Evidence map›Paper›PMID 39709141›Full record

ArticleJournal of hepatology2025

Single-cell RNA sequencing-derived signatures define response patterns to atezolizumab + bevacizumab in advanced hepatocellular carcinoma.

Sarah Cappuyns, Marta Piqué-Gili, Roger Esteban-Fabró, Gino Philips, Ugne Balaseviciute, Roser Pinyol, Albert Gris-Oliver, Vincent Vandecaveye, Jordi Abril-Fornaguera, Carla Montironi and 31 more

Abstract read
In one paragraph

Article in Journal of hepatology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
48citing papers in PubMed, 1 pooled it
–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

48 citing papers in PubMed, 1 synthesis or guideline pooled it.

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  7. Immunotherapy Rechallenge in HCC: A Second Chance for Response?Liver international : official journal of the International Association for the Study of the Liver · 2026
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  19. From Theory to Practice: Which Biomarkers Are Ready for Predicting Response in Advanced HCC?Liver international : official journal of the International Association for the Study of the Liver · 2026
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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.

Sarah CappuynsDigestive Oncology, Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium; Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; VIB Centre for Cancer Biology, Leuven, Belgium; Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA.
Marta Piqué-GiliMount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA; Liver Cancer Translational Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain.
Roger Esteban-FabróMount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA; Liver Cancer Translational Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain.
Gino PhilipsLaboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; VIB Centre for Cancer Biology, Leuven, Belgium.
Ugne BalaseviciuteLiver Cancer Translational Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain.
Roser PinyolLiver Cancer Translational Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain.
Albert Gris-OliverLiver Cancer Translational Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain.
Vincent VandecaveyeRadiology Department, University Hospitals Leuven, Leuven, Belgium; Laboratory of Translational MRI, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium.
Jordi Abril-FornagueraMount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA; Liver Cancer Translational Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain.
Carla MontironiLiver Cancer Translational Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain; Pathology Department and Molecular Biology Core, Hospital Clínic of Barcelona, Barcelona, Spain.
Laia BassaganyasInstitut de Génomique Fonctionnelle, Univ. Montpellier, CNRS, INSERM, Montpellier, France.
Judit PeixLiver Cancer Translational Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain.
Marcus ZeitlhoeflerMount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA.
Agavni MesropianMount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA; Liver Cancer Translational Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain.
Júlia Huguet-PradellMount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA; Liver Cancer Translational Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain.
Philipp K HaberDepartment of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany.
Igor FigueiredoDepartment of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Giorgio IoannouDepartment of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Edgar Gonzalez-KozlovaDepartment of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Antonio D'AlessioDepartment of Surgery & Cancer, Imperial College London, Hammersmith Hospital, London, UK.
Raphael MohrDepartment of Hepatology and Gastroenterology, Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum (CVK) and Campus Charité Mitte (CCM), Berlin, Germany.
Tim MeyerResearch Department of Oncology, UCL Cancer Institute, University College London, Royal Free Hospital, London, UK.
Anja LachenmayerDepartment of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
Jens U MarquardtDepartment of Medicine I, University Medical Center Schleswig Holstein Campus Lübeck, Lübeck, Germany.
Helen L ReevesHepatopancreatobiliary Multidisciplinary Team, Newcastle upon Tyne NHS Foundation Trust, Freeman Hospital, Newcastle upon Tyne, UK; Newcastle University Translational and Clinical Research Institute and Newcastle University Centre for Cancer, Medical School, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK.
Julien EdelineDepartment of Medical Oncology, Centre Eugène Marquis, Rennes, France.
Fabian FinkelmeierDepartment of Gastroenterology, University Liver and Cancer Centre, Frankfurt, Germany.
Jörg TrojanDepartment of Gastroenterology, University Liver and Cancer Centre, Frankfurt, Germany.
Peter R GalleDepartment of Medicine I, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany.
Friedrich FoersterDepartment of Medicine I, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany.
Beatriz MínguezLiver Unit, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Liver Diseases Research Group, Vall d'Hebron Institute of Research (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; CIBERehd, Universitat Autònoma de Barcelona, Barcelona, Spain.
Robert MontalDepartment of Medical Oncology, Cancer Biomarkers Research Group, Hospital Universitari Arnau de Vilanova, IRBLleida, University of Lleida (UdL), Catalonia, Spain.
Sacha GnjaticDepartment of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
David J PinatoDepartment of Surgery & Cancer, Imperial College London, Hammersmith Hospital, London, UK; Department of Translational Medicine, Università Del Piemonte Orientale "A. Avogadro", Novara, Italy.
Mathias HeikenwalderDivision of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Chris VerslypeDigestive Oncology, Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium.
Eric Van CutsemDigestive Oncology, Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium.
Diether LambrechtsLaboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; VIB Centre for Cancer Biology, Leuven, Belgium.
Augusto VillanuevaMount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA.
Jeroen DekervelDigestive Oncology, Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium. Electronic address: jeroen.dekervel@uzleuven.be.
Josep M LlovetMount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA; Liver Cancer Translational Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, 08010, Spain. Electronic address: josep.llovet@mountsinai.org.

