Gene map of the extended human MHC

Integration of transcriptome-wide association study and gene-based association analysis identifies candidate genes for Hodgkin lymphoma

BACKGROUND

Genome-wide association studies (GWASs) have pinpointed many susceptibility loci for Hodgkin Lymphoma (HL), but their underlying biological mechanisms remain unclear.

METHODS

Utilizing GWAS data from the UK Biobank and FinnGen, along with expression quantitative trait loci (eQTL) statistics from the Genotype-Tissue Expression (GTEx) and the eQTL Catalogue, we carried out a large-scale gene-level association study using Omnibus Transcriptome Test with Expression Reference Summary data (OTTERS), and gene-based analysis with eQTL Multi-marker Analysis of Genomic Annotation (E-MAGMA).

RESULTS

We identified sixteen susceptibility genes for HL (FDR < 0.01), primarily immune-related, including HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DRB1, HLA-DRB5, HLA-DMA, and HLA-DPB1, alongside genes involved in apoptosis, RNA processing, transcriptional regulation, and signal transduction. We identified five novel plausible genes, including HLA-DMA, HLA-DPB1, LSM2, AAR2, and NOTCH4.

CONCLUSION

These findings highlight the role of the exogenous antigen presentation pathway in HL, shedding light on potential mechanisms.

Synergistic Effects of 2-Deoxyglucose and Diclofenac Sodium on Breast Cancer Cells: A Comparative Evaluation of MDA-231 and MCF7 Cells

Resistance of breast cancers to chemotherapy remains a global challenge to date. Drug combination studies between anti-cancer agents are increasingly becoming therapeutic strategies, geared towards alleviating breast cancers. Previously, 2-deoxyglucose has been shown to target and interrupt glycolysis. Available evidence also suggests that diclofenac, which was originally designed as a pain reliever, could inhibit the proliferation of breast cancer cells. However, the reverse Warburg effect and other metabolic reprogramming mechanisms in breast cancers limit the pharmacological application of both 2-deoxyglucose and diclofenac as mono-therapeutic agents. The present study explores the additive anti-cancer effects of 2-deoxyglucose and diclofenac sodium on breast cancer cells. In this study, MDA-231 and MCF7 cells were treated with 2-deoxyglucose and diclofenac sodium in single and combination doses before being evaluated for viability, cell growth, reactive oxygen species, apoptotic and necrotic phases, and migration abilities. Additionally, immunoblotting of pro-apoptotic proteins, Caspase-3 and Caspase-9, and a hypoxia-inducible factor-1 alpha, was also performed. The results showed that combination treatments of the cells with the drugs exhibited additive anti-cancer effects by limiting proliferation, enhancing cytotoxic reactive oxygen species generation, enhancing apoptosis and necrosis, limiting colony formation and expansion of cells, and inhibiting cell migration. The degrees of cytotoxicity of combined treatments were almost similar in both cell lines, although with minimal differences. Put together, these results reveal the novel synergistic effects of 2-deoxyglucose and diclofenac sodium on breast cancer cells, hence potentially elevating their pharmacological profile in the overall breast cancer therapy.

Genome-wide diversity and MHC characterisation in a critically endangered freshwater turtle susceptible to disease

Small, isolated populations are often vulnerable to increased inbreeding and genetic drift, both of which elevate the risk of extinction. The Bellinger River turtle (Myuchelys georgesi) is a critically endangered species endemic to a single river catchment in New South Wales, Australia. The only extant wild population, along with the breeding program, face significant threats from viral outbreaks, most notably a nidovirus outbreak in 2015 that led to a 90% population decline. To enhance our understanding of genomic characteristics in the species, including genome-wide and functional gene diversity, we re-sequenced, assembled, and analysed 31 re-sequenced genomes for pure M. georgesi (N = 31). We manually annotated the major histocompatibility complex (MHC), identifying five MHC class I and ten MHC class II genes and investigated genetic diversity across both classes in M. georgesi. Our results showed that genome-wide diversity is critically low in pure M. georgesi, contexualised through comparison with opportunistically sampled backcross animals-offspring of F1 hybrids (M. georgesi × Emydura macquarii) backcrossed to pure M. georgesi (N = 4). However, the variation observed within the core MHC region of pure M. georgesi, extending across scaffold 10, exceeded that of all other macrochromosomes. Additionally, no significant short-term changes in either genome-wide or immunogenetic diversity were detected following the 2015 nidovirus outbreak (before; N = 19, after; N = 12). Demographic history reconstructions indicated a sustained, long-term decline in effective population size since the last interglacial period, accompanied by more recent steep declines. These patterns suggested that prolonged isolation and reduced population size have significantly influenced the dynamics of genome-wide diversity. It is likely that contemporary stressors, including the recent nidovirus outbreak, are acting on an already genetically depleted population. This study offers new insights into genome-wide and immune gene diversity, including immune gene annotation data with broader implications for testudines. These findings provide crucial information to support future management strategies for the species.

Genomic Full-Length Sequence of the HLA-DRB1*03:19 Allele Was Identified in a Chinese Bone Marrow Donor by PacBio Sequencing

Genomic full-length sequence of HLA-DRB1*03:19 was identified in a Chinese individual by PacBio sequencing.

Genetic burden of lupus increases the risk of transition from normal to preclinical autoimmune conditions via antinuclear antibody development

OBJECTIVES

This study aimed to investigate the association between the genetic burden of systemic lupus erythematosus (SLE) and the loss of tolerance to self-nuclear antigens in the preclinical stage.

METHODS

We analysed genetic data from 349 Korean individuals who tested positive for autoantibodies in the preclinical stage, along with 33,596 healthy controls and 2057 patients with SLE. Genome-wide and pathway-specific polygenic risk scores (PRSs) of SLE were calculated based on 180 known non-human leukocyte antigen (non-HLA) SLE loci, HLA-DRB1 classical alleles, and predefined immune-related pathways to subsequently correlate with clinical phenotypes, particularly the presence of antinuclear antibodies (ANAs) at various titre thresholds.

RESULTS

Individuals with preclinical autoimmune conditions exhibited significantly higher SLE PRSs than healthy controls (P = 2.99 × 10-5), with a significantly upward trend between ANA titres and PRS (P = 1.12 × 10-3). Stratification analysis revealed that preclinical-stage individuals with PRSs exceeding the means of age- and sex-matched PRSs among patients with SLE were at a significantly higher risk of ANA development (odds ratio = 2.25; P = 8.12 × 10-3 at a dilution factor of 1:80). Pathway-specific PRS analysis identified the significant enrichment of SLE-risk effects in nine pathways, such as signalling related to reactive oxygen species production, T cell receptor, B cell receptor, and cytokines, in ANA-positive preclinical individuals (Padjusted < 0.05).

CONCLUSIONS

Our findings illustrate that the genetic burden of SLE may lead to a crucial transition from normal to preclinical autoimmune conditions prior to the pathogenic stage by increasing the susceptibility to and levels of ANAs.

MultiCook: A Tool That Improves Accuracy of HLA Imputation by Combining Probabilities From Multiple Reference Panels and Methods

HLA molecules are produced by genes within the Major Histocompatibility Complex (MHC). Although the identification of HLA genotype is costly, fortunately, recent computational methods have made it possible to impute HLA genotypes using inexpensive single nucleotide polymorphism (SNP) markers. These imputation methods perform well if ethnicity-matched reference panels are provided. However, the availability of large-sized panels specific to each ethnicity remains limited. As a result, to achieve better imputation for each population, we need to utilise available multiple reference panels together. In this study, we introduce MultiCook, which enables users to simultaneously utilise existing multiple HLA imputation methods with multiple reference panels. MultiCook is versatile in that panels typed with different SNP genotyping platforms can seamlessly be merged, outputs from multiple imputation methods can be combined and the output from the Michigan imputation server with a multiethnic reference panel can also be incorporated. We compared MultiCook to the existing single-reference-panel approaches and the Michigan HLA imputation server. In evaluation with a cohort of 413 Koreans, MultiCook reduced the imputation error rate by about one third, from 4.70% to 3.31%, by combining 1KG EAS (N = 504) and HAN Chinese (N = 9773) reference panels compared to the single-panel approach. Moreover, MultiCook achieved better accuracy for imputing low-frequency alleles in evaluation benchmarks.

