1
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Kinget L, Naulaerts S, Govaerts J, Vanmeerbeek I, Sprooten J, Laureano RS, Dubroja N, Shankar G, Bosisio FM, Roussel E, Verbiest A, Finotello F, Ausserhofer M, Lambrechts D, Boeckx B, Wozniak A, Boon L, Kerkhofs J, Zucman-Rossi J, Albersen M, Baldewijns M, Beuselinck B, Garg AD. A spatial architecture-embedding HLA signature to predict clinical response to immunotherapy in renal cell carcinoma. Nat Med 2024:10.1038/s41591-024-02978-9. [PMID: 38773341 DOI: 10.1038/s41591-024-02978-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 04/05/2024] [Indexed: 05/23/2024]
Abstract
An important challenge in the real-world management of patients with advanced clear-cell renal cell carcinoma (aRCC) is determining who might benefit from immune checkpoint blockade (ICB). Here we performed a comprehensive multiomics mapping of aRCC in the context of ICB treatment, involving discovery analyses in a real-world data cohort followed by validation in independent cohorts. We cross-connected bulk-tumor transcriptomes across >1,000 patients with validations at single-cell and spatial resolutions, revealing a patient-specific crosstalk between proinflammatory tumor-associated macrophages and (pre-)exhausted CD8+ T cells that was distinguished by a human leukocyte antigen repertoire with higher preference for tumoral neoantigens. A cross-omics machine learning pipeline helped derive a new tumor transcriptomic footprint of neoantigen-favoring human leukocyte antigen alleles. This machine learning signature correlated with positive outcome following ICB treatment in both real-world data and independent clinical cohorts. In experiments using the RENCA-tumor mouse model, CD40 agonism combined with PD1 blockade potentiated both proinflammatory tumor-associated macrophages and CD8+ T cells, thereby achieving maximal antitumor efficacy relative to other tested regimens. Thus, we present a new multiomics and spatial map of the immune-community architecture that drives ICB response in patients with aRCC.
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Affiliation(s)
- Lisa Kinget
- Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
- Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Stefan Naulaerts
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Jannes Govaerts
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Isaure Vanmeerbeek
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Jenny Sprooten
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Raquel S Laureano
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Nikolina Dubroja
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Gautam Shankar
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Francesca M Bosisio
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Eduard Roussel
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | | | - Francesca Finotello
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Markus Ausserhofer
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Bram Boeckx
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | | | | | - Johan Kerkhofs
- Histocompatibility and Immunogenetics Laboratory, Belgian Red Cross-Flanders, Mechelen, Belgium
| | - Jessica Zucman-Rossi
- Inserm, UMRS-1138, Génomique fonctionnelle des tumeurs solides, Centre de recherche des Cordeliers, Paris, France
| | - Maarten Albersen
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | | | - Benoit Beuselinck
- Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium.
- Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.
| | - Abhishek D Garg
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
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2
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Geukens T, De Schepper M, Van Den Bogaert W, Van Baelen K, Maetens M, Pabba A, Mahdami A, Leduc S, Isnaldi E, Nguyen HL, Bachir I, Hajipirloo M, Zels G, Van Cauwenberge J, Borremans K, Vandecaveye V, Weynand B, Vermeulen P, Leucci E, Baietti MF, Sflomos G, Battista L, Brisken C, Derksen PWB, Koorman T, Visser D, Scheele CLGJ, Thommen DS, Hatse S, Fendt SM, Vanderheyden E, Van Brussel T, Schepers R, Boeckx B, Lambrechts D, Marano G, Biganzoli E, Smeets A, Nevelsteen I, Punie K, Neven P, Wildiers H, Richard F, Floris G, Desmedt C. Rapid autopsies to enhance metastatic research: the UPTIDER post-mortem tissue donation program. NPJ Breast Cancer 2024; 10:31. [PMID: 38658604 PMCID: PMC11043338 DOI: 10.1038/s41523-024-00637-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 04/05/2024] [Indexed: 04/26/2024] Open
Abstract
Research on metastatic cancer has been hampered by limited sample availability. Here we present the breast cancer post-mortem tissue donation program UPTIDER and show how it enabled sampling of a median of 31 (range: 5-90) metastases and 5-8 liquids per patient from its first 20 patients. In a dedicated experiment, we show the mild impact of increasing time after death on RNA quality, transcriptional profiles and immunohistochemical staining in tumor tissue samples. We show that this impact can be counteracted by organ cooling. We successfully generated ex vivo models from tissue and liquid biopsies from distinct histological subtypes of breast cancer. We anticipate these and future findings of UPTIDER to elucidate mechanisms of disease progression and treatment resistance and to provide tools for the exploration of precision medicine strategies in the metastatic setting.
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Affiliation(s)
- Tatjana Geukens
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of General Medical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Maxim De Schepper
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | | | - Karen Van Baelen
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Marion Maetens
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Anirudh Pabba
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Amena Mahdami
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sophia Leduc
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Edoardo Isnaldi
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Ha-Linh Nguyen
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Imane Bachir
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Anesthesiology, Institut Jules Bordet, Brussels, Belgium
| | - Maysam Hajipirloo
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Gitte Zels
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Josephine Van Cauwenberge
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Kristien Borremans
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | | | - Birgit Weynand
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Peter Vermeulen
- Centre for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
| | - Eleonora Leucci
- TRACE and Laboratory for RNA Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Maria Francesca Baietti
- TRACE and Laboratory for RNA Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - George Sflomos
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Laura Battista
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Cathrin Brisken
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Patrick W B Derksen
- Department of Pathology, University Medical Center, Utrecht, The Netherlands
| | - Thijs Koorman
- Department of Pathology, University Medical Center, Utrecht, The Netherlands
| | - Daan Visser
- Department of Pathology, University Medical Center, Utrecht, The Netherlands
| | - Colinda L G J Scheele
- Laboratory of Intravital Microscopy and Dynamics of Tumor Progression, Department of Oncology, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
| | - Daniela S Thommen
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sigrid Hatse
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Evy Vanderheyden
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium, and VIB Center for Cancer Biology, Leuven, Belgium
| | - Thomas Van Brussel
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium, and VIB Center for Cancer Biology, Leuven, Belgium
| | - Rogier Schepers
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium, and VIB Center for Cancer Biology, Leuven, Belgium
| | - Bram Boeckx
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium, and VIB Center for Cancer Biology, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium, and VIB Center for Cancer Biology, Leuven, Belgium
| | - Giuseppe Marano
- Unit of Medical Statistics, Biometry and Epidemiology, Department of Biomedical and Clinical Sciences (DIBIC) "L. Sacco" & DSRC, LITA Vialba campus, Università degli Studi di Milano, Milan, Italy
| | - Elia Biganzoli
- Unit of Medical Statistics, Biometry and Epidemiology, Department of Biomedical and Clinical Sciences (DIBIC) "L. Sacco" & DSRC, LITA Vialba campus, Università degli Studi di Milano, Milan, Italy
| | - Ann Smeets
- Department of Surgical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Ines Nevelsteen
- Department of Surgical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Kevin Punie
- Department of General Medical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Patrick Neven
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Hans Wildiers
- Department of General Medical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - François Richard
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Giuseppe Floris
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium.