Funding

Conduits: Mount Sinai Health System Translational Science HubUL1TR004419 · NCATS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Rosalind J Wright · 2022 to 2026
$46.4M
THE TISCH CANCER INSTITUTE - CANCER CENTER SUPPORT GRANTP30CA196521 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Ramon E Parsons · 2015 to 2026
$35.4M
Characterizing and predicting colitis in immune checkpoint blockade-treated cancer patientsU01DK124165 · NIDDK · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI COLOMBEL, JEAN-FREDERIC, FAITH, JEREMIAH JAMES · 2020 to 2024
$2.9M
COVID and Translational Science supercomputer (CATS)S10OD030463 · OD · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI KOVATCH, PATRICIA · 2021 to 2021
$2.0M
Big Omics Data Engine 2 SupercomputerS10OD026880 · OD · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI KOVATCH, PATRICIA · 2019 to 2019
$2.0M
Determinants of immunotherapy response in NASH-Hepatocellular carcinomaR01CA273932 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI JOSEP M LLOVET · 2023 to 2026
$2.0M
NCATS NIH HHS UL1 TR004419NCI NIH HHS P30 CA196521NCI NIH HHS R01 CA273932NIDDK NIH HHS U01 DK124165NIH HHS S10 OD026880NIH HHS S10 OD030463
6 · The paper itself

Abstract

BACKGROUND &

aimsThe combination of atezolizumab and bevacizumab (atezo+bev) is the current standard of care for advanced hepatocellular carcinoma (HCC), providing a median overall survival (OS) of 19.2 months. Here, we aim to uncover the underlying cellular processes driving clinical benefit vs. resistance to atezo+bev.

methodsWe harnessed the power of single-cell RNA sequencing in advanced HCC to derive gene expression signatures recapitulating 21 cell phenotypes. These signatures were applied to 422 RNA-sequencing samples of patients with advanced HCC treated with atezo+bev (n = 317) vs. atezolizumab (n = 47) or sorafenib (n = 58) as comparators.

resultsWe unveiled two distinct patterns of response to atezo+bev. First, an immune-mediated response characterised by the combined presence of CD8+ T effector cells and pro-inflammatory CXCL10+ macrophages, representing an immune-rich microenvironment. Second, a non-immune, angiogenesis-related response distinguishable by a reduced expression of the VEGF co-receptor neuropilin-1 (NRP1), a biomarker that specifically predicts improved OS upon atezo+bev vs. sorafenib (p = 0.039). Primary resistance was associated with an enrichment of immunosuppressive myeloid populations, namely CD14+ monocytes and TREM2+ macrophages, and Notch pathway activation. Based on these mechanistic insights we define "Immune-competent" and "Angiogenesis-driven" molecular subgroups, each associated with a significantly longer OS with atezo+bev vs. sorafenib (p of interaction = 0.027), and a "Resistant" subset.

conclusionOur study unveils two distinct molecular subsets of clinical benefit to atezolizumab plus bevacizumab in advanced HCC ("Immune-competent" and "Angiogenesis-driven") as well as the main traits of primary resistance to this therapy, thus providing a molecular framework to stratify patients based on clinical outcome and guiding potential strategies to overcome resistance. IMPACT AND IMPLICATIONS: Atezolizumab + bevacizumab (atezo+bev) is standard of care in advanced hepatocellular carcinoma (HCC), yet molecular determinants of clinical benefit to the combination remain unclear. This study harnesses the power of single-cell RNA sequencing, deriving gene expression signatures representing 21 cell subtypes in the advanced HCC microenvironment. By applying these signatures to RNA-sequencing samples, we reveal two distinct response patterns to atezo+bev and define molecular subgroups of patients ("Immune-competent" and "Angiogenesis-driven" vs. "Resistant") with differential clinical outcomes upon treatment with atezo+bev, pointing towards the role of immunosuppressive myeloid cell types and Notch pathway activation in primary resistance to atezo+bev. These results may help refine treatment strategies and improve outcomes for patients with advanced HCC, while also guiding future research aimed at overcoming resistance mechanisms.

Indexed as

Antibodies, Monoclonal, HumanizedAntineoplastic Combined Chemotherapy ProtocolsBevacizumabCarcinoma, HepatocellularLiver NeoplasmsDrug Resistance, NeoplasmFemaleHumansMaleMiddle AgedSequence Analysis, RNASingle-Cell AnalysisSorafenibTumor MicroenvironmentAntibodies, Monoclonal, HumanizedatezolizumabBevacizumabSorafenibAdvanced Hepatocellular CarcinomaAtezolizumab and bevacizumabBiomarkers of ResponsePrimary ResistanceSingle-Cell RNA-Sequencing

Identifiers

PMID39709141
PMCPMC12086051

What Socratic 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 Socratic graph.