The MHC (Major Histocmpatibility Complex) Exceptional Molecules of Birds and Their Relationship to Diseases

There are about 5000 species of Passeriformes birds, which are half of the extant ones. Their class I MHC molecules are found to be different from all other studied vertebrates, including other bird species; i.e., amino acid residues 10 and 96 are not the seven canonic residues extant in all other vertebrate molecules. Thus, the canonic residues in MHC class I vertebrate molecules are reduced to five. These differences have physical effects in MHC (Major Histocompatibility Complex) class I alpha chain interaction with beta-2-microglobulin but have yet unknown functional effects. Also, introns show specific Passeriformes distinction both in size and invariance. The studies reviewed in this paper on MHC structure have been done in wild birds that cover most of the world's passerine habitats. In this context, we are going to expose the most commonly occurring bird diseases with the caveat that MHC and disease linkage pathogenesis is not resolved. In addition, this field is poorly studied in birds; however, common bird diseases like malaria and Marek's disease are linked to MHC. On the other hand, the main established function of MHC molecules is presenting microbial and other antigens to T cells in order to start immune responses, and they also may modulate the immune system through NK receptors and other receptors (non-classical class I MHC molecules). Also, structural and polymorphic differences between classical class I molecules and non-classical class I molecules are at present not clear, and their definition is blurred. These passerine exceptional MHC class I molecules may influence linkage to diseases, transplantation, and other MHC presentation and self-protection functions. Further studies in more Passeriformes species are ongoing and needed.

Newborn blood DNA methylation and childhood asthma: findings from the ECHO program

BACKGROUND

DNA methylation (DNAm) at birth has been linked to childhood asthma in epigenome-wide association studies (EWASs). However, existing EWASs have limited representation of non-European and extremely preterm participants and have not explored sex-specific DNAm differences. This study examined the association between DNAm in newborn blood and subsequent childhood asthma risk in a diverse population.

METHODS

Data from the Environmental influences on Child Health Outcomes (ECHO) Program were used for EWAS meta-analyses in United States (US) cohorts of children born before and after 28 weeks of gestation. DNAm was measured in newborn blood using Illumina arrays. Childhood asthma was defined as provider-diagnosed asthma with persistent symptoms beyond age 5. Linear regression was used to identify differentially methylated positions (DMPs), and "comb-p" was used to identify differentially methylated regions (DMRs). Sex-stratified analyses were performed.

RESULTS

The meta-analysis included 942 children (369 asthma cases) born after 28 weeks of gestation. We identified a novel DMP (cg24749470 in CADM1, P = 9.31 × 10-8) and 18 DMRs (Šidák P-value <.001) associated with asthma, with four DMRs in the human leukocyte antigen region. At these four DMRs, the association between DNAm and asthma differed by sex. In the extremely preterm cohort (n = 271, 106 asthma cases), we identified 20 DMRs, with two novel asthma-associated DMPs (cg03237868 in SPATA18, P = 2.71 × 10-8; cg20681219 in IRF2, P = 5.18 × 10-8) identified in males.

CONCLUSION

In US children born before and after 28 weeks of gestation, we discovered novel genomic loci linking newborn blood DNAm to childhood asthma, suggesting DNAm involvement in early asthma development.

Allele and Haplotype Frequencies of 17 HLA-Related Loci in Shenzhen Chinese Population by Next-Generation Sequencing

Although the allele and haplotype frequencies of 11 HLA loci (HLA-A, B, C, DRB1, DRB3/4/5, DQA1, DQB1, DPA1 and DPB1) have been reported in different populations, rare studies have simultaneously assessed the allele distributions of non-classical HLA class I genes (HLA-E/F/G/H) and MICA/MICB together with the 11 classical HLA loci, or further analysed the haplotype frequencies covering the 17 loci. The present study aims to investigate the allele diversity and haplotype frequencies of 17 HLA-related loci including HLA genes and MICA/MICB simultaneously using a hybrid capture (HC)-based NGS method. A total of 358 HLA alleles including 177 class I and 137 class II alleles, as well as 29 MICA and 15 MICB alleles were identified in this project. The most frequent alleles at each locus were A*11:01 (29.10%), B*40:01 (14.46%), C*01:02 (19.90%), DRB1*09:01 (15.61%), DQB1*03:01 (18.48%), DPB1*05:01 (40.13%), DQA1*01:02 (22.58%), DPA1*02:02 (55.27%), DRB3*02:02 (65.95%), DRB4*01:03 (95.20%), DRB5*01:01 (75.97%), E*01:03 (62.63%), F*01:01 (97.07%), G*01:01 (70.74%), H*01:01 (35.87%), MICA*010:01 (19.90%) and MICB*005:02 (57.53%), respectively. The haplotype frequencies for different combinations of HLA loci were estimated and linkage disequilibrium (LD) between alleles for all pairs of neighbouring loci were calculated. The most frequent haplotype covering 17 loci was F*01:01-G*01:01-H*01:01-A*02:07-E*01:03-C*01:02-B*46:01-MICA*010:01-MICB*005:02-DRB4*01:03-DRB1*09:01-DQA1*03:02-DQB1*03:03-DPA1*02:02-DPB1*05:01 with a frequency of 3.18%. This is the first study on allelic polymorphism, haplotype inference and LD covering 17 HLA-related loci simultaneously in the Shenzhen Chinese population. These results will extend our knowledge of the allelic diversity of the HLA complex and provide population genetics data for transplantation and HLA-associated disease studies.

Admixed gene expression models expand molecular and neurological insights into 6 major psychiatric disorders

Our understanding of the influence of ancestral background on genetically determined expression remains limited, especially when gene expression models are applied to studies from different or multiple populations. We performed transcriptome wide association studies (TWAS) in 6 different psychiatric conditions, leveraging gene expression models trained in cohorts with different proportions of African, European, and Indigenous American genetic ancestries. For comparison we repeated each TWAS using a model trained in individuals of predominantly European ancestry. We identified 1,416 statistically significant TWAS associations (FDR p < 0.05) across the 6 diagnoses, of which 62% were uniquely detected by the admixed gene models. We observed > 92% correlation in the gene-level effects on disease risk, a statistic that remained robust for TWAS results that only reached statistical significance in one population. Using admixed gene expression models validated and greatly extended the yield of TWAS. The resulting transcriptomic signatures implicated neuroimaging features associated with diagnostic symptoms.

Identification of a Risk Allele at SLC41A3 and a Protective Allele HLA-DPB1*02:01 Associated with Sarcopenia in Japanese

INTRODUCTION

Age-related alterations in muscle tissue morphology and function, as well as chronic pro-inflammatory conditions, contribute to the development of sarcopenia. To elucidate the multidimensional pathogenesis of sarcopenia, we performed a comprehensive genetic analysis, including common variants, rare variants, and human leukemia antigen (HLA).

METHODS

A total of 129 older adults were analyzed using whole-genome sequencing (WGS), including 67 sarcopenia patients and 62 normal controls. Sarcopenia was diagnosed according to the Asian Working Group for Sarcopenia 2019 consensus. WGS data and associated clinical data were obtained from the National Center for Geriatrics and Gerontology Biobank in Japan. We performed logistic regression adjusted for age, sex, and body mass index for common variant (minor allele frequency [MAF] ≧0.01), rare variant (MAF <0.01), and HLA analyses. For the functional analysis, we performed RNA interference using human myoblasts and estimated gene expressions (MYOG, MYMK, MYMG) by quantitative PCR.

