Variation in the Untranslated Genome and Susceptibility to Infections

Investigating the role of killer cell immunoglobulin-like receptors and human leukocyte antigen genetic variants in hepatitis C virus infection

The genetic diversity of killer cell immunoglobulin-like receptors (KIRs) and human leukocyte antigen (HLA) genes influences the host's immune response to viral pathogens. This study aims to explore the impact of five single nucleotide polymorphisms (SNPs) in KIR3DL2 and HLA-A genes on hepatitis C virus (HCV) infection. A total of 2251 individuals were included in the case-control study. SNPs including KIR3DL2 rs11672983, rs3745902, rs1654644, and HLA-A rs3869062, rs12202296 were genotyped. By controlling various confounding factors using a modified logistic regression model, as well as incorporating stratified analysis, joint effects analysis, and multidimensional bioinformatics analysis, we analyzed the relationship between SNPs and HCV infection. The logistic regression analysis showed a correlation between KIR3DL2 rs11672983 AA, KIR3DL2 rs3745902 TT, and increased HCV susceptibility (p < 0.01). Stratified analysis indicated that KIR3DL2 rs1654644 and HLA-A rs3869062 also heightened HCV susceptibility in certain subgroups. A linear trend of rising HCV infection rates was observed when combining KIR3DL2 rs11672983 AA and KIR3DL2 rs3745902 TT (ptrend = 0.007). Bioinformatics analysis suggested these SNPs' regulatory potential and their role in altering messenger RNA secondary structure, implying their functional relevance in HCV susceptibility. Our findings indicate that KIR3DL2 rs11672983 AA and KIR3DL2 rs3745902 TT are significantly associated with increased susceptibility to HCV infection.

The 5' untranslated region variant rs3811050 C/T of the interleukin-38 encoding gene is associated with susceptibility to rheumatoid arthritis in Iraqi women

BACKGROUND

Interleukin (IL)-38, the latest member of the IL-1 cytokine family, is proposed to have a pathogenic role in rheumatoid arthritis (RA). It is encoded by the IL1F10 gene, which harbors single nucleotide polymorphisms (SNPs) that may predict the risk of autoimmune diseases. Among them are 5' untranslated region (UTR) SNPs, which play a key role in post-transcriptional control, but have not been studied in Iraqi RA patients.

METHODS

Two novel IL1F10 5'UTR SNPs (rs3811050 C/T and rs3811051 T/G) were explored in RA and control women (n = 120 and 110, respectively). SNPs were genotyped using TaqMan assay. An ELISA kit was used to measure serum IL-38 concentrations.

RESULTS

A reduced risk of RA was associated with rs3811050 T allele and CT genotype (corrected probability [pc] = 0.01 and < 0.001, respectively), while there was no significant association with rs3811051. Haplotype analysis demonstrated that C-T haplotype was associated with a 1.65-fold greater risk of RA, whereas a reduced risk was linked to T-G haplotype. IL-38 concentrations were higher in patients than in controls (p < 0.001). In addition, IL-38 showed acceptable performance in distinguishing between RA and control women (p < 0.001). When IL-38 concentrations were stratified according to SNP genotypes, no significant differences were found.

CONCLUSIONS

The rs3811050 variant was more likely to affect RA susceptibility in Iraqi women, and the T allele may play a role in reducing disease risk. IL-38 concentrations were elevated in RA patients, but were not affected by the rs3811050 and rs3811051 genotypes.

Processing genome-wide association studies within a repository of heterogeneous genomic datasets

BACKGROUND

Genome Wide Association Studies (GWAS) are based on the observation of genome-wide sets of genetic variants - typically single-nucleotide polymorphisms (SNPs) - in different individuals that are associated with phenotypic traits. Research efforts have so far been directed to improving GWAS techniques rather than on making the results of GWAS interoperable with other genomic signals; this is currently hindered by the use of heterogeneous formats and uncoordinated experiment descriptions.

RESULTS

To practically facilitate integrative use, we propose to include GWAS datasets within the META-BASE repository, exploiting an integration pipeline previously studied for other genomic datasets that includes several heterogeneous data types in the same format, queryable from the same systems. We represent GWAS SNPs and metadata by means of the Genomic Data Model and include metadata within a relational representation by extending the Genomic Conceptual Model with a dedicated view. To further reduce the gap with the descriptions of other signals in the repository of genomic datasets, we perform a semantic annotation of phenotypic traits. Our pipeline is demonstrated using two important data sources, initially organized according to different data models: the NHGRI-EBI GWAS Catalog and FinnGen (University of Helsinki). The integration effort finally allows us to use these datasets within multi-sample processing queries that respond to important biological questions. These are then made usable for multi-omic studies together with, e.g., somatic and reference mutation data, genomic annotations, epigenetic signals.