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3
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Lecomte K, Toniolo A, Hoste E. Cell death as an architect of adult skin stem cell niches. Cell Death Differ 2024:10.1038/s41418-024-01297-3. [PMID: 38649745 DOI: 10.1038/s41418-024-01297-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
Our skin provides a physical and immunological barrier against dehydration and environmental insults ranging from microbial attacks, toxins and UV irradiation to wounding. Proper functioning of the skin barrier largely depends on the interplay between keratinocytes- the epithelial cells of the skin- and immune cells. Two spatially distinct populations of keratinocyte stem cells (SCs) maintain the epidermal barrier function and the hair follicle. These SCs are inherently long-lived, but cell death can occur within their niches and impacts their functionality. The default cell death programme in skin is apoptosis, an orderly and non-inflammatory suicide programme. However, recent findings are shedding light on the significance of various modes of regulated necrotic cell death, which are lytic and can provoke inflammation within the local skin environment. While the presence of dying cells was generally regarded as a mere consequence of inflammation, findings in various human dermatological conditions and experimental mouse models of aberrant cell death control demonstrated that cell death programmes in keratinocytes (KCs) can drive skin inflammation and even tumour initiation. When cells die, they need to be removed by phagocytosis and KCs can function as non-professional phagocytes of apoptotic cells with important implications for their SC capacities. It is becoming apparent that in conditions of heightened SC activity, distinct cell death modalities differentially impact the different skin SC populations in their local niches. Here, we describe how regulated cell death modalities functionally affect epidermal SC niches along with their relevance to injury repair, inflammatory skin disorders and cancer.
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Affiliation(s)
- Kim Lecomte
- VIB Center for Inflammation Research, 9052, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9052, Ghent, Belgium
| | - Annagiada Toniolo
- VIB Center for Inflammation Research, 9052, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9052, Ghent, Belgium
| | - Esther Hoste
- VIB Center for Inflammation Research, 9052, Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, 9052, Ghent, Belgium.
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4
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Van Baelen K, Van Cauwenberge J, Maetens M, Beck G, Camden A, Chase MC, Fraser V, Freeney S, Hutcheson L, Levine JK, Lien T, Terveer R, Turner C, Senkus E, Jankowitz RC, Vandecaveye V, Floris G, Neven P, Wildiers H, Sawyer E, Vincent-Salomon A, Derksen PWB, Desmedt C. Reporting on invasive lobular breast cancer in clinical trials: a systematic review. NPJ Breast Cancer 2024; 10:23. [PMID: 38509112 PMCID: PMC10954721 DOI: 10.1038/s41523-024-00627-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Invasive lobular breast cancer (ILC) differs from invasive breast cancer of no special type in many ways. Evidence on treatment efficacy for ILC is, however, lacking. We studied the degree of documentation and representation of ILC in phase III/IV clinical trials for novel breast cancer treatments. Trials were identified on Pubmed and clinicaltrials.gov. Inclusion/exclusion criteria were reviewed for requirements on histological subtype and tumor measurability. Documentation of ILC was assessed and ILC inclusion rate, central pathology and subgroup analyses were evaluated. Inclusion restrictions concerning tumor measurability were found in 39/93 manuscripts. Inclusion rates for ILC were documented in 13/93 manuscripts and varied between 2.0 and 26.0%. No central pathology for ILC was reported and 3/13 manuscripts had ILC sub-analyses. ILC is largely disregarded in most trials with poor representation and documentation. The current inclusion criteria using RECIST v1.1, fall short in recognizing the unique non-measurable metastatic infiltration of ILC.
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Affiliation(s)
- Karen Van Baelen
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Gynecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Josephine Van Cauwenberge
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Gynecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Marion Maetens
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Gabriela Beck
- European Lobular Breast Cancer Consortium, Utrecht, the Netherlands
| | - Ann Camden
- Lobular Breast Cancer Alliance inc., Plymouth, MA, USA
| | | | | | - Siobhan Freeney
- European Lobular Breast Cancer Consortium, Utrecht, the Netherlands
- Lobular Ireland, Dublin, Ireland
| | | | | | - Tone Lien
- European Lobular Breast Cancer Consortium, Utrecht, the Netherlands
| | - Rian Terveer
- European Lobular Breast Cancer Consortium, Utrecht, the Netherlands
- Borstkankervereniging Nederland, Utrecht, the Netherlands
| | - Claire Turner
- European Lobular Breast Cancer Consortium, Utrecht, the Netherlands
- Lobular Breast Cancer UK, Manchester, UK
| | - Elzbieta Senkus
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, Gdańsk, Poland
| | - Rachel C Jankowitz
- Division of Hematology/Oncology, Abramsom Cancer Center, University of Pennsylvania, Philadelphia, USA
| | - Vincent Vandecaveye
- Department of Radiology, University Hospitals Leuven, Leuven, Belgium
- Division of Translational MRI, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Giuseppe Floris
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Patrick Neven
- Department of Gynecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Hans Wildiers
- Department of General Medical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Elinor Sawyer
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Anne Vincent-Salomon
- Department of Pathology, Institut Curie, Paris Sciences Lettres University, Paris, France
| | - Patrick W B Derksen
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium.