RESULTS

Rare variant analysis identified five rare coding variants of genes - SLC41A3, SYNRG, CLUAP1, CCHCR1, and ALDH2 - expressed in skeletal muscle. Of these, a deleterious frameshift deletion in SLC41A3 was associated with the pathogenesis of sarcopenia (p = 0.0012, odds ratio [OR] = 11.52, 95% confidence interval [CI] = 2.62-50.69). This deletion significantly reduced expression of myogenin (MYOG), a factor involved in myoblast differentiation (p = 0.0094), but did not affect the fusion of myogenic cells. We also discovered a new protective allele, HLA-DPB1*02:01 associated with sarcopenia (OR = 0.17, 95% CI = 0.060-0.51, p = 0.0015), which has a high occurrence rate in the Northeast Asian population.

CONCLUSION

Rare variant analysis identified a deleterious frameshift deletion in SLC41A3 as a risk factor for sarcopenia. Our findings suggest that the suppression of MYOG could play a role in myogenesis or muscle maintenance, although this mutation did not impact the terminal differentiation of human myoblasts. Additionally, HLA analysis revealed that HLA-DPB1*02:01 has a protective effect, especially in Northeast Asian populations. Our study enhances the understanding of the etiology of sarcopenia and provides new insights into the mechanisms of its pathogenesis.

Characterisation of the Novel HLA-C*04:533 Allele

HLA-C*04:533 differs from C*04:01:01:14 by a single non-synonymous nucleotide change in codon 216 (ACC>AAC).

The Case of a Missing HLA-B Gene

The Major Histocompatibility Complex (MHC) of human chromosome 6 contains multiple genes critical for immunity. The exceptional polymorphism of this genomic region that establishes and maintains immune diversity can be technically challenging to characterise and analyse. In this study, we present a family where the mother and one of her children have no HLA-B allele in common, implying the absence of HLA-B from the maternal haplotype. Homozygosity of the mother and child was confirmed using three independent PCR-based methods and high throughput DNA sequencing. Through probe-based MHC region enrichment, sequencing, and read mapping, we located the breakpoints of a large (36.5 kbp) deletion encompassing the entire HLA-B gene. Accordingly, the deletion was present on the maternal haplotype and transmitted to the child. This study demonstrates strategies for locating large deletions in complex genomic regions and highlights the dynamic nature of MHC structure and variation.

Characterisation of the Novel HLA-C*02:231 Allele

HLA-C*02:231 differs from C*02:02:02:79 by a single non-synonymous nucleotide change in codon 124 (ATC>GTC).

Effect of major ABO blood group mismatched HSCT on blood transfusion and clinical outcomes in AA patients

To investigate the impact of the ABO blood group major match type on stem cell engraftment, blood transfusion and clinical outcomes in aplastic anemia patients with hematopoietic stem cell transplantation (HSCT), we retrospectively analyzed the data of 361 aplastic anemia patients treated with HSCT, and found ABO major mismatched resulted in delayed red blood cells (RBCs) engraftment and ABO blood group conversion. The patients in the ABO major mismatched group required more units of RBCs and PLTs transfusions. Multivariate linear regression analysis showed that ABO mismatched, acute graft-versus-host disease (aGVHD), time to RBCs and PLTs engraftment and blood group conversion, and baseline hemoglobin were significantly associated with RBCs transfusion, the factors associated with PLTs transfusion were the PLTs, RBCs and neutrophils engraftment, graft rejection, baseline PLTs, aGVHD grade II-IV, and severe chronic GVHD. Multivariate analysis showed that the time to neutrophils engraftment, baseline hemoglobin, and aGVHD were independent poor prognostic factors to both overall survival and failure-free survival. Moreover, the major ABO-mismatched HSCT group were hospitalized more often. These findings suggest that it's better to select a donor with an ABO major match to reduce the burden of transfusion and the impact of hospitalization, if conditions permit.

Immunometabolism of Liver Xenotransplantation and Prospective Solutions

End-stage liver diseases, such as hepatocellular carcinoma or acute liver failure, critically necessitate liver transplantation. However, the shortage of available organ donors fails to meet the rapidly growing transplantation demand. Due to the high similarity of liver tissue structure and metabolism between miniature pigs and humans, xenotransplantation of pig livers is considered as a potentially viable solution to organ scarcity. In the 2024, teams from China first time have successfully transplanted a genetically modified Bama miniature pig liver into a clinically brain-dead man lasting for 10 days. This milestone in human xenotransplantation research not only confirms the feasibility of clinical application of xenotransplantation, but also underscores the daunting and protracted nature of this pathway. Despite advanced gene-editing technologies theoretically circumventing the occurrence of most transplant rejection reactions, patients still face challenges such as chronic immune rejection, coagulation disorders, and thrombotic microangiopathy after receiving xenografts. Moreover, prolonged use of immunosuppressive drugs may induce irreversible immune dysfunction, leading to opportunistic infections and metabolic disorders. This article compares the similarities and differences in livers between humans and pigs, summarizes the immunometabolism of xenotransplantation based on current findings, and provides research perspectives on pre-transplantation and post-transplantation strategies for prolonging the survival time of xenografts.

GWAS meta-analysis of psoriasis identifies new susceptibility alleles impacting disease mechanisms and therapeutic targets

Psoriasis is a common, debilitating immune-mediated skin disease. Genetic studies have identified biological mechanisms of psoriasis risk, including those targeted by effective therapies. However, the genetic liability to psoriasis is not fully explained by variation at robustly identified risk loci. To refine the genetic map of psoriasis susceptibility we meta-analysed 18 GWAS comprising 36,466 cases and 458,078 controls and identified 109 distinct psoriasis susceptibility loci, including 46 that have not been previously reported. These include susceptibility variants at loci in which the therapeutic targets IL17RA and AHR are encoded, and deleterious coding variants supporting potential new drug targets (including in STAP2, CPVL and POU2F3). We conducted a transcriptome-wide association study to identify regulatory effects of psoriasis susceptibility variants and cross-referenced these against single cell expression profiles in psoriasis-affected skin, highlighting roles for the transcriptional regulation of haematopoietic cell development and epigenetic modulation of interferon signalling in psoriasis pathobiology.

The epidemiology, pathology and pathogenesis of MS: Therapeutic implications

Multiple sclerosis (MS) is a chronic, and potentially disabling, inflammatory disease of the central nervous system (CNS). MS is generally characterized by recurrent, and self-limited, episodes of neurological dysfunction, which occur unpredictably and often result in multifocal tissue injury within the CNS. Currently, women are affected two to three times as often as men although this may not have been the case during earlier Time-Periods. The pathogenesis of MS is known to involve both critical genetic and environmental mechanisms. Nevertheless, in addition to these two mechanisms, disease-pathogenesis also involves a "truly" random event. Indeed, it is this random mechanism, which is responsible for the currently-observed (and increasing) excess of women among patients with MS. This review summarizes the current state of knowledge regarding the pathogenesis of MS (includong its epidemiology, pathology, and genetics) and considers the therapeutic implications that these pathogenetic mechanisms have both for our currently available therapies as well as for the possible therapeutic approaches to the management of this potentially disabling condition in the future.

Genetics in Congenital Adrenal Hyperplasia Due to 21-Hydroxylase Deficiency and Clinical Implications

Of all congenital adrenal hyperplasia (CAH), 95% to 99% is 21-hydroxylase deficiency (21OHD), an autosomal recessive disease. 21OHD is due to an insufficiency of 21-hydroxylase enzyme, which is encoded by the CYP21A2 gene and involved in cortisol and aldosterone production. The clinical presentation differs widely from severe classic to mild nonclassic CAH. 21OHD represents one of the most complex and at the same time intriguing topics in human genetics and its molecular diagnosis involves ongoing challenges. To provide a meticulous presentation of the topic, we searched the past and present literature, including original articles and reviews from PubMed, ScienceDirect, Web of Science, Embase, and Scopus, using search terms for genetics of 21OHD, 21OHD variants, molecular diagnosis of 21OHD, and 21OHD genetic testing. We offer a comprehensive review focusing on recent developments, new concepts, and conclusions.

