HLA-A Research Articles

Letter to the Editor: Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection

Letter to the Editor: Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection

Active immunological participation and metabolic shutdown of kidney structural cells during kidney transplant rejection

Contrary to immune cells, the response of the kidney structural cells in rejection is less established. We performed single-cell RNA sequencing on 18 kidney transplant biopsies from 14 recipients.Single-cell RNA sequencing identified cells from the major compartments of the kidney, next to infiltrated immune cells. Endothelial cells from the glomerulus, peritubular capillaries and vasa recta showed upregulation of class I and II HLA genes, adhesion molecules and cytokines and chemokines, suggesting an active participation in the alloimmune process, with compartment-specific differences. Epithelial cells including proximal tubular, loop of Henle and collecting duct cells, also showed increased expression of immune genes. Strikingly, in proximal tubule cells a strong downregulation of energy metabolism upon inflammation was observed. There was a large overlap between the cell-specific expression changes upon alloimmune inflammation and those observed in two large micro-array biopsy cohorts.In conclusion, the kidney structural cells, being the main target of the alloimmune process, appear to actively contribute herein, enhancing the damaging effects of the infiltrating immune cells. In epithelial cells, a profound shutdown of metabolism was seen upon inflammation, which associated with poor kidney function. These observations highlight the critical role of the graft in triggering and sustaining rejection after transplantation.

Transcriptomic Analysis of the Effect of Glabridin on Biofilm Formation in Staphylococcus Aureus.

Staphylococcus aureus (S. aureus) is among the major skin infection-causing pathogens in animals and humans. Its ability to form biofilms has become a foremost cause of bacterial infections and the extensive spread of drug resistance, which poses a great difficulty in clinical treatment. Glabridin (Glb), an extract of licorice with antibacterial and anti-infective properties, has a partially understood biofilm-inhibitory mechanism. This study investigated the inhibitory and antibiofilm activities of subinhibitory concentrations of Glb against S. aureus. The crystal violet assay revealed that Glb significantly suppressed biofilm expression. Scanning electron microscopy observations unveiled that Glb reduced S. aureus adhesion and accumulation by disrupting the spatial structure of the biofilm. In vitro extracellular DNA (eDNA) inhibition assays demonstrated that Glb inhibited biofilm formation by S. aureus by suppressing eDNA secretion. In total, 184 differentially expressed genes were obtained through transcriptomic (RNA-seq) sequencing, of which 81 and 103 genes were upregulated and downregulated, respectively. Glb regulated the transcript levels of biofilm-related genes through the phosphatase transfer system, two-component regulatory system, and nitrogen metabolism. The qPCR analysis was performed to confirm whether Glb interfered with the expression of regulatory genes involved in S. aureus biofilm formation (SarA, ArlR, FnbA, ClfA, icaD, and icaR) as well as the virulence gene Hla. In conclusion, this study demonstrates that Glb has a significant inhibitory effect on biofilm activity and is expected to be a good antibiofilm drug.

TMT-Based Quantitative Proteomics Revealed the Antibacterial Mechanism of Cinnamaldehyde against MRSA.

Natural plant extracts have demonstrated significant potential in alternative antibiotic therapies. Cinnamaldehyde (CA) has garnered considerable attention as a natural antibacterial agent. In this study, Tandem mass tag (TMT) quantitative proteomics combined with Western blot and RT-qPCR methods were employed to explore the antibacterial mechanism of CA against Methicillin-Resistant Staphylococcus aureus (MRSA) at the protein level. The results showed that a total of 254 differentially expressed proteins (DEPs) were identified in the control group and CA treatment group, of which 161 were significantly upregulated and 93 were significantly downregulated. DEPs related to nucleotide synthesis, homeostasis of the internal environment, and protein biosynthesis were significantly upregulated, while DEPs involved in the cell wall, cell membrane, and virulence factors were significantly downregulated. The results of GO and KEGG enrichment analyses demonstrated that CA could exert its antibacterial effects by influencing pyruvate metabolism, the tricarboxylic acid (TCA) cycle, teichoic acid biosynthesis, and the Staphylococcus aureus (S. aureus) infection pathway in MRSA. CA significantly inhibited the expression of recombinant protein MgrA (p < 0.05), significantly reduced the mRNA transcription levels of mgrA, hla, and sdrD genes (p < 0.05), and thermostability migration assays demonstrated that CA can directly interact with MgrA protein, thereby inhibiting its activity. These findings suggest that CA exerts its antibacterial mechanism by regulating the expression of related proteins, providing a theoretical basis for further development of clinical applications of antimicrobial agents derived from natural plant essential oils in the treatment of dairy cow mastitis.

