 79 relationships. A Continuous Integration/Continuous Update pipeline ensures MedKG remains current, addressing a critical limitation of static knowledge bases. The integration of molecular embeddings enhances semantic analysis capabilities, bridging the gap between chemical structures and biological entities. To demonstrate MedKG's utility, a novel hybrid Relational Graph Convolutional Network for disease-drug link prediction, MedLINK was developed and used in case studies on clinical trial data for disease drug link prediction. Furthermore, a web-based application with user-friendly APIs and visualization tools was built, making MedKG accessible to both technical and non-technical users, which is freely available at http://pitools.niper.ac.in/medkg/.

Genome-wide SNPs reveal novel genetic relationships among Atlantic cod (Gadus morhua) from the south coast of Newfoundland, Canada (subdivision 3Ps), Northern cod stock complex, and Gulf of St Lawrence

The south coast of Newfoundland, Canada (Northwest Atlantic Fisheries Organization (NAFO) Subdivision 3Ps) is known to be a mixing zone for Atlantic cod (Gadus morhua). Tagging and genetic studies have shown cod from the Northern and Southern Gulf of St. Lawrence (NAFO Divisions 3Pn, 4RST), Southern Grand Banks (3NO), and the Northern cod stock complex (2J3KL) frequent the waters of 3Ps at various times throughout the year, but the extent of genetic mixing is unknown. However, 3Ps has not been the central focus of previous large-scale genomic analyses of population structure, a knowledge gap that we address using single nucleotide polymorphisms. Using 38,111 neutral markers from reduced representation next-generation sequencing data, we determined the provenance of 3Ps cod relative to the Northern stock complex, Gulf of St. Lawrence, Bay of Fundy, and Gulf of Maine. We present evidence for genetic similarity between 3Ps and the Northern stock complex, particularly NAFO Division 3L. Additionally, genetic clustering analyses suggest 3Ps to be a mixed stock, containing individuals from the Northern stock complex and Gulf of St. Lawrence. Genetic clustering also suggests that there are two subtle subclusters of Northern stock complex and 3Ps cod, indicating there may be subtle population structure within the Northern stock complex and surrounding zones. This new information on population structure gives insight into connectivity and may be useful in future management for rebuilding cod populations.

Altered Cellular Pathways in the Blood of Patients With Guillain-Barre Syndrome

BACKGROUND AND AIMS

Guillain-Barré syndrome (GBS) is a rare disorder, with a global incidence ranging from 1 to 2 individuals per 100,000 people/year. Infections and vaccines have been implicated as causes triggering GBS. The aim of the study was to identify host genes involved in the pathogenesis of GBS when Zika (ZIKV) and Chikungunya viruses (CHIKV) were introduced in Brazil.

METHODS

A case-control study of GBS was performed when ZIKV and CHIKV were introduced into a naïve population. GBS was studied during both acute and postacute phases. RNA sequencing was conducted using whole blood.

RESULTS

GBS typically manifested a week after rash and fever; acute inflammatory demyelinating polyradiculoneuropathy was more frequent. None of the GBS cases had a poor outcome. Serological assays for ZIKV and CHIKV revealed high titers of immunoglobulin G for both viruses in 9 out of 11 subjects. Metatranscriptomic analyses unveiled an increased abundance of reads attributed to Pseudomonas tolaasii and Toxoplasma gondii in the acute phase. Analysis of differentially expressed host genes during the acute phase revealed altered expression of genes associated with axogenesis, synapse assembly, and presynapse organization. Moreover, genes upregulated during acute GBS were primarily related to inflammation and the inflammasome pathways, including AIM2, NLR family genes and LRR-protein genes, and IL-10.

INTERPRETATION

These findings suggest that inflammasome activation via AIM2 could play a role in tissue damage during GBS. Further investigation into the general activation of innate inflammatory responses is warranted to elucidate their potential contribution to the pathology of GBS.

TMEM106B deficiency leads to alterations in lipid metabolism and obesity in the TDP-43Q331K knock-in mouse model

The TMEM106B gene, encoding a lysosomal membrane protein, is closely linked with brain aging and neurodegeneration. TMEM106B has been identified as a risk factor for several neurodegenerative diseases characterized by aggregation of the RNA-binding protein TDP-43, including frontotemporal lobar degeneration (FTLD) and limbic-predominant age-related TDP-43 encephalopathy (LATE). To investigate the role of TMEM106B in TDP-43 proteinopathy, we ablated TMEM106B in the TDP-43Q331K knock-in mouse line, which expresses an ALS-linked TDP-43 mutation at endogenous levels. We found that TMEM106B deficiency leads to glial activation, Purkinje cell loss, and behavioral deficits in TDP-43Q331K mice without inducing typical TDP-43 pathology. Interestingly, ablation of TMEM106B results in significant body weight gain, increased fat deposition, and hepatic triglyceride (TG) accumulation in TDP-43Q331K mice. In addition, lipidomic and transcriptome analysis shows a profound alteration in lipid metabolism in the liver of TDP-43Q331KTmem106b-/- mice. Our studies reveal a novel function of TMEM106B and TDP-43 in lipid metabolism and provide new insights into their roles in neurodegeneration.

Genomic correlation, shared loci, and causal association between obesity, periodontitis and tooth loss

Observational studies have reported an association of obesity with periodontitis and tooth loss, yet findings remain inconsistent. We aim to investigate the genetic link underlying obesity-related traits (BMI [body mass index], WHR [waist-to-hip ratio], WHRadjBMI and childhood BMI), periodontitis and tooth loss. Leveraging summary statistics from large-scale genome-wide association studies, we comprehensively investigated the pair-wise genetic correlation using linkage disequilibrium score regression (LDSC) and SUPERGNOVA, identified shared loci using cross-phenotype association analysis (CPASSOC), and estimated causal association using Mendelian randomization. We identified a significant genetic correlation of obesity with tooth loss, but not with periodontitis. Partitioning the genome into LD-independent regions revealed 10 significantly shared local signals across six regions. Genome-wide cross-trait analysis uncovered 14 shared loci, four of which were colocalized: rs2064044 (PP4 = 0.94), rs6000329 (PP4 = 0.86), rs7134628 (PP4 = 0.86), and rs1286769 (PP4 = 0.90). Notably, rs1286769, identified via CPASSOC and validated through colocalization analysis, is located near RARβ, a gene associated with both BMI and denture use. Mendelian randomization revealed a nominally-significant causal association of obesity with periodontitis (P = 0.045) but a robust causal association with tooth loss represented by number of teeth (BMI: beta = [Formula: see text]0.20, 95%CI = [Formula: see text]0.26 to [Formula: see text]0.14, P = 5.27 × 10-11; WHR: beta = [Formula: see text]0.16, 95%CI = [Formula: see text]0.24 to [Formula: see text]0.08, P = 3.71 × 10-5). Results of CAUSE were consistent with main findings. From a genetic perspective, our work highlights an intrinsic link between obesity, periodontitis and tooth loss, which may add new lines of evidence and provide insights for clinical and public oral health applications.