Identification and validation of depression-associated genetic variants in the UK Biobank cohort with transcriptome and DNA methylation analyses in independent cohorts

Depression is one of the most common psychiatric conditions resulting from a complex interaction of genetic, epigenetic and environmental factors. The present study aimed to identify independent genetic variants in the protein-coding genes that associate with depression and to analyze their transcriptomic and methylation profile. Data from the GWAS Catalogue was used to identify independent genetic variants for depression. The identified genetic variants were validated in the UK Biobank cohort and used to calculate a genetic risk score for depression. Data was also used from publicly available cohorts to conduct transcriptome and methylation analyses. Eight SNPs corresponding to six protein-coding genes (TNXB, NCAM1, LTBP3, BTN3A2, DAG1, FHIT) were identified that were highly associated with depression. These validated genetic variants for depression were used to calculate a genetic risk score that showed a significant association with depression (p < 0.05) but not with co-morbid traits. The transcriptome and methylation analyses suggested nominal significance for some gene probes (TNXB- and NCAM1) with depressed phenotype. The present study identified six protein-coding genes associated with depression and primarily involved in inflammation (TNXB), neuroplasticity (NCAM1 and LTBP3), immune response (BTN3A2), cell survival (DAG1) and circadian clock modification (FHIT). Our findings confirmed previous evidence for TNXB- and NCAM1 in the pathophysiology of depression and suggested new potential candidate genes (LTBP3, BTN3A2, DAG1 and FHIT) that warrant further investigation.

Sarcopenia and immune-mediated inflammatory diseases: Evaluating causality and exploring therapeutic targets for sarcopenia through Mendelian randomization

BACKGROUND

An increasing body of evidence has revealed the association between immune-mediated inflammatory diseases (IMIDs) and sarcopenia. However, a genetically direct causality between IMIDs and sarcopenia remains elusive.

METHODS

To investigate the relationship between IMIDs and sarcopenia-related traits and identify potential therapeutic targets, a Mendelian randomization (MR) was performed. We collected publicly available genome-wide association studies (GWAS) data for seven common IMIDs, including systemic lupus erythematosus (SLE), inflammatory bowel disease (IBD), Crohn's disease (CD), ulcerative colitis (UC), psoriasis (PSO), ankylosing spondylitis (AS), and rheumatoid arthritis (RA). Additionally, summary-level GWAS data for sarcopenia-related traits, including appendicular lean mass (ALM), left-hand grip strength, and right-hand grip strength were collected. To search for therapeutic targets, we used two types of genetic instruments to proxy the exposure of druggable genes, including genetic variants within or nearby drug targets and expression quantitative trait loci (eQTLs) of drug targets. Two-sample MR and summary-data-based MR (SMR) were used to calculate effect estimates, and sensitivity analyses were implemented for robustness. Drug tractability, gene enrichment analysis, and protein-protein interaction (PPI) analysis were used to validate the biological and clinical significance of the selected drug targets.

RESULTS

The two-sample MR analysis indicated the existence of casual associations between IMIDs and sarcopenia-related traits in the overall and sex-stratified populations. In particular, PSO had causal effects on decreased ALM, which showed significance in all six MR analysis tests with directional consistency in the overall population. Grounded in this robust association, HLA-DRB5, HLA-DRB1, and AGER were identified as potential therapeutic targets for ALM decline by drug target MR and further confirmed by SMR analysis. These genes were associated with therapeutic agents currently undergoing evaluations in clinical trials. Gene enrichment and PPI analysis indicated a strong association of these genes with immune functions.

CONCLUSIONS

This MR study contributes novel genetic evidence supporting the causal link between IMIDs and sarcopenia, with a particular emphasis on the association between PSO and decreased ALM. Additionally, AGER, HLA-DRB1, and HLA-DRB5 emerge as potential therapeutic targets for ALM decline.

Association of the Immunity Genes with Type 1 Diabetes Mellitus

Type 1 diabetes mellitus (T1D) is a complicated illness marked by the death of insulin- producing pancreatic beta cells, which ultimately leads to insulin insufficiency and hyperglycemia. T lymphocytes are considered to destroy pancreatic beta cells in the etiology of T1D as a result of hereditary and environmental factors. Although the latter factors are very important causes of T1D development, this disease is very genetically predisposed, so there is a significant genetic component to T1D susceptibility. Among the T1D-associated gene mutations, those that affect genes that encode the traditional Human Leukocyte Antigens (HLA) entail the highest risk of T1D development. Accordingly, the results of decades of genetic linkage and association studies clearly demonstrate that mutations in the HLA genes are the most associated mutations with T1D. They can, therefore, be used as biomarkers for prediction strategies and may even prove to be of value for personalized treatments. Other immunity-associated genetic loci are also associated with higher T1D risk. Indeed, T1D is considered an autoimmune disease. Its prevalence is rising globally, especially among children and young people. Given the global rise of, and thus interest in, autoimmune diseases, here we present a short overview of the link between immunity, especially HLA, genes and T1D.

Shared genetic factors and the interactions with fresh fruit intake contributes to four types squamous cell carcinomas

Studies have reported risk factors for a single-squamous cell carcinoma(Single-SCCs). However, the shared common germline genetic factors and environmental factors have not been well elucidated with respect to augmented risk of pan-squamous cell carcinoma(Pan-SCCs). By integrating a large-scale genotype data of 1,928 Pan-SCCs cases and 7,712 age- and sex-matched controls in the UK Biobank cohort, as well as multiple transcriptome and protein databases, we conducted a multi-omics analysis. Genome-wide association analysis (GWAS) was used to identify genetic susceptibility loci of SCCs. High resolution human leucocyte antigen (HLA) alleles and corresponding amino acid sequences were imputed using SNP2HLA and tested for association with SCCs. Credible risk variants (CRVs) were combined risk SNPs reported in GWAS Catalog and our study, followed by comprehensive bioinformatics analyses. We identified six novel index SNPs in the progression of SCCs, which were also strongly interacted with fresh fruit intake. Moreover, our study systematically characterize the HLA variants and their relationship to SCCs susceptibility. We identified HLA-A*01 and six HLA-A amino acid position were associated independently with SCCs. Credible risk variants were annotated to 469 target genes, further GO and KEGG Pathway Enrichment Analysis showed that SCCs genes were primarily involved in immune-related pathways, espechially regulated by HLA region. The transcriptome analysis showed that there were 270 differentially expressed genes(DEGs), with the upregulated genes were enriched in the regulation of stem cell differentiation, proliferation, development, and maintenance. The PPI Network and Modular Analysis uncovered the Keratin(KRT) genes may serve as a potential marker in SCCs. Our results illustrate the molecular basis of both well-studied and new susceptibility loci of SCCs, providing not only novel insights into the genetic commonality among SCCs but also a set of plausible gene targets for post-GWAS functional experiments.

Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and implicates causal proteins for Alzheimer's disease

The integration of quantitative trait loci (QTLs) with disease genome-wide association studies (GWASs) has proven successful in prioritizing candidate genes at disease-associated loci. QTL mapping has been focused on multi-tissue expression QTLs or plasma protein QTLs (pQTLs). We generated a cerebrospinal fluid (CSF) pQTL atlas by measuring 6,361 proteins in 3,506 samples. We identified 3,885 associations for 1,883 proteins, including 2,885 new pQTLs, demonstrating unique genetic regulation in CSF. We identified CSF-enriched pleiotropic regions on chromosome (chr)3q28 near OSTN and chr19q13.32 near APOE that were enriched for neuron specificity and neurological development. We integrated our associations with Alzheimer's disease (AD) through proteome-wide association study (PWAS), colocalization and Mendelian randomization and identified 38 putative causal proteins, 15 of which have drugs available. Finally, we developed a proteomics-based AD prediction model that outperforms genetics-based models. These findings will be instrumental to further understand the biology and identify causal and druggable proteins for brain and neurological traits.

