Evidence map›Paper›PMID 42020604›Full record

ArticleNature genetics2026

Systematic design of combination therapy by targeting master regulators of coexisting diffuse midline glioma cell states.

Ester Calvo Fernández, Lorenzo Tomassoni, Xu Zhang, Junqiang Wang, Aleksandar Obradovic, Pasquale Laise, Aaron T Griffin, Lukas Vlahos, Hanna E Minns, Diana V Morales and 16 more

Abstract read
In one paragraph

Article in Nature genetics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
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

26 authors.

Ester Calvo FernándezDepartment of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0001-6307-8452
Lorenzo Tomassoni *Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
Xu Zhang *Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.
Junqiang Wang *Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
Aleksandar ObradovicDepartment of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
Pasquale LaiseDepartment of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0003-1469-4704
Aaron T GriffinDepartment of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
Lukas VlahosDepartment of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
Hanna E MinnsDepartment of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.
Diana V MoralesOncology Precision Therapeutics and Imaging Core, Columbia University Irving Medical Center, New York, NY, USA.ORCID http://orcid.org/0009-0005-8590-861X
Christian SimmonsOncology Precision Therapeutics and Imaging Core, Columbia University Irving Medical Center, New York, NY, USA.
Matthew GallittoDepartment of Radiation Oncology, Columbia University Irving Medical Center, New York, NY, USA.
Hong-Jian WeiDepartment of Radiation Oncology, Columbia University Irving Medical Center, New York, NY, USA.
Timothy J MartinsQuellos High Throughput Screening Core, University of Washington School of Medicine, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-2133-7281
Pamela S BeckerDepartments of Hematology and Hematopoietic Cell Transplantation and Hematologic Malignancies Translational Science, City of Hope, Duarte, CA, USA.ORCID http://orcid.org/0000-0001-6235-9463
John R CrawfordDepartment of Pediatrics, University of California Irvine, Irvine, CA, USA.
Theophilos TzaridisCancer Genome and Epigenetics Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
Robert J Wechsler-ReyaCancer Genome and Epigenetics Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
James GarvinDepartment of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0003-4709-1088
Robyn D GartrellDepartment of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.
Luca SzalontayBrain Tumor Institute, Children's National Hospital, Washington, DC, USA.
Stergios ZacharoulisDepartment of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.
Cheng-Chia WuDepartment of Radiation Oncology, Columbia University Irving Medical Center, New York, NY, USA.
Zhiguo ZhangInstitute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-9451-2685
Andrea CalifanoDepartment of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA. ac2248@cumc.columbia.edu.ORCID http://orcid.org/0000-0003-4742-3679
Jovana PavisicDepartment of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-6968-600X

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026
$347.4M
Predicting Cancer Cell Response to Endogenous and Exogenous Perturbations at the Single Cell LevelR35CA197745 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI ANDREA CALIFANO · 2015 to 2026
$11.5M
Elucidating and Targeting tumor dependencies and drug resistance determinants at the single cell levelU01CA272610 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI ANDREA CALIFANO · 2022 to 2026
$4.8M
Roles of Chromatin Remodeler CHD2 in Diffuse Midline Glioma with Onco-Histone MutationsR01NS132344 · NINDS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Zhiguo Zhang · 2023 to 2026
$1.8M
Epigenetic dependence of diffuse midline glioma with H3K27M mutationR01CA277605 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Zhiguo Zhang · 2023 to 2026
$1.8M
NCI NIH HHS P30 CA008748NCI NIH HHS R01 CA277605NCI NIH HHS R35 CA197745NCI NIH HHS U01 CA272610NINDS NIH HHS R01 NS132344
6 · The paper itself

Abstract

Intratumor heterogeneity fundamentally challenges cancer treatment, as coexisting, molecularly distinct cell states with non-overlapping drug sensitivities can drive therapeutic resistance. We establish and validate a generalizable, network-based framework to systematically identify combination therapies targeting complementary tumor cell states. Applied to diffuse midline glioma (DMG)-a universally fatal pediatric malignancy-this approach identified master regulator protein dependencies in seven coexisting cell states, confirmed by pooled CRISPR-Cas9 assays. Perturbational transcriptional profiles for 372 clinically relevant drugs prioritized candidates predicted to invert state-specific master regulator activity. State-selective drug sensitivity was validated for eight out of nine (89%) drugs in vivo, including avapritinib, ruxolitinib and larotrectinib. Compared with monotherapy, co-administering drugs targeting complementary states significantly prolonged survival across virtually all combinations, with avapritinib plus ruxolitinib extending median survival nearly threefold versus vehicle and 1.5-fold versus avapritinib alone. These findings establish clinically actionable DMG combinations and a tumor-agnostic and mutation-agnostic framework for rational combination therapy design.

Indexed as

Antineoplastic Combined Chemotherapy ProtocolsBrain NeoplasmsGliomaAnimalsAvapritinibCell Line, TumorDrug Resistance, NeoplasmGene Expression Regulation, NeoplasticHumansMiceNitrilesPyrazolesPyrimidinesPyrrolesXenograft Model Antitumor AssaysAvapritinibNitrilesPyrazolesPyrimidinesPyrrolesruxolitinib

Identifiers

PMID42020604
PMCPMC13175895

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.