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.

C G composition in transposon-derived genes is increased in FXD with perturbed immune system.

Increasing incidence of Fragile X disorders (FXD) and of immune-mediated disorders in FXD suggests that additional factors besides FMR1 mutations contribute to the pathogenesis. Here, we discovered that the expression levels or splicing of specific transposon element (TE)-derived genes, regulating purine metabolism and immune responses against viral infections are altered in FXD. These genes include HLA genes clustered in chr6p21.3 and viral responsive genes in chr5q15. Remarkably, these TE-derived genes contain a low A T/C G suggesting base substitutions of A T to C G. The TE-derived genes with changed expression levels contained a higher content of 5'-CG-3' dinucleotides in FXD compared to healthy donors. This resembles the genomes of some RNA viruses, which maintain high contents of CG dinucleotides to sustain their latent infection exploiting antiviral responses. Thus, past viral infections may have persisted as TEs, provoking immune-mediated disorders in FXD.

Schizophrenia and Rheumatoid Arthritis Genetic Scenery: Potential Non-HLA Genes Involved in Both Diseases Relationship.

Background: The link between rheumatoid arthritis (RA) and schizophrenia (SZ) has long been a hot topic of deliberation among scientists from various fields. Especially when it comes to genetics, the connection between RA and SZ is still up for discussion, as can be observed in this study. The HLA genes are the most disputed in identifying a connection between the two diseases, but a more thorough investigation of other genes that may be ignored could yield something even more interesting. Thus, finding the genes responsible for this long-sought relationship will necessitate looking for them. Materials and Methods: Shared and overlapped associated genes involved between SZ and RA were extracted from four databases. The overlapping genes were examined using Database for Annotation, Visualization and Integrated Discovery (DAVID) and InnateDB to search the pertinent genes that concatenate between these two disorders. Results: A total of 91 overlapped genes were discovered, and that 13 genes, divided into two clusters, showed a similarity in function, suggesting that they may serve as an important meeting point. FCGR2A, IL18R, BTNL2, AGER, and CTLA4 are five non-HLA genes related to the immune system, which could lead to new discoveries about the connection between these two disorders. Conclusion: An in-depth investigation of these functionally comparable non-HLA genes that overlap could reveal new interesting information in both diseases. Understanding the molecular and immune-related aspects of RA and SZ may shed light on their etiology and inform future research on targeted treatment strategies.

Detection of Virulence Genes Hla (α-hemolysis), CrtN (staphyloxanthin) for Staphylococcus aureus Isolated from Patients with Otitis and Rhinitis

Staphylococcus aureus is a bacterium that is capable of causing several types of infections acquired in hospitals and other healthcare facilities. The presence of S. aureus in the nasal cavity is significant for both the spread and development of infection. The goal of this study is to detect some virulence genes hla and CrtN of S. aureus. Thirty samples were collected from patients with otitis, and nose and throat infection from Al-Ramadi Teaching Hospital and external Labs for the period December 2021 to February 2022. Oti¬tis and Rhinitis swabs were taken from the patients and cultured on Mannitol salt agar and blood agar then gram stain and biochemical test were done. DNA was extracted from these isolates, and PCR was used to detect 16s rRNA, hla, and CrtN genes. The results showed after the phenotypic, microscopic, and biochem¬ical test, 20 isolates were referred to as S. aureus, which is approximately 66.6% of the total samples. The infection rate among youth and children was higher than that of the elderly and children in particular. Most bacterial infections of the pharynx, nose, and throat are the cause of S. aureus about 90%. DNA extract from 20 positive samples for S. aureus, the diagnosis of the samples was confirmed by 16s rRNA gene. The PCR results showed 18 samples carrying the hla gene by 90% of the total samples, while only 14 samples were carrying the CrtN gene at 80%.