Imaging flow cytometry-based cellular screening elucidates pathophysiology in individuals with Variants of Uncertain Significance

BACKGROUND

Deciphering variants of uncertain significance (VUS) represents a major diagnostic challenge, partially due to the lack of easy-to-use and versatile cellular readouts that aid the interpretation of pathogenicity and pathophysiology. To address this challenge, we propose a high-throughput screening of cellular functionality through an imaging flow cytometry (IFC)-based platform.

METHODS

Six assays to evaluate autophagic-, lysosomal-, Golgi- health, mitochondrial function, ER stress, and NF-κβ activity were developed in fibroblasts. Assay sensitivity was verified with compounds (N = 5) and positive control patients (N = 6). Eight healthy controls and 20 individuals with VUS were screened.

RESULTS

All molecular compounds and positive controls showed significant changes on their cognate assays, confirming assay sensitivity. Simultaneous screening of positive control patients on all six assays revealed distinct phenotypic profiles. In addition, individuals with VUS(es) in well-known disease genes showed distinct - but similar-phenotypic profiles compared to patients with pathogenic variants in the same gene.. For all individuals with VUSes in Genes of Uncertain Significance (GUS), we found one or more of six assays were significantly altered. Broadening the screening to an untargeted approach led to the identification of two clusters that allowed for the recognition of altered cell cycle dynamics and DNA damage repair defects. Experimental follow-up of the 'DNA damage repair defect cluster' led to the discovery of highly specific defects in top2cc release from double-strand DNA breaks in one of these individuals, harboring a VUS in the RAD54L2 gene.

CONCLUSIONS

Our high-throughput IFC-based platform simplifies the process of identifying VUS pathogenicity through six assays and allows for the recognition of useful pathophysiological markers that structure follow-up experiments, thereby representing a novel valuable tool for precise functional diagnostics in genomics.

The impaired response of nasal epithelial cells to microplastic stimulation in asthma and COPD

Microplastic particles from the air are inhaled and accumulate in the lungs, potentially causing immunological reactions and airway tissue injury. This study aimed to evaluate the biological effects of polyamide fibres on nasal epithelium co-cultivated with macrophages in control, asthma, and COPD groups. Nasal epithelial cells alone or in co-culture with monocyte-derived macrophages were exposed to polyamide fibres for 48 h. We identified 8 differentially expressed genes (DEGs) in controls, 309 DEGs in asthma (including ANKRD36C, BCL2L15, FCGBP, and IL-19), and 22 DEGs in COPD (e.g., BCL2L15, IL-19, CAPN14, PGBD5, PTPRH), particularly in epithelial/moMφ co-cultures. Microplastic exposure induced inflammatory cytokine secretion only for IL-8 production in controls (epithelial/ moMφs co-culture) and asthmatic (monoculture) epithelial cells in contrast to PM2.5, which was a strong inflammatory inducer. Gene Ontology analysis revealed that microplastic exposure affected sterol and cholesterol biosynthesis, secondary alcohol metabolism, and acetyl-CoA metabolism in asthma, and cell motility, chemokine signaling, leukocyte migration, and chemotaxis in COPD. Microplastic stimulation altered the response of airway epithelial cells in obstructive lung diseases differently than in controls, linking to Th2 inflammation, stress response modulation, and carcinogenesis. Asthmatic and COPD epithelial cells are more susceptible to damage from microplastic fibre exposure.

A Novel Homozygous Variant in CPLANE1 Gene in a Patient with Developmental Deficits

Background

Oral-facial-digital syndrome (OFDS) type 6 is a rare subtype of Joubert syndrome characterized by orofacial anomalies and polydactyly with neurological features of Joubert syndrome. This rare syndrome is divided into thirteen subtypes, all of which demonstrate autosomal recessive inheritance, except for OFDS type 1 which demonstrates X-linked dominant inheritance.

Case Presentation

A 19-year-old man with mild developmental delay was brought to a rural community clinic, as he had become irritable and angry, in the recent past. There was no history of prior medical conditions. In view of orofacial anomalies, and developmental deficits, a genetic analysis was requested. Karyotype analysis revealed a normal male karyotype (46,XY) in all 30 metaphase spreads analyzed. No numerical or structural chromosomal abnormalities were observed. Clinical exome sequencing and chromosomal microarray detected a variant of uncertain significance in exon 5 of CPLANE1 gene c.365T>G (p.Val122Gly) leading to substitution of Glycine for Valine. This was confirmed by Sanger sequencing. Parents were heterozygous, and the unaffected sibling was homozygous for the wild-type allele. This variant has not been reported earlier in the mutation databases or gnomAD. Runs of homozygosity (ROH) analysis showed a 3.2 Mb ROH around the CPLANE1 gene in the proband, which was absent in both parents and the unaffected sibling.

Conclusion

We find a novel homozygous mutation in the CPLANE1 gene in a patient of non-consanguineous parentage with atypical orofacial features. This suggests that potentially deleterious, rare variants may occur in the heterozygous state in the population. Hence, sequencing of population samples might help understand the genetic epidemiology of rare syndromes.

