1
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Ma W, Tang W, Kwok JS, Tong AH, Lo CW, Chu AT, Chung BH. A review on trends in development and translation of omics signatures in cancer. Comput Struct Biotechnol J 2024; 23:954-971. [PMID: 38385061 PMCID: PMC10879706 DOI: 10.1016/j.csbj.2024.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.
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Affiliation(s)
- Wei Ma
- Hong Kong Genome Institute, Hong Kong, China
| | - Wenshu Tang
- Hong Kong Genome Institute, Hong Kong, China
| | | | | | | | | | - Brian H.Y. Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Kong Genome Project
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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2
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Cañellas-Socias A, Sancho E, Batlle E. Mechanisms of metastatic colorectal cancer. Nat Rev Gastroenterol Hepatol 2024; 21:609-625. [PMID: 38806657 DOI: 10.1038/s41575-024-00934-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2024] [Indexed: 05/30/2024]
Abstract
Despite extensive research and improvements in understanding colorectal cancer (CRC), its metastatic form continues to pose a substantial challenge, primarily owing to limited therapeutic options and a poor prognosis. This Review addresses the emerging focus on metastatic CRC (mCRC), which has historically been under-studied compared with primary CRC despite its lethality. We delve into two crucial aspects: the molecular and cellular determinants facilitating CRC metastasis and the principles guiding the evolution of metastatic disease. Initially, we examine the genetic alterations integral to CRC metastasis, connecting them to clinically marked characteristics of advanced CRC. Subsequently, we scrutinize the role of cellular heterogeneity and plasticity in metastatic spread and therapy resistance. Finally, we explore how the tumour microenvironment influences metastatic disease, emphasizing the effect of stromal gene programmes and the immune context. The ongoing research in these fields holds immense importance, as its future implications are projected to revolutionize the treatment of patients with mCRC, hopefully offering a promising outlook for their survival.
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Affiliation(s)
- Adrià Cañellas-Socias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
| | - Elena Sancho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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3
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Li Z, Zhang B, Chan JJ, Tabatabaeian H, Tong QY, Chew XH, Fan X, Driguez P, Chan C, Cheong F, Wang S, Siew BE, Tan IJW, Lee KY, Lieske B, Cheong WK, Kappei D, Tan KK, Gao X, Tay Y. An isoform-resolution transcriptomic atlas of colorectal cancer from long-read single-cell sequencing. CELL GENOMICS 2024:100641. [PMID: 39216476 DOI: 10.1016/j.xgen.2024.100641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 06/06/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Colorectal cancer (CRC) ranks as the second leading cause of cancer deaths globally. In recent years, short-read single-cell RNA sequencing (scRNA-seq) has been instrumental in deciphering tumor heterogeneities. However, these studies only enable gene-level quantification but neglect alterations in transcript structures arising from alternative end processing or splicing. In this study, we integrated short- and long-read scRNA-seq of CRC samples to build an isoform-resolution CRC transcriptomic atlas. We identified 394 dysregulated transcript structures in tumor epithelial cells, including 299 resulting from various combinations of splicing events. Second, we characterized genes and isoforms associated with epithelial lineages and subpopulations exhibiting distinct prognoses. Among 31,935 isoforms with novel junctions, 330 were supported by The Cancer Genome Atlas RNA-seq and mass spectrometry data. Finally, we built an algorithm that integrated novel peptides derived from open reading frames of recurrent tumor-specific transcripts with mass spectrometry data and identified recurring neoepitopes that may aid the development of cancer vaccines.
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Affiliation(s)
- Zhongxiao Li
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Center of Excellence on Generative AI, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Bin Zhang
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Center of Excellence on Generative AI, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
| | - Jia Jia Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Hossein Tabatabaeian
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Qing Yun Tong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Xiao Hong Chew
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Xiaonan Fan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Patrick Driguez
- Core Labs, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Charlene Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Faith Cheong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Shi Wang
- Department of Pathology, National University Health System, Singapore 119228, Singapore
| | - Bei En Siew
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Ian Jse-Wei Tan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Singapore
| | - Kai-Yin Lee
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Singapore
| | - Bettina Lieske
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Singapore
| | - Wai-Kit Cheong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Singapore
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Ker-Kan Tan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Singapore
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Center of Excellence on Generative AI, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
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4
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Xie Z, Niu L, Du K, Chen L, Zheng G, Dai S, Dan H, Duan L, Dou X, Feng F, Zhang J, Zheng J. Endothelial cell heterogeneity in colorectal cancer: tip cells drive angiogenesis. Cell Mol Life Sci 2024; 81:365. [PMID: 39172168 PMCID: PMC11342913 DOI: 10.1007/s00018-024-05411-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/31/2024] [Accepted: 08/13/2024] [Indexed: 08/23/2024]
Abstract
This study aims to uncover the heterogeneity of endothelial cells (ECs) in colorectal cancer (CRC) and their crucial role in angiogenesis, with a special focus on tip cells. Using single-cell RNA sequencing to profile ECs, our data suggests that CRC ECs predominantly exhibit enhanced angiogenesis and decreased antigen presentation, a shift in phenotype largely steered by tip cells. We also observed that an increase in the density and proportion of tip cells correlates with CRC occurrence, progression, and poorer patient prognosis. Furthermore, we identified endothelial cell-specific molecule 1 (ESM1), specifically expressed in tip cells, sustains a VEGFA-KDR-ESM1 positive feedback loop, promoting angiogenesis and CRC proliferation and migration. We also found the enrichment of KDR in tip cells and spotlight a unique long-tail effect in VEGFA expression: while VEGFA is primarily expressed by epithelial cells, the highest level of VEGFA expression is found in individual myeloid cells. Moreover, we observed that effective PD-1 blockade immunotherapy significantly reduced tip cells, disrupting the VEGFA-KDR-ESM1 positive feedback loop in the process. Our investigation into the heterogeneity of ECs in CRC at a single-cell level offers important insights that may contribute to the development of more effective immunotherapies targeting tip cells in CRC.
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Affiliation(s)
- Zhenyu Xie
- Department of Digestive Surgery, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 169 Changle Road, Xi'an, Shaanxi, 710032, China
| | - Liaoran Niu
- Department of Digestive Surgery, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 169 Changle Road, Xi'an, Shaanxi, 710032, China
| | - Kunli Du
- Department of Digestive Surgery, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 169 Changle Road, Xi'an, Shaanxi, 710032, China
| | - Ling Chen
- Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Gaozan Zheng
- Department of Digestive Surgery, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 169 Changle Road, Xi'an, Shaanxi, 710032, China
| | - Songchen Dai
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Shenyang, 110016, China
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110016, China
| | - Hanjun Dan
- Department of Digestive Surgery, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 169 Changle Road, Xi'an, Shaanxi, 710032, China
| | - Lili Duan
- Department of Digestive Surgery, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 169 Changle Road, Xi'an, Shaanxi, 710032, China
| | - Xinyu Dou
- Xi'an Medical University, Xi'an, Shaanxi, 710021, China
| | - Fan Feng
- Department of Digestive Surgery, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 169 Changle Road, Xi'an, Shaanxi, 710032, China.
| | - Jian Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, 169 Changle Road, Xi'an, Shaanxi, 710032, China.
| | - Jianyong Zheng
- Department of Digestive Surgery, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 169 Changle Road, Xi'an, Shaanxi, 710032, China.
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5
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Chu X, Li X, Zhang Y, Dang G, Miao Y, Xu W, Wang J, Zhang Z, Cheng S. Integrative single-cell analysis of human colorectal cancer reveals patient stratification with distinct immune evasion mechanisms. NATURE CANCER 2024:10.1038/s43018-024-00807-z. [PMID: 39147986 DOI: 10.1038/s43018-024-00807-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 07/16/2024] [Indexed: 08/17/2024]
Abstract
The tumor microenvironment (TME) considerably influences colorectal cancer (CRC) progression, therapeutic response and clinical outcome, but studies of interindividual heterogeneities of the TME in CRC are lacking. Here, by integrating human colorectal single-cell transcriptomic data from approximately 200 donors, we comprehensively characterized transcriptional remodeling in the TME compared to noncancer tissues and identified a rare tumor-specific subset of endothelial cells with T cell recruitment potential. The large sample size enabled us to stratify patients based on their TME heterogeneity, revealing divergent TME subtypes in which cancer cells exploit different immune evasion mechanisms. Additionally, by associating single-cell transcriptional profiling with risk genes identified by genome-wide association studies, we determined that stromal cells are major effector cell types in CRC genetic susceptibility. In summary, our results provide valuable insights into CRC pathogenesis and might help with the development of personalized immune therapies.
