Evidence map›Paper›PMID 40578362›Full record

ArticleCancer cell2025

Gene context drift identifies drug targets to mitigate cancer treatment resistance.

Amir Jassim, Birgit V Nimmervoll, Sabrina Terranova, Erica Nathan, Linda Hu, Jessica T Taylor, Katherine E Masih, Lisa Ruff, Matilde Duarte, Elizabeth Cooper and 20 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cancer cell, 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. Review
  2. Review
  3. Review
  4. Review
  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

30 authors.

Amir JassimCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK. Electronic address: amir.jassim@cruk.cam.ac.uk.
Birgit V NimmervollCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Sabrina TerranovaCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Erica NathanCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Linda HuCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Jessica T TaylorCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Katherine E MasihCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethseda, MD 20892, USA.
Lisa RuffCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Matilde DuarteCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Elizabeth CooperCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Gunjan KatyalCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Melika AkhbariCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Reuben J GilbertsonCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Jennifer C ColemanCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Joseph S TokerCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Colton TerhuneCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Gabriel BalmusUK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0AH, UK; Department of Molecular Neuroscience, Transylvanian Institute of Neuroscience, 400191 Cluj-Napoca, Romania.
Stephen P JacksonCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Hailong LiuDepartment of Radiotherapy, Beijing Tiantan Hospital Capital Medical University, Beijing 100070, China.
Tao JiangDepartment of Pediatric Neurosurgery, Beijing Tiantan Hospital Capital Medical University, Beijing 100070, China.
Michael D TaylorTexas Children's Cancer and Hematology Center, Houston, TX 77030, USA; Department of Pediatrics, Hematology/Oncology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurosurgery, Texas Children's Hospital, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
Kui HuaCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Jean E AbrahamDepartment of Oncology, University of Cambridge, Box 197 Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK; Precision Breast Cancer Institute, Box 197 Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.
Mariella G FilbinBoston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA.
Anthony HillSchaller Research Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
Anarita PatriziSchaller Research Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
Neil DaniDepartment of Cell and Developmental Biology, Vanderbilt School of Medicine, Nashville, TN 37232, USA.
Aviv RegevBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Maria K LehtinenBoston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA.
Richard J GilbertsonCancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Box 197 Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK. Electronic address: richard.gilbertson@cruk.cam.ac.uk.

Funding

Medical Scientist Training ProgramT32GM144273 · NIGMS · HARVARD MEDICAL SCHOOL · PI David Shumway Jones, Jacqueline A. Lees · 2022 to 2026
$14.7M
Control of neural stem cells by the nascent cerebrospinal fluidR01NS088566 · NINDS · BOSTON CHILDREN'S HOSPITAL · PI LEHTINEN, MARIA · 2014 to 2024
$5.5M
NIGMS NIH HHS T32 GM144273NINDS NIH HHS R01 NS088566
6 · The paper itself

Abstract

Cancer treatment often fails because combinations of different therapies evoke complex resistance mechanisms that are hard to predict. We introduce REsistance through COntext DRift (RECODR): a computational pipeline that combines co-expression graph networks of single-cell RNA sequencing profiles with a graph-embedding approach to measure changes in gene co-expression context during cancer treatment. RECODR is based on the idea that gene co-expression context, rather than expression level alone, reveals important information about treatment resistance. Analysis of tumors treated in preclinical and clinical trials using RECODR unmasked resistance mechanisms -invisible to existing computational approaches- enabling the design of highly effective combination treatments for mice with choroid plexus carcinoma, and the prediction of potential new treatments for patients with medulloblastoma and triple-negative breast cancer. Thus, RECODR may unravel the complexity of cancer treatment resistance by detecting context-specific changes in gene interactions that determine the resistant phenotype.

Indexed as

Drug Resistance, NeoplasmNeoplasmsAnimalsFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticGene Regulatory NetworksHumansMedulloblastomaMiceSingle-Cell AnalysisTriple Negative Breast Neoplasmscancerchoroid plexuschoroid plexus carcinomacombination therapyDNA repairgraph networksmachine learningradiationtreatment resistancetriple-negative breast cancer

Identifiers

PMID40578362
PMCPMC7619360

What OpenQuestion holds

Textmetadata
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.