The role of SELE gene polymorphism in ST-elevation myocardial infarction

Ischemic heart disease (IHD) is an important medical and social problem. ST-elevation myocardial infarction (STEMI) is the most severe form of IHD, affecting all layers of the heart muscle. One of the diagnostic criteria for endothelial dysfunction in myocardial infarction is the level of sE-selectin, a cell adhesion molecule that recruits neutrophils and induces neutrophil inflammation. The aim of this study is to investigate intronic polymorphisms rs5353, rs3917412 and rs1534904 of the E-selectin coding gene SELE in patients with STEMI. We have analyzed a group of patients with STEMI (n = 74) and a population sample of Tomsk (n = 136) as the control group. The frequencies of the rs5353 genotypes in the SELE gene have shown statistically significant differences between patients and the control sample (p = 0.004). The CC genotype is a predisposing factor to STEMI (OR = 6.93, CI:95 % (1.84-26.04), χ2 = 8.69, p = 0.002). The analyzed markers were not studied previously in cardiovascular diseases (CVDs) and were rarely involved in association studies at all; there is no information on these SNPs in the leading databases. At the same time, all three variants, according to the RegulomeDB classification, belong to the functional class 1f, and are highly likely to have regulatory potential relative not only to the SELE gene, but also to other genes in the nearby region. The analysis of the functional significance of the studied markers has shown the presence of a region more extensive than one gene, which is co-regulated by the studied nucleotide substitutions. The association of rs5353 with STEMI identified in this study once again confirms the involvement of the SELE gene in the pathogenesis of CVDs. It is possible that this entire region of the genome may be involved indirectly in the pathogenesis of CVD through the systems of inflammation, immune response and DNA repair.

Extracellular Vesicles Derived From Lipopolysaccharide-Challenged Gingival Fibroblast Reveal Distinct miRNA Expression Patterns Associated With Reduced Cancer Survival

OBJECTIVES

Periodontitis is a prevalent inflammatory disease with established systemic implications. Extracellular vesicles (EVs) have emerged as key mediators of intercellular communication, potentially linking periodontitis to systemic diseases. However, the molecular cargo of EVs from inflamed periodontal cells remains poorly characterized. This study investigates the EV cargo of human gingival fibroblasts (hGF-hTERT) following lipopolysaccharide (LPS) stimulation and explores their potential role in cancer progression.

MATERIALS AND METHODS

EVs were isolated from LPS-treated and untreated fibroblasts via ultracentrifugation. Dynamic light scattering and scanning electron microscopy characterized EV size and morphology. RNA sequencing identified differentially expressed miRNAs, validated by qPCR. Functional pathway enrichment and in-silico analyses using The Cancer Genome Atlas (TCGA) were performed to assess EV-associated miRNA impact on tumorigenesis.

RESULTS

EV size and concentration remained unchanged after LPS stimulation. However, LPS-derived EVs exhibited a 2.6-fold increase in miRNA content, with three significantly upregulated miRNAs: miR-146a-5p, miR-486-5p, and miR-451a. Functional enrichment analysis revealed their involvement in inflammation, immune modulation, and cancer pathways. In vitro, LPS-derived EVs significantly enhanced prostate cancer (LnCap) cell proliferation. TCGA analysis linked the upregulated miRNAs to poor cancer prognosis.

CONCLUSIONS

LPS stimulation alters the miRNA cargo of gingival fibroblast-derived EVs, enhancing pathways associated with inflammation and cancer progression. These findings suggest a mechanistic role for periodontal EVs in systemic disease pathogenesis, warranting further investigation into their diagnostic and therapeutic potential.

Co-occurrence of Parkinson's disease and Retinitis Pigmentosa: A genetic and in silico analysis

INTRODUCTION

Parkinson's disease (PD) is primarily driven by the protein Alpha Synuclein (A-Syn) accumulation. Synphilin-1 protein, encoded by the SNCAIP gene, which co-localizes with A-Syn is a known risk factor for PD. Retinitis pigmentosa (RP), is a cluster of retinal degenerative disorders, and Cyclic Nucleotide Gated channel subunit Alpha 1 (CNGA1) is one of the initial genes associated with RP. Patients with PD can have various kinds of visual dysfunction as a non-motor manifestation, but to date, CNGA1 mutation and RP as a PD associated visual symptom has not been reported. We report a mutation in the SNCAIP gene in a PD patient, not reported earlier, and its co-occurrence with RP-associated CNGA1 gene mutation.

METHOD

Whole exome sequencing (WES) of the patient DNA sample and in-silico protein-protein interaction (PPI) analysis performed to find out proteins interacting with SNCAIP relevant concerning reported mutation of SNCAIP and further, CNGA1 interaction with SNCAIP.

RESULT

We are reporting, a missense mutation (p.Thr64Ser) at the SNCAIP gene, co-occurring with a missense variation (p.Gly509Arg) in the CNGA1 gene. In silico PPI analysis suggests SIAH1 as an important protein affected by SNCAIP mutation. LGALS4 and SNCA (gene encoding A-Syn) are common interactors between SNCAIP and CNGA1.

CONCLUSION

The current study has determined the co-occurrence of RP and PD, whole exome sequencing ascertains the mutations in SNCAIP and CNGA1 genes, which could be the cause of PD and RP co-occurrence.

Herpesviruses mimic zygotic genome activation to promote viral replication

Zygotic genome activation (ZGA) is crucial for maternal to zygotic transition at the 2-8-cell stage in order to overcome silencing of genes and enable transcription from the zygotic genome. In humans, ZGA is induced by DUX4, a pioneer factor that drives expression of downstream germline-specific genes and retroelements. Here we show that herpesviruses from all subfamilies, papillomaviruses and Merkel cell polyomavirus actively induce DUX4 expression to promote viral transcription and replication. Analysis of single-cell sequencing data sets from patients shows that viral DUX4 activation is of relevance in vivo. Herpes-simplex virus 1 (HSV-1) immediate early proteins directly induce expression of DUX4 and its target genes, which mimics zygotic genome activation. Upon HSV-1 infection, DUX4 directly binds to the viral genome and promotes viral transcription. DUX4 is functionally required for infection, since genetic depletion by CRISPR/Cas9 as well as degradation of DUX4 by nanobody constructs abrogates HSV-1 replication. Our results show that DNA viruses including herpesviruses mimic an embryonic-like transcriptional program that prevents epigenetic silencing of the viral genome and facilitates herpesviral gene expression.