CONCLUSIONS

As a result of the our work on GWAS datasets, we enable 1) their interoperable use with several other homogenized and processed genomic datasets in the context of the META-BASE repository; 2) their big data processing by means of the GenoMetric Query Language and associated system. Future large-scale tertiary data analysis may extensively benefit from the addition of GWAS results to inform several different downstream analysis workflows.

Multi-omics research in sarcopenia: Current progress and future prospects

Sarcopenia is a systemic disease with progressive and generalized skeletal muscle dysfunction defined by age-related low muscle mass, high content of muscle slow fibers, and low muscle function. Muscle phenotypes and sarcopenia risk are heritable; however, the genetic architecture and molecular mechanisms underlying sarcopenia remain largely unclear. In recent years, significant progress has been made in determining susceptibility loci using genome-wide association studies. In addition, recent advances in omics techniques, including genomics, epigenomics, transcriptomics, proteomics, and metabolomics, offer new opportunities to identify novel targets to help us understand the pathophysiology of sarcopenia. However, each individual technology cannot capture the entire view of the biological complexity of this disorder, while integrative multi-omics analyses may be able to reveal new insights. Here, we review the latest findings of multi-omics studies for sarcopenia and provide an in-depth summary of our current understanding of sarcopenia pathogenesis. Leveraging multi-omics data could give us a holistic understanding of sarcopenia etiology that may lead to new clinical applications. This review offers guidance and recommendations for fundamental research, innovative perspectives, and preventative and therapeutic interventions for sarcopenia.

Competitive endogenous RNA network and pathway-based analysis of LncRNA single-nucleotide polymorphism in myasthenia gravis

Myasthenia gravis (MG) is a complex neurological autoimmune disease with a pathogenetic mechanism that has yet to be elucidated. Emerging evidence has revealed that genes, non-coding RNAs and genetic variants play significant roles in the pathogenesis of MG. However, the molecular mechanisms of single nucleotide polymorphisms (SNPs) located on lncRNAs could disturb lncRNA-mediated ceRNA regulatory functions still unclear in MG. In this study, we collated 276 experimentally confirmed MG risk genes and 192 MG risk miRNAs. We then constructed a lncRNA-mediated ceRNA network for MG based on multi-step computational strategies. Next, we systematically integrated risk pathways and identified candidate SNPs in lncRNAs for MG based on data acquired from public databases. In addition, we constructed a pathway-based lncRNA-SNP mediated network (LSPN) that contained 128 lncRNAs targeting 8 MG risk pathways. By analyzing network, we propose a latent mechanism for how the “lncRNA-SNP-mRNA-pathway” axis affects the pathogenesis of MG. Moreover, 25 lncRNAs and 51 SNPs on lncRNAs were extracted from the “lncRNA-SNP-mRNA-pathway” axis. Finally, functional analyses demonstrated lncRNA-SNPs mediated ceRNA regulation pairs associated with MG participated in the MAPK signaling pathway. In summary, we constructed MG-specific lncRNA-SNPs mediated ceRNA regulatory networks based on pathway in the present study, which was helpful to elucidate the roles of lncRNA-SNPs in the pathogenesis of MG and provide novel insights into mechanism of lncRNA-SNPs as potential genetic risk biomarkers of MG.

The role of the X chromosome in infectious diseases

Many infectious diseases in humans present with a sex bias. This bias arises from a combination of environmental factors, hormones and genetics. In this study, we review the contribution of the X chromosome to the genetic factor associated with infectious diseases. First, we give an overview of the X-linked genes that have been described in the context of infectious diseases and group them in four main pathways that seem to be dysregulated in infectious diseases: nuclear factor kappa-B, interleukin 2 and interferon γ cascade, toll-like receptors and programmed death ligand 1. Then, we review the infectious disease associations in existing genome-wide association studies (GWAS) from the GWAS Catalog and the Pan-UK Biobank, describing the main associations and their possible implications for the disease. Finally, we highlight the importance of including the X chromosome in GWAS analysis and the importance of sex-specific analysis.

Impact of rare and common genetic variation in the interleukin-1 pathway on human cytokine responses

Background

The interleukin (IL)-1 pathway is primarily associated with innate immunological defense and plays a major role in the induction and regulation of inflammation. Both common and rare genetic variation in this pathway underlies various inflammation-mediated diseases, but the role of rare variants relative to common variants in immune response variability in healthy individuals remains unclear.

Methods

We performed molecular inversion probe sequencing on 48 IL-1 pathway-related genes in 463 healthy individuals from the Human Functional Genomics Project. We functionally grouped common and rare variants, over gene, subpathway, and inflammatory levels and performed the Sequence Kernel Association Test to test for association with in vitro stimulation-induced cytokine responses; specifically, IL-1β and IL-6 cytokine measurements upon stimulations that represent an array of microbial infections: lipopolysaccharide (LPS), phytohaemagglutinin (PHA), Candida albicans (C. albicans), and Staphylococcus aureus (S. aureus).

