Some considerations on the current debate about typing resolution in solid organ transplantation

Advancements in HLA Typing Techniques and Their Impact on Transplantation Medicine

HLA typing serves as a standard practice in hematopoietic stem cell transplantation to ensure compatibility between donors and recipients, preventing the occurrence of allograft rejection and graft-versus-host disease. Conventional laboratory methods that have been widely employed in the past few years, including sequence-specific primer PCR and sequencing-based typing (SBT), currently face the risk of becoming obsolete. This risk stems not only from the extensive diversity within HLA genes but also from the rapid advancement of next-generation sequencing and third-generation sequencing technologies. Third-generation sequencing systems like single-molecule real-time (SMRT) sequencing and Oxford Nanopore (ONT) sequencing have the capability to analyze long-read sequences that span entire intronic-exonic regions of HLA genes, effectively addressing challenges related to HLA ambiguity and the phasing of multiple short-read fragments. The growing dominance of these advanced sequencers in HLA typing is expected to solidify further through ongoing refinements, cost reduction, and error rate minimization. This review focuses on hematopoietic stem cell transplantation (HSCT) and explores prospective advancements and application of HLA DNA typing techniques. It explores how the adoption of third-generation sequencing technologies can revolutionize the field by offering improved accuracy, reduced ambiguity, and enhanced assessment of compatibility in HSCT. Embracing these cutting-edge technologies is essential to advancing the success rates and outcomes of hematopoietic stem cell transplantation. This review underscores the importance of staying at the forefront of HLA typing techniques to ensure the best possible outcomes for patients undergoing HSCT.

On the clinical relevance of using complete high-resolution HLA typing for an accurate interpretation of posttransplant immune-mediated graft outcomes

Complete and high-resolution (HR) HLA typing improves the accurate assessment of donor–recipient compatibility and pre-transplant donor-specific antibodies (DSA). However, the value of this information to identify de novo immune-mediated graft events and its impact on outcomes has not been assessed. In 241 donor/recipient kidney transplant pairs, DNA samples were re-evaluated for six-locus (A/B/C/DRB1/DQB1+A1/DPB1) HR HLA typing. De novo anti-HLA antibodies were assessed using solid-phase assays, and dnDSA were classified either (1) as per current clinical practice according to three-locus (A/B/DRB1) low-resolution (LR) typing, estimating donor HLA-C/DQ typing with frequency tables, or (2) according to complete six-locus HR typing. The impact on graft outcomes was compared between groups. According to LR HLA typing, 36 (15%) patients developed dnDSA (LR_dnDSA+). Twenty-nine out of 36 (80%) were confirmed to have dnDSA by HR typing (LR_dnDSA+/HR_dnDSA+), whereas 7 (20%) did not (LR_dnDSA+/HR_dnDSA−). Out of 49 LR_dnDSA specificities, 34 (69%) were confirmed by HR typing whereas 15 (31%) LR specificities were not confirmed. LR_dnDSA+/HR_dnDSA+ patients were at higher risk of ABMR as compared to dnDSA− and LR_dnDSA+/HR_dnDSA− (logRank < 0.001), and higher risk of death-censored graft loss (logRank = 0.001). Both LR_dnDSA+ (HR: 3.51, 95% CI = 1.25–9.85) and LR_dnDSA+/HR_dnDSA+ (HR: 4.09, 95% CI = 1.45–11.54), but not LR_dnDSA+/HR_dnDSA− independently predicted graft loss. The implementation of HR HLA typing improves the characterization of biologically relevant de novo anti-HLA DSA and discriminates patients with poorer graft outcomes.

Next-generation sequencing technologies: An overview

Since the days of Sanger sequencing, next-generation sequencing technologies have significantly evolved to provide increased data output, efficiencies, and applications. These next generations of technologies can be categorized based on read length. This review provides an overview of these technologies as two paradigms: short-read, or "second-generation," technologies, and long-read, or "third-generation," technologies. Herein, short-read sequencing approaches are represented by the most prevalent technologies, Illumina and Ion Torrent, and long-read sequencing approaches are represented by Pacific Biosciences and Oxford Nanopore technologies. All technologies are reviewed along with reported advantages and disadvantages. Until recently, short-read sequencing was thought to provide high accuracy limited by read-length, while long-read technologies afforded much longer read-lengths at the expense of accuracy. Emerging developments for third-generation technologies hold promise for the next wave of sequencing evolution, with the co-existence of longer read lengths and high accuracy.

