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Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation

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Published on: September 6, 2017

Snowflake: A deep learning-based human leukocyte antigen matching algorithm considering allele-specific surface

Matthias Niemann¹, Benedict M Matern², Eric Spierings^2,3

¹Research and Development, PIRCHE AG, Berlin, Germany.

Frontiers in Immunology

|August 15, 2022

Summary

Histocompatibility in solid-organ transplantation relies on understanding Human Leukocyte Antigen (HLA) allele-specific surface accessibility. This study refines B-cell epitope prediction by analyzing HLA solvent accessibility, improving graft survival predictions.

Keywords:

3D-structures HLA antibodies deep-learning epitope epitope matching neural network structure prediction

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Generation of Human Alloantigen-specific T Cells from Peripheral Blood

Generation of Human Alloantigen-specific T Cells from Peripheral Blood

Published on: November 21, 2014

Area of Science:

Immunology
Computational Biology
Transplantation Science

Background:

Solid-organ transplantation success is significantly influenced by histocompatibility.
Current understanding of allorecognition, despite advances in epitope matching, is incomplete regarding immunogenic determinants.

Purpose of the Study:

To investigate the hypothesis that Human Leukocyte Antigen (HLA) solvent accessibility is allele-specific.
To refine Human Leukocyte Antigen (HLA) B-cell epitope prediction by incorporating allele-specific solvent accessibility data.

Main Methods:

Developed the Snowflake computational pipeline to calculate solvent accessibility of HLA Class I proteins using experimental and predicted structures.
Utilized AlphaFold for structure prediction and APE-Gen for peptide binding.
Trained a deep learning model (long short-term memory bidirectional recurrent neural network) to infer solvent accessibility for all known HLA Class I proteins.

Main Results:

Found significant variation in solvent accessibility between different HLA alleles, indicating protein-specific surface characteristics.
Demonstrated that residue accessibility can differ even between closely related HLA alleles (e.g., HLA-A*02:01 vs. HLA-A*01:01).
Mapped these findings to antibody-verified epitopes, revealing patterns of consistent, partial, or variable residue accessibility.

Conclusions:

Allele-specific solvent accessibility provides a more refined approach to B-cell epitope definition in transplantation.
This approach offers improved accuracy compared to aggregating HLA surface maps by class or locus.
A cloud-based web service was developed to facilitate the calculation of donor-allele-specific solvent-accessible amino acid mismatches for transplantation research.