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Related Concept Videos

CRISPR01:59

CRISPR

Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced Short...
CRISPR/Cas9 Genome Editing01:28

CRISPR/Cas9 Genome Editing

The CRISPR-Cas system serves as a bacterial defense mechanism against invading genetic elements such as viruses and plasmids, forming the foundation for its adaptation as a powerful genome-editing tool. Originally discovered in prokaryotes, this system has been repurposed to revolutionize genetic engineering across a wide range of organisms, including plants, animals, and humans. The core component, Cas9, is an endonuclease derived from Streptococcus pyogenes, capable of introducing...

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Updated: Jul 1, 2026

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Innovative CRISPR/Cas9-Based Strategy for Allele-Specific HLA Peptidome Analysis Using a Pan-HLA Antibody.

Laura Cobos-Figueroa1, Ana Pintor-Poveda2, Carmen Mir2

  • 1Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain; Centro Láser, Universidad Politécnica de Madrid, Madrid, Spain.

Molecular & Cellular Proteomics : MCP
|May 2, 2026
PubMed
Summary

CRISPR gene editing allows precise deletion of human leukocyte antigen (HLA) alleles, enabling allele-specific immunopeptidome profiling with a general HLA antibody. This method overcomes limitations of allele-specific antibodies and overexpression systems.

Keywords:
CRISPR/Cas9HLA-A∗02immunopeptidomicsmass spectrometrypeptide repertoire

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Area of Science:

  • Immunology
  • Genetics
  • Proteomics

Background:

  • Human leukocyte antigen (HLA) immunopeptidomics faces challenges due to limited allele-specific antibodies and potential artifacts from HLA overexpression systems.
  • Accurate profiling of HLA-presented peptides is crucial for understanding immune responses and developing targeted therapies.

Purpose of the Study:

  • To develop and validate a CRISPR/Cas9-based strategy for allele-specific immunopeptidome analysis.
  • To overcome limitations of current immunopeptidomics methods by enabling the use of pan-HLA antibodies.

Main Methods:

  • CRISPR/Cas9 gene editing was used to selectively delete specific classical class I HLA alleles (HLA-B*07:02 and HLA-C*07:02) in JY cells, retaining HLA-A*02:01 (ΔBC clones).
  • Immunoprecipitation of peptide-HLA complexes was performed using pan-HLA class I (W6/32) and allele-specific (PA2.1 for A*02:01) antibodies.
  • NanoLC-MS/MS analysis followed by computational HLA assignment was used to profile the eluted peptides.

Main Results:

  • CRISPR editing successfully reduced surface expression of targeted HLA alleles by approximately 55%.
  • Pan-HLA antibody (W6/32) immunoprecipitation from edited cells yielded a comparable peptide yield to allele-specific antibody (PA2.1) in wild-type cells.
  • Computational analysis confirmed that peptides identified in edited cells primarily originated from the retained HLA-A*02:01 allele, with minimal peptides from deleted alleles.
  • High overlap (~88%) was observed between the immunopeptidome obtained using W6/32 on edited cells and PA2.1 on wild-type cells, validating the approach's specificity.

Conclusions:

  • CRISPR-based HLA allele editing is a viable strategy for allele-specific immunopeptidome profiling using pan-HLA antibodies.
  • This approach reduces reliance on scarce allele-specific reagents and facilitates the study of underrepresented HLA alleles.
  • The method holds potential for broader applications in immunology and personalized medicine beyond the proof-of-concept system.