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Affiliation(s)
| | | | - Yu Zhang
- Changping Laboratory, Beijing, China
| | - Guohui Dang
- Changping Laboratory, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | | | - Wenbin Xu
- Changping Laboratory, Beijing, China
| | | | - Zemin Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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6
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Djordjevic J, Cisneros Romero NS, Cascione L, Mele V, Cremonesi E, Sorrenti E, Basso C, Villa M, Cianfarani A, Roesel R, Galafassi J, Majno-Hurst PE, Spagnoli G, Christoforidis D, Iezzi G. Direct toll-like receptor triggering in colorectal cancer-associated stromal cells elicits immunostimulatory properties leading to enhanced immune cell recruitment. Gut 2024:gutjnl-2023-331759. [PMID: 39122362 DOI: 10.1136/gutjnl-2023-331759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 07/10/2024] [Indexed: 08/12/2024]
Affiliation(s)
- Julija Djordjevic
- Laboratory for Surgical Research, EOC Laboratories for Translational Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
| | - Nubia Sarahi Cisneros Romero
- Faculty of Natural Sciences, University of Basel, Basel, Switzerland
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Luciano Cascione
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Bioinformatics Core Unit, Institute of Oncology Research (IOR), Bellinzona, Switzerland
| | - Valentina Mele
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Eleonora Cremonesi
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Elisa Sorrenti
- Laboratory for Surgical Research, EOC Laboratories for Translational Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
| | - Camilla Basso
- Laboratory for Surgical Research, EOC Laboratories for Translational Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
| | - Martina Villa
- Laboratory for Surgical Research, EOC Laboratories for Translational Research, Bellinzona, Switzerland
| | - Agnese Cianfarani
- Laboratory for Surgical Research, EOC Laboratories for Translational Research, Bellinzona, Switzerland
- Department of Surgery, Ente Ospedaliero Cantonale (EOC), Bellinzona, Switzerland
| | - Raffaello Roesel
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Surgery, Ente Ospedaliero Cantonale (EOC), Bellinzona, Switzerland
| | - Jacopo Galafassi
- Department of Surgery, Ente Ospedaliero Cantonale (EOC), Bellinzona, Switzerland
| | - Pietro Edoardo Majno-Hurst
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Surgery, Ente Ospedaliero Cantonale (EOC), Bellinzona, Switzerland
| | - Giulio Spagnoli
- Institute of Translational Pharmacology, National Research Council, Roma, Italy
| | - Dimitrios Christoforidis
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Surgery, Ente Ospedaliero Cantonale (EOC), Bellinzona, Switzerland
| | - Giandomenica Iezzi
- Laboratory for Surgical Research, EOC Laboratories for Translational Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
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7
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Cornish AJ, Gruber AJ, Kinnersley B, Chubb D, Frangou A, Caravagna G, Noyvert B, Lakatos E, Wood HM, Thorn S, Culliford R, Arnedo-Pac C, Househam J, Cross W, Sud A, Law P, Leathlobhair MN, Hawari A, Woolley C, Sherwood K, Feeley N, Gül G, Fernandez-Tajes J, Zapata L, Alexandrov LB, Murugaesu N, Sosinsky A, Mitchell J, Lopez-Bigas N, Quirke P, Church DN, Tomlinson IPM, Sottoriva A, Graham TA, Wedge DC, Houlston RS. The genomic landscape of 2,023 colorectal cancers. Nature 2024:10.1038/s41586-024-07747-9. [PMID: 39112709 DOI: 10.1038/s41586-024-07747-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 06/24/2024] [Indexed: 08/17/2024]
Abstract
Colorectal carcinoma (CRC) is a common cause of mortality1, but a comprehensive description of its genomic landscape is lacking2-9. Here we perform whole-genome sequencing of 2,023 CRC samples from participants in the UK 100,000 Genomes Project, thereby providing a highly detailed somatic mutational landscape of this cancer. Integrated analyses identify more than 250 putative CRC driver genes, many not previously implicated in CRC or other cancers, including several recurrent changes outside the coding genome. We extend the molecular pathways involved in CRC development, define four new common subgroups of microsatellite-stable CRC based on genomic features and show that these groups have independent prognostic associations. We also characterize several rare molecular CRC subgroups, some with potential clinical relevance, including cancers with both microsatellite and chromosomal instability. We demonstrate a spectrum of mutational profiles across the colorectum, which reflect aetiological differences. These include the role of Escherichia colipks+ colibactin in rectal cancers10 and the importance of the SBS93 signature11-13, which suggests that diet or smoking is a risk factor. Immune-escape driver mutations14 are near-ubiquitous in hypermutant tumours and occur in about half of microsatellite-stable CRCs, often in the form of HLA copy number changes. Many driver mutations are actionable, including those associated with rare subgroups (for example, BRCA1 and IDH1), highlighting the role of whole-genome sequencing in optimizing patient care.
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Affiliation(s)
- Alex J Cornish
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Andreas J Gruber
- Department of Biology, University of Konstanz, Konstanz, Germany
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- University College London Cancer Institute, London, UK
| | - Daniel Chubb
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Anna Frangou
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Boris Noyvert
- Cancer Research UK Centre and Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Eszter Lakatos
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Henry M Wood
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Steve Thorn
- Department of Oncology, University of Oxford, Oxford, UK
| | - Richard Culliford
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Claudia Arnedo-Pac
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Jacob Househam
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - William Cross
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Philip Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | | | - Aliah Hawari
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Connor Woolley
- Department of Oncology, University of Oxford, Oxford, UK
| | - Kitty Sherwood
- Department of Oncology, University of Oxford, Oxford, UK
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Nathalie Feeley
- Department of Oncology, University of Oxford, Oxford, UK
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Güler Gül
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Luis Zapata
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Nirupa Murugaesu
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Alona Sosinsky
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Jonathan Mitchell
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Philip Quirke
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - David N Church
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Andrea Sottoriva
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Trevor A Graham
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - David C Wedge
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
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8
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Nunes L, Li F, Wu M, Luo T, Hammarström K, Torell E, Ljuslinder I, Mezheyeuski A, Edqvist PH, Löfgren-Burström A, Zingmark C, Edin S, Larsson C, Mathot L, Osterman E, Osterlund E, Ljungström V, Neves I, Yacoub N, Guðnadóttir U, Birgisson H, Enblad M, Ponten F, Palmqvist R, Xu X, Uhlén M, Wu K, Glimelius B, Lin C, Sjöblom T. Prognostic genome and transcriptome signatures in colorectal cancers. Nature 2024:10.1038/s41586-024-07769-3. [PMID: 39112715 DOI: 10.1038/s41586-024-07769-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/01/2024] [Indexed: 08/17/2024]
Abstract
Colorectal cancer is caused by a sequence of somatic genomic alterations affecting driver genes in core cancer pathways1. Here, to understand the functional and prognostic impact of cancer-causing somatic mutations, we analysed the whole genomes and transcriptomes of 1,063 primary colorectal cancers in a population-based cohort with long-term follow-up. From the 96 mutated driver genes, 9 were not previously implicated in colorectal cancer and 24 had not been linked to any cancer. Two distinct patterns of pathway co-mutations were observed, timing analyses identified nine early and three late driver gene mutations, and several signatures of colorectal-cancer-specific mutational processes were identified. Mutations in WNT, EGFR and TGFβ pathway genes, the mitochondrial CYB gene and 3 regulatory elements along with 21 copy-number variations and the COSMIC SBS44 signature correlated with survival. Gene expression classification yielded five prognostic subtypes with distinct molecular features, in part explained by underlying genomic alterations. Microsatellite-instable tumours divided into two classes with different levels of hypoxia and infiltration of immune and stromal cells. To our knowledge, this study constitutes the largest integrated genome and transcriptome analysis of colorectal cancer, and interlinks mutations, gene expression and patient outcomes. The identification of prognostic mutations and expression subtypes can guide future efforts to individualize colorectal cancer therapy.
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Affiliation(s)
- Luís Nunes
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Fuqiang Li
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Meizhen Wu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Tian Luo
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Klara Hammarström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Emma Torell
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ingrid Ljuslinder
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Artur Mezheyeuski
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Carl Zingmark
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Sofia Edin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Chatarina Larsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucy Mathot
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Erik Osterman
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Emerik Osterlund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Inês Neves
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Nicole Yacoub
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Unnur Guðnadóttir
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Helgi Birgisson
- Department of Surgical Sciences, Uppsala University, Akademiska sjukhuset, Uppsala, Sweden
| | - Malin Enblad
- Department of Surgical Sciences, Uppsala University, Akademiska sjukhuset, Uppsala, Sweden
| | - Fredrik Ponten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Richard Palmqvist
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Xun Xu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
| | - Mathias Uhlén
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kui Wu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China.
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China.
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China.
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Cong Lin
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China.
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China.
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China.
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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9
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Deng J, Pan T, Wang D, Hong Y, Liu Z, Zhou X, An Z, Li L, Alfano G, Li G, Dolcetti L, Evans R, Vicencio JM, Vlckova P, Chen Y, Monypenny J, Gomes CADC, Weitsman G, Ng K, McCarthy C, Yang X, Hu Z, Porter JC, Tape CJ, Yin M, Wei F, Rodriguez-Justo M, Zhang J, Tejpar S, Beatson R, Ng T. The MondoA-dependent TXNIP/GDF15 axis predicts oxaliplatin response in colorectal adenocarcinomas. EMBO Mol Med 2024:10.1038/s44321-024-00105-2. [PMID: 39103698 DOI: 10.1038/s44321-024-00105-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/21/2024] [Accepted: 07/03/2024] [Indexed: 08/07/2024] Open
Abstract
Chemotherapy, the standard of care treatment for cancer patients with advanced disease, has been increasingly recognized to activate host immune responses to produce durable outcomes. Here, in colorectal adenocarcinoma (CRC) we identify oxaliplatin-induced Thioredoxin-Interacting Protein (TXNIP), a MondoA-dependent tumor suppressor gene, as a negative regulator of Growth/Differentiation Factor 15 (GDF15). GDF15 is a negative prognostic factor in CRC and promotes the differentiation of regulatory T cells (Tregs), which inhibit CD8 T-cell activation. Intriguingly, multiple models including patient-derived tumor organoids demonstrate that the loss of TXNIP and GDF15 responsiveness to oxaliplatin is associated with advanced disease or chemotherapeutic resistance, with transcriptomic or proteomic GDF15/TXNIP ratios showing potential as a prognostic biomarker. These findings illustrate a potentially common pathway where chemotherapy-induced epithelial oxidative stress drives local immune remodeling for patient benefit, with disruption of this pathway seen in refractory or advanced cases.
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Affiliation(s)
- Jinhai Deng
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
- Clinical Research Centre (CRC), Medical Pathology Centre (MPC), Cancer Early Detection and Treatment Centre (CEDTC), Translational Medicine Research Centre (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Wanzhou, Chongqing, China
| | - Teng Pan
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), 518172, Shenzhen, China
| | - Dan Wang
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
| | - Yourae Hong
- Digestive Oncology Unit and Centre for Human Genetics, Universitair Ziekenhuis (UZ) Leuven, Leuven, Belgium
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xingang Zhou
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Zhengwen An
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
| | - Lifeng Li
- Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, China
| | - Giovanna Alfano
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
| | - Gang Li
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Luigi Dolcetti
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
| | - Rachel Evans
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Jose M Vicencio
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
| | - Petra Vlckova
- Cell Communication Lab, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Yue Chen
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - James Monypenny
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
| | | | - Gregory Weitsman
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
| | - Kenrick Ng
- Department of Medical Oncology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Caitlin McCarthy
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
| | - Xiaoping Yang
- Centre of Excellence for Mass Spectrometry, Proteomics Facility, The James Black Centre, King's College London, London, UK
| | - Zedong Hu
- Digestive Oncology Unit and Centre for Human Genetics, Universitair Ziekenhuis (UZ) Leuven, Leuven, Belgium
| | - Joanna C Porter
- Centre for Inflammation and Tissue Repair, UCL Respiratory, Division of Medicine, University College London (UCL), Rayne Building, London, UK
| | - Christopher J Tape
- Cell Communication Lab, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Mingzhu Yin
- Clinical Research Centre (CRC), Medical Pathology Centre (MPC), Cancer Early Detection and Treatment Centre (CEDTC), Translational Medicine Research Centre (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Wanzhou, Chongqing, China
| | - Fengxiang Wei
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), 518172, Shenzhen, China
| | | | - Jin Zhang
- 3rd Department of Breast Cancer Prevention, Treatment and Research Centre, Tianjin, PR China
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin, PR China
- Tianjin's Clinical Research Centre for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, PR China
- National Clinical Research Centre for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
| | - Sabine Tejpar
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), 518172, Shenzhen, China
| | - Richard Beatson
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK.
