ArticleCell reports. Medicine2023
Deep learning integrates histopathology and proteogenomics at a pan-cancer level.
Open access · goldAbstract read
In one paragraph
Article in Cell reports. Medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
0numbers the graph read from it
0cells of the map it votes in
26citing papers in PubMed
6.9field-weighted citation impact, top 2% of its field
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.
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.
Who cites it
26 citing papers in PubMed, 30 citations in OpenAlex.
- Molecular histomorphometry and the emerging role of transcriptomics in celiac disease diagnosis and therapeutic trials.Annals of medicine · 2026Review
- Effective tumor kinetics inferred from single routine H&E biopsies enable counterfactual virtual radiotherapy trials.medRxiv : the preprint server for health sciences · 2026Article
- Deep Learning-Based Multi-Cancer Analysis for Predicting Disease-Free Survival Across Multiple Cancer Types.Cancers · 2026Article
- Cancer of unknown primary: the evolution of tissue of origin identification in the artificial intelligence era.Biomarker research · 2026Review
- Human genetics across levels of biological organization.Nature reviews. Genetics · 2026Review
- The consensus molecular subtypes of esophageal squamous cell carcinoma.Signal transduction and targeted therapy · 2026Article
- Pathomic model to predict the expression of UQCRH and overall survival of lung adenocarcinoma patients.Diagnostic pathology · 2026Article
- Panorama: a database for the oncogenic evaluation of somatic mutations in pan-cancer.Database : the journal of biological databases and curation · 2026Article
- AI-Guided Discovery of Oncogenic Signaling Crosstalk in Tumor Progression and Drug Resistance.Oncology research · 2026Review
- Integrating chemokine signatures and multi-omic biomarkers to predict immunotherapy response in non-small cell lung cancer: a comprehensive narrative review.Frontiers in oncology · 2026Review
- Exploring the Role of Transcriptomics, Proteomics, and Machine Learning in HPV Infection and Cardiovascular Disease.Biomedicines · 2025Review
- Review
- Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures.Cancer cell · 2025Article
- Building digital histology models of transcriptional tumor programs with generative deep learning for pathology-based precision medicine.Genome medicine · 2025Article
- Image-based inference of tumor cell trajectories enables large-scale cancer progression analysis.Science advances · 2025Article
- Pan-cancer analysis shapes the understanding of cancer biology and medicine.Cancer communications (London, England) · 2025Review
- Multimodal data integration in early-stage breast cancer.Breast (Edinburgh, Scotland) · 2025Review
- Deep learning-based multi-task prediction of response to neoadjuvant chemotherapy using multiscale whole slide images in breast cancer: A multicenter study.Chinese journal of cancer research = Chung-kuo yen cheng yen chiu · 2025Article
- A predictive system comprising serum microRNAs and radiomics for residual retroperitoneal masses in metastatic nonseminomatous germ cell tumors.Cell reports. Medicine · 2024Article
- The 2024 Report on the Human Proteome from the HUPO Human Proteome Project.Journal of proteome research · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
24 authors at 10 institutions in 2 countries.
Joshua M WangInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
Runyu HongInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
Elizabeth G DemiccoDepartment of Pathology and Laboratory Medicine, Mount Sinai Hospital and Laboratory Medicine and Pathobiology, University of Toronto, Toronto M5G 1X5, ON, Canada.
Jimin TanInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA.
Rossana LazcanoDepartment of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Andre L MoreiraDepartment of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA.
Yize LiDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
Anna CalinawanDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Narges RazavianDepartment of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Radiology, NYU Grossman School of Medicine, New York, NY 10016, USA.
Tobias SchrainkInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA.
Michael A GilletteThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Massachusetts General Hospital Division of Pulmonary and Critical Care Medicine, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA.
Gilbert S OmennDepartments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA.
Eunkyung AnOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA.
Henry RodriguezOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA.
Aristotelis TsirigosDepartment of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA; Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA.
Kelly V RugglesInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA.
Li DingDepartment of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
Ana I RoblesOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA.
D R ManiThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Karin D RodlandBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA.
Alexander J LazarDepartment of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: alazar@mdanderson.org.
Wenke LiuInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA. Electronic address: wenke.liu@nyulangone.org.
David FenyöInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA. Electronic address: david@fenyolab.org.