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5
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Mah CY, Nguyen ADT, Niijima T, Helm M, Dehairs J, Ryan FJ, Ryan N, Quek LE, Hoy AJ, Don AS, Mills IG, Swinnen JV, Lynn DJ, Nassar ZD, Butler LM. Peroxisomal β-oxidation enzyme, DECR2, regulates lipid metabolism and promotes treatment resistance in advanced prostate cancer. Br J Cancer 2024; 130:741-754. [PMID: 38216720 PMCID: PMC10912652 DOI: 10.1038/s41416-023-02557-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/05/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Peroxisomes are central metabolic organelles that have key roles in fatty acid homoeostasis. As prostate cancer (PCa) is particularly reliant on fatty acid metabolism, we explored the contribution of peroxisomal β-oxidation (perFAO) to PCa viability and therapy response. METHODS Bioinformatic analysis was performed on clinical transcriptomic datasets to identify the perFAO enzyme, 2,4-dienoyl CoA reductase 2 (DECR2) as a target gene of interest. Impact of DECR2 and perFAO inhibition via thioridazine was examined in vitro, in vivo, and in clinical prostate tumours cultured ex vivo. Transcriptomic and lipidomic profiling was used to determine the functional consequences of DECR2 inhibition in PCa. RESULTS DECR2 is upregulated in clinical PCa, most notably in metastatic castrate-resistant PCa (CRPC). Depletion of DECR2 significantly suppressed proliferation, migration, and 3D growth of a range of CRPC and therapy-resistant PCa cell lines, and inhibited LNCaP tumour growth and proliferation in vivo. DECR2 influences cell cycle progression and lipid metabolism to support tumour cell proliferation. Further, co-targeting of perFAO and standard-of-care androgen receptor inhibition enhanced suppression of PCa cell proliferation. CONCLUSION Our findings support a focus on perFAO, specifically DECR2, as a promising therapeutic target for CRPC and as a novel strategy to overcome lethal treatment resistance.
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Affiliation(s)
- Chui Yan Mah
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - An Dieu Trang Nguyen
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Takuto Niijima
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
| | - Madison Helm
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Jonas Dehairs
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, KU Leuven, Leuven, Belgium
| | - Feargal J Ryan
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | - Natalie Ryan
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Lake-Ee Quek
- School of Medical Sciences, Charles Perkins Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Andrew J Hoy
- School of Medical Sciences, Charles Perkins Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Anthony S Don
- School of Medical Sciences, Charles Perkins Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Ian G Mills
- Patrick G Johnston Centre for Cancer Research, Queen's University, Belfast, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Johannes V Swinnen
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, KU Leuven, Leuven, Belgium
| | - David J Lynn
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | - Zeyad D Nassar
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia.
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.
| | - Lisa M Butler
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia.
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.
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6
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Bravo González-Blas C, Matetovici I, Hillen H, Taskiran II, Vandepoel R, Christiaens V, Sansores-García L, Verboven E, Hulselmans G, Poovathingal S, Demeulemeester J, Psatha N, Mauduit D, Halder G, Aerts S. Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation. Nat Cell Biol 2024; 26:153-167. [PMID: 38182825 PMCID: PMC10791584 DOI: 10.1038/s41556-023-01316-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 11/15/2023] [Indexed: 01/07/2024]
Abstract
In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based on their location within the liver lobule. However, it is unclear whether this spatial variation, called zonation, is governed by a well-defined gene regulatory code. Here, using a combination of single-cell multiomics, spatial omics, massively parallel reporter assays and deep learning, we mapped enhancer-gene regulatory networks across mouse liver cell types. We found that zonation affects gene expression and chromatin accessibility in hepatocytes, among other cell types. These states are driven by the repressors TCF7L1 and TBX3, alongside other core hepatocyte transcription factors, such as HNF4A, CEBPA, FOXA1 and ONECUT1. To examine the architecture of the enhancers driving these cell states, we trained a hierarchical deep learning model called DeepLiver. Our study provides a multimodal understanding of the regulatory code underlying hepatocyte identity and their zonation state that can be used to engineer enhancers with specific activity levels and zonation patterns.
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Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irina Matetovici
- VIB Center for Brain & Disease Research, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
| | - Hanne Hillen
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Roel Vandepoel
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Leticia Sansores-García
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Elisabeth Verboven
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | | | - Jonas Demeulemeester
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nikoleta Psatha
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - David Mauduit
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Georg Halder
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium.
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7
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Leduc S, De Schepper M, Richard F, Maetens M, Pabba A, Borremans K, Jaekers J, Latacz E, Zels G, Bohlok A, Van Baelen K, Nguyen HL, Geukens T, Dirix L, Larsimont D, Vankerckhove S, Santos E, Oliveira RC, Dede K, Kulka J, Borbala S, Salamon F, Madaras L, Marcell Szasz A, Lucidi V, Meyer Y, Topal B, Verhoef C, Engstrand J, Moro CF, Gerling M, Bachir I, Biganzoli E, Donckier V, Floris G, Vermeulen P, Desmedt C. Histopathological growth patterns and tumor-infiltrating lymphocytes in breast cancer liver metastases. NPJ Breast Cancer 2023; 9:100. [PMID: 38102162 PMCID: PMC10724185 DOI: 10.1038/s41523-023-00602-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
Liver is the third most common organ for breast cancer (BC) metastasis. Two main histopathological growth patterns (HGP) exist in liver metastases (LM): desmoplastic and replacement. Although a reduced immunotherapy efficacy is reported in patients with LM, tumor-infiltrating lymphocytes (TIL) have not yet been investigated in BCLM. Here, we evaluate the distribution of the HGP and TIL in BCLM, and their association with clinicopathological variables and survival. We collect samples from surgically resected BCLM (n = 133 patients, 568 H&E sections) and post-mortem derived BCLM (n = 23 patients, 97 H&E sections). HGP is assessed as the proportion of tumor liver interface and categorized as pure-replacement ('pure r-HGP') or any-desmoplastic ('any d-HGP'). We score the TIL according to LM-specific guidelines. Associations with progression-free (PFS) and overall survival (OS) are assessed using Cox regressions. We observe a higher prevalence of 'any d-HGP' (56%) in the surgical samples and a higher prevalence of 'pure r-HGP' (83%) in the post-mortem samples. In the surgical cohort, no evidence of the association between HGP and clinicopathological characteristics is observed except with the laterality of the primary tumor (p value = 0.049) and the systemic preoperative treatment before liver surgery (p value = .039). TIL is less prevalent in 'pure r-HGP' as compared to 'any d-HGP' (p value = 0.001). 'Pure r-HGP' predicts worse PFS (HR: 2.65; CI: (1.45-4.82); p value = 0.001) and OS (HR: 3.10; CI: (1.29-7.46); p value = 0.011) in the multivariable analyses. To conclude, we demonstrate that BCLM with a 'pure r-HGP' is associated with less TIL and with the worse outcome when compared with BCLM with 'any d-HGP'. These findings suggest that HGP could be considered to refine treatment approaches.