- Centre for Inflammation and Tissue Repair, UCL Respiratory, Division of Medicine, University College London (UCL), Rayne Building, London, UK.
- Centre for the Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Tony Ng
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK.
- UCL Cancer Institute, University College London, London, UK.
- Cancer Research UK City of London Centre, London, UK.
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10
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Kinoshita H, Martinez-Ordoñez A, Cid-Diaz T, Han Q, Duran A, Muta Y, Zhang X, Linares JF, Nakanishi Y, Kasashima H, Yashiro M, Maeda K, Albaladejo-Gonzalez A, Torres-Moreno D, García-Solano J, Conesa-Zamora P, Inghirami G, Diaz-Meco MT, Moscat J. Epithelial aPKC deficiency leads to stem cell loss preceding metaplasia in colorectal cancer initiation. Dev Cell 2024; 59:1972-1987.e8. [PMID: 38815584 PMCID: PMC11303105 DOI: 10.1016/j.devcel.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/19/2023] [Accepted: 05/03/2024] [Indexed: 06/01/2024]
Abstract
The early mechanisms of spontaneous tumor initiation that precede malignancy are largely unknown. We show that reduced aPKC levels correlate with stem cell loss and the induction of revival and metaplastic programs in serrated- and conventional-initiated premalignant lesions, which is perpetuated in colorectal cancers (CRCs). Acute inactivation of PKCλ/ι in vivo and in mouse organoids is sufficient to stimulate JNK in non-transformed intestinal epithelial cells (IECs), which promotes cell death and the rapid loss of the intestinal stem cells (ISCs), including those that are LGR5+. This is followed by the accumulation of revival stem cells (RSCs) at the bottom of the crypt and fetal-metaplastic cells (FMCs) at the top, creating two spatiotemporally distinct cell populations that depend on JNK-induced AP-1 and YAP. These cell lineage changes are maintained during cancer initiation and progression and determine the aggressive phenotype of human CRC, irrespective of their serrated or conventional origin.
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Affiliation(s)
- Hiroto Kinoshita
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Anxo Martinez-Ordoñez
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Tania Cid-Diaz
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Qixiu Han
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Angeles Duran
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yu Muta
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Xiao Zhang
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Juan F Linares
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yuki Nakanishi
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiroaki Kasashima
- Department of Gastroenterological Surgery, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka city 545-8585, Japan
| | - Masakazu Yashiro
- Department of Gastroenterological Surgery, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka city 545-8585, Japan
| | - Kiyoshi Maeda
- Department of Gastroenterological Surgery, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka city 545-8585, Japan
| | - Ana Albaladejo-Gonzalez
- Department of Histology and Pathology, Faculty of Life Sciences, Universidad Católica de Murcia (UCAM), 30107 Murcia, Spain; Department of Pathology, Santa Lucía General University Hospital (HGUSL), Calle Mezquita sn, 30202 Cartagena, Spain
| | - Daniel Torres-Moreno
- Department of Histology and Pathology, Faculty of Life Sciences, Universidad Católica de Murcia (UCAM), 30107 Murcia, Spain; Department of Clinical Analysis, Santa Lucía General University Hospital (HGUSL), Calle Mezquita sn, 30202 Cartagena, Spain
| | - José García-Solano
- Department of Histology and Pathology, Faculty of Life Sciences, Universidad Católica de Murcia (UCAM), 30107 Murcia, Spain; Department of Pathology, Santa Lucía General University Hospital (HGUSL), Calle Mezquita sn, 30202 Cartagena, Spain
| | - Pablo Conesa-Zamora
- Department of Histology and Pathology, Faculty of Life Sciences, Universidad Católica de Murcia (UCAM), 30107 Murcia, Spain; Department of Clinical Analysis, Santa Lucía General University Hospital (HGUSL), Calle Mezquita sn, 30202 Cartagena, Spain
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Maria T Diaz-Meco
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Jorge Moscat
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA.
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11
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Guo DZ, Zhang X, Zhang SQ, Zhang SY, Zhang XY, Yan JY, Dong SY, Zhu K, Yang XR, Fan J, Zhou J, Huang A. Single-cell tumor heterogeneity landscape of hepatocellular carcinoma: unraveling the pro-metastatic subtype and its interaction loop with fibroblasts. Mol Cancer 2024; 23:157. [PMID: 39095854 PMCID: PMC11295380 DOI: 10.1186/s12943-024-02062-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/05/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Tumor heterogeneity presents a formidable challenge in understanding the mechanisms driving tumor progression and metastasis. The heterogeneity of hepatocellular carcinoma (HCC) in cellular level is not clear. METHODS Integration analysis of single-cell RNA sequencing data and spatial transcriptomics data was performed. Multiple methods were applied to investigate the subtype of HCC tumor cells. The functional characteristics, translation factors, clinical implications and microenvironment associations of different subtypes of tumor cells were analyzed. The interaction of subtype and fibroblasts were analyzed. RESULTS We established a heterogeneity landscape of HCC malignant cells by integrated 52 single-cell RNA sequencing data and 5 spatial transcriptomics data. We identified three subtypes in tumor cells, including ARG1+ metabolism subtype (Metab-subtype), TOP2A+ proliferation phenotype (Prol-phenotype), and S100A6+ pro-metastatic subtype (EMT-subtype). Enrichment analysis found that the three subtypes harbored different features, that is metabolism, proliferating, and epithelial-mesenchymal transition. Trajectory analysis revealed that both Metab-subtype and EMT-subtype originated from the Prol-phenotype. Translation factor analysis found that EMT-subtype showed exclusive activation of SMAD3 and TGF-β signaling pathway. HCC dominated by EMT-subtype cells harbored an unfavorable prognosis and a deserted microenvironment. We uncovered a positive loop between tumor cells and fibroblasts mediated by SPP1-CD44 and CCN2/TGF-β-TGFBR1 interaction pairs. Inhibiting CCN2 disrupted the loop, mitigated the transformation to EMT-subtype, and suppressed metastasis. CONCLUSION By establishing a heterogeneity landscape of malignant cells, we identified a three-subtype classification in HCC. Among them, S100A6+ tumor cells play a crucial role in metastasis. Targeting the feedback loop between tumor cells and fibroblasts is a promising anti-metastatic strategy.
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Affiliation(s)
- De-Zhen Guo
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xin Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Sen-Quan Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Shi-Yu Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xiang-Yu Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jia-Yan Yan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - San-Yuan Dong
- Department of Radiology, Zhongshan Hospital, Shanghai Institute of Medical Imaging, Fudan University, Shanghai, 200032, China
| | - Kai Zhu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xin-Rong Yang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China.
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| | - Ao Huang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China.
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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12
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Menche C, Schuhwerk H, Armstark I, Gupta P, Fuchs K, van Roey R, Mosa MH, Hartebrodt A, Hajjaj Y, Clavel Ezquerra A, Selvaraju MK, Geppert CI, Bärthel S, Saur D, Greten FR, Brabletz S, Blumenthal DB, Weigert A, Brabletz T, Farin HF, Stemmler MP. ZEB1-mediated fibroblast polarization controls inflammation and sensitivity to immunotherapy in colorectal cancer. EMBO Rep 2024; 25:3406-3431. [PMID: 38937629 PMCID: PMC11315988 DOI: 10.1038/s44319-024-00186-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/29/2024] Open
Abstract
The EMT-transcription factor ZEB1 is heterogeneously expressed in tumor cells and in cancer-associated fibroblasts (CAFs) in colorectal cancer (CRC). While ZEB1 in tumor cells regulates metastasis and therapy resistance, its role in CAFs is largely unknown. Combining fibroblast-specific Zeb1 deletion with immunocompetent mouse models of CRC, we observe that inflammation-driven tumorigenesis is accelerated, whereas invasion and metastasis in sporadic cancers are reduced. Single-cell transcriptomics, histological characterization, and in vitro modeling reveal a crucial role of ZEB1 in CAF polarization, promoting myofibroblastic features by restricting inflammatory activation. Zeb1 deficiency impairs collagen deposition and CAF barrier function but increases NFκB-mediated cytokine production, jointly promoting lymphocyte recruitment and immune checkpoint activation. Strikingly, the Zeb1-deficient CAF repertoire sensitizes to immune checkpoint inhibition, offering a therapeutic opportunity of targeting ZEB1 in CAFs and its usage as a prognostic biomarker. Collectively, we demonstrate that ZEB1-dependent plasticity of CAFs suppresses anti-tumor immunity and promotes metastasis.
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Affiliation(s)
- Constantin Menche
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Harald Schuhwerk
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Isabell Armstark
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Pooja Gupta
- Core Unit for Bioinformatics, Data Integration and Analysis, Center for Medical Information and Communication Technology, University Hospital Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Kathrin Fuchs
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Ruthger van Roey
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Mohammed H Mosa
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Anne Hartebrodt
- Biomedical Network Science Lab, Department Artificial Intelligence in Biomedical Engineering (AIBE), FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Yussuf Hajjaj
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Ana Clavel Ezquerra
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Manoj K Selvaraju
- Core Unit for Bioinformatics, Data Integration and Analysis, Center for Medical Information and Communication Technology, University Hospital Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Carol I Geppert
- Institute of Pathology, University Hospital Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Stefanie Bärthel
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Florian R Greten
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
- German Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
| | - Simone Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - David B Blumenthal
- Biomedical Network Science Lab, Department Artificial Intelligence in Biomedical Engineering (AIBE), FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Weigert
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
- Institute of Biochemistry I, Goethe University, Frankfurt am Main, Germany
| | - Thomas Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, FAU Erlangen-Nürnberg, Erlangen, Germany.
| | - Henner F Farin
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany.
