Regulatory noncoding and predicted pathogenic coding variants of ccr5 predispose to severe covid-19

Genome-wide association studies (GWAS) found locus 3p21.31 associated with severe COVID-19. CCR5 resides at the same locus and, given its known biological role in other infection diseases, we investigated if common noncoding and rare coding variants, affecting CCR5, can predispose to severe COVID-19. We combined single nucleotide polymorphisms (SNPs) that met the suggestive significance level (P ≤ 1 × 10−5 ) at the 3p21.31 locus in public GWAS datasets (6406 COVID-19 hospitalized patients and 902,088 controls) with gene expression data from 208 lung tissues, Hi-C, and Chip-seq data. Through whole exome sequencing (WES), we explored rare coding variants in 147 severe COVID-19 patients. We identified three SNPs (rs9845542, rs12639314, and rs35951367) associated with severe COVID-19 whose risk alleles correlated with low CCR5 expression in lung tissues. The rs35951367 resided in a CTFC binding site that interacts with CCR5 gene in lung tissues and was confirmed to be associated with severe COVID-19 in two independent datasets. We also identified a rare coding variant (rs34418657) associated with the risk of developing severe COVID-19. Our results suggest a biological role of CCR5 in the progression of COVID-19 as common and rare genetic variants can increase the risk of developing severe COVID-19 by affecting the functions of CCR5

G protein-coupled receptor (GPCR) pharmacogenomics

The field of pharmacogenetics, the investigation of the influence of one or more sequence variants on drug response phenotypes, is a special case of pharmacogenomics, a discipline that takes a genome-wide approach. Massively parallel, next generation sequencing (NGS), has allowed pharmacogenetics to be subsumed by pharmacogenomics with respect to the identification of variants associated with responders and non-responders, optimal drug response, and adverse drug reactions. A plethora of rare and common naturally-occurring GPCR variants must be considered in the context of signals from across the genome. Many fundamentals of pharmacogenetics were established for G protein-coupled receptor (GPCR) genes because they are primary targets for a large number of therapeutic drugs. Functional studies, demonstrating likely-pathogenic and pathogenic GPCR variants, have been integral to establishing models used for in silico analysis. Variants in GPCR genes include both coding and non-coding single nucleotide variants and insertion or deletions (indels) that affect cell surface expression (trafficking, dimerization, and desensitization/downregulation), ligand binding and G protein coupling, and variants that result in alternate splicing encoding isoforms/variable expression. As the breadth of data on the GPCR genome increases, we may expect an increase in the use of drug labels that note variants that significantly impact the clinical use of GPCR-targeting agents. We discuss the implications of GPCR pharmacogenomic data derived from the genomes available from individuals who have been well-phenotyped for receptor structure and function and receptor-ligand interactions, and the potential benefits to patients of optimized drug selection. Examples discussed include the renin-angiotensin system in SARS-CoV-2 (COVID-19) infection, the probable role of chemokine receptors in the cytokine storm, and potential protease activating receptor (PAR) interventions. Resources dedicated to GPCRs, including publicly available computational tools, are also discussed.</p

Int J Med Sci

Hypertension, diabetes mellitus, and coronary artery disease are common comorbidities and dangerous factors for infection and serious COVID-19. Polymorphisms in genes associated with comorbidities may help observe susceptibility and disease severity variation. However, specific genetic factors and the extent to which they can explain variation in susceptibility of severity are unclear. Therefore, we evaluated candidate genes associated with COVID-19 and hypertension, diabetes mellitus, and coronary artery disease. In particular, we performed searches against OMIM, NCBI, and other databases, protein-protein interaction network construction, and GO and KEGG pathway enrichment analyses. Results showed that the associated overlapping genes were |, |, |, |, |, |, |, |, |, |, and |. GO and KEGG analyses yielded 302 GO terms (q < 0.05) and 29 signaling pathways (q < 0.05), respectively, mainly including coronavirus disease-COVID-19 and cytokine-cytokine receptor interaction. | and | were central in the PPI, with 8 and 5 connections, respectively. In this study, we identified 11 genes associated with both COVID-19 and three comorbidities that may contribute to infection and disease severity. The key genes IL6 and AGT are involved in regulating immune response, cytokine activity, and viral infection. Therefore, RAAS inhibitors, AGT antisense nucleotides, cytokine inhibitors, vitamin D, fenofibrate, and vaccines regulating non-immune and immune factors could be potential strategies to prevent and cure COVID-19. The study provides a basis for further investigation of genes and pathways with predictive value for the risk of infection and prognosis and could help guide drug and vaccine development to improve treatment efficacy and the development of personalised treatments, especially for COVID-19 individuals with common comorbidities.35165525PMC87958081102