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Affiliation(s)
- Sophia Leduc
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Maxim De Schepper
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - François Richard
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Marion Maetens
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Anirudh Pabba
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Kristien Borremans
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Gynecological Oncology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Joris Jaekers
- Department of Abdominal Surgery, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Emily Latacz
- Translational Cancer Research Unit, GZA Hospitals & CORE, MIPRO, University of Antwerp, Antwerp, Belgium
| | - Gitte Zels
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Ali Bohlok
- Department of Surgical Oncology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Karen Van Baelen
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Gynecological Oncology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Ha Linh Nguyen
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Tatjana Geukens
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Luc Dirix
- Translational Cancer Research Unit, GZA Hospitals & CORE, MIPRO, University of Antwerp, Antwerp, Belgium
| | - Denis Larsimont
- Department of Anatomopathology, Institut Jules Bordet, Brussels, Belgium
| | - Sophie Vankerckhove
- Department of Surgical Oncology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Eva Santos
- General Surgery Department, Centro Hospitalar e Universitario de Coimbra, Coimbra, Portugal
| | - Rui Caetano Oliveira
- General Surgery Department, Centro Hospitalar e Universitario de Coimbra, Coimbra, Portugal
| | - Kristòf Dede
- Department of Surgical Oncology, Uzsoki Hospital, Budapest, Hungary
| | - Janina Kulka
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Székely Borbala
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Ferenc Salamon
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Lilla Madaras
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
- Department of Pathology, Uzsoki Hospital, Budapest, Hungary
| | - A Marcell Szasz
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Valerio Lucidi
- Department of Abdominal Surgery, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Yannick Meyer
- Department of Surgical Oncology and Gastrointestinal Surgery, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Baki Topal
- Department of Abdominal Surgery, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Cornelis Verhoef
- Department of Surgical Oncology and Gastrointestinal Surgery, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Jennie Engstrand
- Division of Surgery, Department of Clinical Science, Intervention and Technology, Karolinska Institutet at Karolinska University Hospital, Stockholm, Sweden
| | - Carlos Fernandez Moro
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge and Karolinska University Hospital, Solna, Sweden
| | - Marco Gerling
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge and Karolinska University Hospital, Solna, Sweden
| | - Imane Bachir
- Department of Anesthesiology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Elia Biganzoli
- Unit of Medical Statistics, Biometry and Epidemiology, Department of Biomedical and Clinical Sciences (DIBIC) "L. Sacco" & DSRC, LITA Vialba campus, University of Milan, Milan, Italy
| | - Vincent Donckier
- Department of Surgical Oncology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Giuseppe Floris
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Peter Vermeulen
- Translational Cancer Research Unit, GZA Hospitals & CORE, MIPRO, University of Antwerp, Antwerp, Belgium
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium.
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8
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Cappuyns S, Philips G, Vandecaveye V, Boeckx B, Schepers R, Van Brussel T, Arijs I, Mechels A, Bassez A, Lodi F, Jaekers J, Topal H, Topal B, Bricard O, Qian J, Van Cutsem E, Verslype C, Lambrechts D, Dekervel J. PD-1 - CD45RA + effector-memory CD8 T cells and CXCL10 + macrophages are associated with response to atezolizumab plus bevacizumab in advanced hepatocellular carcinoma. Nat Commun 2023; 14:7825. [PMID: 38030622 PMCID: PMC10687033 DOI: 10.1038/s41467-023-43381-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
The combination of atezolizumab plus bevacizumab (atezo/bev) has dramatically changed the treatment landscape of advanced HCC (aHCC), achieving durable responses in some patients. Using single-cell transcriptomics, we characterize the intra-tumoural and peripheral immune context of patients with aHCC treated with atezo/bev. Tumours from patients with durable responses are enriched for PDL1+ CXCL10+ macrophages and, based on cell-cell interaction analysis, express high levels of CXCL9/10/11 and are predicted to attract peripheral CXCR3+ CD8+ effector-memory T cells (CD8 TEM) into the tumour. Based on T cell receptor sharing and pseudotime trajectory analysis, we propose that CD8 TEM preferentially differentiate into clonally-expanded PD1- CD45RA+ effector-memory CD8+ T cells (CD8 TEMRA) with pronounced cytotoxicity. In contrast, in non-responders, CD8 TEM remain frozen in their effector-memory state. Finally, in responders, CD8 TEMRA display a high degree of T cell receptor sharing with blood, consistent with their patrolling activity. These findings may help understand the possible mechanisms underlying response to atezo/bev in aHCC.
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Affiliation(s)
- Sarah Cappuyns
- 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
| | - Gino Philips
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
| | - Vincent Vandecaveye
- Radiology Department, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Translational MRI, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Bram Boeckx
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
| | - Rogier Schepers
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
| | - Thomas Van Brussel
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
| | - Ingrid Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
| | - Aurelie Mechels
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
| | - Ayse Bassez
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
| | - Francesca Lodi
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
| | - Joris Jaekers
- Hepatobiliary- and pancreas Surgery, Department of Abdominal Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Halit Topal
- Hepatobiliary- and pancreas Surgery, Department of Abdominal Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Baki Topal
- Hepatobiliary- and pancreas Surgery, Department of Abdominal Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Orian Bricard
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
| | - Junbin Qian
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynaecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Eric Van Cutsem
- Digestive Oncology, Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Clinical Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Chris Verslype
- Digestive Oncology, Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Clinical Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
- VIB Centre for Cancer Biology, Leuven, Belgium.
| | - Jeroen Dekervel
- Digestive Oncology, Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium.