Results

We identified a burden of NCF4 rare variants with PHA-induced IL-6 cytokine and showed that the respective carriers are in the 1% lowest IL-6 producers. Collapsing rare variants in IL-1 subpathway genes produces a bidirectional association with LPS-induced IL-1β cytokine levels, which is reflected by a significant Spearman correlation. On the inflammatory level, we identified a burden of rare variants in genes encoding for proteins with an anti-inflammatory function with S. aureus-induced IL-6 cytokine. In contrast to these rare variant findings which were based on different types of stimuli, common variant associations were exclusively identified with C. albicans-induced cytokine over various levels of grouping, from the gene, to subpathway, to inflammatory level.

Conclusions

In conclusion, this study shows that functionally grouping common and rare genetic variants enables the elucidation IL-1-mediated biological mechanisms, specifically, for IL-1β and IL-6 cytokine responses induced by various stimuli. The framework used in this study may allow for the analysis of rare and common genetic variants in a wider variety of (non-immune) complex phenotypes and therefore has the potential to contribute to better understanding of unresolved, complex traits and diseases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13073-021-00907-w.

Genetic variations associated with long noncoding RNAs

Genetic variations, including single nucleotide polymorphisms (SNPs) and structural variations, are widely distributed in the genome, including the long noncoding RNA (lncRNA) regions. The changes at locus might produce numerous effects in a variety of aspects. Multiple bioinformatics resources and tools were also developed for systematically dealing with genetic variations associated with lncRNAs. Moreover, correlation of the genetic variations in lncRNAs with immune disease, cancers, and other disease as well as development process were all included for discussion. In this essay, we summarized how and in what aspects these changes would affect lncRNA functions.

Disease-Causing Mutations and Rearrangements in Long Non-coding RNA Gene Loci

The classic understanding of molecular disease-mechanisms is largely based on protein-centric models. During the past decade however, genetic studies have identified numerous disease-loci in the human genome that do not encode proteins. Such non-coding DNA variants increasingly gain attention in diagnostics and personalized medicine. Of particular interest are long non-coding RNA (lncRNA) genes, which generate transcripts longer than 200 nucleotides that are not translated into proteins. While most of the estimated ~20,000 lncRNAs currently remain of unknown function, a growing number of genetic studies link lncRNA gene aberrations with the development of human diseases, including diabetes, AIDS, inflammatory bowel disease, or cancer. This suggests that the protein-centric view of human diseases does not capture the full complexity of molecular patho-mechanisms, with important consequences for molecular diagnostics and therapy. This review illustrates well-documented lncRNA gene aberrations causatively linked to human diseases and discusses potential lessons for molecular disease models, diagnostics, and therapy.

Loci Associated With Antibody Response in Feral Swine (Sus scrofa) Infected With Brucella suis

Feral swine (Sus scrofa) are a destructive invasive species widespread throughout the United States that disrupt ecosystems, damage crops, and carry pathogens of concern for the health of domestic stock and humans including Brucella suis-the causative organism for swine brucellosis. In domestic swine, brucellosis results in reproductive failure due to abortions and infertility. Contact with infected feral swine poses spillover risks to domestic pigs as well as humans, companion animals, wildlife, and other livestock. Genetic factors influence the outcome of infectious diseases; therefore, genome wide association studies (GWAS) of differential immune responses among feral swine can provide an understanding of disease dynamics and inform management to prevent the spillover of brucellosis from feral swine to domestic pigs. We sought to identify loci associated with differential antibody responses among feral swine naturally infected with B. suis using a case-control GWAS. Tissue, serum, and genotype data (68,516 bi-allelic single nucleotide polymorphisms) collected from 47 feral swine were analyzed in this study. The 47 feral swine were culture positive for Brucella spp. Of these 47, 16 were antibody positive (cases) whereas 31 were antibody negative (controls). Single-locus GWAS were performed using efficient mixed-model association eXpedited (EMMAX) methodology with three genetic models: additive, dominant, and recessive. Eight loci associated with seroconversion were identified on chromosome 4, 8, 9, 10, 12, and 18. Subsequent bioinformatic analyses revealed nine putative candidate genes related to immune function, most notably phagocytosis and induction of an inflammatory response. Identified loci and putative candidate genes may play an important role in host immune responses to B. suis infection, characterized by a detectable bacterial presence yet a differential antibody response. Given that antibody tests are used to evaluate brucellosis infection in domestic pigs and for disease surveillance in invasive feral swine, additional studies are needed to fully understand the genetic component of the response to B. suis infection and to more effectively translate estimates of Brucella spp. antibody prevalence among feral swine to disease control management action.