Functional genomics in the regulation of the immune response

Genetics contribute substantially to the ability of the immune system to respond appropriately to a challenge. Consequently, many infectious and inflammatory diseases have a heritable component. As genome-wide association studies provide increasing data linking genetic variants to disease, we can leverage this information to gain insights into disease biology if we can elucidate the mechanisms underlying an observed association. Data-driven bioinformatic approaches, in vitro mechanistic studies and whole-organism approaches to study integrated pathophysiological systems provide complementary information to help establish causal links between specific variants and their effects on a target gene, and between that gene and disease pathogenesis. Cells of the mononuclear phagocyte system play key roles in regulation of innate and adaptive immune responses, either via secreted mediators or through direct cell-to-cell contacts. To advance understanding of how these regulatory processes, and genetic variations therein, shape the course of disease, I have combined experimental and bioinformatic approaches to explore novel genetic associations between genes for macrophage surface receptors and human disease. Specifically, functional follow-up of an association between adhesion G-protein-coupled receptor CD97 and severe influenza showed, using a mouse model, that deficiency of this receptor reduces the efficiency of the CD8+ T-lymphocyte response, a process critical to clearance of infected cells. Secondly, I addressed the question of how to identify causal variants in a disease-associated linkage disequilibrium block, for an association between macrophage regulatory receptor SIRPα and schizophrenia. To achieve this, I developed novel methodology for targeted locus screening using CRISPR/Cas9 mutagenesis, and identified a number of plausible causal regulatory variants that could affect expression of this receptor. Combining variant-level information with gene-level studies of disease pathophysiology can provide valuable insights into genetic causation of immune dys-regulation leading to disease, which may be harnessed for improved personalised disease risk prediction, or to identify therapeutically targetable pathways

In vitro expanded human CD4+CD25+ regulatory T cells suppress effector T cell proliferation.

Regulatory T cells (Tregs) have been shown to be critical in the balance between autoimmunity and tolerance and have been implicated in several human autoimmune diseases. However, the small number of Tregs in peripheral blood limits their therapeutic potential. Therefore, we developed a protocol that would allow for the expansion of Tregs while retaining their suppressive activity. We isolated CD4+CD25 hi cells from human peripheral blood and expanded them in vitro in the presence of anti-CD3 and anti-CD28 magnetic Xcyte Dynabeads and high concentrations of exogenous Interleukin (IL)-2. Tregs were effectively expanded up to 200-fold while maintaining surface expression of CD25 and other markers of Tregs: CD62L, HLA-DR, CCR6, and FOXP3. The expanded Tregs suppressed proliferation and cytokine secretion of responder PBMCs in co-cultures stimulated with anti-CD3 or alloantigen. Treg expansion is a critical first step before consideration of Tregs as a therapeutic intervention in patients with autoimmune or graft-versus-host disease

Program and abstracts

We are pleased that the program in 2022 will be more interesting than ever and it will include the following topics: Mathematical Modeling in Cancer Therapy, Gene Therapy, Archaeological Genetics, New perspectives in Human Forensic Molecular Biology, Genomics in Medicine, Pharmacogenomics and Drug Development, Stem Cells in Medicine, Regenerative Medicine, Ribosomes in Medicine, Epigenomics, Crime Scene Investigation, Forensic Genetics, and Mass Catastrophes Managements. This year, the third "Nobel Spirit" will provide a forum to the three Nobel laureates to stimulate public discussion on the role of science in solving global health issues, acute regional problems such as brain drain, demographic decline, as well as cultural and social change. In addition, we are organizing a very stimulating Session on Bioanthropology and global health in the times of crisis, as well as Joint Event ISABS and Ministry of the Interior - Crime Scene Investigation Training Course: Mystery on the ship —Investigation of the water-related crime scene

A stew of mixed ingredients: Observational omics in the post-GWAS era

The past 20 years have seen extensive profiling of the DNA. Collectively, scientists all across the world have identified many places in the DNA, known as loci, that impact human traits such as disease state or immune function. However, interpreting the results from these studies, known as genome wide association studies (GWAS), has been challenging. This thesis studies several approaches for interpreting GWAS results, with a specific focus on our immune system given its important role in preventing and causing disease. This is done through the use of so called ‘omics’ technologies, that can study the role of thousands of genes, proteins and genetic variants at the same time. By doing this, maps can be constructed of which genes and proteins interact to impact human traits. The ultimate goal of this research is to provide a better understanding of the cascade between the DNA and human traits. The hope is that building a specific understanding of how the variation in the DNA leads to the development of human traits, such as disease, will ultimately aid the development of drugs for these diseases