Clinical application of sparse canonical correlation analysis to detect genetic associations with cortical thickness in Alzheimer's disease.

Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by cerebral cortex atrophy. In this study, we used sparse canonical correlation analysis (SCCA) to identify associations between single nucleotide polymorphisms (SNPs) and cortical thickness in the Korean population. We also investigated the role of the SNPs in neurological outcomes, including neurodegeneration and cognitive dysfunction. We recruited 1125 Korean participants who underwent neuropsychological testing, brain magnetic resonance imaging, positron emission tomography, and microarray genotyping. We performed group-wise SCCA in Aβ negative (-) and Aβ positive (+) groups. In addition, we performed mediation, expression quantitative trait loci, and pathway analyses to determine the functional role of the SNPs. We identified SNPs related to cortical thickness using SCCA in Aβ negative and positive groups and identified SNPs that improve the prediction performance of cognitive impairments. Among them, rs9270580 was associated with cortical thickness by mediating Aβ uptake, and three SNPs (rs2271920, rs6859, rs9270580) were associated with the regulation of CHRNA2, NECTIN2, and HLA genes. Our findings suggest that SNPs potentially contribute to cortical thickness in AD, which in turn leads to worse clinical outcomes. Our findings contribute to the understanding of the genetic architecture underlying cortical atrophy and its relationship with AD.

HLA gene polymorphism is a modifier of age-related breast cancer penetrance in carriers of BRCA1 pathogenic alleles

HLA gene polymorphism is a modifier of age-related breast cancer penetrance in carriers of BRCA1 pathogenic alleles

Prevalence of Human Leukocyte Antigen Alleles Polymorphism in North Indian Population

Background Human leukocyte antigens (HLA) are highly polymorphic glycoproteins required for immune response and recognizing self or non-self. Knowing the HLA diversity in a population may be helpful in the selection of organ allocation for transplantation. We aimed to retrospectively analyze the prevalence of HLA, A, B, C, DRB1, and DQA1 alleles frequency in the north Indian population. Materials and Methods HLA antigen allele data were retrospectively analyzed from a transplant cohort of 2259 subjects. HLA-A, B, and DRB1 frequency were determined in 2259, HLA-C in 759 and DQA1 in 751 subjects. Results The most abundant HLA-A antigen alleles were HLA-A*01(25.41%), HLA-A*02 (24.83%), HLA-A*11 (17.53%), HLA-A*24 (10.27%), HLA-A*03 (9.07%). HLA-B antigen alleles were HLA-B*35 (20.54%), HLA-B*15 (15.36%), HLA-B*40 (13.59%), HLA-B*07 (10.14%), HLA-B*44 (7.79). HLA-C antigen alleles were HLA-C*07 (28.06%), HLA-C*04 (20.42%), HLA-C*03 (15.55%), HLA-C*06 (13.04%), HLA-C*12 (5.27%). HLA-DRB1 alleles were HLA-DRB1*07 (21.60%), HLA-DRB1*04 (19.74%), HLA-DRB1*10 (13.15%), HLA-DRB1*03 (10.80%), HLA-DRB1*11 (8.63%). HLA-DQA1 antigen alleles were HLA-DQA1*03 (35.42%), HLA-DQA1*02 (30.89%), HLA-DQA1*05 (21.84%), HLA-DQA1* 06 (10.12%), HLA-DQA1*04 (1.07%). Conclusion The most frequent HLA alleles were HLA-A*01(25.41%), HLA-B*35 (20.54%), HLA-C*07 (28.06%), HLA-DRB1*07(21.60%), HLA-DQA1*03(35.42%) in north Indian population.