New challenges, new opportunities: Next generation sequencing and its place in the advancement of HLA typing

The Human Leukocyte Antigen (HLA) system has a critical role in immunorecognition, transplantation, and disease association. Early typing techniques provided the foundation for genotyping methods that revealed HLA as one of the most complex, polymorphic regions of the human genome. Next Generation Sequencing (NGS), the latest molecular technology introduced in clinical tissue typing laboratories, has demonstrated advantages over other established methods. NGS offers high-resolution sequencing of entire genes in time frames and price points considered unthinkable just a few years ago, contributing a wealth of data informing histocompatibility assessment and standards of clinical care. Although the NGS platforms share a high-throughput massively parallel processing model, differing chemistries provide specific strengths and weaknesses. Research-oriented Third Generation Sequencing and related advances in bioengineering continue to broaden the future of NGS in clinical settings. These diverse applications have demanded equally innovative strategies for data management and computational bioinformatics to support and analyze the unprecedented volume and complexity of data generated by NGS. We discuss some of the challenges and opportunities associated with NGS technologies, providing a comprehensive picture of the historical developments that paved the way for the NGS revolution, its current state and future possibilities for HLA typing.

Utilizing nanopore sequencing technology for the rapid and comprehensive characterization of eleven HLA loci; addressing the need for deceased donor expedited HLA typing

The comprehensive characterization of human leukocyte antigen (HLA) genomic sequences remains a challenging problem. Despite the significant advantages of next-generation sequencing (NGS) in the field of Immunogenetics, there has yet to be a single solution for unambiguous, accurate, simple, cost-effective, and timely genotyping necessary for all clinical applications. This report demonstrates the benefits of nanopore sequencing introduced by Oxford Nanopore Technologies (ONT) for HLA genotyping. Samples (n = 120) previously characterized at high-resolution three-field (HR-3F) for 11 loci were assessed using ONT sequencing paired to a single-plex PCR protocol (Holotype) and to two multiplex protocols OmniType (Omixon) and NGSgo^®-MX6-1 (GenDx). The results demonstrate the potential of nanopore sequencing for delivering accurate HR-3F typing with a simple, rapid, and cost-effective protocol. The protocol is applicable to time-sensitive applications, such as deceased donor typings, enabling better assessments of compatibility and epitope analysis. The technology also allows significantly shorter turnaround time for multiple samples at a lower cost. Overall, the nanopore technology appears to offer a significant advancement over current next-generation sequencing platforms as a single solution for all HLA genotyping needs.

Engineering Microvascularized 3D Tissue Using Alginate-Chitosan Microcapsules

Construction of vascularized tissues is one of the major challenges of tissue engineering. The goal of this study was to engineer 3D microvascular tissues by incorporating the HUVEC-CS cells with a collagen/alginate-chitosan (AC) microcapsule scaffold. In the presence of AC microcapsules, a 3D vascular-like network was clearly observable. The results indicated the importance of AC microcapsules in engineering microvascular tissues -- providing support and guiding alignment of HUVEC-CS cells. This approach provides an alternative and promising method for constructing vascularized tissues.

A Novel Method for Anti-HLA Antibody Detection Using Personalized Peptide Arrays

Background

HLA mismatches are the primary cause of alloantibody-mediated rejection (AMR) in organ transplantation. To delineate antigenic and immunogenic potentials among individual HLA mismatches, information regarding antibody specificity at the epitope level, instead of the allelic level, is needed.

Methods

This study explores a direct screening method for HLA linear epitopes in kidney transplant patients. We custom synthesized a large panel of 15-residue HLA peptides in an array format and measured alloantibody reactivity to these peptides from the sera of post and/or pretransplant patients. Two design concepts for the arrays were followed: a standard array of a fixed panel of peptides or personalized arrays. The standard array contains 420 peptides derived from a predetermined set of HLA-DQ allelic antigens based on templates also used in the single-antigen beads assay.

Results

The array detected distinct antiserum patterns among transplant subjects and revealed epitope levels of specificity largely in accordance with the single-antigen results. Two personalized arrays that each included donor-derived peptides of HLA-A, -B, -C, -DQ, and -DR sequences were separately designed for 2 transplant subjects. The personalized arrays detected de novo antibodies following transplantation. The new method also showed superior sensitivity to a single-antigen assay in one of the cases whose pathological diagnosis of AMR occurred before single-antigen assay could detect antibodies.

Conclusions

This pilot study proved the feasibility of using personalized peptide arrays to achieve detection of alloantibodies for linear HLA epitopes associated with distinct donor-recipient mismatches. Single or multiple reactive epitopes may occur on an individual HLA molecule, and donor-specific HLA-DQ-reactivity among 5 kidney transplant subjects revealed patterns of shared epitopes.