Human REXO4 is Required for Cell Cycle Progression

Human REXO4 is a poorly characterized exonuclease that is overexpressed in human cancers. To better understand the function of REXO4 and its relationship to cellular proliferation, we have undertaken multidisciplinary approaches to characterize its cell cycle phase-dependent subcellular localization and the cis determinants required for this localization, its importance to cell cycle progression and cell viability, its protein-protein association network, and its activity. We show that the localization of REXO4 to the nucleolus in interphase depends on an N-terminal nucleolar localization sequence and that its localization to the perichromosomal layer of mitotic chromosomes is dependent on Ki67. Depletion of REXO4 led to a G1/S cell cycle arrest, and reduced cell viability. REXO4 associated with ribosome components and other proteins involved in rRNA metabolism. We propose a model where REXO4 is important for proper rRNA processing, which is required for ribosome biogenesis, cell cycle progression, and proliferation.

Tau mediates the reshaping of the transcriptional landscape toward intermediate Alzheimer's disease stages

Introduction

Recent research revealed that Tau plays critical roles in various neuronal functions. We previously demonstrated that destabilization and nuclear delocalization of Tau alter the expression of glutamatergic genes, mediating early neuronal damage.

Methods

In this study, we discovered that changes in Tau availability are linked to global alterations in gene expression that affect multiple neuronal pathways. Comparison with the human temporal region showed that the Tau-dependent modulation of gene expression closely resembles the intermediate stages of Alzheimer's disease (AD) that precede the definitive pathological condition.

Results

Furthermore, we identified the chromatin remodeling pathway as being significantly affected by Tau in both our cellular model and AD brains, with reductions in heterochromatin markers. Our findings indicate that Tau is able to globally affect the neuronal transcriptome and that its subcellular unbalance changes gene expression in the intermediate stages of AD development. In addition, we found that the chromatin architecture is affected by Tau during the progression of AD.

Discussion

These results provide new insights into the molecular mechanisms underlying early stages of AD development and highlight the central role of Tau and the contribution of nuclear Tau in this process.

From Gene to Whole Cell: Modeling, Visualization, and Analysis

Proteogenomics combines proteomic and genetic data to gain new insights in molecular mechanisms. Here, we extend this approach toward structural biology from a tool perspective. The chapter starts with tools which can be used to explore genetic information and then enrich those with proteomic data. Based on the corresponding identifiers, three-dimensional structures of proteins are identified and used to embed them in their molecular environment, here the surrounding membrane. This membrane is then mapped onto the surface of an interpretative three-dimensional cell model. Then, the embedded protein and the cell environment are associated with a metabolic pathway, again based on the identifiers provided by biomedical databases. Accompanying the different chapters, related work is discussed which can alternatively be used. Finally, an outlook toward immersive analytics is given.

Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform

Proteogenomics is a growing "multi-omics" research area that combines mass spectrometry-based proteomics and high-throughput nucleotide sequencing technologies. Proteogenomics has helped in genomic annotation for organisms whose complete genome sequences became available by using high-throughput DNA sequencing technologies. Apart from genome annotation, this multi-omics approach has also helped researchers confirm expression of variant proteins belonging to unique proteoforms that could have resulted from single-nucleotide polymorphism (SNP), insertion and deletions (Indels), splice isoforms, or other genome or transcriptome variations.A proteogenomic study depends on a multistep informatics workflow, requiring different software at each step. These integrated steps include creating an appropriate protein sequence database, matching spectral data against these sequences, and finally identifying peptide sequences corresponding to novel proteoforms followed by variant classification and functional analysis. The disparate software required for a proteogenomic study is difficult for most researchers to access and use, especially those lacking computational expertise. Furthermore, using them disjointedly can be error-prone as it requires setting up individual parameters for each software. Consequently, reproducibility suffers. Managing output files from each software is an additional challenge. One solution for these challenges in proteogenomics is the open-source Web-based computational platform Galaxy. Its capability to create and manage workflows comprised of disparate software while recording and saving all important parameters promotes both usability and reproducibility. Here, we describe a workflow that can perform proteogenomic analysis on a Galaxy-based platform. This Galaxy workflow facilitates matching of spectral data with a customized protein sequence database, identifying novel protein variants, assessing quality of results, and classifying variants along with visualization against the genome.

Antigen presentation for central tolerance induction

The extent of central T cell tolerance is determined by the diversity of self-antigens that developing thymocytes 'see' on thymic antigen-presenting cells (APCs). Here, focusing on insights from the past decade, we review the functional adaptations of medullary thymic epithelial cells, thymic dendritic cells and thymic B cells for the purpose of tolerance induction. Their distinct cellular characteristics range from unconventional phenomena, such as promiscuous gene expression or mimicry of peripheral cell types, to strategic positioning in distinct microenvironments and divergent propensities to preferentially access endogenous or exogenous antigen pools. We also discuss how 'tonic' inflammatory signals in the thymic microenvironment may extend the intrathymically visible 'self' to include autoantigens that are otherwise associated with highly immunogenic peripheral environments.

Gone with the Species: From Gene Loss to Gene Extinction

BACKGROUND

Vertebrae protein-coding genes exhibit remarkable diversity and are organized into many gene families. These gene families have emerged through various gene duplication events, the most prominent being the two rounds of whole-genome duplication (WGD). The current research project analyzed a unique class of genes called "singletons". Notably, we introduce the concept of "super-singletons": genes that stand as the last representatives of their ancestral families and the sole representatives of their genetic makeup with no ortholog in any other species.

METHODS

We used the Ensembl/Biomart pipeline to identify duplicated and unduplicated protein-coding genes in different vertebrate species and found orthologs of human genes.

RESULTS

We showed the frequency of duplicated genes and singletons, demonstrating that singletons are more vulnerable to evolutionary loss than duplicated genes. Additionally, we found that contractions in vertebrate gene families are more prevalent than expansion.

CONCLUSION

Our study provides insight into the evolution of gene families and presents a novel scenario where the extinction of species would lead to the extinction of a gene, ultimately shifting the narrative from the impact of genetics on species extinction to the extinction of genes.

