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Nakagawa T, Santos J, Nasamran CA, Sen P, Sadat S, Monther A, Bendik J, Ebisumoto K, Hu J, Preissl S, Guo T, Vavinskaya V, Fisch KM, Califano JA. Defining the relationship of salivary gland malignancies to novel cell subpopulations in human salivary glands using single nucleus RNA-sequencing. Int J Cancer 2024; 154:1492-1503. [PMID: 37971144 DOI: 10.1002/ijc.34790] [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: 02/20/2023] [Revised: 09/26/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023]
Abstract
Salivary glands have essential roles in maintaining oral health, mastication, taste and speech, by secreting saliva. Salivary glands are composed of several types of cells, and each cell type is predicted to be involved in the carcinogenesis of different types of cancers including adenoid cystic carcinoma (ACC), acinic cell carcinoma (AciCC), salivary duct carcinoma (SDC), myoepithelial carcinoma (MECA) and other histology. In our study, we performed single nucleus RNA-seq on three human salivary gland samples to clarify the gene expression profile of each complex cellular component of the salivary glands and related these expression patterns to expression found in salivary gland cancers (SGC) to infer cell of origin. By single nucleus RNA-seq, salivary gland cells were stratified into four clusters: acinar cells, ductal cells 1, ductal cells 2 and myoepithelial cells/stromal cells. The localization of each cell group was verified by IHC of each cluster marker gene, and one group of ductal cells was found to represent intercalated ductal cells labeled with HES1. Furthermore, in comparison with SGC RNA-seq data, acinar cell markers were upregulated in AciCC, but downregulated in ACC and ductal cell markers were upregulated in SDC but downregulated in MECA, suggesting that markers of origin are highly expressed in some SGC. Cell type expressions in specific SGC histology are similar to those found in normal salivary gland populations, indicating a potential etiologic relationship.
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Affiliation(s)
- Takuya Nakagawa
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Jessica Santos
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, California, USA
| | - Prakriti Sen
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Sayed Sadat
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Abdula Monther
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Joseph Bendik
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Koji Ebisumoto
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Jingjing Hu
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Sebastian Preissl
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Theresa Guo
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of California San Diego, La Jolla, California, USA
| | - Vera Vavinskaya
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, California, USA
| | - Joseph A Califano
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of California San Diego, La Jolla, California, USA
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de Rooij LPMH, Becker LM, Teuwen LA, Boeckx B, Jansen S, Feys S, Verleden S, Liesenborghs L, Stalder AK, Libbrecht S, Van Buyten T, Philips G, Subramanian A, Dumas SJ, Meta E, Borri M, Sokol L, Dendooven A, Truong ACK, Gunst J, Van Mol P, Haslbauer JD, Rohlenova K, Menter T, Boudewijns R, Geldhof V, Vinckier S, Amersfoort J, Wuyts W, Van Raemdonck D, Jacobs W, Ceulemans LJ, Weynand B, Thienpont B, Lammens M, Kuehnel M, Eelen G, Dewerchin M, Schoonjans L, Jonigk D, van Dorpe J, Tzankov A, Wauters E, Mazzone M, Neyts J, Wauters J, Lambrechts D, Carmeliet P. The pulmonary vasculature in lethal COVID-19 and idiopathic pulmonary fibrosis at single cell resolution. Cardiovasc Res 2022; 119:520-535. [PMID: 35998078 PMCID: PMC9452154 DOI: 10.1093/cvr/cvac139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/18/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022] Open
Abstract
Aims SARS-CoV-2 infection causes COVID-19, which in severe cases evokes life-threatening acute respiratory distress syndrome (ARDS). Transcriptome signatures and the functional relevance of non-vascular cell types (e.g. immune and epithelial cells) in COVID-19 are becoming increasingly evident. However, despite its known contribution to vascular inflammation, recruitment/invasion of immune cells, vascular leakage and perturbed hemostasis in the lungs of severe COVID-19 patients, an in-depth interrogation of the endothelial cell (EC) compartment in lethal COVID-19 is lacking. Moreover, progressive fibrotic lung disease represents one of the complications of COVID-19 pneumonia and ARDS. Analogous features between idiopathic pulmonary fibrosis (IPF) and COVID-19 suggest partial similarities in their pathophysiology, yet, a head-to-head comparison of pulmonary cell transcriptomes between both conditions has not been implemented to date. Methods and Results We performed single nucleus RNA-seq (snRNA-seq) on frozen lungs from 7 deceased COVID-19 patients, 6 IPF explant lungs and 12 controls. The vascular fraction, comprising 38,794 nuclei, could be subclustered into 14 distinct EC subtypes. Non-vascular cell types, comprising 137,746 nuclei, were subclustered and used for EC-interactome analyses. Pulmonary ECs of deceased COVID-19 patients showed an enrichment of genes involved in cellular stress, as well as signatures suggestive of dampened immunomodulation and impaired vessel wall integrity. In addition, increased abundance of a population of systemic capillary and venous ECs was identified in COVID-19 and IPF. COVID-19 systemic ECs closely resembled their IPF counterparts, and a set of 30 genes was found congruently enriched in systemic ECs across studies. Receptor-ligand interaction analysis of ECs with non-vascular cell types in the pulmonary micro-environment revealed numerous previously unknown interactions specifically enriched/depleted in COVID-19 and/or IPF. Conclusions This study uncovered novel insights into the abundance, expression patterns and interactomes of EC subtypes in COVID-19 and IPF, relevant for future investigations into the progression and treatment of both lethal conditions. Translational perspective While assessing clinical and molecular characteristics of severe and lethal COVID-19 cases, the vasculature’s undeniable role in disease progression has been widely acknowledged. COVID-19 lung pathology moreover shares certain clinical features with late-stage IPF – yet an in-depth interrogation and direct comparison of the endothelium at single-cell level in both conditions is still lacking. By comparing the transcriptomes of ECs from lungs of deceased COVID-19 patients to those from IPF explant and control lungs, we gathered key insights the heterogeneous composition and potential roles of ECs in both lethal diseases, which may serve as a foundation for development of novel therapeutics.
