Evidence map›Paper›PMID 40067759›Full record

ArticleeLife2025

Unraveling the power of NAP-CNB's machine learning-enhanced tumor neoantigen prediction.

Almudena Mendez-Perez, Andres M Acosta-Moreno, Carlos Wert-Carvajal, Pilar Ballesteros-Cuartero, Ruben Sánchez-García, Jose R Macias, Rebeca Sanz-Pamplona, Ramon Alemany, Carlos Oscar Sorzano, Arrate Munoz-Barrutia and 1 more

Abstract read
In one paragraph

Article in eLife, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

11 authors.

Almudena Mendez-PerezCentro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
Andres M Acosta-MorenoCentro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
Carlos Wert-CarvajalCentro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
Pilar Ballesteros-CuarteroCentro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
Ruben Sánchez-GarcíaCentro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
Jose R MaciasCentro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
Rebeca Sanz-PamplonaCatalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.
Ramon AlemanyProcure Program, Institut Català d'Oncologia-Oncobell Program, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.
Carlos Oscar SorzanoCentro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
Arrate Munoz-BarrutiaDepartamento de Bioingenieria, Universidad Carlos III de Madrid, Leganés, Madrid, Spain.ORCID https://orcid.org/0000-0002-1573-1661
Esteban VeigaCentro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.ORCID https://orcid.org/0000-0002-7333-2466

Funding

Agencia Estatal de Investigación 10.13039/501100011033Fundación Fero BFERO2020.04Ministerio de Ciencia e Innovación FPU18/03199JMGGMinisterio de Ciencia e Innovación PID2020-116393RB-I00
6 · The paper itself

Abstract

In this study, we present a proof-of-concept classical vaccination experiment that validates the in silico identification of tumor neoantigens (TNAs) using a machine learning-based platform called NAP-CNB. Unlike other TNA predictors, NAP-CNB leverages RNA-seq data to consider the relative expression of neoantigens in tumors. Our experiments show the efficacy of NAP-CNB. Predicted TNAs elicited potent antitumor responses in mice following classical vaccination protocols. Notably, optimal antitumor activity was observed when targeting the antigen with higher expression in the tumor, which was not the most immunogenic. Additionally, the vaccination combining different neoantigens resulted in vastly improved responses compared to each one individually, showing the worth of multiantigen-based approaches. These findings validate NAP-CNB as an innovative TNA identification platform and make a substantial contribution to advancing the next generation of personalized immunotherapies.

Indexed as

Antigens, NeoplasmCancer VaccinesMachine LearningNeoplasmsAnimalsFemaleHumansImmunotherapyMiceVaccinationAntigens, NeoplasmCancer Vaccinesantigen identificationcancercancer biologyimmunologyinflammationmachine learning-based platformmousevaccination

Identifiers

PMID40067759
PMCPMC11896607

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.