Leading the way: BLEAT, a novel HLA-B Leader Assessment Tool

From the Petersdorf Lab, Clinical Research Division

“How often do you find yourself in a situation where you’ve discovered something new and there is a way to use that information to help patients? We were very fortunate to be in that situation,” stated Dr. Effie Petersdorf, a member of Fred Hutch’s Clinical Research Division when discussing her recent research focused on HLA-B leader peptides, a collaboration with colleagues at the National Marrow Donor Program/Be The Match. Not everyone who is in need of transplantation has a related or perfectly matched donor available, and recent research has highlighted the potential of HLA-B, a member of the human histocompatibility complex that plays a major role in presenting antigens to cells of the immune system, to improve donor selection based on associated risks for mismatched cases. HLA-B differs from its counterparts HLA-A and HLA-C, whereby a dimorphic single nucleotide polymorphism (SNP) can lead to the expression of one of two distinct leader peptides containing threonine (T) or methionine (M) at the second position along the nonamer leader peptide sequence encoded by exon 1. These leader peptides can be critical for mismatched transplant outcomes with research from the International Histocompatibility Working Group in Hematopoietic-Cell Transplantation specifying “when a patient lacks matched donors but has HLA-B-mismatched donors, the studies found that GVHD [graft versus host disease] risk is significantly higher when the mismatched antigens are members of different families compared to mismatching between antigens of the same family. The information can be used to avoid high-risk HLA-B mismatches,” according to Dr. Petersdorf.

Potential transplant donors are HLA-typed by genetic sequencing to match transplant recipients to donors, and the sequencing data include information on the HLA-B leader SNP/peptide. Dr. Petersdorf and colleagues were able to utilize these sequencing data in a cohort of almost 10 million registered donors to confirm that 99.99% of HLA-B alleles encoded a T or M at position 2 of the leader peptide. They leveraged these findings, recently published in Blood Advances, to develop BLEAT - HLA-B LEader Assessment Tool - an application that aids clinical decision making by automating the assignment of the HLA-B leader peptide sequence/genotype to the transplant recipient and candidate donors. In this way, the tool can be used to select optimal donors to reduce the risks associated with HLA-B-mismatched transplantation. 

A computational tool, BLEAT, can accurately assign HLA-B leader genotypes to reduce transplant risk after HLA-B-mismatched unrelated donor transplantation.
A computational tool, BLEAT, can accurately assign HLA-B leader genotypes to reduce transplant risk after HLA-B-mismatched unrelated donor transplantation. This research was originally published in Blood Advances. Sajulga R, Bolon YT, Maiers MJ and Petersdorf EW. Assessment of HLA-B genetic variation with an HLA-B leader tool and implications in clinical transplantation. Blood Adv (2022) 6 (1): 270–280, © the American Society of Hematology.

BLEAT is designed to work in three parts. Firstly, it is required to input the transplant recipient’s HLA-B typing information into the software, alongside HLA-B typing information for any potential donors. BLEAT will then align the HLA-B sequences to reference sequences and assign a leader peptide (M or T) to each allele. Secondly, BLEAT provides a leader genotype to potential candidate donors (MM, TT, or MT). The tool then compares the assigned leader genotypes between the recipient and potential donor, stratifying them into leader match or leader mismatch categories. Importantly, the third and final part of the tool operates by ranking the top candidate donors based on HLA-B reported outcome data, with the goal of reducing clinical risk to the recipient. The authors further tested the capabilities of their tool by evaluating its performance in a validated dataset. Encouragingly, BLEAT showed high performance with respect to genotype assignment and leader matching between transplant donor and recipient. “To aid laboratories and transplant centers, we designed a tool to automate the assignment of the leader sequence to each HLA-B antigen. The user can specify the HLA-B antigen typing for patients and candidate donors; the tool provides the leader genotype for each individual and indicates donors whose mismatched antigens are in the same (favorable) or different (unfavorable) families. We hope this tool will facilitate the use of the leader SNP in prospective donor selection to lower the risks of GVHD in the patient,” explained Dr. Petersdorf.

Next, the authors sought to understand the distribution of leader genotypes across US populations; these data are pertinent to all patients and particularly patients from underserved communities who often have only mismatched donor options for transplant procedures. The T allele was found to be the major allele across all race categories - white, Hispanic/Latino, Asian/Pacific Islander, Black/African American, and American Indian/Alaskan Native - in available donor registries; however, the frequency of individuals with the TT genotype differed markedly. The data are important for searching unrelated donors to achieve optimal leader matching for all patients.

The authors have made BLEAT publicly available here, providing a valuable resource to clinicians and researchers working in the field of transplant research. Summarizing this study and potential next steps, Dr. Petersdorf concluded “we examined over a million US donors from the Be The Match Registry to confirm the physical linkage of the leader SNP to the coding regions that define the peptide-binding region of the HLA-B molecule. These data provide novel information on the frequency of the leader sequences in individuals of diverse ethnic and racial backgrounds. We found that the SNP of interest is not the only position that can be variable; however, the SNP is the most common variant. We then asked whether information on the complete nucleotide HLA-B sequence (allele) is necessary to define the SNP of its linked leader sequence and found an exceptionally high correlation between the SNP and the antigen. These results mean that laboratories and transplant centers require only a serological-level definition of HLA-B to define its leader sequence. Finally, the distribution of the leader genotypes is highly dependent on the race and ethnicity of the individual. At the Seattle Cancer Care Alliance, we are using the HLA-B leader to avoid high-risk HLA-B mismatches.”

This work was funded by grants from the National Institutes of Health National Institute of Allergy and Infectious Diseases and National Cancer Institute, and partly by funding from the Office of Naval Research to the National Marrow Donor Program/Be The Match.

UW/Fred Hutch Cancer Consortium member Effie Petersdorf contributed to this work.

Sajulga R, Bolon YT, Maiers MJ, Petersdorf EW. Assessment of HLA-B genetic variation with an HLA-B leader tool and implications in clinical transplantation. Blood Adv. 2022 Jan 11;6(1):270-280. doi: 10.1182/bloodadvances.2021004561. PMID: 34529780; PMCID: PMC8753210.