WITHDRAWN: Progranulin inhibits phospholipase sPLA2-IIA to control neuroinflammation

The authors have withdrawn this manuscript because more work is needed to fully define the role of sPLA2-IIA. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

HROB Is Implicated in DNA Replication

DNA replication represents a series of precisely regulated events performed by a complex protein machinery that guarantees accurate duplication of the genetic information. Since DNA replication is permanently faced by a variety of exogenous and endogenous stressors, DNA damage response, repair and replication must be closely coordinated to maintain genomic integrity. HROB has been identified recently as a binding partner and activator of the Mcm8/9 helicase involved in DNA interstrand crosslink (ICL) repair. We identified HROB independently as a nuclear protein whose expression is co-regulated with various DNA replication factors. Accordingly, the HROB protein level showed a maximum in S phase and a downregulation in quiescence. Structural prediction and homology searches revealed that HROB is a largely intrinsically disordered protein bearing a helix-rich region and a canonical oligonucleotide/oligosaccharide-binding-fold motif that originated early in eukaryotic evolution. Employing a flow cytometry Förster resonance energy transfer (FRET) assay, we detected associations between HROB and proteins of the DNA replication machinery. Moreover, ectopic expression of HROB protein led to an almost complete shutdown of DNA replication. The available data imply a function for HROB during DNA replication across barriers such as ICLs.

Late-life protein or isoleucine restriction impacts physiological and molecular signatures of aging

Restricting the intake of protein or the branched-chain amino acid isoleucine promotes healthspan and extends lifespan in young or adult mice. However, their effects when initiated in aged animals are unknown. Here we investigate the consequences of consuming a diet with 67% reduction of all amino acids (low AA) or of isoleucine alone (low Ile), in male and female C57BL/6J.Nia mice starting at 20 months of age. Both dietary regimens effectively promote overall metabolic health without reducing calorie intake. Both low AA and low Ile diets improve aspects of frailty and slow multiple molecular indicators of aging rate; however, the low Ile diet reduces grip strength in both sexes and has mixed, sexually dimorphic effects on the heart. These results demonstrate that low AA and low Ile diets can promote aspects of healthy aging in aged mice and suggest that similar interventions might promote healthy aging in older adults.

LPL Gene Mutation in Type 1 Familial Triglyceridemia Presenting as Recurrent Pancreatitis and Complicated by COVID19

A 7-year-old girl with recurrent episodes of pancreatitis with risk factor of poorly controlled hyperglyceridemia presented with an acute episode of pancreatitis. She was managed conservatively and underwent whole exome sequencing which showed a likely pathogenic LPL gene mutation. Incidentally, she was diagnosed with COVID-19 on screening, which we hypothesize to have triggered the recent episode. On further examination, she was found to have bilateral cataracts. Her hypercholesterolemia was effectively managed with dietary therapy, high dose omega 3, and gemfibrozil. Our case report sensitizes the clinician to use a modern diagnostic tool such as whole exome sequencing in children with recurrent pancreatitis where hypertriglyceridemia is a known risk factor. This child is the first case of LPL mutation reported in India.

Molecular Identification and Characterization of Hevein Antimicrobial Peptide Genes in Two-Row and Six-Row Cultivars of Barley (Hordeum vulgare L.)

Heveins are one of the most important groups of plant antimicrobial peptides. So far, various roles in plant growth and development and in response to biotic and abiotic stresses have reported for heveins. The present study aimed to identify and characterize the hevein genes in two-row and six-row cultivars of barley. In total, thirteen hevein genes were identified in the genome of two-row and six-row cultivars of barley. The identified heveins were identical in two-row and six-row cultivars of barley and showed a high similarity with heveins from other plant species. The hevein coding sequences produced open reading frames (ORFs) ranged from 342 to 1002 bp. Most of the identified hevein genes were intronless, and the others had only one intron. The hevein ORFs produced proteins ranged from 113 to 333 amino acids. Search for conserved functional domains showed CBD and LYZ domains in barley heveins. All barley heveins comprised extracellular signal peptides ranged from 19 to 35 amino acids. The phylogenetic analysis divided barley heveins into two groups. The promoter analysis showed regulatory elements with different frequencies between two-row and six-row cultivars. These cis-acting elements included elements related to growth and development, hormone response, and environmental stresses. The expression analysis showed high expression level of heveins in root and reproductive organs of both two-row and six-row cultivars. The expression analysis also showed that barley heveins is induced by both biotic and abiotic stresses. The results of antimicrobial activity prediction showed the highest antimicrobial activity in CBD domain of barley heveins. The findings of the current study can improve our knowledge about the role of hevein genes in plant and can be used for future studies.

Phenotypic Heterogeneity in ORAI-1-Associated Congenital Myopathy

Introduction  ORAI-1 is a plasma membrane calcium release-activated calcium channel that plays a crucial role in the excitation-contraction of skeletal muscles. Loss-of-function mutations of ORAI-1 cause severe combined immunodeficiency, nonprogressive muscle hypotonia, and anhidrotic ectodermal dysplasia. Autosomal dominant gain-of-function mutation causes Stormorken's syndrome, which includes tubular aggregate myopathy along with bleeding diathesis. Methods  This is a description of a genetically confirmed case of ORAI-1-associated myopathy with clinical, histopathological, and imaging characteristics and a detailed literature review. Results  We report an 18-year-old woman who presented with 2-and-a-half year history of slowly progressive proximal lower limb weakness and ophthalmoparesis. Her serum creatine kinase levels were normal. Magnetic resonance imaging of the muscle showed predominant fatty infiltration of the glutei and quadriceps femoris. Histopathological analysis of muscle biopsy was suggestive of congenital fiber-type disproportion (CFTD). Clinical exome sequencing showed novel homozygous nonsense pathogenic variant NC_000012.12 (NM_032790.3): c.205G > T (p.Glu69Ter) in ORAI-1 gene. Conclusion  This report expands the phenotypic spectrum of ORAI-1-related myopathy to include congenital myopathy-CFTD with ophthalmoparesis, a novel manifestation.