Differential modulation of mutant CALR and JAK2 V617F-driven oncogenesis by HLA genotype in myeloproliferative neoplasms.

It has been demonstrated previously that human leukocyte antigen class I (HLA-I) and class II (HLA-II) alleles may modulate JAK2 V617F and CALR mutation (CALRmut)-associated oncogenesis in myeloproliferative neoplasms (MPNs). However, the role of immunogenetic factors in MPNs remains underexplored. We aimed to investigate the potential involvement of HLA genes in CALRmut+ MPNs. High-resolution genotyping of HLA-I and -II loci was conducted in 42 CALRmut+ and 158 JAK2 V617F+ MPN patients and 1,083 healthy controls. A global analysis of the diversity of HLA-I genotypes revealed no significant differences between CALRmut+ patients and controls. However, one HLA-I allele (C*06:02) showed an inverse correlation with presence of CALR mutation. A meta-analysis across independent cohorts and healthy individuals from the 1000 Genomes Project confirmed an inverse correlation between the presentation capabilities of the HLA-I loci for JAK2 V617F and CALRmut-derived peptides in both patients and healthy individuals. scRNA-Seq analysis revealed low expression of TAP1 and CIITA genes in CALRmut+ hematopoietic stem and progenitor cells. In conclusion, the HLA-I genotype differentially restricts JAK2 V617F and CALRmut-driven oncogenesis potentially explaining the mutual exclusivity of the two mutations and differences in their presentation latency. These findings have practical implications for the development of neoantigen-based vaccines in MPNs.

HLA A10 spurious reactivity with single antigen beads investigated

HLA A10 spurious reactivity with single antigen beads investigated

Identification of Biomarkers for Endometrial Cancer Based on Natural Killer Cell-Related Genes

Endometrial cancer (EC) is a malignant tumor. Natural killer (NK) cells play a crucial role in various cancers, but their role in EC is unclear. To this purpose, in this paper, differential expression analysis was performed on transcriptome data from the TCGA database, and the obtained DEGs and the collected NRGs were intersected, and single-factor Cox regression analysis and Lasso-Cox regression analysis were performed on the intersected genes to obtain prognosis-related genes and risk model, respectively. These genes and models were validated by Kaplan-Meier (KM) survival curve analysis and ROC analysis on the internal and external test sets. In addition, nomogram models were constructed based on prognosis-associated genes, sample risk scores, and clinical factors. Finally, we explored the immune landscape of high- and low-risk groups of EC. The results showed that the risk models constructed in this paper exhibited excellent predictive effects, which will facilitate research on the precision treatment of EC. There were significant differences in prognosis, immune cell infiltration abundance, immune checkpoint-associated genes, and HLA gene expression between high- and low-risk groups of EC. The risk model in this paper can provide a reference for the personalized treatment of EC. In addition, we performed RT-qPCR to validate the levels of genes significantly associated with prognosis.

Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data.

In addition to the classical HLA genes, the major histocompatibility complex (MHC) harbors a high number of other polymorphic genes with less established roles in disease associations and transplantation matching. To facilitate studies of the non-classical and non-HLA genes in large patient and biobank cohorts, we trained imputation models for MICA, MICB, HLA-E, HLA-F and HLA-G alleles on genome SNP array data. We show, using both population-specific and multi-population 1000 Genomes references, that the alleles of these genes can be accurately imputed for screening and research purposes. The best imputation model for MICA, MICB, HLA-E, -F and -G achieved a mean accuracy of 99.3% (min, max: 98.6, 99.9). Furthermore, validation of the 1000 Genomes exome short-read sequencing-based allele calling against a clinical-grade reference data showed an average accuracy of 99.8%, testifying for the quality of the 1000 Genomes data as an imputation reference. We also fitted the models for Infinium Global Screening Array (GSA, Illumina, Inc.) and Axiom Precision Medicine Research Array (PMRA, Thermo Fisher Scientific Inc.) SNP content, with mean accuracies of 99.1% (97.2, 100) and 98.9% (97.4, 100), respectively.

