Evidence map›Paper›PMID 40747419›Full record

ArticlebioRxiv : the preprint server for biology2025

Pan-cancer prediction of tumor immune activation and response to immune checkpoint blockade from tumor transcriptomics and histopathology.

Sumit Mukherjee, Sumeet Patiyal, Lipika R Pal, Tian-Gen Chang, Sumona Biswas, Saugato Rahman Dhruba, Amos Stemmer, Arashdeep Singh, Abbas Yousefi-Rad, Tien-Hua Chen and 31 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

41 authors.

Sumit MukherjeeCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0001-9807-7994
Sumeet PatiyalCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0003-1358-292X
Lipika R PalCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Tian-Gen ChangCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0003-1485-1992
Sumona BiswasCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Saugato Rahman DhrubaCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Amos StemmerCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Arashdeep SinghCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Abbas Yousefi-RadGenitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Tien-Hua ChenSchool of Medicine, National Yang Ming Chiao Tung University, Taiwan.
Binbin WangCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Denis MarinoOncoBiobank, Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Wonwoo ShonCedars-Sinai Medical Center, Los Angeles, CA, USA.
Yuan YuanCedars-Sinai Medical Center, Los Angeles, CA, USA.
Mark FariesCedars-Sinai Medical Center, Los Angeles, CA, USA.
Omid HamidCedars-Sinai Medical Center, Los Angeles, CA, USA.
Karen ReckampCedars-Sinai Medical Center, Los Angeles, CA, USA.
Barliz WaissengrinCedars-Sinai Medical Center, Los Angeles, CA, USA.
Beatriz OrnelasCedars-Sinai Medical Center, Los Angeles, CA, USA.
Pen-Yuan ChuDepartment of Otolaryngology, Taipei Veterans General Hospital, Taipei, Taiwan.
Salah BoudjadiGenitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Lisa LeyGenitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Dilara AkbulutGenitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Nourhan El AhmarDepartment of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
Sabina SignorettiDepartment of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
David A BraunCenter of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
Hyunjeong JooJim and Eleanor Randall Department of Surgery and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Hyungsoo KimJim and Eleanor Randall Department of Surgery and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Arsen OsipovOncoBiobank, Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Robert A FiglinOncoBiobank, Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Jair BarDepartment of Pathology, Sheba Medical Center, Ramat Gan, Israel.
Iris BarshackDepartment of Pathology, Sheba Medical Center, Ramat Gan, Israel.
Chi-Ping DayCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Karine SargsyanSchool of Medicine, National Yang Ming Chiao Tung University, Taiwan.
Andrea B ApoloGenitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Kenneth AldapeLaboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Muh-Hwa YangInstitute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
Michael B AtkinsGeorgetown Lombardi Comprehensive Cancer Center, Washington, DC, USA.
Ze'ev A RonaiJim and Eleanor Randall Department of Surgery and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.ORCID 0000-0002-3859-0400
Danh-Tai HoangCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0003-2640-4196
Eytan RuppinCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-7862-3940

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Accurately predicting which patients will respond to immune checkpoint blockade (ICB) remains a major challenge. Here, we present TIME_ACT, an unsupervised 66-gene transcriptomic signature of tumor immune activation derived from TCGA melanoma data. First, TIME_ACT scores accurately identify tumors with activated immune microenvironments across cancer types. Analysis of spatial features of the tumor microenvironment revealed that TIME_ACT-high regions exhibit dense lymphocyte infiltration near tumor cells, indicating localized immune activation. Second, in 15 anti-PD1 transcriptomic cohorts spanning six cancer types, TIME_ACT outperforms 22 established signatures and methods, achieving a mean AUC of 0.76 and a clinically meaningful mean odds ratio of 6.11. Thirdly, TIME_ACT scores can be accurately inferred from tumor histopathology slides. Finally, slide-inferred TIME_ACT scores predict ICB response across eight unseen cohorts, achieving a mean AUC of 0.72 and a mean odds ratio of 5.02. These findings establish TIME_ACT as a robust, pan-cancer, and low-cost predictor of ICB response.

Identifiers

PMID40747419
PMCPMC12312174

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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.