Underestimated risk of secondary complications in pathogenic and glucose-elevating GCK variant carriers with type 2 diabetes

BACKGROUND

Natural HbA1c levels in GCK Maturity-onset diabetes of the young (GCK-MODY) patients often sit above the diagnostic threshold for type 2 diabetes (T2D). Treatments to lower HbA1c levels show reduced effectiveness in these individuals, yet in case studies to date, GCK-MODY patients often evade secondary T2D complications. Given these deviations, genetic screening of GCK may be clinically useful, but population studies are needed to more broadly understand T2D-related complications in GCK variant carriers.

METHODS

To identify GCK variant carriers at the population level, we used both ACMG/AMP variant interpretation for GCK-MODY pathogenicity and a state-of-the-art variant interpretation strategy based on functional and statistical evidence to predict glucose elevations. Presence of pathogenic and glucose-elevating GCK variants was assessed in two cohorts (n~535,000). We identified 442 individuals with GCK variants predicted to increase glucose (~1/1200), with 150 (34%) of these individuals harboring variants reaching a pathogenic interpretation.

RESULTS

In a retrospective analysis, we show that in addition to elevated HbA1c, pathogenic variant carriers are 10x as likely, and all other glucose-elevating GCK variant carriers are 3x as likely, to receive a T2D diagnosis compared to non-GCK carriers. Surprisingly, carriers of pathogenic and glucose-elevating GCK variants with T2D develop T2D-related complications at rates more than double that of individuals without T2D, comparable to non-GCK individuals with T2D.

CONCLUSIONS

This population-level assessment shows secondary complications in individuals with pathogenic and glucose-elevating GCK variants and T2D and suggests that genotyping for these variants should be considered in a precision medicine approach for T2D treatment and prevention.

Understanding perspectives and research trends in Down syndrome neuropathogenesis: A bibliometric analysis

Down syndrome (DS), characterised by compromised brain development and intellectual challenges, often manifests Alzheimer's disease (AD) -like symptoms. Utilising the Web of Science Core Collection (WOSCC) database from January 1, 2000, to July 31, 2023, we conducted a comprehensive bibliometric analysis using VOSviewer, CiteSpace, and the R package "bibliometrix." Analyses included co-authorship, co-citation, co-occurrence, cooperative network, reference, and keyword burst citation. Analysing 5,082 papers, the U.S. demonstrated prominence with the highest number of research organisations and citations. Keyword analysis revealed promising research areas, including "Alzheimer's disease," "development," "inflammation," and "neurogenesis". This 22-year survey of the brain with trisomy 21 research unveils key trends, contributors, and focal areas in DS neuropathogenesis. Notably, Alzheimer 's-related genes and proteins play a pervasive role in DS neuropathological processes across patients' lifespans. The study contributes foundational knowledge for advancing research and care in the DS neuropathogenesis domain.

Oviductal extracellular matrix hydrogels enhance in vitro culture of rabbit embryos and reduce deficiencies during assisted reproductive technologies

In vitro embryo culture often falls short of mimicking the physiological dynamism occurring in the reproductive tract, prompting developmental plasticity in mammalian embryos with consequential genotypic and phenotypic deviations. Recent research highlights the potential of biological derivatives in in vitro culture to mitigate these effects, being the extracellular matrix (ECM) one of the most important components in retaining structural and biological signals derived from the native source tissue. Current bioengineering techniques could provide ECM-based biomaterials mimicking the native environment and offering optimal embryonic development. Rabbit oviducts (n = 24) were decellularized and solubilized to create tissue-specific ECM (OviECM) hydrogels. Following physicochemical characterization, these hydrogels were applied as coatings for the in vitro culture of two-cell embryos over 48 h, along with embryos cultured under In vitro control conditions (n = 218/group), which were subsequently transferred to recipient females. A subset of embryos was recovered on day 6 for transcriptomic analysis (n = 75-80/group), while the remaining embryos were used to assess implantation and birth rates. Rabbit weights were monitored over 20 weeks post-delivery, with blood tests conducted at weeks 8 and 20. Bayesian inference methods were used for statistical analysis. Differences were considered relevant if P ≥ 0.8 (80%). No differences in embryo development and morphology were detected between the OviECM coating and In vitro control conditions. However, embryos cultured on these coatings exhibited upregulation of pathways involved in antigen presentation and immune system activation, as well as, increased cellular response to external stimulus and intracellular protein transport. The implantation and live birth rates were significantly higher in the coating group than in the In vitro control group (30.8% vs. 26.1% and 21.2% vs. 18.1%, respectively). During the first 20 weeks of life, the animals from the coating group showed higher weights than the In vitro control group P0 > 0.8. The animals of both experimental groups showed normal blood parameters. Implementation of OviECM coatings allows for improving in vitro conditions and decreases postnatal phenotypic deviations after assisted reproductive technology (ART). This study could initiate a new embryo culture techniques era to guarantee that ART is utilized in the most efficient and safest possible practice.

Molecular and Functional Assessment of TSC1 and TSC2 in Individuals with Tuberous Sclerosis Complex

Tuberous sclerosis complex (TSC) is an autosomal dominant neurodevelopmental disorder and multisystem disease caused by pathogenic DNA alterations in the TSC1 and TSC2 tumor suppressor genes. A molecular genetic diagnosis of TSC confirms the clinical diagnosis, facilitating the implementation of appropriate care and surveillance. TSC1 and TSC2 encode the core components of the TSC1/2 complex (TSC1/2), a negative regulator of the mechanistic target of rapamycin (MTOR) complex 1 (TORC1). Functional analysis of the effects of TSC1 and TSC2 variants on TORC1 activity can help establish variant pathogenicity. We searched for pathogenic alterations to TSC1 and TSC2 in DNA isolated from 116 individuals with a definite clinical diagnosis of TSC. Missense variants and in-frame deletions were functionally assessed. Pathogenic DNA alterations were identified in 106 cases (91%); 18 (17%) in TSC1 and 88 (83%) in TSC2. Of these, 35 were novel. Disruption of TSC1/2 activity was demonstrated for seven TSC2 variants. Molecular diagnostics confirms the clinical diagnosis of TSC in a large proportion of cases. Functional assessment can help establish variant pathogenicity and is a useful adjunct to DNA analysis.