- Laboratory of Clinical Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium.
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9
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Dondelinger Y, Priem D, Huyghe J, Delanghe T, Vandenabeele P, Bertrand MJM. NINJ1 is activated by cell swelling to regulate plasma membrane permeabilization during regulated necrosis. Cell Death Dis 2023; 14:755. [PMID: 37980412 PMCID: PMC10657445 DOI: 10.1038/s41419-023-06284-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/25/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Plasma membrane permeabilization (PMP) is a defining feature of regulated necrosis. It allows the extracellular release of damage-associated molecular patterns (DAMPs) that trigger sterile inflammation. The pore forming molecules MLKL and GSDMs drive PMP in necroptosis and pyroptosis, respectively, but the process of PMP remains unclear in many other forms of regulated necrosis. Here, we identified NINJ1 as a crucial regulator of PMP and consequent DAMP release during ferroptosis, parthanatos, H2O2-induced necrosis and secondary necrosis. Importantly, the membrane-permeabilizing function of NINJ1 takes place after the metabolic death of the cells and is independent of the pore-forming molecules MLKL, GSDMD and GSDME. During ferroptosis, NINJ1 acts downstream of lipid peroxidation, which suggested a role for reactive oxygen species (ROS) in NINJ1 activation. Reactive oxygen species were however neither sufficient nor required to trigger NINJ1-dependent PMP. Instead, we found that NINJ1 oligomerization is induced by the swelling of the cell and that its permeabilizing potential still requires an addition, and yet to be discovered, activation mechanism.
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Affiliation(s)
- Yves Dondelinger
- Inflammation Research Center, VIB, Technologiepark 71, 9052, Zwijnaarde-Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Zwijnaarde-Ghent, Belgium.
| | - Dario Priem
- Inflammation Research Center, VIB, Technologiepark 71, 9052, Zwijnaarde-Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Zwijnaarde-Ghent, Belgium
| | - Jon Huyghe
- Inflammation Research Center, VIB, Technologiepark 71, 9052, Zwijnaarde-Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Zwijnaarde-Ghent, Belgium
| | - Tom Delanghe
- Inflammation Research Center, VIB, Technologiepark 71, 9052, Zwijnaarde-Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Zwijnaarde-Ghent, Belgium
| | - Peter Vandenabeele
- Inflammation Research Center, VIB, Technologiepark 71, 9052, Zwijnaarde-Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Zwijnaarde-Ghent, Belgium
| | - Mathieu J M Bertrand
- Inflammation Research Center, VIB, Technologiepark 71, 9052, Zwijnaarde-Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Zwijnaarde-Ghent, Belgium.
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10
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Deprez J, Verbeke R, Meulewaeter S, Aernout I, Dewitte H, Decruy T, Coudenys J, Van Duyse J, Van Isterdael G, Peer D, van der Meel R, De Smedt SC, Jacques P, Elewaut D, Lentacker I. Transport by circulating myeloid cells drives liposomal accumulation in inflamed synovium. Nat Nanotechnol 2023; 18:1341-1350. [PMID: 37430039 DOI: 10.1038/s41565-023-01444-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/07/2023] [Indexed: 07/12/2023]
Abstract
The therapeutic potential of liposomes to deliver drugs into inflamed tissue is well documented. Liposomes are believed to largely transport drugs into inflamed joints by selective extravasation through endothelial gaps at the inflammatory sites, known as the enhanced permeation and retention effect. However, the potential of blood-circulating myeloid cells for the uptake and delivery of liposomes has been largely overlooked. Here we show that myeloid cells can transport liposomes to inflammatory sites in a collagen-induced arthritis model. It is shown that the selective depletion of the circulating myeloid cells reduces the accumulation of liposomes up to 50-60%, suggesting that myeloid-cell-mediated transport accounts for more than half of liposomal accumulation in inflamed regions. Although it is widely believed that PEGylation inhibits premature liposome clearance by the mononuclear phagocytic system, our data show that the long blood circulation times of PEGylated liposomes rather favours uptake by myeloid cells. This challenges the prevailing theory that synovial liposomal accumulation is primarily due to the enhanced permeation and retention effect and highlights the potential for other pathways of delivery in inflammatory diseases.
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Affiliation(s)
- Joke Deprez
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent Research Group on Nanomedicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Unit Molecular Immunology and Inflammation, VIB Centre for Inflammation Research, Ghent University and Department of Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - Rein Verbeke
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent Research Group on Nanomedicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Sofie Meulewaeter
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent Research Group on Nanomedicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Ilke Aernout
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent Research Group on Nanomedicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Heleen Dewitte
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent Research Group on Nanomedicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Tine Decruy
- Unit Molecular Immunology and Inflammation, VIB Centre for Inflammation Research, Ghent University and Department of Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - Julie Coudenys
- Unit Molecular Immunology and Inflammation, VIB Centre for Inflammation Research, Ghent University and Department of Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - Julie Van Duyse
- VIB Flow Core, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Gert Van Isterdael
- VIB Flow Core, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Dan Peer
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Roy van der Meel
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Stefaan C De Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent Research Group on Nanomedicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Peggy Jacques
- Unit Molecular Immunology and Inflammation, VIB Centre for Inflammation Research, Ghent University and Department of Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - Dirk Elewaut
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
- Unit Molecular Immunology and Inflammation, VIB Centre for Inflammation Research, Ghent University and Department of Rheumatology, Ghent University Hospital, Ghent, Belgium.
| | - Ine Lentacker
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent Research Group on Nanomedicine, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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11
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Lambrechts Y, Garg AD, Floris G, Punie K, Neven P, Nevelsteen I, Govaerts J, Richard F, Laenen A, Desmedt C, Wildiers H, Hatse S. Circulating biomarkers at diagnosis correlate with distant metastases of early luminal-like breast cancer. Genes Immun 2023; 24:270-279. [PMID: 37759086 PMCID: PMC10575765 DOI: 10.1038/s41435-023-00220-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023]
Abstract
There is an urgent need for new and better biomarker modalities to estimate the risk of recurrence within the luminal-like breast cancer (BC) population. Molecular diagnostic tests used in the clinic lack accuracy in identifying patients with early luminal BC who are likely to develop metastases. This study provides proof of concept that various liquid biopsy read-outs could serve as valuable candidates to build a multi-modal biomarker model distinguishing, already at diagnosis, between early metastasizing and non-metastasizing patients. All these blood biomarkers (chemokines, microRNAs, leukemia inhibitory factor, osteopontin, and serum-induced functional myeloid signaling responses) can be measured in baseline plasma/serum samples and could be added to the existing prognostic factors to improve risk stratification and more patient-tailored treatment in early luminal BC.