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany.
- German Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany.
| | - Marc P Stemmler
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, FAU Erlangen-Nürnberg, Erlangen, Germany.
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13
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de Back TR, Wu T, Schafrat PJ, Ten Hoorn S, Tan M, He L, van Hooff SR, Koster J, Nijman LE, Vink GR, Beumer IJ, Elbers CC, Lenos KJ, Sommeijer DW, Wang X, Vermeulen L. A consensus molecular subtypes classification strategy for clinical colorectal cancer tissues. Life Sci Alliance 2024; 7:e202402730. [PMID: 38782602 PMCID: PMC11116811 DOI: 10.26508/lsa.202402730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Consensus Molecular Subtype (CMS) classification of colorectal cancer (CRC) tissues is complicated by RNA degradation upon formalin-fixed paraffin-embedded (FFPE) preservation. Here, we present an FFPE-curated CMS classifier. The CMSFFPE classifier was developed using genes with a high transcript integrity in FFPE-derived RNA. We evaluated the classification accuracy in two FFPE-RNA datasets with matched fresh-frozen (FF) RNA data, and an FF-derived RNA set. An FFPE-RNA application cohort of metastatic CRC patients was established, partly treated with anti-EGFR therapy. Key characteristics per CMS were assessed. Cross-referenced with matched benchmark FF CMS calls, the CMSFFPE classifier strongly improved classification accuracy in two FFPE datasets compared with the original CMSClassifier (63.6% versus 40.9% and 83.3% versus 66.7%, respectively). We recovered CMS-specific recurrence-free survival patterns (CMS4 versus CMS2: hazard ratio 1.75, 95% CI 1.24-2.46). Key molecular and clinical associations of the CMSs were confirmed. In particular, we demonstrated the predictive value of CMS2 and CMS3 for anti-EGFR therapy response (CMS2&3: odds ratio 5.48, 95% CI 1.10-27.27). The CMSFFPE classifier is an optimized FFPE-curated research tool for CMS classification of clinical CRC samples.
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Affiliation(s)
- Tim R de Back
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- https://ror.org/01n92vv28 Oncode Institute, Amsterdam, Netherlands
| | - Tan Wu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Pascale Jm Schafrat
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- https://ror.org/01n92vv28 Oncode Institute, Amsterdam, Netherlands
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Medical Oncology, Amsterdam, Netherlands
| | - Sanne Ten Hoorn
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- https://ror.org/01n92vv28 Oncode Institute, Amsterdam, Netherlands
| | - Miaomiao Tan
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
- Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, China
| | - Lingli He
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sander R van Hooff
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- https://ror.org/01n92vv28 Oncode Institute, Amsterdam, Netherlands
| | - Jan Koster
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
| | - Lisanne E Nijman
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- https://ror.org/01n92vv28 Oncode Institute, Amsterdam, Netherlands
| | - Geraldine R Vink
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Research and Development, Netherlands Comprehensive Cancer Organisation, Utrecht, Netherlands
| | | | - Clara C Elbers
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- https://ror.org/01n92vv28 Oncode Institute, Amsterdam, Netherlands
| | - Kristiaan J Lenos
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- https://ror.org/01n92vv28 Oncode Institute, Amsterdam, Netherlands
| | - Dirkje W Sommeijer
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- Flevohospital, Department of Internal Medicine, Almere, Netherlands
| | - Xin Wang
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Louis Vermeulen
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, Netherlands
- https://ror.org/01n92vv28 Oncode Institute, Amsterdam, Netherlands
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14
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Borrelli C, Roberts M, Eletto D, Hussherr MD, Fazilaty H, Valenta T, Lafzi A, Kretz JA, Guido Vinzoni E, Karakatsani A, Adivarahan S, Mannhart A, Kimura S, Meijs A, Baccouche Mhamedi F, Acar IE, Handler K, Ficht X, Platt RJ, Piscuoglio S, Moor AE. In vivo interaction screening reveals liver-derived constraints to metastasis. Nature 2024; 632:411-418. [PMID: 39048831 PMCID: PMC11306111 DOI: 10.1038/s41586-024-07715-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 06/14/2024] [Indexed: 07/27/2024]
Abstract
It is estimated that only 0.02% of disseminated tumour cells are able to seed overt metastases1. While this suggests the presence of environmental constraints to metastatic seeding, the landscape of host factors controlling this process remains largely unclear. Here, combining transposon technology2 and fluorescence niche labelling3, we developed an in vivo CRISPR activation screen to systematically investigate the interactions between hepatocytes and metastatic cells. We identify plexin B2 as a critical host-derived regulator of liver colonization in colorectal and pancreatic cancer and melanoma syngeneic mouse models. We dissect a mechanism through which plexin B2 interacts with class IV semaphorins on tumour cells, leading to KLF4 upregulation and thereby promoting the acquisition of epithelial traits. Our results highlight the essential role of signals from the liver parenchyma for the seeding of disseminated tumour cells before the establishment of a growth-promoting niche. Our findings further suggest that epithelialization is required for the adaptation of CRC metastases to their new tissue environment. Blocking the plexin-B2-semaphorin axis abolishes metastatic colonization of the liver and therefore represents a therapeutic strategy for the prevention of hepatic metastases. Finally, our screening approach, which evaluates host-derived extrinsic signals rather than tumour-intrinsic factors for their ability to promote metastatic seeding, is broadly applicable and lays a framework for the screening of environmental constraints to metastasis in other organs and cancer types.
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Affiliation(s)
- Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Morgan Roberts
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Davide Eletto
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Hassan Fazilaty
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Tomas Valenta
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Atefeh Lafzi
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Jonas A Kretz
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Elena Guido Vinzoni
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | | | - Ardian Mannhart
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Shoichiro Kimura
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ab Meijs
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Ilhan E Acar
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Kristina Handler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Xenia Ficht
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Salvatore Piscuoglio
- IRCCS Humanitas Research Hospital, Milan, Italy
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
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15
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Kenakin T. Know your molecule: pharmacological characterization of drug candidates to enhance efficacy and reduce late-stage attrition. Nat Rev Drug Discov 2024; 23:626-644. [PMID: 38890494 DOI: 10.1038/s41573-024-00958-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 06/20/2024]
Abstract
Despite advances in chemical, computational and biological sciences, the rate of attrition of drug candidates in clinical development is still high. A key point in the small-molecule discovery process that could provide opportunities to help address this challenge is the pharmacological characterization of hit and lead compounds, culminating in the selection of a drug candidate. Deeper characterization is increasingly important, because the 'quality' of drug efficacy, at least for G protein-coupled receptors (GPCRs), is now understood to be much more than activation of commonly evaluated pathways such as cAMP signalling, with many more 'efficacies' of ligands that could be harnessed therapeutically. Such characterization is being enabled by novel assays to characterize the complex behaviour of GPCRs, such as biased signalling and allosteric modulation, as well as advances in structural biology, such as cryo-electron microscopy. This article discusses key factors in the assessments of the pharmacology of hit and lead compounds in the context of GPCRs as a target class, highlighting opportunities to identify drug candidates with the potential to address limitations of current therapies and to improve the probability of them succeeding in clinical development.
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Affiliation(s)
- Terry Kenakin
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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16
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Hissong E, Bhinder B, Kim J, Ohara K, Ravichandran H, Assaad MA, Elsoukkary S, Shusterman M, Khan U, Eng KW, Bareja R, Manohar J, Sigouros M, Rendeiro AF, Jessurun J, Ocean AJ, Sboner A, Elemento O, Mosquera JM, Shah MA. Integrative Transcriptomic and Single-Cell Protein Characterization of Colorectal Carcinoma Delineates Distinct Tumor Immune Microenvironments Associated with Overall Survival. RESEARCH SQUARE 2024:rs.3.rs-4751101. [PMID: 39108491 PMCID: PMC11302706 DOI: 10.21203/rs.3.rs-4751101/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Colorectal carcinoma (CRC) is a heterogeneous group of tumors with varying therapeutic response and prognosis, and evidence suggests the tumor immune microenvironment (TIME) plays a pivotal role. Using advanced molecular and spatial biology technologies, we aimed to evaluate the TIME in patients with CRC to determine whether specific alterations in the immune composition correlated with prognosis. We identified primary and metastatic tumor samples from 31 consented patients, which were profiled with whole-exome sequencing and bulk RNA-seq. Immune cell deconvolution followed by gene set enrichment analysis and unsupervised clustering was performed. A subset of tumors underwent in situ analysis of the TIME spatial composition at single-cell resolution through Imaging Mass Mass Cytometry. Gene set enrichment analysis revealed two distinct groups of advanced CRC, one with an immune activated phenotype and the other with a suppressed immune microenvironment. The activated TIME phenotype contained increased Th1 cells, activated dendritic cells, tertiary lymphoid structures, and higher counts of CD8+ T cells whereas the inactive or suppressed TIME contained increased macrophages and a higher M2/M1 ratio. Our findings were further supported by RNA-seq data analysis from the TCGA CRC database, in which unsupervised clustering also identified two separate groups. The immunosuppressed CRC TIME had a lower overall survival probability (HR 1.66, p=0.007). This study supports the pertinent role of the CRC immune microenvironment in tumor progression and patient prognosis. We characterized the immune cell composition to better understand the complexity and vital role that immune activity states of the TIME play in determining patient outcome.