Unraveling the susceptibility of paracoccidioidomycosis: Insights towards the pathogen-immune interplay and immunogenetics

Paracoccidioidomycosis (PCM) is a life-threatening systemic mycosis caused by Paracoccidioides spp. This disease comprises three clinical forms: symptomatic acute and chronic forms (PCM disease) and PCM infection, a latent form without clinical symptoms. PCM disease differs markedly according to severity, clinical manifestations, and host immune response. Fungal virulence factors and adhesion molecules are determinants for entry, latency, immune escape and invasion, and dissemination in the host. Neutrophils and macrophages play a paramount role in first-line defense against the fungus through the recognition of antigens by pattern recognition receptors (PRRs), activating their microbicidal machinery. Furthermore, the clinical outcome of the PCM is strongly associated with the variability of cytokines and immunoglobulins produced by T and B cells. While the mechanisms that mediate susceptibility or resistance to infection are dictated by the immune system, some genetic factors may alter gene expression and its final products and, hence, modulate how the organism responds to infection and injury. This review outlines the main findings relative to this topic, addressing the complexity of the immune response triggered by Paracoccidioides spp. infection from preclinical investigations to studies in humans. Here, we focus on mechanisms of fungal pathogenesis, the patterns of innate and adaptive immunity, and the genetic and molecular basis related to immune response and susceptibility to the development of the PCM and its clinical forms. Immunogenetic features such as HLA system, cytokines/cytokines receptors genes and other immune-related genes, and miRNAs are likewise discussed. Finally, we point out the occurrence of PCM in patients with primary immunodeficiencies and call attention to the research gaps and challenges faced by the PCM field.

Regulatory genome variants in human susceptibility to infection

Genome studies have accelerated the discovery of common and rare genetic variants associated with susceptibility to infection and with disease severity. Genome-wide association studies identified many common genetic variants associated with modest risk for infection. Over 80% of these common variants map to the non-coding genome and are thought to modulate the regulatory networks. Exome sequencing has rapidly expanded the number of recognized primary immunodeficiencies through the identification of rare coding variants. In contrast, less than 29 primary immunodeficiencies have causative rare variation mapped outside protein-coding regions. In the future, whole genome sequencing will accelerate the identification of rare variants of substantial phenotypic impact that disrupt essential regulatory elements and the three-dimensional structure of chromatin.

The challenge of determining the impact of FUT3 tumor-associated polymorphism rs2306969 (-6951 C> T) in invasive breast cancer cells

FUT3 gene is responsible for encode an homonymous α1,3/4-fucosyltransferase involved in the synthesis of sialyl-Lewis antigens. FUT3-fucosylated glycoconjugates play key roles in pathways involved in tumor biology and metastasis, such as cellular ligation to E-selectins, TGF-β-induced epithelial-mesenchymal transition, NK cell-mediated tumor cytotoxicity and apoptosis. Tumor-associated FUT3 promoter polymorphism rs2306969 (-6951 C> T, position related to the gene's translation start site) has been linked to breast, ovarian and intestinal gastric cancer. Although non-coding polymorphisms accounts for the majority of variations founded in breast cancer, their functional roles are still poorly understood. This study aimed to investigate the impact of different alleles for this variation in FUT3 expression of invasive breast tumors. A luciferase reporter assay was performed using two breast tumor cell lines to evaluate respectively the impact of FUT3 rs2306969 (-6951 CC) and (-6951 TT) on protein expression. Gene and protein expressions were also measured in twenty-nine fresh biopsies of invasive breast tumors. Rs2306969 did not significantly influence FUT3 expression in both used systems. However, this study is defiant since the biological role of this polymorphism in breast cancer and other tumor types could be linked to cis/trans modulation of other genes, respond to different environmental stimuli or impact gene expression only in association with other variations. Rs2306969 did not modulate FUT3 expression in breast tumors under non-stimulated conditions. Nevertheless, our study contributes to the notably challenging task that is to understand how non-coding polymorphisms can drive the overall risk in cancer development.

Host and Graft Factors Impacting Infection Risk in Hematopoietic Cell Transplantation

Infection contributes significantly to morbidity and mortality in hematopoietic cell transplantation. A complex interplay of host, graft, and technical factors contributes to infectious risk in the recipient. Host factors such as age, underlying disease, and comorbidities; central venous access; and the preparative regimen contribute to mucosal disruption, organ dysfunction, and immunodeficiency before hematopoietic cell transplantation. Graft factors, including donor histocompatibility, cell source, and graft components, along with immunosuppression and graft-versus-host disease, contribute to the speed of immune reconstitution. Evaluation of these factors, plus previous and posttransplant exposure to pathogens, is necessary to best assess an individual recipient's infection risk.