Description of the Novel HLA-B*48:01:14 Allele Identified in a Northern Chinese Han Individual

Identification of the novel HLA-B*48:01:14 allele, which differs from HLA-B*48:01:01 at one position.

Animal models of lupus nephritis: the past, present and a future outlook

Lupus nephritis (LN) is the most severe end-organ pathology in Systemic Lupus Erythematosus (SLE). Research has enhanced our understanding of immune effectors and inflammatory pathways in LN. However, even with the best available therapy, the rate of complete remission for proliferative LN remains below 50%. A deeper understanding of the resistance or susceptibility of renal cells to injury during the progression of SLE is critical for identifying new targets and developing effective long-term therapies. The complex and heterogeneous nature of LN, combined with the limitations of clinical research, make it challenging to investigate the aetiology of this disease directly in patients. Hence, multiple murine models resembling SLE-driven nephritis are utilised to dissect LN's cellular and genetic mechanisms, identify therapeutic targets, and screen novel compounds. This review discusses commonly used spontaneous and inducible mouse models that have provided insights into pathogenic mechanisms and long-term maintenance therapies in LN.

A review of the advances in understanding the genetic basis of spondylarthritis and emerging clinical benefit

Spondyloarthropathies (SpA), including ankylosing spondylitis (AS) and psoriatic arthritis (PsA), have been shown to have a substantial genetic predisposition based on heritability estimates derived from family studies and genome-wide association studies (GWAS). GWAS have uncovered numerous genetic loci associated with susceptibility to SpA, with significant associations to human leukocyte antigen (HLA) genes, which are major genetic risk factors for both AS and PsA. Specific loci differentiating PsA from cutaneous-only psoriasis have been identified, though these remain limited. Further research with larger sample sizes is necessary to identify more PsA-specific genetic markers. Current research focuses on translating these genetic insights into clinical applications. For example, polygenic risk scores are showing promise for the classification of disease risk and diagnosis and future research should focus on refining these risk assessment tools to improve clinical outcomes for individuals with SpA. Addressing these challenges will help integrate genetic testing into patients care and impact clinical practice.

Association of immunity-related gene SNPs with Alzheimer's disease

Alzheimer's disease (AD) is a prevalent neurodegenerative disorder characterized by progressive cognitive decline. Genetic factors have been implicated in disease susceptibility as its etiology remains multifactorial. The CD33 and the HLA-DRB1 genes, involved in immune responses, have emerged as potential candidates influencing AD risk. In this study, 644 Lebanese individuals, including 127 AD patients and 250 controls, were genotyped, by KASP assay, for six SNPs selected from the largest GWAS study in 2021. Logistic regression analysis assessed the association between SNP genotypes and AD risk, adjusting for potential confounders. Among the six SNPs analyzed, rs1846190G>A in HLA-DRB1 and rs1354106T>G in CD33 showed significant associations with AD risk in the Lebanese population (p < 0.05). Carriers of the AG and AA genotypes of rs1846190 in HLA-DRB1 exhibited a protective effect against AD (AG: OR = 0.042, p = 0.026; AA: OR = 0.052, p = 0.031). The GT genotype of rs1354106T>G in CD33 was also associated with reduced risk (OR = 0.173, p = 0.005). Following Bonferroni correction, a significant correlation of rs1354106T > G with AD risk was established. Our results might highlight the complex interplay between genetic and immunological factors contributing to the development of the disease.

New Associations with the HIV Predisposing and Protective Alleles of the Human Leukocyte Antigen System in a Peruvian Population

The accurate determination of an individual's unique human leukocyte antigen (HLA) allele holds important significance in evaluating the risk associated with autoimmune and infectious diseases, such as human immunodeficiency virus (HIV) infection. Several allelic variants within the HLA system have been linked to either increased protection or susceptibility in the context of infectious and autoimmune diseases. This study aimed to determine the frequency and association of HLA alleles between people living with HIV (PLHIV) as the case group and Peruvian individuals without HIV with high-risk behaviors of sexually transmitted diseases as the control group. Whole exome sequencing (WES) was used to determine high-resolution HLA allelotypes using the OptiType and arcas HLA tools. The HLA alleles present in HLA classes I (A, B, and C loci) and II (DPB1, DQA1, DQB1, and DRB1 loci) were determined in a cohort of 59 PLHIV (cases) and 44 individuals without HIV (controls). The most frequent HLA alleles were A*02:01, DPB1*04:02, and DQB1*03:419 at 36%, 30%, and 28% prevalence in general population. We found that C*07:01 (p = 0.0101; OR = 10.222, 95% IC: 1.40-74.55), DQA1*03:02 (p = 0.0051; OR = 5.297, 95% IC: 1.48-19.02), and DRB1*09:01 (p = 0.0119; OR = 4.788, 95% IC: 1.39-16.44) showed an association with susceptibility to HIV infection, while DQB1*03:419 (p = 0.0478; OR = 0.327, 95% IC: 0.11-0.96) was associated with protection from HIV infection. Our findings contribute to the knowledge of HLA allele diversity in the Peruvian population (around 70% South American indigenous ancestry) lays the groundwork for further valuable large-scale use of HLA typing and offers a novel association with HIV infection that is relevant to vaccine studies.

Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples

The human major histocompatibility complex (MHC) is a ∼4 Mb genomic segment on Chromosome 6 that plays a pivotal role in the immune response. Despite its importance in various traits and diseases, its complex nature makes it challenging to accurately characterize on a routine basis. We present a novel approach allowing targeted sequencing and de novo haplotypic assembly of the MHC region in heterozygous samples, using long-read sequencing technologies. Our approach is validated using two reference samples, two family trios, and an African-American sample. We achieved excellent coverage (96.6%-99.9% with at least 30× depth) and high accuracy (99.89%-99.99%) for the different haplotypes. This methodology offers a reliable and cost-effective method for sequencing and fully characterizing the MHC without the need for whole-genome sequencing, facilitating broader studies on this important genomic segment and having significant implications in immunology, genetics, and medicine.

Host-pathobiont interactions in Crohn's disease

The mammalian intestine is colonized by trillions of microorganisms that are collectively referred to as the gut microbiota. The majority of symbionts have co-evolved with their host in a mutualistic relationship that benefits both. Under certain conditions, such as in Crohn's disease, a subtype of inflammatory bowel disease, some symbionts bloom to cause disease in genetically susceptible hosts. Although the identity and function of disease-causing microorganisms or pathobionts in Crohn's disease remain largely unknown, mounting evidence from animal models suggests that pathobionts triggering Crohn's disease-like colitis inhabit certain niches and penetrate the intestinal tissue to trigger inflammation. In this Review, we discuss the distinct niches occupied by intestinal symbionts and the evidence that pathobionts triggering Crohn's disease live in the mucus layer or near the intestinal epithelium. We also discuss how Crohn's disease-associated mutations in the host disrupt intestinal homeostasis by promoting the penetration and accumulation of pathobionts in the intestinal tissue. Finally, we discuss the potential role of microbiome-based interventions in precision therapeutic strategies for the treatment of Crohn's disease.

