Evidence map›Paper›PMID 40664650›Full record

ArticleNature communications2025

Genome-level selection in tumors as a universal marker of resistance to therapy.

Erez Persi, Praneeth R Sudalagunta, Yuri I Wolf, Rafael R Canevarolo, Mehdi Damaghi, Kenneth H Shain, Ariosto S Silva, Eugene V Koonin

Abstract read
In one paragraph

Article in Nature communications, 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. Article
  4. Review
  5. A Darwinian Perspective on Tumor Evolution.International journal of biological sciences · 2026
    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

8 authors.

Erez PersiComputational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA. erezpersi@gmail.com.ORCID http://orcid.org/0009-0001-3228-5552
Praneeth R SudalaguntaDepartment of Metabolism and Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.ORCID http://orcid.org/0000-0003-1283-9332
Yuri I WolfComputational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-0247-8708
Rafael R CanevaroloDepartment of Metabolism and Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.ORCID http://orcid.org/0000-0002-8722-8512
Mehdi DamaghiDepartment of Pathology, School of Medicine, Stony Brook University, Stony Brook, NY, USA.ORCID http://orcid.org/0000-0002-7744-6161
Kenneth H ShainDepartments of Malignant Hematology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
Ariosto S SilvaDepartment of Metabolism and Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA. Ariosto.Silva@moffitt.org.ORCID http://orcid.org/0000-0003-3237-9986
Eugene V KooninComputational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA. koonin@ncbi.nlm.nih.gov.ORCID http://orcid.org/0000-0003-3943-8299

Funding

TRANSLATIONAL RESEARCHP30CA076292 · NCI · UNIVERSITY OF SOUTH FLORIDA · PI John L. Cleveland · 1998 to 2026
$93.5M
"Research Supplement to Promote Diversity in Health-Related Research", as part of Moffitt PS-OC, "Cancer as a Complex adaptive System"U54CA193489 · NCI · H. LEE MOFFITT CANCER CTR & RES INST · PI ANDERSON, ALEXANDER ROBERTSON ALLAN, GATENBY, ROBERT A · 2015 to 2020
$12.5M
Ecology and Evolution of Breast CarcinogenesisU01CA261841 · NCI · STATE UNIVERSITY NEW YORK STONY BROOK · PI DAMAGHI, MEHDI, SIQUEIRA SILVA, ARIOSTO S · 2021 to 2025
$3.0M
NCI NIH HHS P30 CA076292NCI NIH HHS U01 CA261841NCI NIH HHS U54 CA193489
6 · The paper itself

Abstract

Tumor evolution is shaped by selective pressures imposed by physiological factors as the tumor naturally progresses to colonize local and distant tissues, as well as by therapy. However, the distinction between these two types of pressures and their impact on tumor evolution remain elusive, mainly, due to extensive intra-tumor heterogeneity. To disentangle the effects of these selective pressures, we analyze data from diverse cohorts of patients, of both treated and untreated cancers. We find that, despite the wide variation across patients, the selection strength on tumor genomes in individual patients is stable and largely unaffected by tumor progression in the primary settings, with some cancer-specific signatures detectable in the progression to metastases. However, we identify a nearly universal shift toward neutral evolution in tumors that resist treatment and demonstrate that this regime is associated with worse prognosis. We validate these findings on both published and original datasets. We suggest that monitoring the selection regime during cancer treatment can assist clinical decision-making in many cases.

Indexed as

Biomarkers, TumorDrug Resistance, NeoplasmNeoplasmsSelection, GeneticDisease ProgressionGenome, HumanHumansPrognosisBiomarkers, Tumor

Identifiers

PMID40664650
PMCPMC12263839

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.