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Affiliation(s)
- Erika Hissong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 525 E 68th St, New York, NY 10065; Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA
| | - Bhavneet Bhinder
- Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA
| | - Junbum Kim
- Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA
| | - Kentaro Ohara
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 525 E 68th St, New York, NY 10065; Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA
| | - Hiranmayi Ravichandran
- Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA
| | - Majd Al Assaad
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 525 E 68th St, New York, NY 10065; Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA
| | - Sarah Elsoukkary
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 525 E 68th St, New York, NY 10065, USA
| | - Michael Shusterman
- Department of Medicine, Hematology and Medical Oncology, Weill Cornell Medicine, 525 E 68th St New York, NY, USA
| | - Uqba Khan
- Department of Medicine, Hematology and Medical Oncology, Weill Cornell Medicine, 525 E 68th St New York, NY, USA
| | - Kenneth Wha Eng
- Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA
| | - Rohan Bareja
- Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA
| | - Jyothi Manohar
- Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA
| | - Michael Sigouros
- Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA
| | - Andre F Rendeiro
- Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Wien, Austria
| | - Jose Jessurun
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 525 E 68th St, New York, NY 10065, USA
| | - Allyson J Ocean
- Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA; Department of Medicine, Hematology and Medical Oncology, Weill Cornell Medicine, 525 E 68th St New York, NY, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 525 E 68th St, New York, NY 10065; Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, 525 E 68th St. New York, NY, USA
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, 525 E 68th St. New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, 525 E 68th St. New York, NY, USA
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 525 E 68th St, New York, NY 10065; Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA
| | - Manish A Shah
- Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, 413 E 69th St, New York, NY 10021, USA; Department of Medicine, Hematology and Medical Oncology, Weill Cornell Medicine, 525 E 68th St New York, NY, USA
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17
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Ran R, Trapecar M, Brubaker DK. Systematic Analysis of Human Colorectal Cancer scRNA-seq Revealed Limited Pro-tumoral IL-17 Production Potential in Gamma Delta T Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.604156. [PMID: 39071278 PMCID: PMC11275756 DOI: 10.1101/2024.07.18.604156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Gamma delta (γδ) T cells play a crucial role in anti-tumor immunity due to their cytotoxic properties. However, the role and extent of γδ T cells in production of pro-tumorigenic interleukin- 17 (IL-17) within the tumor microenvironment (TME) of colorectal cancer (CRC) remains controversial. In this study, we re-analyzed nine published human CRC whole-tissue single-cell RNA sequencing (scRNA-seq) datasets, identifying 18,483 γδ T cells out of 951,785 total cells, in the neoplastic or adjacent normal tissue of 165 human CRC patients. Our results confirm that tumor-infiltrating γδ T cells exhibit high cytotoxicity-related transcription in both tumor and adjacent normal tissues, but critically, none of the γδ T cell clusters showed IL-17 production potential. We also identified various γδ T cell subsets, including Teff, TRM, Tpex, and Tex, and noted an increased expression of cytotoxic molecules in tumor-infiltrating γδ T cells compared to their normal area counterparts. Our work demonstrates that γδ T cells in CRC primarily function as cytotoxic effector cells rather than IL-17 producers, mitigating the concerns about their potential pro-tumorigenic roles in CRC, highlighting the importance of accurately characterizing these cells for cancer immunotherapy research and the unneglectable cross-species discrepancy between the mouse and human immune system in the study of cancer immunology.
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Affiliation(s)
- Ran Ran
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH
| | - Martin Trapecar
- Department of Medicine, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Douglas K. Brubaker
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH
- The Blood, Heart, Lung, and Immunology Research Center, Case Western Reserve University, University Hospitals of Cleveland, Cleveland, OH
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18
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Wei TT, Blanc E, Peidli S, Bischoff P, Trinks A, Horst D, Sers C, Blüthgen N, Beule D, Morkel M, Obermayer B. High-confidence calling of normal epithelial cells allows identification of a novel stem-like cell state in the colorectal cancer microenvironment. Int J Cancer 2024. [PMID: 39031967 DOI: 10.1002/ijc.35079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/29/2024] [Accepted: 06/10/2024] [Indexed: 07/22/2024]
Abstract
Single-cell analyses can be confounded by assigning unrelated groups of cells to common developmental trajectories. For instance, cancer cells and admixed normal epithelial cells could adopt similar cell states thus complicating analyses of their developmental potential. Here, we develop and benchmark CCISM (for Cancer Cell Identification using Somatic Mutations) to exploit genomic single nucleotide variants for the disambiguation of cancer cells from genomically normal non-cancer cells in single-cell data. We find that our method and others based on gene expression or allelic imbalances identify overlapping sets of colorectal cancer versus normal colon epithelial cells, depending on molecular characteristics of individual cancers. Further, we define consensus cell identities of normal and cancer epithelial cells with higher transcriptome cluster homogeneity than those derived using existing tools. Using the consensus identities, we identify significant shifts of cell state distributions in genomically normal epithelial cells developing in the cancer microenvironment, with immature states increased at the expense of terminal differentiation throughout the colon, and a novel stem-like cell state arising in the left colon. Trajectory analyses show that the new cell state extends the pseudo-time range of normal colon stem-like cells in a cancer context. We identify cancer-associated fibroblasts as sources of WNT and BMP ligands potentially contributing to increased plasticity of stem cells in the cancer microenvironment. Our analyses advocate careful interpretation of cell heterogeneity and plasticity in the cancer context and the consideration of genomic information in addition to gene expression data when possible.
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Affiliation(s)
- Tzu-Ting Wei
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Peidli
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Philip Bischoff
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium Partner Site Berlin, German Cancer Research Center, Heidelberg, Germany
| | - Alexandra Trinks
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Unit Bioportal Single Cells, Berlin, Germany
| | - David Horst
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium Partner Site Berlin, German Cancer Research Center, Heidelberg, Germany
| | - Christine Sers
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium Partner Site Berlin, German Cancer Research Center, Heidelberg, Germany
| | - Nils Blüthgen
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
- German Cancer Consortium Partner Site Berlin, German Cancer Research Center, Heidelberg, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Morkel
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Unit Bioportal Single Cells, Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
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19
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van Baarle L, De Simone V, Schneider L, Santhosh S, Abdurahiman S, Biscu F, Schneider R, Zanoletti L, Siqueira de Mello R, Verbandt S, Hu Z, Stakenborg M, Ke BJ, Stakenborg N, Salvador Laureano R, García-Reyes B, Henn J, Toma M, Vanmechelen M, Boeckxstaens G, De Smet F, Garg AD, Ibiza S, Tejpar S, Wehner S, Matteoli G. IL-1R signaling drives enteric glia-macrophage interactions in colorectal cancer. Nat Commun 2024; 15:6079. [PMID: 39030280 PMCID: PMC11271635 DOI: 10.1038/s41467-024-50438-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 07/11/2024] [Indexed: 07/21/2024] Open
Abstract
Enteric glia have been recently recognized as key components of the colonic tumor microenvironment indicating their potential role in colorectal cancer pathogenesis. Although enteric glia modulate immune responses in other intestinal diseases, their interaction with the colorectal cancer immune cell compartment remains unclear. Through a combination of single-cell and bulk RNA-sequencing, both in murine models and patients, here we find that enteric glia acquire an immunomodulatory phenotype by bi-directional communication with tumor-infiltrating monocytes. The latter direct a reactive enteric glial cell phenotypic and functional switch via glial IL-1R signaling. In turn, tumor glia promote monocyte differentiation towards pro-tumorigenic SPP1+ tumor-associated macrophages by IL-6 release. Enteric glia cell abundancy correlates with worse disease outcomes in preclinical models and colorectal cancer patients. Thereby, our study reveals a neuroimmune interaction between enteric glia and tumor-associated macrophages in the colorectal tumor microenvironment, providing insights into colorectal cancer pathogenesis.
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Affiliation(s)
- Lies van Baarle
- Laboratory of Mucosal Immunology, Department of Chronic Diseases and Metabolism (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Veronica De Simone
- Laboratory of Mucosal Immunology, Department of Chronic Diseases and Metabolism (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Linda Schneider
- Department of Surgery, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Sneha Santhosh
- Laboratory of Mucosal Immunology, Department of Chronic Diseases and Metabolism (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC, Australia
| | - Saeed Abdurahiman
- Laboratory of Mucosal Immunology, Department of Chronic Diseases and Metabolism (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Francesca Biscu
- Laboratory of Mucosal Immunology, Department of Chronic Diseases and Metabolism (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Reiner Schneider
- Department of Surgery, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Lisa Zanoletti
- Laboratory of Mucosal Immunology, Department of Chronic Diseases and Metabolism (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Renata Siqueira de Mello
- Laboratory of Mucosal Immunology, Department of Chronic Diseases and Metabolism (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Sara Verbandt
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Zedong Hu
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Michelle Stakenborg
- Laboratory of Mucosal Immunology, Department of Chronic Diseases and Metabolism (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Bo-Jun Ke
- Laboratory of Mucosal Immunology, Department of Chronic Diseases and Metabolism (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Nathalie Stakenborg
- Laboratory for Intestinal Neuro-Immune Interaction, Department of Chronic Diseases and Metabolism (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Raquel Salvador Laureano
- Cell Stress and Immunity (CSI) Lab, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Balbina García-Reyes
- Department of Surgery, University Hospital Bonn, Medical Faculty, Bonn, Germany
- Mildred Scheel School of Oncology, Aachen Bonn Cologne Düsseldorf (MSSO ABCD), University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Jonas Henn
- Department of Surgery, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Marieta Toma
- Department of Pathology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Maxime Vanmechelen
- Translational Cell and Tissue Research Unit, Department of Imaging & Pathology, Laboratory for Precision Cancer Medicine, KU Leuven, Leuven, Belgium
- Leuven Institute for Single-Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | - Guy Boeckxstaens
- Laboratory for Intestinal Neuro-Immune Interaction, Department of Chronic Diseases and Metabolism (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Frederik De Smet
- Translational Cell and Tissue Research Unit, Department of Imaging & Pathology, Laboratory for Precision Cancer Medicine, KU Leuven, Leuven, Belgium
- Leuven Institute for Single-Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | - Abhishek D Garg
- Cell Stress and Immunity (CSI) Lab, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Sales Ibiza
- Laboratory of Cell Biology & Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Sabine Tejpar
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sven Wehner
- Department of Surgery, University Hospital Bonn, Medical Faculty, Bonn, Germany.
| | - Gianluca Matteoli
- Laboratory of Mucosal Immunology, Department of Chronic Diseases and Metabolism (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium.
- Leuven Institute for Single-Cell Omics (LISCO), KU Leuven, Leuven, Belgium.
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20
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de Back TR, van Hooff SR, Sommeijer DW, Vermeulen L. Transcriptomic subtyping of gastrointestinal malignancies. Trends Cancer 2024:S2405-8033(24)00120-1. [PMID: 39019673 DOI: 10.1016/j.trecan.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/19/2024]
Abstract
Gastrointestinal (GI) cancers are highly heterogeneous at multiple levels. Tumor heterogeneity can be captured by molecular profiling, such as genetic, epigenetic, proteomic, and transcriptomic classification. Transcriptomic subtyping has the advantage of combining genetic and epigenetic information, cancer cell-intrinsic properties, and the tumor microenvironment (TME). Unsupervised transcriptomic subtyping systems of different GI malignancies have gained interest because they reveal shared biological features across cancers and bear prognostic and predictive value. Importantly, transcriptomic subtypes accurately reflect complex phenotypic states varying not only per tumor region, but also throughout disease progression, with consequences for clinical management. Here, we discuss methodologies of transcriptomic subtyping, proposed taxonomies for GI malignancies, and the challenges posed to clinical implementation, highlighting opportunities for future transcriptomic profiling efforts to optimize clinical impact.
