Evidence map›Paper›PMID 40721532›Full record

ArticleNature genetics2025

Massively parallel immunopeptidome by DNA sequencing provides insights into cancer antigen presentation.

Quanming Shi, Elana P Simon, Cansu Cimen Bozkus, Anna Kaminska, Leandra Velazquez, Mansi Saxena, Zilin Zhang, Julia A Belk, Shuo Wang, Nuoya Yang and 13 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Article
  5. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

23 authors.

Quanming ShiDepartment of Dermatology, Stanford University, Stanford, CA, USA.
Elana P SimonDepartment of Dermatology, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-2433-4390
Cansu Cimen BozkusTisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID http://orcid.org/0000-0001-7834-4792
Anna KaminskaTisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Leandra VelazquezTisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Mansi SaxenaTisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Zilin ZhangDepartment of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
Julia A BelkDepartment of Dermatology, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-4724-6158
Shuo WangDepartment of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
Nuoya YangDepartment of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0001-6130-0291
Yaowen ZhangDepartment of Dermatology, Stanford University, Stanford, CA, USA.
Ashley KwongDepartment of Dermatology, Stanford University, Stanford, CA, USA.
Yonglu CheDepartment of Dermatology, Stanford University, Stanford, CA, USA.
Robert R StickelsDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-4326-4084
Charles R CrainRagon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.
Laura Schmidt-HongRagon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0009-0009-0711-3570
Cheryl F LichtiDepartment of Pathology and Immunology, Washington University, St. Louis, MO, USA.
Gaurav D GaihaRagon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-6875-4472
Theodore L RothDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-3970-9573
Nina BhardwajTisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID http://orcid.org/0000-0003-1865-4187
Ansuman T SatpathyDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-5167-537X
Bingfei YuDepartment of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA. bingfeiy@usc.edu.ORCID http://orcid.org/0000-0001-5550-6701
Howard Y ChangDepartment of Dermatology, Stanford University, Stanford, CA, USA. howchang@stanford.edu.ORCID http://orcid.org/0000-0002-9459-4393

Funding

Project 3: T CellsU54CA260517 · NCI · STANFORD UNIVERSITY · PI WANG, TAIA · 2020 to 2024
$10.4M
NCI NIH HHS U54 CA260517
6 · The paper itself

Abstract

Human leukocyte antigens (HLAs) are encoded by the most polymorphic genes in the human genome. HLA class I alleles control antigen presentation for T cell recognition, which is pivotal for autoimmunity, infectious diseases and cancer. Current knowledge of HLA-bound peptides is limited, skewed and falls short of population-wide HLA binding profiles for high-value targets. Here we present ESCAPE-seq (enhanced single-chain antigen presentation sequencing), a massively parallel platform for comprehensive screening of class I HLA-peptide combinations for antigen presentation via deep DNA sequencing. ESCAPE-seq demonstrates programmability, high throughput, sensitivity and nominated viral and cancer epitopes. We simultaneously assessed over 75,000 peptide-HLA combinations, revealing broadly presented epitopes from oncogenic driver mutations and fusions across diverse HLA-A, HLA-B and HLA-C alleles that cover 90% of the human population. We further identified epitopes that are differentially presented, comparing oncogenic hotspot mutations versus wild type. ESCAPE-seq enables one-shot population-wide antigen presentation discovery, offering insights into HLA specificity and immune recognition of genomic mutations.

Indexed as

Antigen PresentationAntigens, NeoplasmHigh-Throughput Nucleotide SequencingNeoplasmsAllelesEpitopesHistocompatibility Antigens Class IHLA AntigensHumansMutationPeptidesSequence Analysis, DNAAntigens, NeoplasmEpitopesHistocompatibility Antigens Class IHLA AntigensPeptides

Identifiers

PMID40721532
PMCPMC12339365

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.