Novel alleles in the era of next-generation sequencing-based HLA typing calls for standardization and policy

Anti-HLA antibodies may be a subset of polyreactive immunoglobulins generated after viral superinfection

Chronic rejection remains an obstacle to long-term allograft survival. Donor-specific anti-HLA antibodies (DSA) play a significant role in causing chronic antibody-mediated allograft rejection. Exposure to mismatched HLA antigens via transfusion, pregnancy, or transplanted tissue has been described in the literature as an immunogenic stimulus of anti-HLA antibodies. Yet anti-HLA antibodies also develop in the absence of traditional sensitization events and molecular mimicry has been postulated as a stimulus for these naturally occurring alloantibodies. While heterologous reactivity has been documented between virus components and allogeneic T cells, there is insufficient evidence to support the development of anti-HLA antibodies from viral components. We hypothesized that anti-HLA antibodies may develop following viral coinfection or superinfection. The objectives of this investigation included: 1) developing an in-silico algorithm to identify viral peptide components that exhibit HLA-specific homology, and 2) identifying cellular changes that take place during ischemia/reperfusion injury which could facilitate the generation of novel anti-HLA antibodies from viral sources. We developed the neoepitope transplant rejection and autoimmune disease (NETRAD) algorithm to identify amino acid sequence homology between viral envelope proteins and HLA. The algorithm integrates post-translational protein modifications that are consistent with ischemia/reperfusion injury. Seventy-two HLA-specific epitopes were demarcated as examples using this approach. In conclusion, we present in-silico evidence which supports the identification of anti-HLA antibodies as a subset of polyreactive antibodies generated from stress-modified viral envelope proteins. Remarkably, each targeted HLA epitope associated with a distinct anti-HLA antibody could be consistently attributed to a major envelope glycoprotein component of Epstein Barr virus. Transplant Immunology manuscript # TRIM-D-24-00351. Dryad data repository:https://doi.org/10.5061/dryad.qjq2bvqpq.

Kidney transplantation in Lupus Nephritis: a comprehensive review of challenges and strategies

PURPOSE OF REVIEW: Lupus nephritis (LN) is a severe complication of systemic lupus erythematosus (SLE), significantly impacting patient outcomes. Despite advances in immunosuppressive therapies, many patients progress to end-stage renal disease (ESRD), and kidney transplantation becomes essential for improving survival. However, the unique characteristics of autoimmune diseases make the timing of kidney transplantation and post-transplant management challenging. This review evaluates authoritative guidelines and recent studies to identify optimal timing for kidney transplantation and effective pre- and post-transplant management measures for patients with LN. RECENT FINDINGS: Advancements in immunosuppressive therapies, including calcineurin inhibitors, Voclosporin, and biologic agents such as belimumab, have significantly improved LN management. Emerging biomarkers, such as urinary MCP-1 and BAFF, offer promising tools for monitoring LN activity and predicting recurrence risk post-transplantation. Current guidelines emphasize the importance of achieving disease quiescence before transplantation, while new evidence supports the benefits of preemptive transplantation and personalized immunosuppressive regimens in improving patient and graft survival. This review highlights the latest evidence and strategies for optimizing kidney transplantation outcomes in LN patients, focusing on timing, immunosuppression, and disease monitoring.

Identification of Two Novel Alleles HLA-B*14:136 and HLA-B*58:159 by Next-Generation Sequencing

Two novel HLA-B alleles, HLA-B*14:136 and -B*58:159, identified by NGS during the routine HLA typing.

Identification of the new allele HLA-C*04:01:01:186 in a Greek individual using next generation sequencing

The newly discovered HLA-C*04:01:01:186 allele differs from HLA-C*04:01:01:01 by a single nucleotide substitution in intron 3.

Identification of novel HLA alleles discovered in 2022-2023

In this paper, we describe 10 novel HLA alleles discovered, submitted and officially named in the calendar years 2022 through the end of 2023.

A novel HLA-C*03 variant, HLA-C*03:620, identified in a Chinese individual

HLA-C*03:620 differs from the HLA-C*03:04:01:02 allele by one nucleotide substitution in the exon 3.

Identification of the novel HLA-DPA1*02:02:15 allele by next-generation sequencing

The novel HLA-DPA1*02:02:15 allele differs from HLA-DPA1*02:02:02:01 by one nucleotide substitution in exon 1.

Utilizing Massively Parallel Sequencing (MPS) of Human Leukocyte Antigen (HLA) Gene Polymorphism to Assess Relatedness in Deficiency Parentage Testing

In the realm of DNA testing with legal implications, the reliability and precision of genetic markers play a pivotal role in confirming or negating paternity claims. This study aimed to assess the potential utility of human leukocyte antigen (HLA) gene polymorphism through massively parallel sequencing (MPS) technology as robust forensic markers for parentage testing involving genetic deficiencies. It sought to redefine the significance of HLA genes in this context. Data on autosomal short tandem repeat (aSTR) mutational events across 18 paternity cases involving 16 commonly employed microsatellite loci were presented. In instances where traditional aSTR analysis failed to establish statistical certainty, kinship determination was pursued via HLA genotyping, encompassing the amplification of 17 linked HLA loci. Within the framework of this investigation, phase-resolved genotypes for HLA genes were meticulously generated, resulting in the definition of 34 inherited HLA haplotypes. An impressive total of 274 unique HLA alleles, which were classified at either the field 3 or 4 level, were identified, including the discovery of four novel HLA alleles. Likelihood ratio (LR) values, which indicated the likelihood of the observed data under a true biological relationship versus no relationship, were subsequently calculated. The analysis of the LR values demonstrated that the HLA genes significantly enhanced kinship determination compared with the aSTR analysis. Combining LR values from aSTR markers and HLA loci yielded conclusive outcomes in duo paternity cases, showcasing the potential of HLA genes and MPS technology for deeper insights and diversity in genetic testing. Comprehensive reference databases and high-resolution HLA typing across diverse populations are essential. Reintegrating HLA alleles into forensic identification complements existing markers, creating a potent method for future forensic analysis.

Update on HLA-B*15:02 allele associated with adverse drug reactions

HLA alleles, part of the major histocompatibility complex, are strongly associated with adverse drug reactions (ADRs). This review focuses on HLA-B*15:02 and explores its association with ADRs in various ethnic populations and with different drugs, aiming to provide insights into the safe clinical use of drugs and minimize the occurrence of ADRs. Furthermore, the review explores the potential mechanisms by which HLA-B*15:02 may be associated with ADRs, aiming to gain new insights into drug modification and identification of haptens. In addition, it analyzes the frequency of the HLA-B*15:02, genotyping methods, cost-effectiveness and treatment measures for adverse reactions, thereby providing a theoretical basis for formulating clinical treatment plans.