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Affiliation(s)
- Tim R de Back
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Sander R van Hooff
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Dirkje W Sommeijer
- Flevohospital, Department of Internal Medicine, Hospitaalweg 1, 1315 RA, Almere, The Netherlands
| | - Louis Vermeulen
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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21
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Wang J, Fonseca GJ, Ding J. scSemiProfiler: Advancing large-scale single-cell studies through semi-profiling with deep generative models and active learning. Nat Commun 2024; 15:5989. [PMID: 39013867 PMCID: PMC11252419 DOI: 10.1038/s41467-024-50150-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/28/2024] [Indexed: 07/18/2024] Open
Abstract
Single-cell sequencing is a crucial tool for dissecting the cellular intricacies of complex diseases. Its prohibitive cost, however, hampers its application in expansive biomedical studies. Traditional cellular deconvolution approaches can infer cell type proportions from more affordable bulk sequencing data, yet they fall short in providing the detailed resolution required for single-cell-level analyses. To overcome this challenge, we introduce "scSemiProfiler", an innovative computational framework that marries deep generative models with active learning strategies. This method adeptly infers single-cell profiles across large cohorts by fusing bulk sequencing data with targeted single-cell sequencing from a few rigorously chosen representatives. Extensive validation across heterogeneous datasets verifies the precision of our semi-profiling approach, aligning closely with true single-cell profiling data and empowering refined cellular analyses. Originally developed for extensive disease cohorts, "scSemiProfiler" is adaptable for broad applications. It provides a scalable, cost-effective solution for single-cell profiling, facilitating in-depth cellular investigation in various biological domains.
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Affiliation(s)
- Jingtao Wang
- Meakins-Christe Laboratories, Research Institute of McGill University Health Centre, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada
| | - Gregory J Fonseca
- Meakins-Christe Laboratories, Research Institute of McGill University Health Centre, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada
- Quantitative Life Sciences, McGill University, 845 Rue Sherbrooke Ouest, Montreal, H3A 0G4, Quebec, Canada
| | - Jun Ding
- Meakins-Christe Laboratories, Research Institute of McGill University Health Centre, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada.
- Quantitative Life Sciences, McGill University, 845 Rue Sherbrooke Ouest, Montreal, H3A 0G4, Quebec, Canada.
- School of Computer Science, McGill University, 3480 Rue University, Montreal, H3A 2A7, Quebec, Canada.
- Mila-Quebec AI Institute, 6666 Rue Saint-Urbain, Montreal, H2S 3H1, Quebec, Canada.
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22
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Liu Z, Zhou X, Tang F. Epigenetic regulators as the foundation for molecular classification of colorectal cancer. Cancer Biol Med 2024; 21:j.issn.2095-3941.2024.0176. [PMID: 39015014 PMCID: PMC11271224 DOI: 10.20892/j.issn.2095-3941.2024.0176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 06/24/2024] [Indexed: 07/18/2024] Open
Affiliation(s)
- Zhenyu Liu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Xin Zhou
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing 100871, China
- Peking University Third Hospital Cancer Center, Beijing 100191, China
| | - Fuchou Tang
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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23
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Yuan X, Ma Y, Gao R, Cui S, Wang Y, Fa B, Ma S, Wei T, Ma S, Yu Z. HEARTSVG: a fast and accurate method for identifying spatially variable genes in large-scale spatial transcriptomics. Nat Commun 2024; 15:5700. [PMID: 38972896 PMCID: PMC11228050 DOI: 10.1038/s41467-024-49846-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 06/19/2024] [Indexed: 07/09/2024] Open
Abstract
Identifying spatially variable genes (SVGs) is crucial for understanding the spatiotemporal characteristics of diseases and tissue structures, posing a distinctive challenge in spatial transcriptomics research. We propose HEARTSVG, a distribution-free, test-based method for fast and accurately identifying spatially variable genes in large-scale spatial transcriptomic data. Extensive simulations demonstrate that HEARTSVG outperforms state-of-the-art methods with higherF 1 scores (averageF 1 Score=0.948), improved computational efficiency, scalability, and reduced false positives (FPs). Through analysis of twelve real datasets from various spatial transcriptomic technologies, HEARTSVG identifies a greater number of biologically significant SVGs (average AUC = 0.792) than other comparative methods without prespecifying spatial patterns. Furthermore, by clustering SVGs, we uncover two distinct tumor spatial domains characterized by unique spatial expression patterns, spatial-temporal locations, and biological functions in human colorectal cancer data, unraveling the complexity of tumors.
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Affiliation(s)
- Xin Yuan
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China
| | - Yanran Ma
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ruitian Gao
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuya Cui
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China
| | - Yifan Wang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Botao Fa
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Shiyang Ma
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ting Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangge Ma
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China.
- Department of Biostatistics, Yale University, New Haven, USA.
| | - Zhangsheng Yu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China.
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Center for Biomedical Data Science, Translational Science Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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24
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Liu B, Li S, Cheng Y, Song P, Xu M, Li Z, Shao W, Xin J, Fu Z, Gu D, Du M, Zhang Z, Wang M. Distinctive multicellular immunosuppressive hubs confer different intervention strategies for left- and right-sided colon cancers. Cell Rep Med 2024; 5:101589. [PMID: 38806057 PMCID: PMC11228667 DOI: 10.1016/j.xcrm.2024.101589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/11/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024]
Abstract
Primary colon cancers arising from the left and right sides exhibit distinct clinical and molecular characteristics. Sidedness-associated heterogeneity relies intricately on the oncogenic properties of cancer cells and multicellular interactions in tumor microenvironments. Here, combining transcriptomic profiling of 426,863 single cells from 105 colon cancer patients and validation with spatial transcriptomics and large-scale histological analysis, we capture common transcriptional heterogeneity patterns between left- and right-sided malignant epithelia through delineating two side-specific expression meta-programs. The proliferation stemness meta-program is notably enriched in left-sided malignant epithelia that colocalize with Mph-PLTP cells, activated regulatory T cells (Tregs), and exhausted CD8-LAYN cells, constituting the glucose metabolism reprogramming niche. The immune secretory (IS) meta-program exhibits specific enrichment in right-sided malignant epithelia, especially in smoking patients with right-sided colon cancer. The IShigh malignant epithelia spatially localize in hypoxic regions and facilitate immune evasion through attenuating Mph-SPP1 cell antigen presentation and recruiting innate-like cytotoxicity-reduced CD8-CD161 cells.
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Affiliation(s)
- Bingxin Liu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuwei Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yifei Cheng
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Peng Song
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Menghuan Xu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengyi Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wei Shao
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zan Fu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Dongying Gu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
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25
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Fang C, Selega A, Campbell KR. Beyond benchmarking and towards predictive models of dataset-specific single-cell RNA-seq pipeline performance. Genome Biol 2024; 25:159. [PMID: 38886757 PMCID: PMC11184819 DOI: 10.1186/s13059-024-03304-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND The advent of single-cell RNA-sequencing (scRNA-seq) has driven significant computational methods development for all steps in the scRNA-seq data analysis pipeline, including filtering, normalization, and clustering. The large number of methods and their resulting parameter combinations has created a combinatorial set of possible pipelines to analyze scRNA-seq data, which leads to the obvious question: which is best? Several benchmarking studies compare methods but frequently find variable performance depending on dataset and pipeline characteristics. Alternatively, the large number of scRNA-seq datasets along with advances in supervised machine learning raise a tantalizing possibility: could the optimal pipeline be predicted for a given dataset? RESULTS Here, we begin to answer this question by applying 288 scRNA-seq analysis pipelines to 86 datasets and quantifying pipeline success via a range of measures evaluating cluster purity and biological plausibility. We build supervised machine learning models to predict pipeline success given a range of dataset and pipeline characteristics. We find that prediction performance is significantly better than random and that in many cases pipelines predicted to perform well provide clustering outputs similar to expert-annotated cell type labels. We identify characteristics of datasets that correlate with strong prediction performance that could guide when such prediction models may be useful. CONCLUSIONS Supervised machine learning models have utility for recommending analysis pipelines and therefore the potential to alleviate the burden of choosing from the near-infinite number of possibilities. Different aspects of datasets influence the predictive performance of such models which will further guide users.
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Affiliation(s)
- Cindy Fang
- Lunenfeld-Tanenbaum Research Institute, Toronto, Canada
- Program in Bioinformatics and Computational Biology, University of Toronto, Toronto, Canada
- Present address: Department of Biostatistics, Johns Hopkins University, Baltimore, USA
| | - Alina Selega
- Lunenfeld-Tanenbaum Research Institute, Toronto, Canada
- Vector Institute, Toronto, Canada
| | - Kieran R Campbell
- Lunenfeld-Tanenbaum Research Institute, Toronto, Canada.
- Vector Institute, Toronto, Canada.
- Departments of Molecular Genetics, Statistical Sciences, Computer Science, University of Toronto, Toronto, Canada.
- Ontario Institute for Cancer Research, Toronto, Canada.
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26
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Zhang JP, Yan BZ, Liu J, Wang W. Action of circulating and infiltrating B cells in the immune microenvironment of colorectal cancer by single-cell sequencing analysis. World J Gastrointest Oncol 2024; 16:2671-2684. [DOI: 10.4251/wjgo.v16.i6.2671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/10/2024] [Accepted: 04/09/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND The complexity of the immune microenvironment has an impact on the treatment of colorectal cancer (CRC), one of the most prevalent malignancies worldwide. In this study, multi-omics and single-cell sequencing techniques were used to investigate the mechanism of action of circulating and infiltrating B cells in CRC. By revealing the heterogeneity and functional differences of B cells in cancer immunity, we aim to deepen our understanding of immune regulation and provide a scientific basis for the development of more effective cancer treatment strategies.