Like a Rolling Stone? A Review on Spontaneous Clearance of Hepatitis C Virus Infection.

Elimination of hepatitis C virus (HCV) without the need for medical intervention, known as spontaneous clearance (SC), occurs at a significantly lower rate than in the case of hepatitis B virus infection and only in selected individuals, such as reportedly in Keith Richards, a guitarist of The Rolling Stones. The present paper provides an updated narrative review of the research devoted to the phenomenon in order to identify and discuss the demographic, lifestyle-related, clinical, viral genotype-related, and host genetic factors underpinning the SC occurrence. The body of evidence indicates that the likelihood of SC is decreased in older individuals, men, Black people, HIV-coinfected subjects, and intravenous drug and alcohol users. In turn, HBV coinfection and specific polymorphism of the genes encoding interferon lambda 3 (particularly at rs8099917) and interferon lambda 4 (particularly at rs12979860) and HLA genes increase the odds of SC. Numerous other host-specific genetic factors could be implicated in SC, but the evidence is limited only to certain ethnic groups and often does not account for confounding variables. SC of HCV infection is a complex process arising from a combination of various factors, though a genetic component may play a leading role in some cases. Understanding factors influencing the likelihood of this phenomenon justifies better surveillance of high-risk groups, decreasing health inequities in particular ethnic groups, and may guide the development of a prophylactic vaccine, which at present is not available, or novel therapeutic strategies. Further research is needed to elucidate the exact mechanisms underlying SC and to explore potential interventions that could enhance this natural antiviral response.

Telomere Length, HLA, and Longevity-Results from a Multicenter Study.

Aging is an exceptionally complex process that depends on genetic, environmental, and lifestyle factors. Previous studies within the International HLA and Immunogenetics Workshop (IHIWS) component "Immunogenetics of Ageing" showed that longevity is associated with positive selection of HLA-DRB1*11- and DRB1*16-associated haplotypes, shown to be protective against diseases. Within the 18th IHIWS, we aimed to investigate the relevance of telomere length for successful aging and its association with classical HLAs. In total 957 individuals from Bulgaria, Turkey, Romania, and Poland in two age groups, elderly individuals (age 65-99 years) and ethnically matched young group (age 18-64 years), were investigated. The obtained results confirmed interpopulation differences in the distribution of HLA alleles, documented the lengths of telomeres in analyzed populations, and demonstrated significant associations of telomere length with aging as well as with the presence of some HLA class I or class II alleles. They suggest that telomere length assessment combined with HLA genotyping may help identify immunogenetic profiles associated with longevity. The associations between HLA and telomeres support the theory that HLA genes influence the aging process. However, further research is needed to clarify the biological basis of the observed relationships.