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Affiliation(s)
- Yentl Lambrechts
- Laboratory of Experimental Oncology (LEO), Department of Oncology, KU Leuven, Leuven, Belgium
| | - Abhishek D Garg
- Laboratory of Cell Stress & Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Giuseppe Floris
- Laboratory for Cell and Tissue Translational Research, Department of Imaging and Radiology, KU Leuven - Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Kevin Punie
- Department of General Medical Oncology and Multidisciplinary Breast Center, University Hospitals Leuven, Leuven, Belgium
| | - Patrick Neven
- Department of General Medical Oncology and Multidisciplinary Breast Center, University Hospitals Leuven, Leuven, Belgium
| | - Ines Nevelsteen
- Department of General Medical Oncology and Multidisciplinary Breast Center, University Hospitals Leuven, Leuven, Belgium
| | - Jannes Govaerts
- Laboratory of Cell Stress & Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - François Richard
- Laboratory for Translational Breast Cancer Research (LTBCR), Department of Oncology, KU Leuven, Leuven, Belgium
| | - Annouschka Laenen
- Leuven Biostatistics and Statistical Bioinformatics Center, KU Leuven, Leuven, Belgium
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research (LTBCR), Department of Oncology, KU Leuven, Leuven, Belgium
| | - Hans Wildiers
- Laboratory of Experimental Oncology (LEO), Department of Oncology, KU Leuven, Leuven, Belgium
- Department of General Medical Oncology and Multidisciplinary Breast Center, University Hospitals Leuven, Leuven, Belgium
| | - Sigrid Hatse
- Laboratory of Experimental Oncology (LEO), Department of Oncology, KU Leuven, Leuven, Belgium.
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12
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Yu Q, Van Minsel P, Galle E, Thienpont B. GiRAFR improves gRNA detection and annotation in single-cell CRISPR screens. Commun Biol 2023; 6:975. [PMID: 37741886 PMCID: PMC10518011 DOI: 10.1038/s42003-023-05351-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
Novel methods that combine single cell RNA-seq with CRISPR screens enable high-throughput characterization of transcriptional changes caused by genetic perturbations. Dedicated software is however lacking to annotate CRISPR guide RNA (gRNA) libraries and associate them with single cell transcriptomes. Here, we describe a CRISPR droplet sequencing (CROP-seq) dataset. During analysis, we observed that the most commonly used method fails to detect mutant gRNAs. We therefore developed a python tool to identify and characterize intact and mutant gRNAs, called GiRAFR. We show that mutant gRNAs are dysfunctional, and failure to detect and annotate them leads to an inflated estimate of the number of untransformed cells, attenuated downregulation of target genes, as well as an underestimated multiplet frequency. These findings are mirrored in publicly available datasets, where we find that up to 35% of cells are transduced with a mutant gRNA. Applying GiRAFR hence stands to improve the annotation and quality of single cell CRISPR screens.
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Affiliation(s)
- Qian Yu
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Paulien Van Minsel
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Eva Galle
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
- Leuven Institute for Single Cell Omics, KU Leuven, 3000, Leuven, Belgium.
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13
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Bravo González-Blas C, De Winter S, Hulselmans G, Hecker N, Matetovici I, Christiaens V, Poovathingal S, Wouters J, Aibar S, Aerts S. SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks. Nat Methods 2023; 20:1355-1367. [PMID: 37443338 PMCID: PMC10482700 DOI: 10.1038/s41592-023-01938-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 06/06/2023] [Indexed: 07/15/2023]
Abstract
Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present a method for the inference of enhancer-driven GRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TFs) and links these enhancers to candidate target genes. To improve both recall and precision of TF identification, we curated and clustered a motif collection with more than 30,000 motifs. We benchmarked SCENIC+ on diverse datasets from different species, including human peripheral blood mononuclear cells, ENCODE cell lines, melanoma cell states and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers and GRNs between human and mouse cell types in the cerebral cortex. Finally, we use SCENIC+ to study the dynamics of gene regulation along differentiation trajectories and the effect of TF perturbations on cell state. SCENIC+ is available at scenicplus.readthedocs.io .
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Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seppe De Winter
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nikolai Hecker
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irina Matetovici
- VIB Center for Brain & Disease Research, Leuven, Belgium
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Jasper Wouters
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
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14
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Bögürcü-Seidel N, Bergers G. R-2-HG assists IDH1-mutant solid tumors by promoting angiogenesis. Cell Res 2022; 32:795-796. [PMID: 35931821 PMCID: PMC9437032 DOI: 10.1038/s41422-022-00708-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Nuray Bögürcü-Seidel
- Laboratory of Tumor Microenvironment and Therapeutic Resistance, VIB Center for Cancer Biology, Leuven, Belgium
| | - Gabriele Bergers
- Laboratory of Tumor Microenvironment and Therapeutic Resistance, VIB Center for Cancer Biology, Leuven, Belgium.
- Department of Oncology, KU Leuven, Leuven, Belgium.
