Systematic design of combination therapy by targeting master regulators of coexisting diffuse midline glioma cell states
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.
Authors
- Junqiang Wang (ORCID: https://orcid.org/0000-0002-3064-0936)
- Ester Calvo Fernández (ORCID: https://orcid.org/0000-0001-6307-8452)
- Lukas J. Vlahos (ORCID: https://orcid.org/0000-0002-4083-6924)
- Aaron Timothy Griffin (ORCID: https://orcid.org/0000-0002-8027-0822)
- Timothy J. Martins (ORCID: https://orcid.org/0000-0002-2133-7281)
- Cheng–Chia Wu (ORCID: https://orcid.org/0000-0002-5908-0143)
- Luca Szalontay (ORCID: https://orcid.org/0000-0002-7341-0014)
- Stergios Zacharoulis
- Pasquale Laise (ORCID: https://orcid.org/0000-0003-1469-4704)
- Jovana Pavisic (ORCID: https://orcid.org/0000-0002-6968-600X)
- Christian Simmons (ORCID: https://orcid.org/0000-0001-9368-1236)
- Pamela S. Becker (ORCID: https://orcid.org/0000-0001-6235-9463)
- Hanna E. Minns (ORCID: https://orcid.org/0000-0001-7120-5511)
- Theophilos Tzaridis (ORCID: https://orcid.org/0000-0001-9651-1144)
- Matthew Gallitto (ORCID: https://orcid.org/0000-0002-5210-742X)
- Hong-Jian Wei (ORCID: https://orcid.org/0000-0002-5962-7831)
- A Califano
- Lorenzo Tomassoni (ORCID: https://orcid.org/0000-0002-7720-9166)
- James H. Garvin (ORCID: https://orcid.org/0000-0003-4709-1088)
- Xu Zhang (ORCID: https://orcid.org/0000-0002-9817-4492)
- Aleksandar Obradovic
- Diana V. Morales
- Robyn D. Gartrell
- Robert J. Wechsler-Reya
- Zhiguo Zhang (ORCID: https://orcid.org/0000-0002-9451-2685)
- John R. Crawford
Institutions
- Children's Hospital of Orange County (US)
- Memorial Sloan Kettering Cancer Center (US)
- Children's National (US)
- Johns Hopkins University (US)
- Oregon Health & Science University (US)
- Sanford Burnham Prebys Medical Discovery Institute (US)
- University of Washington (US)
- University of California, Irvine (US)
- Discovery Institute (US)
- Columbia University Irving Medical Center (US)
- Johns Hopkins Medicine (US)
- Doheny Eye Institute (US)
- City of Hope (US)
- Biomedical Research Institute (US)
- Cancer Genetics (United States) (US)
- DarwinHealth (United States) (US)
- High Throughput Biology (United States) (US)
- Columbia University (US)
- Virginia Tech (US)
Publication Details
- Journal
- Nature Genetics
- Published
- 2026-04-22
- DOI
- https://doi.org/10.1038/s41588-026-02550-w
- Primary Topic
- Glioma Diagnosis and Treatment
- Type
- article
- Field-Weighted Citation Impact
- 0.00