Unveiling the Molecular Features of SCLC With a Clinical RNA Expression Panel

IntroductionThe translation of gene expression profiles of SCLC to clinical testing remains relatively unexplored. In this study, gene expression variations in SCLC were evaluated to identify potential biomarkers. MethodsRNA expression profiling was performed on 44 tumor samples from 35 patients diagnosed with SCLC using the clinically validated RNA Salah Targeted Expression Panel (RNA STEP). RNA sequencing (RNA-Seq) and immunohistochemistry were performed on two different SCLC cohorts, and correlation analyses were performed for the ASCL1, NEUROD1, POU2F3, and YAP1 genes and their corresponding proteins. RNA STEP and RNA-Seq results were evaluated for gene expression profiles and heterogeneity between SCLC primary and metastatic sites. RNA STEP gene expression profiles of independent SCLC samples (n = 35) were compared with lung adenocarcinoma (n = 160) and squamous cell carcinoma results (n = 25). ResultsThe RNA STEP results were highly correlated with RNA-Seq and immunohistochemistry results. The dominant transcription regulator by RNA STEP was ASCL1 in 74.2% of the samples, NEUROD1 in 20%, and POU2F3 in 2.9%. The ASCL1, NEUROD1, and POU2F3 gene expression profiles were heterogeneous between primary and metastatic sites. SCLCs displayed markedly high expression for targetable genes DLL3, EZH2, TERT, and RET. SCLCs were found to have relatively colder immune profiles than lung adenocarcinomas and squamous cell carcinomas, characterized by lower expression of HLA genes, immune cell, and immune checkpoint genes, except the LAG3 gene. ConclusionsClinical-grade SCLC RNA expression profiling has value for SCLC subtyping, design of clinical trials, and identification of patients for trials and potential targeted therapy.

RNAseq-differentiated gene expression profile of people living with HTLV-1 in the Brazilian Amazon region: a pilot study

In this study, we aimed investigated the differential gene expression profiles of samples from uninfected individuals (control group) and study groups of asymptomatic human T-lymphotropic virus 1 (HTLV-1) carriers and patients with HTLV-1-associated myelopathy (HAM) by exploratory RNA sequencing (RNA-Seq) analysis. The gene expression profiles of individuals in the asymptomatic group were represented by 3 genes, most associated with cell cycle regulation. The gene expression profiles of individuals in the HAM group were represented by 12 genes, the majority of which are associated with the immune response. The HLA-A gene and the non-coding RNA LINC02470 were upregulated in the asymptomatic and HAM groups. The HLA-DQB1 and HLA-C genes were downregulated in the asymptomatic and HAM groups. In this pilot study, although limited in terms of methodological rigor, we showed differential gene expression profiles in different clinical groups of HTLV-1 infection. However, further studies are needed to confirm these findings.

HLA-DQA1*05 associates with anti-TNF immunogenicity and low adalimumab trough concentrations in inflammatory bowel disease patients from the SERENE UC and CD studies.

Anti-tumor necrosis factor (anti-TNF) therapies are commonly prescribed treatments for Crohn's Disease (CD) and Ulcerative Colitis (UC). Many patients treated with anti-TNF therapy eventually develop anti-drug antibodies (ADA). Understanding the factors associated with immunogenicity in anti-TNF treated patients can help guide treatment. The Humira SERENE studies were phase 3 trials studying adalimumab induction regimens in CD and UC patients. We imputed alleles for 7 HLA genes in 1100 patients from the SERENE CD and SERENE UC trials. We tested these alleles for association with time to immunogenicity. We then tested loci significantly associated with immunogenicity for association with patients that had consistently low drug-serum concentrations. This study replicated the association of HLA-DQA1*05 with time to immunogenicity (Hazard Ratio (HR) 1.42, P=2.22E-06). Specifically, HLA-DQA1*05:05 was strongly associated (HR 1.76, P=2.02E-10) and we detected a novel association represented by HLA-DRB1*01:02 (HR 3.16, P=2.92E-07). Carriage of HLA-DQA1*05:05 and HLA-DRB1*01:02 were both associated with patients who experienced consistently low adalimumab trough concentrations (HLA-DQA1*05:05 OR 1.98, P=0.0049; HLA DRB1*01:02 OR 7.06, P=7.44E-05). We found a significant association between alleles at genes in the human HLA locus and the formation of adalimumab immunogenicity and low adalimumab drug-serum concentrations in large clinical studies of CD and UC patients. This work extends previous results in Crohn's disease to ulcerative colitis and directly shows a genetic association in patients with low drug concentrations. This work builds on existing literature to suggest genetic screening as a useful tool for clinicians concerned with patient anti-TNF immunogenicity.