The role of genetically predicted serum iron levels on neurodegenerative and cardiovascular traits

Iron is an essential mineral that supports numerous biological functions. Studies have reported associations between iron dysregulation and certain cardiovascular and neurodegenerative diseases, but the direction of influence is not clear. Our goal was to use computational approaches to better understand the role of genetically predicted iron levels on disease risk. We meta-analyzed genome-wide association study summary statistics for serum iron levels from two cohorts and two previous meta-analyses. We then obtained summary statistics from 11 neurodegenerative, cerebrovascular, cardiovascular or lipid traits to assess global and regional genetic correlation between iron levels and these traits. We used two-sample Mendelian randomization (MR) to estimate causal effects. Sex-stratified analyses were also carried out to identify effects potentially differing by sex. Overall, we identified three significant global correlations between iron levels and (i) coronary heart disease, (ii) triglycerides, and (iii) high-density lipoprotein (HDL) cholesterol levels. A total of 194 genomic regions had significant (after correction for multiple testing) local correlations between iron levels and the 11 tested traits. MR analysis revealed two potential causal relationships, between genetically predicted iron levels and (i) total cholesterol or (ii) non-HDL cholesterol. Sex-stratified analyses suggested a potential protective effect of iron levels on Parkinson's disease risk in females, but not in males. Our results will contribute to a better understanding of the genetic basis underlying iron in cardiovascular and neurological health in aging, and to the eventual identification of new preventive interventions or therapeutic avenues for diseases which affect women and men worldwide.

The Immune Modulation HLA-G*01:01:01 Full Allele Is Associated with Gastric Adenocarcinoma Development

The Human Leukocyte Antigen (HLA) system contains a set of genes involved at many levels in the innate and adaptive immune response. Among the non-classical HLA class I genes, HLA-G stands out for the numerous studies about its pivotal role in regulating/modulating immune responses. Also, its involvement in extravillous cytotrophoblast function, viral infections, autoimmunity, and cancer has been extensively documented. The present study explores for the first time the relationship between natural alleles of HLA-G, rather than STSs, SNPs, or partial gene polymorphisms, and the development of gastric adenocarcinoma, by analyzing the genetic profile of a cohort of 40 Spanish patients with this type of tumor using DNA extracted from paired biopsies of tumoral and adjacent non-tumoral gastric tissue. Our results reveal a significant statistical relationship between the presence of the HLA-G*01:01:01 allele and the development of gastric cancer, while other common alleles such as -G*01:04 or -G*01:05N did not demonstrate a significant correlation. Studying the involvement of HLA genes in the development of many diseases is relevant to understanding their pathophysiology. However, the absence of specific mechanisms underlying these associations suggests that investigating complete HLA natural alleles' extended haplotypes or complotypes may offer a more precise and valuable approach to elucidating the association of HLA with the pathogenesis of disease.

Associations of classical HLA alleles with sleep behaviours

Immune dysregulation has been observed in individuals with sleep disturbance, with HLA molecules play a crucial role in the immune response. This study aimed to investigate the associations between HLA alleles and sleep behaviours, considering several environmental factors. Data were sourced from the UK Biobank. Logistic regression analyses were performed to explore the associations between 359 HLA alleles and 4 sleep behaviours, including chronotype (n = 204,636), insomnia (n = 227,553), snoring (n = 214,350) and daytime dozing (n = 227,197). Furthermore, gene-environmental interaction studies (GEIS) were conducted to evaluate the interactions of HLA alleles with environmental factors on sleep behaviours. This study analysed a total sample and subgroups stratified by sex to elucidate the impact of HLA alleles on sleep behaviours. Our findings revealed several associations between specific HLA alleles and sleep behaviours. Notably, HLA-A*23:01 was associated with evening chronotype in the total sample (OR = 0.918, 95%CI: 0.872-0.965), while HLA-A*32:01 was associated with evening chronotype in males (OR = 1.089, 95%CI: 1.037-1.144). Furthermore, GEIS identified multiple sets of interactions associated with sleep behaviours. For example, the interaction of HLA-DPA1*01:04 with alcohol consumption was associated with daytime dozing in the total sample (OR = 1.993, 95%CI: 1.351-2.941), while the interaction of HLA-DQB1*05:04 with ever suffered mental distress preventing usual activities was associated with insomnia in males (OR = 0.409, 95%CI: 0.254-0.658). Our findings highlight the involvement of HLA in sleep regulation and underscore the potential interactions between HLA alleles and environmental factors in modulating susceptibility to sleep behaviours.

Genotype imputation methods for whole and complex genomic regions utilizing deep learning technology

The imputation of unmeasured genotypes is essential in human genetic research, particularly in enhancing the power of genome-wide association studies and conducting subsequent fine-mapping. Recently, several deep learning-based genotype imputation methods for genome-wide variants with the capability of learning complex linkage disequilibrium patterns have been developed. Additionally, deep learning-based imputation has been applied to a distinct genomic region known as the major histocompatibility complex, referred to as HLA imputation. Despite their various advantages, the current deep learning-based genotype imputation methods do have certain limitations and have not yet become standard. These limitations include the modest accuracy improvement over statistical and conventional machine learning-based methods. However, their benefits include other aspects, such as their "reference-free" nature, which ensures complete privacy protection, and their higher computational efficiency. Furthermore, the continuing evolution of deep learning technologies is expected to contribute to further improvements in prediction accuracy and usability in the future.

Distributions of MICA and MICB Alleles Typed by Amplicon-Based Next-Generation Sequencing in South Koreans

Major histocompatibility complex class I chain-related genes A and B (MICA and MICB) play a role as ligands in activating the NKG2D receptor expressed in natural killer cells, γδ T-cells and αβ CD8 T-cells and have been defined in human diseases and haematopoietic stem cell transplantation (HSCT). MICA and MICB alleles were genotyped at the three-field level by amplicon-based next-generation sequencing (NGS) using a MiSeqDx system and compared with the results from previous studies in healthy South Korean donors. Exons 2-5 of MICA and exons 2-4 of MICB were amplified using a multiplex polymerase chain reaction (PCR). Sequence reads of ≥ 51 depth counts were consistently obtained for each sample exon, and target exons were determined to match reference sequences contained in the IPD-IMGT/HLA database. MICA and MICB alleles were tested using exon combinations. The program was designed to recognise specific sequences and discriminate between the MICA*008:01:01/*027 alleles. A total of 22 alleles were found in MICA and MICB. We observed 1 HLA-C ~ HLA-B ~ MICA ~ MICB ~ HLA-DRB1 haplotype with significant linkage disequilibrium between alleles at all neighbouring HLA loci. These results are consistent with previous microarray results. Genotyping of MICA and MICB was possible using 11-loci HLA genes. We updated the distribution of MICA and MICB based on three-field allele and haplotype frequencies containing linkage disequilibrium in South Koreans using amplicon-based NGS. These data suggest that high-resolution MICA and MICB typing data obtained using NGS may aid in performing HSCT and disease association studies.

Risk of inflammatory bowel disease following hospitalisation with infectious mononucleosis: nationwide cohort study from Denmark

Infectious mononucleosis (IM) is suspected to be associated with inflammatory bowel disease (IBD) development. Using a Danish nationwide cohort of people developing severe IM and their age-, sex-, and socioeconomic (SES) index-matched counterparts, we investigated the subsequent risk of IBD, Crohn's disease (CD), or ulcerative colitis (UC) development from 1977 to 2021. Among 39,684 severe IM patients we find a sex-, age-, and SES index-adjusted HR for IBD of 1.35 (95% CI: 1.22-1.49). This significantly increased risk was seen for both CD (HR: 1.56; 95% CI: 1.34-1.83) and to a lesser extent UC (HR: 1.23; 95% CI: 1.08-1.40) and remains following negative control matching with a cohort diagnosed with Chlamydia trachomatis infection (HR: 1.39; 95% CI: 1.01-1.91). Those with severe IM at 0-9 years had a particularly increased risk for CD (HR: 1.77; 95% CI: 1.26-2.49). Here we show an increased risk for IBD diagnosis following IM hospitalisation, indicating an association between severe EBV disease and later IBD development. Further exploration of the potential factors contributing to IBD susceptibility following EBV disease is warranted.