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15
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Rufo N, Korovesis D, Van Eygen S, Derua R, Garg AD, Finotello F, Vara-Perez M, Rožanc J, Dewaele M, de Witte PA, Alexopoulos LG, Janssens S, Sinkkonen L, Sauter T, Verhelst SHL, Agostinis P. Stress-induced inflammation evoked by immunogenic cell death is blunted by the IRE1α kinase inhibitor KIRA6 through HSP60 targeting. Cell Death Differ 2022; 29:230-245. [PMID: 34453119 PMCID: PMC8738768 DOI: 10.1038/s41418-021-00853-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 08/02/2021] [Accepted: 08/08/2021] [Indexed: 12/13/2022] Open
Abstract
Mounting evidence indicates that immunogenic therapies engaging the unfolded protein response (UPR) following endoplasmic reticulum (ER) stress favor proficient cancer cell-immune interactions, by stimulating the release of immunomodulatory/proinflammatory factors by stressed or dying cancer cells. UPR-driven transcription of proinflammatory cytokines/chemokines exert beneficial or detrimental effects on tumor growth and antitumor immunity, but the cell-autonomous machinery governing the cancer cell inflammatory output in response to immunogenic therapies remains poorly defined. Here, we profiled the transcriptome of cancer cells responding to immunogenic or weakly immunogenic treatments. Bioinformatics-driven pathway analysis indicated that immunogenic treatments instigated a NF-κB/AP-1-inflammatory stress response, which dissociated from both cell death and UPR. This stress-induced inflammation was specifically abolished by the IRE1α-kinase inhibitor KIRA6. Supernatants from immunogenic chemotherapy and KIRA6 co-treated cancer cells were deprived of proinflammatory/chemoattractant factors and failed to mobilize neutrophils and induce dendritic cell maturation. Furthermore, KIRA6 significantly reduced the in vivo vaccination potential of dying cancer cells responding to immunogenic chemotherapy. Mechanistically, we found that the anti-inflammatory effect of KIRA6 was still effective in IRE1α-deficient cells, indicating a hitherto unknown off-target effector of this IRE1α-kinase inhibitor. Generation of a KIRA6-clickable photoaffinity probe, mass spectrometry, and co-immunoprecipitation analysis identified cytosolic HSP60 as a KIRA6 off-target in the IKK-driven NF-κB pathway. In sum, our study unravels that HSP60 is a KIRA6-inhibitable upstream regulator of the NF-κB/AP-1-inflammatory stress responses evoked by immunogenic treatments. It also urges caution when interpreting the anti-inflammatory action of IRE1α chemical inhibitors.
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Affiliation(s)
- Nicole Rufo
- Cell Death Research and Therapy Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology Research, Leuven, Belgium
| | - Dimitris Korovesis
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Sofie Van Eygen
- Cell Death Research and Therapy Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology Research, Leuven, Belgium
| | - Rita Derua
- Laboratory of Protein Phosphorylation and Proteomics, Department of Cellular and Molecular Medicine and SyBioMa, KU Leuven, Leuven, Belgium
| | - Abhishek D Garg
- Cell Death Research and Therapy Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Monica Vara-Perez
- Cell Death Research and Therapy Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology Research, Leuven, Belgium
| | - Jan Rožanc
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
- ProtATonce Ltd, Science Park Demokritos, Athens, Greece
| | - Michael Dewaele
- VIB Center for Cancer Biology Research, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Peter A de Witte
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Leonidas G Alexopoulos
- ProtATonce Ltd, Science Park Demokritos, Athens, Greece
- BioSys Lab, Department of Mechanical Engineering, National Technical University of Athens, Zografou, Greece
| | - Sophie Janssens
- Laboratory for ER stress and Inflammation, VIB Center for Inflammation Research and Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Thomas Sauter
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Steven H L Verhelst
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS, e.V., Dortmund, Germany
| | - Patrizia Agostinis
- Cell Death Research and Therapy Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
- VIB Center for Cancer Biology Research, Leuven, Belgium.
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16
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Debackere K, Marcelis L, Demeyer S, Vanden Bempt M, Mentens N, Gielen O, Jacobs K, Broux M, Verhoef G, Michaux L, Graux C, Wlodarska I, Gaulard P, de Leval L, Tousseyn T, Cools J, Dierickx D. Fusion transcripts FYN-TRAF3IP2 and KHDRBS1-LCK hijack T cell receptor signaling in peripheral T-cell lymphoma, not otherwise specified. Nat Commun 2021; 12:3705. [PMID: 34140493 PMCID: PMC8211700 DOI: 10.1038/s41467-021-24037-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023] Open
Abstract
Peripheral T-cell lymphoma (PTCL) is a heterogeneous group of non-Hodgkin lymphomas with poor prognosis. Up to 30% of PTCL lack distinctive features and are classified as PTCL, not otherwise specified (PTCL-NOS). To further improve our understanding of the genetic landscape and biology of PTCL-NOS, we perform RNA-sequencing of 18 cases and validate results in an independent cohort of 37 PTCL cases. We identify FYN-TRAF3IP2, KHDRBS1-LCK and SIN3A-FOXO1 as new in-frame fusion transcripts, with FYN-TRAF3IP2 as a recurrent fusion detected in 8 of 55 cases. Using ex vivo and in vivo experiments, we demonstrate that FYN-TRAF3IP2 and KHDRBS1-LCK activate signaling pathways downstream of the T cell receptor (TCR) complex and confer therapeutic vulnerability to clinically available drugs.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Cell Line, Tumor
- Cell Membrane/metabolism
- Cohort Studies
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Forkhead Box Protein O1/genetics
- Forkhead Box Protein O1/metabolism
- Gene Expression Regulation, Neoplastic/genetics
- Humans
- Intracellular Signaling Peptides and Proteins/metabolism
- Kaplan-Meier Estimate
- Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/genetics
- Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/metabolism
- Lymphoma, T-Cell, Peripheral/genetics
- Lymphoma, T-Cell, Peripheral/metabolism
- Lymphoma, T-Cell, Peripheral/pathology
- Mice
- Mice, Inbred C57BL
- NF-kappa B/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Proto-Oncogene Proteins c-fyn/genetics
- Proto-Oncogene Proteins c-fyn/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- RNA-Seq
- Receptors, Antigen, T-Cell/metabolism
- Signal Transduction/genetics
- Sin3 Histone Deacetylase and Corepressor Complex/genetics
- Sin3 Histone Deacetylase and Corepressor Complex/metabolism
- bcl-X Protein/antagonists & inhibitors
- bcl-X Protein/metabolism
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Affiliation(s)
- Koen Debackere
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lukas Marcelis
- Translational Cell & Tissue Research, KU Leuven, Leuven, Belgium
| | - Sofie Demeyer
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Marlies Vanden Bempt
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Nicole Mentens
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Olga Gielen
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Kris Jacobs
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Michael Broux
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Gregor Verhoef
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Lucienne Michaux
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Carlos Graux
- Mont-Godinne University Hospital, Yvoir, Belgium
| | - Iwona Wlodarska
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Philippe Gaulard
- Département de Pathologie, Groupe Hospitalier Henri Mondor, AP-HP, Créteil, France
- INSERM U955 and Université Paris-Est, Créteil, France
| | - Laurence de Leval
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Thomas Tousseyn
- Translational Cell & Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Jan Cools
- Center for Cancer Biology, VIB, Leuven, Belgium.