AIM To explore the role of circulating and infiltrating B cell subsets in the immune microenvironment of CRC, explore the potential driving mechanism of B cell development, analyze the interaction between B cells and other immune cells in the immune microenvironment and the functions of communication molecules, and search for possible regulatory pathways to promote the anti-tumor effects of B cells.
METHODS A total of 69 paracancer (normal), tumor and peripheral blood samples were collected from 23 patients with CRC from The Cancer Genome Atlas database (https://portal.gdc.cancer.gov/). After the immune cells were sorted by multicolor flow cytometry, the single cell transcriptome and B cell receptor group library were sequenced using the 10X Genomics platform, and the data were analyzed using bioinformatics tools such as Seurat. The differences in the number and function of B cell infiltration between tumor and normal tissue, the interaction between B cell subsets and T cells and myeloid cell subsets, and the transcription factor regulatory network of B cell subsets were explored and analyzed.
RESULTS Compared with normal tissue, the infiltrating number of CD20+B cell subsets in tumor tissue increased significantly. Among them, germinal center B cells (GCB) played the most prominent role, with positive clone expansion and heavy chain mutation level increasing, and the trend of differentiation into memory B cells increased. However, the number of plasma cells in the tumor microenvironment decreased significantly, and the plasma cells secreting IgA antibodies decreased most obviously. In addition, compared with the immune microenvironment of normal tissues, GCB cells in tumor tissues became more closely connected with other immune cells such as T cells, and communication molecules that positively regulate immune function were significantly enriched.
CONCLUSION The role of GCB in CRC tumor microenvironment is greatly enhanced, and its affinity to tumor antigen is enhanced by its significantly increased heavy chain mutation level. Meanwhile, GCB has enhanced its association with immune cells in the microenvironment, which plays a positive anti-tumor effect.
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Affiliation(s)
- Jing-Po Zhang
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Hebei Medical University, Shijiazhuang 050032, Hebei Province, China
| | - Bing-Zheng Yan
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Hebei Medical University, Shijiazhuang 050032, Hebei Province, China
| | - Jie Liu
- Department of Hepatobiliary Surgery, Hunan Provincial People’s Hospital, Changsha 410002, Hunan Province, China
| | - Wei Wang
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Hebei Medical University, Shijiazhuang 050032, Hebei Province, China
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27
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Zhang JP, Yan BZ, Liu J, Wang W. Action of circulating and infiltrating B cells in the immune microenvironment of colorectal cancer by single-cell sequencing analysis. World J Gastrointest Oncol 2024; 16:2683-2696. [PMID: 38994150 PMCID: PMC11236258 DOI: 10.4251/wjgo.v16.i6.2683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/10/2024] [Accepted: 04/09/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND The complexity of the immune microenvironment has an impact on the treatment of colorectal cancer (CRC), one of the most prevalent malignancies worldwide. In this study, multi-omics and single-cell sequencing techniques were used to investigate the mechanism of action of circulating and infiltrating B cells in CRC. By revealing the heterogeneity and functional differences of B cells in cancer immunity, we aim to deepen our understanding of immune regulation and provide a scientific basis for the development of more effective cancer treatment strategies. AIM To explore the role of circulating and infiltrating B cell subsets in the immune microenvironment of CRC, explore the potential driving mechanism of B cell development, analyze the interaction between B cells and other immune cells in the immune microenvironment and the functions of communication molecules, and search for possible regulatory pathways to promote the anti-tumor effects of B cells. METHODS A total of 69 paracancer (normal), tumor and peripheral blood samples were collected from 23 patients with CRC from The Cancer Genome Atlas database (https://portal.gdc.cancer.gov/). After the immune cells were sorted by multicolor flow cytometry, the single cell transcriptome and B cell receptor group library were sequenced using the 10X Genomics platform, and the data were analyzed using bioinformatics tools such as Seurat. The differences in the number and function of B cell infiltration between tumor and normal tissue, the interaction between B cell subsets and T cells and myeloid cell subsets, and the transcription factor regulatory network of B cell subsets were explored and analyzed. RESULTS Compared with normal tissue, the infiltrating number of CD20+B cell subsets in tumor tissue increased significantly. Among them, germinal center B cells (GCB) played the most prominent role, with positive clone expansion and heavy chain mutation level increasing, and the trend of differentiation into memory B cells increased. However, the number of plasma cells in the tumor microenvironment decreased significantly, and the plasma cells secreting IgA antibodies decreased most obviously. In addition, compared with the immune microenvironment of normal tissues, GCB cells in tumor tissues became more closely connected with other immune cells such as T cells, and communication molecules that positively regulate immune function were significantly enriched. CONCLUSION The role of GCB in CRC tumor microenvironment is greatly enhanced, and its affinity to tumor antigen is enhanced by its significantly increased heavy chain mutation level. Meanwhile, GCB has enhanced its association with immune cells in the microenvironment, which plays a positive anti-tumor effect.
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Affiliation(s)
- Jing-Po Zhang
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Hebei Medical University, Shijiazhuang 050032, Hebei Province, China
| | - Bing-Zheng Yan
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Hebei Medical University, Shijiazhuang 050032, Hebei Province, China
| | - Jie Liu
- Department of Hepatobiliary Surgery, Hunan Provincial People’s Hospital, Changsha 410002, Hunan Province, China
| | - Wei Wang
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of Hebei Medical University, Shijiazhuang 050032, Hebei Province, China
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28
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Liu Z, Hu Y, Xie H, Chen K, Wen L, Fu W, Zhou X, Tang F. Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers. Cancer Discov 2024; 14:1082-1105. [PMID: 38445965 DOI: 10.1158/2159-8290.cd-23-1445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/06/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024]
Abstract
Colorectal cancer is a highly heterogeneous disease, with well-characterized subtypes based on genome, DNA methylome, and transcriptome signatures. To chart the epigenetic landscape of colorectal cancers, we generated a high-quality single-cell chromatin accessibility atlas of epithelial cells for 29 patients. Abnormal chromatin states acquired in adenomas were largely retained in colorectal cancers, which were tightly accompanied by opposite changes of DNA methylation. Unsupervised analysis on malignant cells revealed two epigenetic subtypes, exactly matching the iCMS classification, and key iCMS-specific transcription factors (TFs) were identified, including HNF4A and PPARA for iCMS2 tumors and FOXA3 and MAFK for iCMS3 tumors. Notably, subtype-specific TFs bind to distinct target gene sets and contribute to both interpatient similarities and diversities for both chromatin accessibilities and RNA expressions. Moreover, we identified CpG-island methylator phenotypes and pinpointed chromatin state signatures and TF regulators for the CIMP-high subtype. Our work systematically revealed the epigenetic basis of the well-known iCMS and CIMP classifications of colorectal cancers. SIGNIFICANCE Our work revealed the epigenetic basis of the well-known iCMS and CIMP classifications of colorectal cancers. Moreover, interpatient minor similarities and major diversities of chromatin accessibility signatures of TF target genes can faithfully explain the corresponding interpatient minor similarities and major diversities of RNA expression signatures of colorectal cancers, respectively. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Zhenyu Liu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yuqiong Hu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Haoling Xie
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Kexuan Chen
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Lu Wen
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Wei Fu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Peking University Third Hospital Cancer Center, Beijing, China
| | - Xin Zhou
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Peking University Third Hospital Cancer Center, Beijing, China
| | - Fuchou Tang
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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Mouillet-Richard S, Cazelles A, Sroussi M, Gallois C, Taieb J, Laurent-Puig P. Clinical Challenges of Consensus Molecular Subtype CMS4 Colon Cancer in the Era of Precision Medicine. Clin Cancer Res 2024; 30:2351-2358. [PMID: 38564259 PMCID: PMC11145159 DOI: 10.1158/1078-0432.ccr-23-3964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/31/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
Over the past decade, our understanding of the diversity of colorectal cancer has expanded significantly, raising hopes of tailoring treatments more precisely for individual patients. A key achievement in this direction was the establishment of the consensus molecular classification, particularly identifying the challenging consensus molecular subtype (CMS) CMS4 associated with poor prognosis. Because of its aggressive nature, extensive research is dedicated to the CMS4 subgroup. Recent years have unveiled molecular and microenvironmental features at the tissue level specific to CMS4 colorectal cancer. This has paved the way for mechanistic studies and the development of preclinical models. Simultaneously, efforts have been made to easily identify patients with CMS4 colorectal cancer. Reassessing clinical trial results through the CMS classification lens has improved our understanding of the therapeutic challenges linked to this subtype. Exploration of the biology of CMS4 colorectal cancer is yielding potential biomarkers and novel treatment approaches. This overview aims to provide insights into the clinico-biological characteristics of the CMS4 subgroup, the molecular pathways driving this subtype, and available diagnostic options. We also emphasize the therapeutic challenges associated with this subtype, offering potential explanations. Finally, we summarize the current tailored treatments for CMS4 colorectal cancer emerging from fundamental and preclinical studies.
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Affiliation(s)
- Sophie Mouillet-Richard
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Antoine Cazelles
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Marine Sroussi
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Claire Gallois
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Gastroenterology and Gastrointestinal Oncology Department, APHP.Centre - Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
| | - Julien Taieb
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Gastroenterology and Gastrointestinal Oncology Department, APHP.Centre - Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
| | - Pierre Laurent-Puig
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Department of Biology, APHP.Centre - Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
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Huang J, Yin Q, Wang Y, Zhou X, Guo Y, Tang Y, Cheng R, Yu X, Zhang J, Huang C, Huang Z, Zhang J, Guo Z, Huo X, Sun Y, Li Y, Wang H, Yang J, Xue L. EZH2 Inhibition Enhances PD-L1 Protein Stability Through USP22-Mediated Deubiquitination in Colorectal Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308045. [PMID: 38520088 PMCID: PMC11187912 DOI: 10.1002/advs.202308045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/26/2024] [Indexed: 03/25/2024]
Abstract
The regulation of PD-L1 is the key question, which largely determines the outcome of the immune checkpoint inhibitors (ICIs) based therapy. However, besides the transcription level, the protein stability of PD-L1 is closely correlated with its function and has drawn increasing attention. In this study, EZH2 inhibition enhances PD-L1 expression and protein stability, and the deubiquitinase ubiquitin-specific peptidase 22 (USP22) is identified as a key mediator in this process. EZH2 inhibition transcriptionally upregulates USP22 expression, and upregulated USP22 further stabilizes PD-L1. Importantly, a combination of EZH2 inhibitors with anti-PD-1 immune checkpoint blockade therapy improves the tumor microenvironment, enhances sensitivity to immunotherapy, and exerts synergistic anticancer effects. In addition, knocking down USP22 can potentially enhance the therapeutic efficacy of EZH2 inhibitors on colon cancer. These findings unveil the novel role of EZH2 inhibitors in tumor immune evasion by upregulating PD-L1, and this drawback can be compensated by combining ICI immunotherapy. Therefore, these findings provide valuable insights into the EZH2-USP22-PD-L1 regulatory axis, shedding light on the optimization of combining both immune checkpoint blockade and EZH2 inhibitor-based epigenetic therapies to achieve more efficacies and accuracy in cancer treatment.