Frameshift mutations at the C-terminus of HIST1H1E result in a specific DNA hypomethylation signature

BACKGROUND: We previously associated HIST1H1E mutations causing Rahman syndrome with a specific genome-wide methylation pattern. RESULTS: Methylome analysis from peripheral blood samples of six affected subjects led us to identify a specific hypomethylated profile. This "episignature" was enriched for genes involved in neuronal system development and function. A computational classifier yielded full sensitivity and specificity in detecting subjects with Rahman syndrome. Applying this model to a cohort of undiagnosed probands allowed us to reach diagnosis in one subject. CONCLUSIONS: We demonstrate an epigenetic signature in subjects with Rahman syndrome that can be used to reach molecular diagnosis

Characterization of the cargo of circulating extracellular vesicles in patients affected with idiopathic inflammatory myopathies and evaluation of clinical correlates in a cross-sectional comparative analysis from a monocentric cohort.

openBackground Idiopathic inflammatory myopathies (IIM) are heterogeneous autoimmune disorders that comprise different clinical entities, characterized by different features. Although several myositis-specific and myositis-associated antibodies have been characterized, the molecular mechanisms underlying these conditions require further exploration. The research field on extracellular vescicles (EVs) is rapidly evolving, highlighting their role in intercellular communication. EVs convoy a cargo of proteins and nucleic acids, such as microRNA (miRNAs), that mediate immune-response regulation in autoimmune diseases. miRNAs regulate gene-expression post-transcriptionally and are involved in multiple molecular pathways of human disease. Evidence of EVs and miRNAs in IIM is still limited and undefined. Aim of the study This study aims to quantify the circulating EVs and characterize their cargo, with a specific focus on miRNAs content to propose novel biomarkers of IIM. Materials and methods A monocentric study was conducted including adult IIM patients (≥18 years old) followed at the Rheumatology Unit of Padua University Hospital, and age- and sex- matched healthy controls (HD). EVs were isolated from platelet-free plasma through size exclusion chromatography followed by ultrafiltration. EVs were quantified by nanoparticle tracking analysis (NTA) and. EV-miRNA cargo was investigated through Next-Generation Sequencing (NGS). Statistical analysis was performed with parametric Student-T test and one-way Anova (Bonferroni correction). Results Sixty-four consecutive IIM patients and sixty-five HDs were included in the study. NTA measurements of EVs concentration showed a significantly higher mean concentration of circulating EVs in IIM patients than in HD (p=0.0073). Across IIM subsets, patients affected with cancer associated myositis (CAM) displayed the highest levels of circulating EVs compared to no CAM patients (p=0.0060) and to HD (p=0.0004). Patients with circulating myositis-associated autoantibodies displayed significantly higher EV levels than HD (p=0.0363). Patients in clinical remission displayed higher levels of circulating EVs compared to those with active disease (p=0.0087). EVs levels were significantly reduced in IIM patients treated with rituximab (RTX) than in patients receiving other treatments (p<0.0001). NGS analysis detected EV-miRNAs with different expression profiles between IIM (n=47) and HDs (n=49): miR-223-3p (p=0.019), miR-15a-5p (p=0.0189), miR-451a (p=0.0074), miR-486-5p (p=0.0052), miR-32-5p (p=0.0146), and miR-222-3p (p=0.0282) were up-regulated in IIM, while miR-141-3p (p=0.0313), miR-142-3p (p=0.0244), and let-7a-5p (p=0.0003) were down-regulated in IIM patients vs. HDs. Other EV-miRNAs expression varied across IIM subsets: CAM patients displayed up-regulated expression of miR-143-3p compared to non-CAM patients (p=0.0085), while miR-148a-3p (p=0.0171) and miR-335-5p (p=0.0171) were up-regulated in dermatomyositis vs. polymyositis/ inclusion body myositis/anti-synthetase syndrome patients. Patients characterized by active disease displayed an up-regulated expression of miR-222-3p (p=0.002) and miR-151-3p (p=0.0233) and down-regulated expression of miR-363-3p (p=0.0001), miR-374a-5p (p=0.0258), miR-144-3p (p=0.0170), miR-181a-5p (p=0.0037) compared to those in clinical remission. Moreover, IIM patients receiving only glucocorticoids (GC) reported up-regulated expression of