Clinical Proteomic Tumor Analysis Consortium
Institute for Systems Biology · USBroad Institute · USCancer Clinic · USJames S. McDonnell Foundation · USNew York University · USMount Sinai Hospital · CAThe University of Texas MD Anderson Cancer Center · USIcahn School of Medicine at Mount Sinai · USPacific Northwest National Laboratory · USUniversity of Michigan · US
Funding
WORK ORDER 126643 B539 EXPAND IC SUITE75N91019D00024 · NIAID · LEIDOS BIOMEDICAL RESEARCH, INC. · PI BRISCOE, LYNN · 2019 to 2025
$3932.6MResearch Education ComponentP30AG066512 · NIA · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI REBECCA A. BETENSKY · 2020 to 2026
$28.4MStrategic Vision & Impact on Environmental HealthP30ES017885 · NIEHS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Dana Dolinoy · 2011 to 2026
$21.3MProject 3: The Evolving Role of Regional Lymph Nodes in Melanoma ProgressionU54CA263001 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Eva Hernando · 2022 to 2026
$11.6MProteogenomic Studies aimed at understanding ovarian tumor responses to agents targeting the DNA damage response and translating this knowledge into clinical benefitU01CA214114 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI BIRRER, MICHAEL, PAULOVICH, AMANDA G · 2017 to 2021
$8.4MMICROSCALED PROTEOGENOMICS FOR CANCER CLINICAL TRIALSU01CA214125 · NCI · BAYLOR COLLEGE OF MEDICINE · PI ANURAG, MEENAKSHI, CARR, STEVEN A · 2017 to 2021
$7.0MProteogenomic Translational Research Center for Clinical ProteomicU01CA214116 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI DRUKER, BRIAN J, RODLAND, KARIN D · 2017 to 2021
$6.8MMedical Scientist Research Service AwardT32GM136573 · NIGMS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI SULMAN, ERIK · 2020 to 2024
$6.8MCenter for Advanced Multi-Omic Characterization of CancerU24CA271012 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI Tao Liu · 2022 to 2026
$6.6MCenter of Excellence for High Throughput Proteogenomic CharacterizationU24CA210986 · NCI · BROAD INSTITUTE, INC. · PI CARR, STEVEN A, GILLETTE, MICHAEL A · 2016 to 2020
$6.4MNRSA Training CoreTL1TR001447 · NCATS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI MICOLI, KEITH J. · 2015 to 2025
$5.9MCenter of Excellence for High Throughput Proteogenomic CharacterizationU24CA270823 · NCI · BROAD INSTITUTE, INC. · PI STEVEN A CARR, MICHAEL A GILLETTE · 2022 to 2026
$5.3MNCATS NIH HHS TL1 TR001447NCI NIH HHS 75N91019D00024NCI NIH HHS 75N91020C00029NCI NIH HHS F30 CA271622NCI NIH HHS U01 CA214114NCI NIH HHS U01 CA214116NCI NIH HHS U01 CA214125NCI NIH HHS U24 CA210954NCI NIH HHS U24 CA210955NCI NIH HHS U24 CA210967NCI NIH HHS U24 CA210972NCI NIH HHS U24 CA210979NCI NIH HHS U24 CA210985NCI NIH HHS U24 CA210986NCI NIH HHS U24 CA210993NCI NIH HHS U24 CA270823NCI NIH HHS U24 CA271012NCI NIH HHS U54 CA263001NIA NIH HHS P30 AG066512NIEHS NIH HHS P30 ES017885NIGMS NIH HHS T32 GM136573
Abstract
We introduce a pioneering approach that integrates pathology imaging with transcriptomics and proteomics to identify predictive histology features associated with critical clinical outcomes in cancer. We utilize 2,755 H&E-stained histopathological slides from 657 patients across 6 cancer types from CPTAC. Our models effectively recapitulate distinctions readily made by human pathologists: tumor vs. normal (AUROC = 0.995) and tissue-of-origin (AUROC = 0.979). We further investigate predictive power on tasks not normally performed from H&E alone, including TP53 prediction and pathologic stage. Importantly, we describe predictive morphologies not previously utilized in a clinical setting. The incorporation of transcriptomics and proteomics identifies pathway-level signatures and cellular processes driving predictive histology features. Model generalizability and interpretability is confirmed using TCGA. We propose a classification system for these tasks, and suggest potential clinical applications for this integrated human and machine learning approach. A publicly available web-based platform implements these models.
Indexed as
Deep LearningNeoplasmsProteogenomicsHumansMachine LearningProteomicscancer imagingcancer proteogenomicscomputational pathologyCPTACmolecular diagnostics
Identifiers
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.