Single-cell RNA seq-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; Laia Bassaganyas; Judit Peix; Marcus Zeitlhoefler; Agavni Mesropian; Júlia Huguet-Pradell; Philipp K Haber; Igor Figueiredo; Giorgio Ioannou; Edgar Gonzalez-Kozlova; Antonio D'Alessio; Raphael Mohr; Tim Meyer; Anja Lachenmayer; Jens U Marquardt; Helen L Reeves; Julien Edeline; Fabian Finkelmeier; Jörg Trojan; Peter R Galle; Friedrich Foerster; Beatriz Mínguez; Robert Montal; Sacha Gnjatic; David J Pinato; Mathias Heikenwalder; Chris Verslype; Eric Van Cutsem; Diether Lambrechts; Augusto Villanueva; Jeroen Dekervel; Josep M Llovet

doi:10.1016/j.jhep.2024.12.016

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

J Hepatol. 2024 Dec 19:S0168-8278(24)02771-5. doi: 10.1016/j.jhep.2024.12.016. Online ahead of print.

Authors

Sarah Cappuyns¹, Marta Piqué-Gili², Roger Esteban-Fabró², Gino Philips³, Ugne Balaseviciute⁴, Roser Pinyol⁴, Albert Gris-Oliver⁴, Vincent Vandecaveye⁵, Jordi Abril-Fornaguera², Carla Montironi⁶, Laia Bassaganyas⁷, Judit Peix⁴, Marcus Zeitlhoefler⁸, Agavni Mesropian², Júlia Huguet-Pradell², Philipp K Haber⁹, Igor Figueiredo¹⁰, Giorgio Ioannou¹⁰, Edgar Gonzalez-Kozlova¹⁰, Antonio D'Alessio¹¹, Raphael Mohr¹², Tim Meyer¹³, Anja Lachenmayer¹⁴, Jens U Marquardt¹⁵, Helen L Reeves¹⁶, Julien Edeline¹⁷, Fabian Finkelmeier¹⁸, Jörg Trojan¹⁸, Peter R Galle¹⁹, Friedrich Foerster¹⁹, Beatriz Mínguez²⁰, Robert Montal²¹, Sacha Gnjatic¹⁰, David J Pinato²², Mathias Heikenwalder²³, Chris Verslype²⁴, Eric Van Cutsem²⁴, Diether Lambrechts³, Augusto Villanueva⁸, Jeroen Dekervel²⁵, Josep M Llovet²⁶

Affiliations

¹ Digestive 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.
² 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; Liver Cancer Translational Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain.
³ Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; VIB Centre for Cancer Biology, Leuven, Belgium.
⁴ Liver Cancer Translational Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain.
⁵ Radiology Department, University Hospitals Leuven, Leuven, Belgium; Laboratory of Translational MRI, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium.
⁶ Liver Cancer Translational Research Laboratory, 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.
⁷ Institut de Génomique Fonctionnelle, Univ. Montpellier, CNRS, INSERM, Montpellier, France.
⁸ 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.
⁹ Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany.
¹⁰ Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
¹¹ Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, London, United Kingdom.
¹² Department of Hepatology and Gastroenterology, Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum (CVK) and Campus Charité Mitte (CCM), Berlin, Germany.
¹³ Research Department of Oncology, UCL Cancer Institute, University College London, Royal Free Hospital, London, UK.
¹⁴ Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
¹⁵ Department of Medicine I, University Medical Center Schleswig Holstein Campus Lübeck, Lübeck, Germany.
¹⁶ Newcastle University Translational and Clinical Research Institute and Newcastle University Centre for Cancer, Medical School, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK; Hepatopancreatobiliary Multidisciplinary Team, Newcastle upon Tyne NHS Foundation Trust, Freeman Hospital, Newcastle upon Tyne, UK.
¹⁷ Department of Medical Oncology, Centre Eugène Marquis, Rennes, France.
¹⁸ Department of Gastroenterology, University Liver and Cancer Centre, Frankfurt, Germany.
¹⁹ Department of Medicine I, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany.
²⁰ Liver 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.
²¹ Department of Medical Oncology, Cancer Biomarkers Research Group, Hospital Universitari Arnau de Vilanova, IRBLleida, University of Lleida (UdL), Catalonia, Spain.
²² Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, London, United Kingdom; Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, London, United Kingdom.
²³ Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
²⁴ Digestive Oncology, Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium.
²⁵ Digestive Oncology, Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium. Electronic address: [email protected].
²⁶ 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; Liver Cancer Translational Research Laboratory, 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: [email protected].

PMID: 39709141
DOI: 10.1016/j.jhep.2024.12.016

Abstract

Background & aims: The 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 versus resistance to atezo+bev.

Methods: We 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 advanced HCC patients treated with atezo+bev (n=317) versus atezolizumab (n=47) or sorafenib (n=58) as comparators.

Results: We unveiled two distinct patterns of response to atezo+bev. First, an immune-mediated response characterized 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 versus sorafenib (p of interaction = 0.027), and a "Resistant" subset.

Conclusion: Our 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.

Keywords: Advanced Hepatocellular Carcinoma; Atezolizumab and bevacizumab; Biomarkers of Response; Primary Resistance; Single-Cell RNA-Sequencing.