miR-4433b-5p (p=0.0439), miR-92a-3p (p=0.0111), let-7f-5p (p=0.0304), and down-regulated expression of miR-27a-3p (p=0.0486) compared to patients receiving GC in combination with immunosuppressants (IS). Conclusions Our results showed significantly increased concentration of circulating EVs in IIM patients. That is confirmed within specific disease phenotypes and pharmacological treatments. EV miRNAs exhibited a differential expression profile between IIM and HD, and significant differences were outlined among IIM subsets.Background Idiopathic inflammatory myopathies (IIM) are heterogeneous autoimmune disorders that comprise different clinical entities, characterized by different features. Although several myositis-specific and myositis-associated antibodies have been characterized, the molecular mechanisms underlying these conditions require further exploration. The research field on extracellular vescicles (EVs) is rapidly evolving, highlighting their role in intercellular communication. EVs convoy a cargo of proteins and nucleic acids, such as microRNA (miRNAs), that mediate immune-response regulation in autoimmune diseases. miRNAs regulate gene-expression post-transcriptionally and are involved in multiple molecular pathways of human disease. Evidence of EVs and miRNAs in IIM is still limited and undefined. Aim of the study This study aims to quantify the circulating EVs and characterize their cargo, with a specific focus on miRNAs content to propose novel biomarkers of IIM. Materials and methods A monocentric study was conducted including adult IIM patients (≥18 years old) followed at the Rheumatology Unit of Padua University Hospital, and age- and sex- matched healthy controls (HD). EVs were isolated from platelet-free plasma through size exclusion chromatography followed by ultrafiltration. EVs were quantified by nanoparticle tracking analysis (NTA) and. EV-miRNA cargo was investigated through Next-Generation Sequencing (NGS). Statistical analysis was performed with parametric Student-T test and one-way Anova (Bonferroni correction). Results Sixty-four consecutive IIM patients and sixty-five HDs were included in the study. NTA measurements of EVs concentration showed a significantly higher mean concentration of circulating EVs in IIM patients than in HD (p=0.0073). Across IIM subsets, patients affected with cancer associated myositis (CAM) displayed the highest levels of circulating EVs compared to no CAM patients (p=0.0060) and to HD (p=0.0004). Patients with circulating myositis-associated autoantibodies displayed significantly higher EV levels than HD (p=0.0363). Patients in clinical remission displayed higher levels of circulating EVs compared to those with active disease (p=0.0087). EVs levels were significantly reduced in IIM patients treated with rituximab (RTX) than in patients receiving other treatments (p<0.0001). NGS analysis detected EV-miRNAs with different expression profiles between IIM (n=47) and HDs (n=49): miR-223-3p (p=0.019), miR-15a-5p (p=0.0189), miR-451a (p=0.0074), miR-486-5p (p=0.0052), miR-32-5p (p=0.0146), and miR-222-3p (p=0.0282) were up-regulated in IIM, while miR-141-3p (p=0.0313), miR-142-3p (p=0.0244), and let-7a-5p (p=0.0003) were down-regulated in IIM patients vs. HDs. Other EV-miRNAs expression varied across IIM subsets: CAM patients displayed up-regulated expression of miR-143-3p compared to non-CAM patients (p=0.0085), while miR-148a-3p (p=0.0171) and miR-335-5p (p=0.0171) were up-regulated in dermatomyositis vs. polymyositis/ inclusion body myositis/anti-synthetase syndrome patients. Patients characterized by active disease displayed an up-regulated expression of miR-222-3p (p=0.002) and miR-151-3p (p=0.0233) and down-regulated expression of miR-363-3p (p=0.0001), miR-374a-5p (p=0.0258), miR-144-3p (p=0.0170), miR-181a-5p (p=0.0037) compared to those in clinical remission. Moreover, IIM patients receiving only glucocorticoids (GC) reported up-regulated expression of miR-4433b-5p (p=0.0439), miR-92a-3p (p=0.0111), let-7f-5p (p=0.0304), and down-regulated expression of miR-27a-3p (p=0.0486) compared to patients receiving GC in combination with immunosuppressants (IS). Conclusions Our results showed significantly increased concentration of circulating EVs in IIM patients. That is confirmed within specific disease phenotypes and pharmacological treatments. EV miRNAs exhibited a differential expression profile between IIM and HD, and significant differences were outlined among IIM subsets