Single-cell RNA sequencing illuminates the ontogeny, conservation and diversification of cartilaginous and bony fish lymphocytes

Elucidating cellular architecture and cell-type evolution across species is central to understanding immune system function and susceptibility to disease. Adaptive immunity is a shared trait of the common ancestor of cartilaginous and bony fishes. However, evolutionary features of lymphocytes in these two jawed vertebrates remain unclear. Here, we present a single-cell RNA sequencing atlas of immune cells from cartilaginous (white-spotted bamboo shark) and bony (zebrafish and Chinese tongue sole) fishes. Cross-species comparisons show that the same cell types across different species exhibit similar transcriptional profiles. In the bamboo shark, we identify a phagocytic B cell population expressing several pattern recognition receptors, as well as a T cell sub-cluster co-expressing both T and B cell markers. In contrast to a division by function in the bony fishes, we show close linkage and poor functional specialization among lymphocytes in the cartilaginous fish. Our cross-species single-cell comparison presents a resource for uncovering the origin and evolution of the gnathostome immune system.

Complex Interactions between the Human Major Histocompatibility Complex (MHC) and Microbiota: Their Roles in Disease Pathogenesis and Immune System Regulation

The relationship between microbiota and the immune system is complex and characterized by the ways in which microbiota directs immune function interactions, both innate and acquired and also keeps activating the immune system throughout an individual's life. In this respect, the human Major Histocompatibility Complex (MHC, referred to as HLA in humans) plays a crucial role and is also established in self-defense against microbes by presenting microbial-derived peptides to the immune cells. However, this assumption has some unclear aspects that should be investigated. For example, how is the microbiota shaped by microbe species diversity, quantity and functions of the immune system, as well as the role and molecular mechanisms of the HLA complex during this process. There are autoimmune diseases related to both HLA and specific microbiota changes or alterations, many of which are mentioned in the present review. In addition, the HLA peptide presenting function should be put in a framework together with its linkage to diseases and also with HLA compatibility necessary for transplants to be successful. These are still quite an enigmatically statistical and phenomenological approach, but no firm pathogenic mechanisms have been described; thus, HLA's real functioning is still to be fully unveiled. After many years of HLA single-genes studies, firm pathogenesis mechanisms underlying disease linkage have been discovered. Finally, microbiota has been defined as conformed by bacteria, protozoa, archaea, fungi, and viruses; notwithstanding, endogenous viral sequences integrated into the human genome and other viral particles (obelisks) recently found in the digestive mucosa should be taken into account because they may influence both the microbiome and the immune system and their interactions. In this context, we propose to integrate these microbial-genetic particle components into the microbiome concept and designate it as "microgenobiota".

Concurrent RB1 Loss and BRCA Deficiency Predicts Enhanced Immunologic Response and Long-term Survival in Tubo-ovarian High-grade Serous Carcinoma

PURPOSE

The purpose of this study was to evaluate RB1 expression and survival across ovarian carcinoma histotypes and how co-occurrence of BRCA1 or BRCA2 (BRCA) alterations and RB1 loss influences survival in tubo-ovarian high-grade serous carcinoma (HGSC).

EXPERIMENTAL DESIGN

RB1 protein expression was classified by immunohistochemistry in ovarian carcinomas of 7,436 patients from the Ovarian Tumor Tissue Analysis consortium. We examined RB1 expression and germline BRCA status in a subset of 1,134 HGSC, and related genotype to overall survival (OS), tumor-infiltrating CD8+ lymphocytes, and transcriptomic subtypes. Using CRISPR-Cas9, we deleted RB1 in HGSC cells with and without BRCA1 alterations to model co-loss with treatment response. We performed whole-genome and transcriptome data analyses on 126 patients with primary HGSC to characterize tumors with concurrent BRCA deficiency and RB1 loss.

RESULTS

RB1 loss was associated with longer OS in HGSC but with poorer prognosis in endometrioid ovarian carcinoma. Patients with HGSC harboring both RB1 loss and pathogenic germline BRCA variants had superior OS compared with patients with either alteration alone, and their median OS was three times longer than those without pathogenic BRCA variants and retained RB1 expression (9.3 vs. 3.1 years). Enhanced sensitivity to cisplatin and paclitaxel was seen in BRCA1-altered cells with RB1 knockout. Combined RB1 loss and BRCA deficiency correlated with transcriptional markers of enhanced IFN response, cell-cycle deregulation, and reduced epithelial-mesenchymal transition. CD8+ lymphocytes were most prevalent in BRCA-deficient HGSC with co-loss of RB1.

CONCLUSIONS

Co-occurrence of RB1 loss and BRCA deficiency was associated with exceptionally long survival in patients with HGSC, potentially due to better treatment response and immune stimulation.

Identification of 43 novel HLA alleles by PacBio single molecule real-time sequencing in haematopoietic cell donors

A total of 43 novel HLA alleles detected in haematopoietic cell donors using single molecule real-time DNA sequencing.

Haplotype Analysis Reveals Pleiotropic Disease Associations in the HLA Region

The human leukocyte antigen (HLA) region plays an important role in human health through involvement in immune cell recognition and maturation. While genetic variation in the HLA region is associated with many diseases, the pleiotropic patterns of these associations have not been systematically investigated. Here, we developed a haplotype approach to investigate disease associations phenome-wide for 412,181 Finnish individuals and 2,459 traits. Across the 1,035 diseases with a GWAS association, we found a 17-fold average per-SNP enrichment of hits in the HLA region. Altogether, we identified 7,649 HLA associations across 647 traits, including 1,750 associations uncovered by haplotype analysis. We find some haplotypes show trade-offs between diseases, while others consistently increase risk across traits, indicating a complex pleiotropic landscape involving a range of diseases. This study highlights the extensive impact of HLA variation on disease risk, and underscores the importance of classical and non-classical genes, as well as non-coding variation.

The influence of HLA genetic variation on plasma protein expression

Genetic variation in the human leukocyte antigen (HLA) loci is associated with risk of immune-mediated diseases, but the molecular effects of HLA polymorphism are unclear. Here we examined the effects of HLA genetic variation on the expression of 2940 plasma proteins across 45,330 Europeans in the UK Biobank, with replication analyses across multiple ancestry groups. We detected 504 proteins affected by HLA variants (HLA-pQTL), including widespread trans effects by autoimmune disease risk alleles. More than 80% of the HLA-pQTL fine-mapped to amino acid positions in the peptide binding groove. HLA-I and II affected proteins expressed in similar cell types but in different pathways of both adaptive and innate immunity. Finally, we investigated potential HLA-pQTL effects on disease by integrating HLA-pQTL with fine-mapped HLA-disease signals in the UK Biobank. Our data reveal the diverse effects of HLA genetic variation and aid the interpretation of associations between HLA alleles and immune-mediated diseases.

Simultaneous de novo calling and phasing of genetic variants at chromosome-scale using NanoStrand-seq

The successful accomplishment of the first telomere-to-telomere human genome assembly, T2T-CHM13, marked a milestone in achieving completeness of the human reference genome. The upcoming era of genome study will focus on fully phased diploid genome assembly, with an emphasis on genetic differences between individual haplotypes. Most existing sequencing approaches only achieved localized haplotype phasing and relied on additional pedigree information for further whole-chromosome scale phasing. The short-read-based Strand-seq method is able to directly phase single nucleotide polymorphisms (SNPs) at whole-chromosome scale but falls short when it comes to phasing structural variations (SVs). To shed light on this issue, we developed a Nanopore sequencing platform-based Strand-seq approach, which we named NanoStrand-seq. This method allowed for de novo SNP calling with high precision (99.52%) and acheived a superior phasing accuracy (0.02% Hamming error rate) at whole-chromosome scale, a level of performance comparable to Strand-seq for haplotype phasing of the GM12878 genome. Importantly, we demonstrated that NanoStrand-seq can efficiently resolve the MHC locus, a highly polymorphic genomic region. Moreover, NanoStrand-seq enabled independent direct calling and phasing of deletions and insertions at whole-chromosome level; when applied to long genomic regions of SNP homozygosity, it outperformed the strategy that combined Strand-seq with bulk long-read sequencing. Finally, we showed that, like Strand-seq, NanoStrand-seq was also applicable to primary cultured cells. Together, here we provided a novel methodology that enabled interrogation of a full spectrum of haplotype-resolved SNPs and SVs at whole-chromosome scale, with broad applications for species with diploid or even potentially polypoid genomes.