An unexpected role of neurite outgrowth inhibitor A as regulator of tooth enamel formation

Neurite outgrowth inhibitor A (Nogo-A) is a major player in neural development and regeneration and the target of clinical trials aiming at promoting the regeneration of the central nervous system upon traumatic and ischemic injury. In this work, we investigated the functions of Nogo-A during tooth development to determine its role in dental physiology and pathology. Using immunohistochemistry and in situ hybridization techniques, we showed that Nogo-A is highly expressed in the developing mouse teeth and, most specifically, in the ameloblasts that are responsible for the formation of enamel. Using both Nogo-A knockout and K14-Cre;Nogo-A fl/fl transgenic mice, we showed that Nogo-A deletion in the dental epithelium leads to the formation of defective enamel. This phenotype is associated with overexpression of a set of specific genes involved in ameloblast differentiation and enamel matrix production, such as amelogenin, ameloblastin and enamelin. By characterising the interactome of Nogo-A in the dental epithelium of wild-type and mutant animals, we found that Nogo-A directly interacts with molecules important for regulating gene expression, and its deletion disturbs their cellular localisation. Furthermore, we demonstrated that inhibition of the intracellular, but not cell-surface, Nogo-A is responsible for gene expression modulation in ameloblasts. Taken together, these results reveal an unexpected function for Nogo-A in tooth enamel formation by regulating gene expression and cytodifferentiation events.

Isolated Lateralized Overgrowth - Phenotypic Spectrum and Molecular Alterations

OBJECTIVES

To evaluate the molecular aberrations at 11p15.5 locus in thirty-two patients with isolated lateralized overgrowth (ILO).

METHODS

Among selected 32 cases of ILO, methylation-sensitive multiplex ligation-dependent probe amplification (MS-MLPA) was performed initially followed by short tandem repeats (STR) marker analysis to confirm uniparental disomy (UPD). In those patients with normal MLPA reports, cyclin dependent kinase inhibitor 1C (CDKN1C) gene and whole exome sequencing was performed.

RESULTS

Molecular analysis by MS-MLPA showed methylation aberrations in 28% (9/32) of patients. Gain of methylation at IC1 imprinting center (H4, H7) and loss of methylation at IC2 (H6, H9) was observed in 2 patients each. Uniparental disomy was observed in 9% cases. Except one, all patients with methylation aberration had more than one limb hypertrophy. Two patients (H22/H29) also had loss of methylation at IC1. Though this molecular alteration is specifically associated with Silver Russel syndrome (SRS), but the affected children did not completely fulfill the diagnostic criteria for SRS. In a recent study, a discrepancy was reported between the diagnosis of Beckwith-Wiedemann syndrome (BWS)/SRS and the molecular findings in the patients. Many times, it is very difficult to differentiate between hemi hypertrophy/hemi hypotrophy. Patients, in whom no aberrations were detected on MS-MLPA, whole exome sequencing (WES) was performed and no pathogenic variant was identified.

CONCLUSIONS

Thus, ILO may be considered as a mild presentation on the extreme edge of BWS spectrum with methylation aberration and UPD in one third of cases which has implications in follow up.

Molecular specializations underlying phenotypic differences in inner ear hair cells of zebrafish and mice

Introduction

Hair cells (HCs) are the sensory receptors of the auditory and vestibular systems in the inner ears of vertebrates that selectively transduce mechanical stimuli into electrical activity. Although all HCs have the hallmark stereocilia bundle for mechanotransduction, HCs in non-mammals and mammals differ in their molecular specialization in the apical, basolateral, and synaptic membranes. HCs of non-mammals, such as zebrafish (zHCs), are electrically tuned to specific frequencies and possess an active process in the stereocilia bundle to amplify sound signals. Mammalian HCs, in contrast, are not electrically tuned and achieve amplification by somatic motility of outer HCs (OHCs).

Methods

To understand the genetic mechanisms underlying differences between adult zebrafish and mammalian HCs, we compared their RNA-seq-characterized transcriptomes, focusing on protein-coding orthologous genes related to HC specialization.

Results

There was considerable shared expression of gene orthologs among the HCs, including those genes associated with mechanotransduction, ion transport/channels, and synaptic signaling. However, there were some notable differences in expression among zHCs, OHCs, and inner HCs (IHCs), which likely underlie the distinctive physiological properties of each cell type. For example, OHCs highly express Slc26a5 which encodes the motor protein prestin that contributes to OHC electromotility. However, zHCs have only weak expression of slc26a5, and subsequently showed no voltage-dependent electromotility when measured. Notably, the zHCs expressed more paralogous genes including those associated with HC-specific functions and transcriptional activity, though it is unknown whether they have functions similar to their mammalian counterparts. There was overlap in the expressed genes associated with a known hearing phenotype.

Discussion

Our analyses unveil substantial differences in gene expression patterns that may explain phenotypic specialization of zebrafish and mouse HCs. This dataset also includes several protein-coding genes to further the functional characterization of HCs and study of HC evolution from non-mammals to mammals.

The pan-cancer landscape presented ITGA7 as a prognostic determinant, tumor suppressor, and oncogene in multiple tumor types

Integrin α7 (ITGA7) is an extracellular matrix-binding protein. Integrins are the main type of cell adhesive molecules in mammals, playing a role in many biological pathways. Although various studies have shown correlations between ITGA7 and various types of cancer, a comprehensive study at a pan-cancer level has not yet been conducted. In this study, we investigated the function of ITGA7 in distinct tumor types using the multi-omics relevant information, then two CeRNA regulatory network was drawn to identify the ITGA7 hub regulatory RNAs. The results indicated that the expression of ITGA7 varies in different tumors. Overexpression of ITGA7 was correlated with a worse OS in BLCA, LGG, and UVM, and the downregulation of ITGA7 was related to a worse OS in PAAD. In addition, BLCA, and UVM showed poor PFS in association with ITGA7 overexpression, and PAAD, SARC, and THCA indicated poor PFS in correlation with ITGA7 under expression. Further analyses of ITGA7 gene alteration data showed that ITGA7 amplifications may have an impact on Kidney Chromophobe prognosis. In 20 types of tumors, ITGA7 expression was linked to cancer-associated fibroblast infiltration. ITGA7 expression was linked to cancer-associated fibroblast infiltration. ITGA7-Related Gene Enrichment Analysis indicated that ITGA7 expression-correlated and functional binding genes were enriched in homotypic cell-cell adhesion, focal adhesion, and ECM-receptor interaction. This pan-cancer study found that abnormal expression of ITGA7 was correlated with poor prognosis and metastasis in different types of tumors. Thus, the ITGA7 gene may prove to be a promising biomarker for the prognosis and complication prevention of different cancers.

