Evidence map›Paper›PMID 40379787›Full record

ArticleNature genetics2025

APOBEC3 mutagenesis drives therapy resistance in breast cancer.

Avantika Gupta, Andrea Gazzo, Pier Selenica, Anton Safonov, Fresia Pareja, Edaise M da Silva, David N Brown, Hong Shao, Yingjie Zhu, Juber Patel and 18 more

Erratum issuedAbstract read
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. An erratum has been issued. Cited by 31 papers.

0numbers the graph read from it
0cells of the map it votes in
31citing 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

31 citing papers in PubMed.

  1. Review
  2. Review
  3. Review
  4. Article
  5. Distinct repair processes produce APOBEC-induced deletions, tandem substitutions, and complex mutations in yeast and human cells.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  6. Cancers · 2026
    Review
  7. Review
  8. Review
  9. Article
  10. Squamous-state excursions activate APOBEC3A in cancer.bioRxiv : the preprint server for biology · 2026
    Article
  11. Article
  12. Article
  13. Article
  14. Article
  15. Acquired High Tumor Mutational Burden and Activity of Immunotherapy after Targeted Therapy in Microsatellite Stable Colorectal Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026
    Article
  16. Article
  17. Two codes of RNA editing by deamination in human diseases.Experimental & molecular medicine · 2026
    Review
  18. Review
  19. HAMMER: Hairpin-based APOBEC3A-mediated mRNA editing reporter.bioRxiv : the preprint server for biology · 2026
    Article
  20. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

28 authors.

Avantika Gupta *Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-8170-6720
Andrea Gazzo *Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Pier SelenicaDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Anton SafonovDepartment of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Fresia ParejaDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0003-3748-8049
Edaise M da SilvaDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0003-3281-7333
David N BrownDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-8249-3632
Hong ShaoHuman Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Yingjie ZhuDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0003-1849-6019
Juber PatelDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Juan Blanco-HerediaDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0001-9526-7450
Bojana StefanovskaDepartment of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA.ORCID http://orcid.org/0000-0003-2212-8200
Michael A CarpenterDepartment of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA.ORCID http://orcid.org/0000-0001-9524-5323
Yanjun ChenDepartment of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA.
Isabella VegasHuman Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0009-0005-2437-7130
Xin PeiDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0001-9961-6152
Denise FrosinaDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Achim A JungbluthDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Marc LadanyiDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0001-9055-7213
Giuseppe CuriglianoDepartment of Oncology and Haemato-Oncology, University of Milano, Milan, Italy.ORCID http://orcid.org/0000-0003-1781-2518
Britta WeigeltDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0001-9927-1270
Nadeem RiazDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0001-9873-5862
Simon N PowellDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-8183-4765
Pedram RazaviDepartment of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0003-4236-0576
Reuben S HarrisDepartment of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA.ORCID http://orcid.org/0000-0002-9034-9112
Jorge S Reis-FilhoDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Antonio MarraDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA. antonio.marra@ieo.it.ORCID http://orcid.org/0000-0002-7310-7824
Sarat ChandarlapatyHuman Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. chandars@mskcc.org.ORCID http://orcid.org/0000-0003-4532-8053

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026
$347.4M
Targeting Polθ to Overcome PARP Inhibitor Resistance in Homologous Recombination Deficient Breast CancerP50CA247749 · NCI · SLOAN-KETTERING INST CAN RESEARCH · PI Sarat Chandarlapaty, Simon N. Powell · 2020 to 2026
$16.3M
PROJECT 3 – BIOLOGY OF DNA DEAMINASES IN CANCERP01CA234228 · NCI · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI Michael Allen Carpenter · 2019 to 2026
$14.5M
NCI NIH HHS P01 CA234228NCI NIH HHS P30 CA008748NCI NIH HHS P50 CA247749U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) P01-CA234228U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) P50-CA247749U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) P50 CA247749 01U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) P50 CA24779
6 · The paper itself

Abstract

Acquired genetic alterations drive resistance to endocrine and targeted therapies in metastatic breast cancer; however, the underlying processes engendering these alterations are largely uncharacterized. To identify the underlying mutational processes, we utilized a clinically annotated cohort of 3,880 patient samples with tumor-normal sequencing. Mutational signatures associated with apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) enzymes were prevalent and enriched in post-treatment hormone receptor-positive cancers. These signatures correlated with shorter progression-free survival on antiestrogen plus CDK4/6 inhibitor therapy in hormone receptor-positive metastatic breast cancer. Whole-genome sequencing of breast cancer models and paired primary-metastatic samples demonstrated that active APOBEC3 mutagenesis promoted therapy resistance through characteristic alterations such as RB1 loss. Evidence of APOBEC3 activity in pretreatment samples illustrated its pervasive role in breast cancer evolution. These studies reveal APOBEC3 mutagenesis to be a frequent mediator of therapy resistance in breast cancer and highlight its potential as a biomarker and target for overcoming resistance.

Indexed as

Breast NeoplasmsCytidine DeaminaseDrug Resistance, NeoplasmMutagenesisAnimalsAPOBEC DeaminasesCell Line, TumorFemaleHumansMiceMutationAPOBEC3 proteins, humanAPOBEC DeaminasesCytidine Deaminase

Identifiers

PMID40379787
PMCPMC12165862

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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.