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Affiliation(s)
| | | | - Laure-Anne Teuwen
- Present address: Department of Oncology, Antwerp University Hospital (UZA), Edegem 2650, Belgium
| | - Bram Boeckx
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB & Department of Genetics, KU Leuven, Leuven 3000, Belgium
| | - Sander Jansen
- Laboratory of Virology & Chemotherapy, KU Leuven, Leuven 3000, Belgium
| | - Simon Feys
- Medical Intensive Care Unit, UZ Gasthuisberg & Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven 3000, Belgium
| | - Stijn Verleden
- Present address: Department of Antwerp Surgical Training, Anatomy and Research Centre, Division of Thoracic and Vascular Surgery, University of Antwerp, Wilrijk, Belgium
| | | | - Anna K Stalder
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel 4031, Switzerland
| | - Sasha Libbrecht
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Tina Van Buyten
- Laboratory of Virology & Chemotherapy, KU Leuven, Leuven 3000, Belgium
| | - Gino Philips
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB & Department of Genetics, KU Leuven, Leuven 3000, Belgium
| | - Abhishek Subramanian
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Sébastien J Dumas
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Elda Meta
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Mila Borri
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Liliana Sokol
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Amélie Dendooven
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
- University of Antwerp, Faculty of Medicine, Wilrijk 2610, Belgium
| | - Anh-Co K Truong
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Jan Gunst
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Pierre Van Mol
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB & Department of Genetics, KU Leuven, Leuven 3000, Belgium
| | - Jasmin D Haslbauer
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Katerina Rohlenova
- Present address: Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec 252 50, Czech Republic
| | - Thomas Menter
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel 4031, Switzerland
| | | | - Vincent Geldhof
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Stefan Vinckier
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Jacob Amersfoort
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Wim Wuyts
- Department of Respiratory Medicine, Unit for Interstitial Lung Diseases, UZ Gasthuisberg, Leuven 3000, Belgium
| | - Dirk Van Raemdonck
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven 3000, Belgium
| | - Werner Jacobs
- Medical CBRNe unit, Queen Astrid Military Hospital, Belgian Defense, Neder-Over-Heembeek 1120, Belgium
- Department of Forensic Pathology, ASTARC Antwerp University Hospital and University of Antwerp, Antwerp 2610, Belgium
| | - Laurens J Ceulemans
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven 3000, Belgium
| | - Birgit Weynand
- Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Martin Lammens
- Department of Pathology Antwerp University Hospital, Edegem 2560, Belgium
- Center for Oncological Research, University of Antwerp, Antwerp 2000, Belgium
| | - Mark Kuehnel
- Medizinische Hochschule Hannover (MHH), Institut für Pathologie, D-30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Member of the German Centre for Lung research (DZL), Hannover 30625, Germany
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Mieke Dewerchin
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Luc Schoonjans
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB & Department of Genetics, KU Leuven, Leuven 3000, Belgium
| | - Danny Jonigk
- Medizinische Hochschule Hannover (MHH), Institut für Pathologie, D-30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Member of the German Centre for Lung research (DZL), Hannover 30625, Germany
| | - Jo van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel 4031, Switzerland
| | - Els Wauters
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven 3000, Belgium
- Respiratory Oncology Unit, University Hospital KU Leuven, Leuven 3000, Belgium
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven 3000, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven 3000, Belgium
| | - Johan Neyts
- Laboratory of Virology & Chemotherapy, KU Leuven, Leuven 3000, Belgium
| | - Joost Wauters
- Medical Intensive Care Unit, UZ Gasthuisberg & Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven 3000, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB & Department of Genetics, KU Leuven, Leuven 3000, Belgium
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