Impact of vaccination with the Anaplasma phagocytophilum MSP4 chimeric antigen on gene expression in the rabbit host

There are currently no vaccines available to prevent and control of Anaplasma phagocytophilum, an intracellular bacterial pathogen transmitted by ticks that occurs in many regions of the world and causes disease in a wide range of domestic and wild hosts, including humans. Vaccines induce long-lasting immunity and could prevent or reduce transmission of this pathogen. Understanding how vaccines induce a protective response can be difficult due to the complexity of the immune system, which operates at many levels throughout the organism. New perspectives in vaccinology, based on systems biology approaches, integrate many scientific disciplines to fully understand the biological responses to vaccination, where a transcriptomic approach could reveal relevant information of the host immune system, allowing profiling for rational design of vaccine formulations, administration, and potential protection. In the present study we report the gene expression profiles by RNA-seq followed by functional analysis using whole blood samples from rabbits immunized with a recombinant chimeric protein containing peptides from the MSP4 protein of A. phagocytophilum, which showed satisfactory results in terms of potential protection. Transcriptomic analysis revealed differential expression of 720 genes, with 346 genes upregulated and 374 genes downregulated. Overrepresentation of biological and metabolic pathways correlated with immune response, protein signaling, cytoskeleton organization and protein synthesis were found. These changes in gene expression could provide a complete and unique picture of the biological response to the epitope candidate vaccine against A. phagocytophilum in the host.

Unlocking the Door for Precision Medicine in Rare Conditions: Structural and Functional Consequences of Missense ACVR1 Variants

Rare diseases and conditions have thus far received relatively less attention in the field of precision/personalized medicine than common chronic diseases. There is a dire need for orphan drug discovery and therapeutics in ways that are informed by the precision/personalized medicine scholarship. Moreover, people with rare conditions, when considered collectively across diseases worldwide, impact many communities. In this overarching context, Activin A Receptor Type 1 (ACVR1) is a transmembrane kinase from the transforming growth factor-β superfamily and plays a critical role in modulating the bone morphogenetic protein signaling. Missense variants of the ACVR1 gene result in modifications in structure and function and, by extension, abnormalities and have been predominantly linked with two rare conditions: fibrodysplasia ossificans progressiva and diffuse intrinsic pontine glioma. We report here an extensive bioinformatic analyses assessing the pool of 50,951 variants and forecast seven highly destabilizing mutations (R206H, G356D, R258S, G328W, G328E, R375P, and R202I) that can significantly alter the structure and function of the native protein. Protein-protein interaction and ConSurf analyses revealed the crucial interactions and localization of highly deleterious mutations in highly conserved domains that may impact the binding and functioning of the protein. cBioPortal, CanSAR Black, and existing literature affirmed the association of these destabilizing mutations with posterior fossa ependymoma, uterine corpus carcinoma, and pediatric brain cancer. The current findings suggest these deleterious nonsynonymous single nucleotide polymorphisms as potential candidates for future functional annotations and validations associated with rare conditions, further aiding the development of precision medicine in rare diseases.

Zebrafish reveal new roles for Fam83f in hatching and the DNA damage-mediated autophagic response

The FAM83 (Family with sequence similarity 83) family is highly conserved in vertebrates, but little is known of the functions of these proteins beyond their association with oncogenesis. Of the family, FAM83F is of particular interest because it is the only membrane-targeted FAM83 protein. When overexpressed, FAM83F activates the canonical Wnt signalling pathway and binds to and stabilizes p53; it therefore interacts with two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development, and here we report the generation of fam83f knock-out (KO) zebrafish, which we have used to study the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the hatching gland of developing zebrafish embryos, and that fam83f KO embryos hatch earlier than their wild-type (WT) counterparts, despite developing at a comparable rate. We also demonstrate that fam83f KO embryos are more sensitive to ionizing radiation than WT embryos-an unexpected finding, bearing in mind the previously reported ability of FAM83F to stabilize p53. Transcriptomic analysis shows that loss of fam83f leads to downregulation of phosphatidylinositol-3-phosphate (PI(3)P) binding proteins and impairment of cellular degradation pathways, particularly autophagy, a crucial component of the DNA damage response. Finally, we show that Fam83f protein is itself targeted to the lysosome when overexpressed in HEK293T cells, and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated suggest that Fam83f plays an important role in autophagic/lysosomal processes, resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo.

A Splice Site Variant in ADAMTS3 Is the Likely Causal Variant for Pulmonary Hypoplasia with Anasarca in Persian/Persian-Cross Sheep

Pulmonary hypoplasia with anasarca, or hydrops fetalis, is characterized by stillbirth, diffuse oedema, and generalized lymph node hypoplasia. The enlarged fetus frequently causes dystocia. The disease has been reported in cattle and sheep as an inherited condition with a recessive mode of inheritance. This is the first report of the disease in Persian/Persian-cross sheep in Australia. Affected fetuses were reported from three flocks, and a total of eleven affected, eleven obligate carrier, and 188 related Persian/Persian-cross animals were available for analysis, as well as unrelated control animals. SNP genotyping revealed a region of homozygosity in affected animals on ovine chromosome six, which contained the functional candidate gene ADAMTS3. Whole genome sequencing of two affected fetuses and one obligate carrier ewe revealed a single nucleotide deletion, ENSOARG00000013204:g.87124344delC, located 3 bp downstream from a donor splice site region in the ADAMTS3 gene. Sanger sequencing of cDNA containing this variant further revealed that it is likely to introduce an early splice site in exon 14, resulting in a loss of 6 amino acids at the junction of exon 14 and intron 14/15. A genotyping assay was developed, and the ENSOARG00000013204:g.87124344delC segregated with disease in 209 animals, allowing for effective identification of carrier animals.