The influence of HLA allele and haplotype on RhE alloimmunization among pregnant females in the Chinese Han population

BACKGROUND AND OBJECTIVES

Anti-E alloantibody is the most common and important red blood cell (RBC) alloantibody during pregnancy. The study aimed to determine the correlation between RhE alloimmunization and human leukocyte antigen (HLA) allele polymorphism, as well as haplotype diversity, among pregnant individuals in the Chinese Han population.

STUDY DESIGN AND METHODS

All individuals included in our study were RhE-negative pregnant women of Chinese Han ethnicity, confirmed through serological testing. Pregnancy could be the only potential stimulating factor in RBC alloimmunization. Given the serological testing, the participants were divided into anti-E (responders) and non-anti-E-producing group (non-responders). The class I and II classical HLA genotyping were determined using next-generation sequencing, and the HLA genotype and haplotype frequencies were compared between the responders and non-responders.

RESULTS

In total, 76 responders and 94 non-responders were enrolled in this study. Comparison results showed that all HLA class I alleles had no difference between the two groups. For HLA class II phenotypes, responders had higher frequencies of HLA-DRB1*09:01, HLA-DQA1*03:02 and HLA-DQB1*03:03 phenotypes than non-responders, and the differences were statistically significant (pc < 0.05). In addition, the haplotype frequency of HLA-DRB1*09:01-DQA1*03:02-DQB1*03:03 in the RhE responders was significantly higher than in the non-responders (31.58% vs. 12.77%; odds ratio, 3.154; 95% confidence interval, 1.823-5.456; pc value, 1.25 × 10-3).

CONCLUSION

Our findings indicated that HLA-DRB1*09:01, HLA-DQA1*03:02 and HLA-DQB1*03:03 might be susceptible alleles for RhE alloimmunization among Chinese Han pregnant females. These three susceptible alleles constituted the unique three-locus haplotype in the RhE responders and collaborated to RhE alloimmunization.

Complex immune microenvironment of chordoma: a road map for future treatment

BACKGROUND

Chordoma, a rare bone tumor, presents limited treatment options and patients typically exhibit poor survival outcomes. While immunotherapy has shown promising results in treating various tumors, research on the immune microenvironment of chordomas is still in its early stages. Therefore, understanding how the immune microenvironment of chordomas influences the outcomes of immunotherapy is crucial.

METHODS

We employed single-cell RNA sequencing (scRNA-seq), bulk RNA-seq, CellChat, gene set variation analysis, as well as calculation of immune features to further dissect the complex immune microenvironment of chordoma.

RESULTS

Previous research by van Oost et al argued that compared with other sarcomas, chordomas typically exhibit an immunologically "hot" microenvironment, a conclusion with which we concur based on their research findings. Additionally, the authors suggest that T cell-mediated immunotherapy is feasible for the majority of chordomas. However, we are inclined to categorize them as an immune-excluded phenotype according to the latest classification methods, rather than persisting with the concepts of "cold" and "hot". Unlike them, we explored immune infiltration scores (IS), T lymphocyte scoring (TLS), and human leucocyte antigen class I (HLA-I) using Bulk RNA-seq data from 126 chordoma patients and found that higher IS, TLS, and higher HLA-I expression were associated with poorer patient prognosis. Additionally, CellChat analysis of scRNA-seq results from six chordoma patients revealed no direct interaction between T cells and tumor cells.

CONCLUSIONS

These findings suggested that the efficacy of T cell-based immunotherapy may be limited or even ineffective for patients with chordoma.

Fast and flexible joint fine-mapping of multiple traits via the Sum of Single Effects model

We introduce mvSuSiE, a multi-trait fine-mapping method for identifying putative causal variants from genetic association data (individual-level or summary data). mvSuSiE learns patterns of shared genetic effects from data, and exploits these patterns to improve power to identify causal SNPs. Comparisons on simulated data show that mvSuSiE is competitive in speed, power and precision with existing multi-trait methods, and uniformly improves on single-trait fine-mapping (SuSiE) in each trait separately. We applied mvSuSiE to jointly fine-map 16 blood cell traits using data from the UK Biobank. By jointly analyzing the traits and modeling heterogeneous effect sharing patterns, we discovered a much larger number of causal SNPs (>3,000) compared with single-trait fine-mapping, and with narrower credible sets. mvSuSiE also more comprehensively characterized the ways in which the genetic variants affect one or more blood cell traits; 68% of causal SNPs showed significant effects in more than one blood cell type.

The 18th International HLA & Immunogenetics workshop project report: Creating fully representative MHC reference haplotypes

A fundamental endeavor of the International Histocompatibility and Immunogenetics Workshop (IHIW) was assembling a collection of DNA samples homozygous through the MHC genomic region. This collection proved invaluable for assay development in the histocompatibility and immunogenetics field, for generating the human reference genome, and furthered our understanding of MHC diversity. Defined by their HLA-A, -B, -C and -DRB1 alleles, the combined frequency of the haplotypes from these individuals is ~20% in Europe. Thus, a significant proportion of MHC haplotypes, both common and rare throughout the world, and including many associated with disease, are not yet represented. In this workshop component, we are collecting the next generation of MHC -homozygous samples, to expand, diversify and modernize this critical community resource that has been foundational to the field. We asked laboratories worldwide to identify samples homozygous through all HLA class I and/or HLA class II genes, or through whole-genome SNP genotyping or sequencing, to have extensive homozygosity tracts within the MHC region. The focus is non-Europeans or those having HLA haplotypes less common in Europeans. Through this effort, we have obtained samples from 537 individuals representing 294 distinct haplotypes, as determined by their HLA class I and II alleles, and an additional 50 haplotypes distinct in HLA class I or II alleles. Although we have expanded the diversity, many populations remain underrepresented, particularly from Africa, and we encourage further participation. The data will serve as a resource for investigators seeking to characterize variation across the MHC genomic region for disease and population studies.

HLA typing: A review of methodologies and clinical impact on haematopoietic cell transplantation

The importance of the HLA gene system in haematopoietic cell transplant outcomes was established early on and advances in both fields have led to ever increasing success of this clinical therapy. In large part, improvements in the understanding of HLA have been driven by the advancement in typing technologies. Each iteration of typing technology has improved the resolution of HLA typing, and often enabled the identification of polymorphism within the HLA loci. The discovery of the enormous amount of variation in the HLA genes, and the need to be able to characterise this for clinical HLA typing, has often resulted in a move away from one typing method to another more suited to typing of this complexity. Today, the gold standard for HLA typing are methods that can produce definitive HLA typing results.

25 years of the IPD-IMGT/HLA Database

Twenty-five years ago, in 1998, the HLA Informatics Group of the Anthony Nolan Research Institute released the IMGT/HLA Database. Since this time, this online resource has acted as the repository for the numerous variant sequences of HLA alleles named by the WHO Nomenclature Committee for Factors of the HLA System. The IPD-IMGT/HLA Database has provided a stable, highly accessible, user-friendly repository for this work. During this time, the technology underlying HLA typing has undergone significant changes. Next generation sequencing (NGS) has superseded previous methodologies of HLA typing and can generate large amounts of high-resolution sequencing data. This has resulted in a drastic increase in the number and complexity of sequences submitted to the database. The challenge for the IPD-IMGT/HLA Database has been to maintain the highest standards of curation, while supporting the core set of tools and functionality to our users with increased numbers of submissions and sequences. Traditional methods of accessing and presenting data have been challenged and new methods utilising new computing technologies have had to be developed to keep pace and support a shifting user demographic.