- Center for Human Genetics, KU Leuven, Leuven, Belgium.
| | - Daan Dierickx
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium.
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium.
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17
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Martens S, Bridelance J, Roelandt R, Vandenabeele P, Takahashi N. MLKL in cancer: more than a necroptosis regulator. Cell Death Differ 2021; 28:1757-1772. [PMID: 33953348 PMCID: PMC8184805 DOI: 10.1038/s41418-021-00785-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 02/03/2023] Open
Abstract
Mixed lineage kinase domain-like protein (MLKL) emerged as executioner of necroptosis, a RIPK3-dependent form of regulated necrosis. Cell death evasion is one of the hallmarks of cancer. Besides apoptosis, some cancers suppress necroptosis-associated mechanisms by for example epigenetic silencing of RIPK3 expression. Conversely, necroptosis-elicited inflammation by cancer cells can fuel tumor growth. Recently, necroptosis-independent functions of MLKL were unraveled in receptor internalization, ligand-receptor degradation, endosomal trafficking, extracellular vesicle formation, autophagy, nuclear functions, axon repair, neutrophil extracellular trap (NET) formation, and inflammasome regulation. Little is known about the precise role of MLKL in cancer and whether some of these functions are involved in cancer development and metastasis. Here, we discuss current knowledge and controversies on MLKL, its structure, necroptosis-independent functions, expression, mutations, and its potential role as a pro- or anti-cancerous factor. Analysis of MLKL expression patterns reveals that MLKL is upregulated by type I/II interferon, conditions of inflammation, and tissue injury. Overall, MLKL may affect cancer development and metastasis through necroptosis-dependent and -independent functions.
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Affiliation(s)
- Sofie Martens
- Cell Death and Inflammation Lab, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jolien Bridelance
- Cell Death and Inflammation Lab, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Ria Roelandt
- Cell Death and Inflammation Lab, VIB Center for Inflammation Research, Ghent, Belgium
| | - Peter Vandenabeele
- Cell Death and Inflammation Lab, VIB Center for Inflammation Research, Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
| | - Nozomi Takahashi
- Cell Death and Inflammation Lab, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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18
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Rapino F, Zhou Z, Roncero Sanchez AM, Joiret M, Seca C, El Hachem N, Valenti G, Latini S, Shostak K, Geris L, Li P, Huang G, Mazzucchelli G, Baiwir D, Desmet CJ, Chariot A, Georges M, Close P. Wobble tRNA modification and hydrophilic amino acid patterns dictate protein fate. Nat Commun 2021; 12:2170. [PMID: 33859181 PMCID: PMC8050329 DOI: 10.1038/s41467-021-22254-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 03/05/2021] [Indexed: 02/07/2023] Open
Abstract
Regulation of mRNA translation elongation impacts nascent protein synthesis and integrity and plays a critical role in disease establishment. Here, we investigate features linking regulation of codon-dependent translation elongation to protein expression and homeostasis. Using knockdown models of enzymes that catalyze the mcm5s2 wobble uridine tRNA modification (U34-enzymes), we show that gene codon content is necessary but not sufficient to predict protein fate. While translation defects upon perturbation of U34-enzymes are strictly dependent on codon content, the consequences on protein output are determined by other features. Specific hydrophilic motifs cause protein aggregation and degradation upon codon-dependent translation elongation defects. Accordingly, the combination of codon content and the presence of hydrophilic motifs define the proteome whose maintenance relies on U34-tRNA modification. Together, these results uncover the mechanism linking wobble tRNA modification to mRNA translation and aggregation to maintain proteome homeostasis.
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Affiliation(s)
- Francesca Rapino
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium.
- GIGA-Institute, University of Liège, Liège, Belgium.
- University of Liège, Liège, Belgium.
- Department of Radiation Oncology (Maastro), GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands.
| | - Zhaoli Zhou
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Ana Maria Roncero Sanchez
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
| | - Marc Joiret
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Biomechanics Research Unit, University of Liège, Liège, Belgium
| | - Christian Seca
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
| | - Najla El Hachem
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
| | - Gianluca Valenti
- University of Liège, Liège, Belgium
- Unité de Recherche Transitions, University of Liège, Liège, Belgium
| | - Sara Latini
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
| | - Kateryna Shostak
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Laboratory of Medical Chemistry, University of Liège, Liège, Belgium
| | - Liesbet Geris
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Biomechanics Research Unit, University of Liège, Liège, Belgium
| | - Ping Li
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Gang Huang
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Gabriel Mazzucchelli
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Mass Spectrometry Laboratory, System Biology and Chemical Biology, University of Liège, Liège, Belgium
| | - Dominique Baiwir
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Mass Spectrometry Laboratory, System Biology and Chemical Biology, University of Liège, Liège, Belgium
| | - Christophe J Desmet
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Laboratory of Cellular and Molecular Immunology, University of Liège, Liège, Belgium
- Faculty of Veterinary Medicine, University of Liege, Liege, Belgium
| | - Alain Chariot
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Laboratory of Medical Chemistry, University of Liège, Liège, Belgium
- WELBIO, University of Liege, Liege, Belgium
| | - Michel Georges
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Faculty of Veterinary Medicine, University of Liege, Liege, Belgium
- Unit of Animal Genomics, University of Liège, Liège, Belgium
| | - Pierre Close
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium.
- GIGA-Institute, University of Liège, Liège, Belgium.
- University of Liège, Liège, Belgium.
- WELBIO, University of Liege, Liege, Belgium.
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