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Park R, Saeed A. Immunotherapy in Colorectal Cancer - Finding the Achilles' Heel. NEJM EVIDENCE 2024; 3:EVIDra2300353. [PMID: 38804784 DOI: 10.1056/evidra2300353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
AbstractColorectal cancer treatment has evolved considerably in the last decade with the development of immunotherapies. Immune checkpoint inhibitor therapies have brisk and durable responses in patients with advanced microsatellite instability-high colorectal cancer, both surgically resectable and unresectable; however, patients with microsatellite stable colorectal cancer in general do not respond to the same therapy. Emerging evidence shows that immune checkpoint inhibitors may elicit responses in subsets of patients with microsatellite stable colorectal cancer, especially when combined with other anticancer agents that can modulate the tumor microenvironment. Therefore, rationally designed therapeutic combinations involving immune checkpoint inhibitors, as well as the development of predictive biomarkers for optimal patient selection, have emerged as two key areas of active research. In addition, other immunotherapeutic agents such as cell-based therapies and bispecific T-cell engagers are beginning to be studied in preclinical and early-phase settings. Although by no means a universal treatment strategy, immunotherapy can elicit responses in microsatellite stable colorectal cancer and further research is needed to extend their benefit to patients with microsatellite stable colorectal cancer. Here, we review the current state of immunotherapeutic regimens for microsatellite stable colorectal cancer.
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Affiliation(s)
- Robin Park
- Division of Hematology and Medical Oncology, Moffitt Cancer Center, Tampa, FL
- Department of Medicine, University of South Florida, Tampa, FL
| | - Anwaar Saeed
- Department of Medicine, Division of Hematology and Oncology, University of Pittsburgh Medical Center, Pittsburgh
- UPMC Hillman Cancer Center, Pittsburgh
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32
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Langerud J, Eilertsen IA, Moosavi SH, Klokkerud SMK, Reims HM, Backe IF, Hektoen M, Sjo OH, Jeanmougin M, Tejpar S, Nesbakken A, Lothe RA, Sveen A. Multiregional transcriptomics identifies congruent consensus subtypes with prognostic value beyond tumor heterogeneity of colorectal cancer. Nat Commun 2024; 15:4342. [PMID: 38773143 PMCID: PMC11109119 DOI: 10.1038/s41467-024-48706-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
Intra-tumor heterogeneity compromises the clinical value of transcriptomic classifications of colorectal cancer. We investigated the prognostic effect of transcriptomic heterogeneity and the potential for classifications less vulnerable to heterogeneity in a single-hospital series of 1093 tumor samples from 692 patients, including multiregional samples from 98 primary tumors and 35 primary-metastasis sets. We show that intra-tumor heterogeneity of the consensus molecular subtypes (CMS) is frequent and has poor-prognostic associations independently of tumor microenvironment markers. Multiregional transcriptomics uncover cancer cell-intrinsic and low-heterogeneity signals that recapitulate the intrinsic CMSs proposed by single-cell sequencing. Further subclassification identifies congruent CMSs that explain a larger proportion of variation in patient survival than intra-tumor heterogeneity. Plasticity is indicated by discordant intrinsic phenotypes of matched primary and metastatic tumors. We conclude that multiregional sampling reconciles the prognostic power of tumor classifications from single-cell and bulk transcriptomics in the context of intra-tumor heterogeneity, and phenotypic plasticity challenges the reconciliation of primary and metastatic subtypes.
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Affiliation(s)
- Jonas Langerud
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Seyed H Moosavi
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Solveig M K Klokkerud
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Henrik M Reims
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Ingeborg F Backe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Merete Hektoen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ole H Sjo
- Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Marine Jeanmougin
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Sabine Tejpar
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Arild Nesbakken
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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33
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Ko KP, Zhang S, Huang Y, Kim B, Zou G, Jun S, Zhang J, Zhao Y, Martin C, Dunbar KJ, Efe G, Rustgi AK, Nakagawa H, Zhang H, Liu Z, Park JI. Tumor niche network-defined subtypes predict immunotherapy response of esophageal squamous cell cancer. iScience 2024; 27:109795. [PMID: 38741711 PMCID: PMC11089351 DOI: 10.1016/j.isci.2024.109795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/16/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024] Open
Abstract
Despite the promising outcomes of immune checkpoint inhibitors (ICIs), resistance to ICI presents a new challenge. Therefore, selecting patients for specific ICI applications is crucial for maximizing therapeutic efficacy. Herein, we curated 69 human esophageal squamous cell cancer (ESCC) patients' tumor microenvironment (TME) single-cell transcriptomic datasets to subtype ESCC. Integrative analyses of the cellular network and transcriptional signatures of T cells and myeloid cells define distinct ESCC subtypes characterized by T cell exhaustion, and interleukin (IL) and interferon (IFN) signaling. Furthermore, this approach classifies ESCC patients into ICI responders and non-responders, as validated by whole tumor transcriptomes and liquid biopsy-based single-cell transcriptomes of anti-PD-1 ICI responders and non-responders. Our study stratifies ESCC patients based on TME transcriptional network, providing novel insights into tumor niche remodeling and potentially predicting ICI responses in ESCC patients.
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Affiliation(s)
- Kyung-Pil Ko
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shengzhe Zhang
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yuanjian Huang
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bongjun Kim
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gengyi Zou
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sohee Jun
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jie Zhang
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yahui Zhao
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Cecilia Martin
- Division of Digestive and Liver Diseases, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Karen J. Dunbar
- Division of Digestive and Liver Diseases, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gizem Efe
- Division of Digestive and Liver Diseases, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Anil K. Rustgi
- Division of Digestive and Liver Diseases, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hiroshi Nakagawa
- Division of Digestive and Liver Diseases, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Haiyang Zhang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jae-Il Park
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Zhu Y, Koleilat MKI, Roszik J, Kwong MK, Wang Z, Maru DM, Kopetz S, Kwong LN. A Gold Standard-Derived Modular Barcoding Approach to Cancer Transcriptomics. Cancers (Basel) 2024; 16:1886. [PMID: 38791964 PMCID: PMC11120226 DOI: 10.3390/cancers16101886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/22/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
A challenge with studying cancer transcriptomes is in distilling the wealth of information down into manageable portions of information. In this resource, we develop an approach that creates and assembles cancer type-specific gene expression modules into flexible barcodes, allowing for adaptation to a wide variety of uses. Specifically, we propose that modules derived organically from high-quality gold standards such as The Cancer Genome Atlas (TCGA) can accurately capture and describe functionally related genes that are relevant to specific cancer types. We show that such modules can: (1) uncover novel gene relationships and nominate new functional memberships, (2) improve and speed up analysis of smaller or lower-resolution datasets, (3) re-create and expand known cancer subtyping schemes, (4) act as a "decoder" to bridge seemingly disparate established gene signatures, and (5) efficiently apply single-cell RNA sequencing information to other datasets. Moreover, such modules can be used in conjunction with native spreadsheet program commands to create a powerful and rapid approach to hypothesis generation and testing that is readily accessible to non-bioinformaticians. Finally, we provide tools for users to create and interpret their own modules. Overall, the flexible modular nature of the proposed barcoding provides a user-friendly approach to rapidly decoding transcriptome-wide data for research or, potentially, clinical uses.
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Affiliation(s)
- Yan Zhu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
| | - Mohamad Karim I. Koleilat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Man Kam Kwong
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China;
| | - Zhonglin Wang
- Social Science Research Institute, Duke University, Durham, NC 27708, USA;
| | - Dipen M. Maru
- Department of Anatomical Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Lawrence N. Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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35
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Zabeti Touchaei A, Vahidi S, Samadani AA. Immune landscape in APC and TP53 related tumor microenvironment in colon adenocarcinoma: A bioinformatic analysis. Eur J Microbiol Immunol (Bp) 2024; 14:154-165. [PMID: 38470482 PMCID: PMC11097784 DOI: 10.1556/1886.2024.00015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction APC and TP53 are the two most regularly mutated genes in colon adenocarcinoma (COAD), especially in progressive malignancies and antitumoral immune response. The current bioinformatics analysis investigates the APC and TP53 gene expression profile in colon adenocarcinoma as a prognostic characteristic for survival, particularly concentrating on the correlated immune microenvironment. Methods Clinical and genetic data of colon cancer and normal tissue samples were obtained from The Cancer Genome Atlas (TCGA)-COAD and Genotype-Tissue Expression (GTEx) online databases, respectively. The genetic differential expressions were analyzed in both groups via the one-way ANOVA test. Kaplan-Meier survival curves were applied to estimate the overall survival (OS). P < 0.05 was fixed as statistically significant. On Tumor Immune Estimation Resource and Gene Expression Profiling Interactive Analysis databases, the linkage between immune cell recruitment and APC and TP53 status was assessed through Spearman's correlation analysis. Results APC and TP53 were found mutated in 66.74% and 85.71% of the 454 and 7 TCGA-COAD patients in colon and rectosigmoid junction primary sites, respectively with a higher log2-transcriptome per million reads compared to the GTEx group (318 samples in sigmoid and 368 samples in transverse). Survival curves revealed a worse significant OS for the high-APC and TP53 profile colon. Spearman's analysis of immune cells demonstrated a strong positive correlation between the APC status and infiltration of T cell CD4+, T cell CD8+, NK cell, and macrophages and also a positive correlation between status and infiltration of T cell CD4+, T cell CD8+. Conclusions APC and TP53 gene mutations prevail in colon cancer and are extremely associated with poor prognosis and shortest survival. The infiltrating T cell CD4+, T cell CD8+, NK cell, and macrophages populate the colon microenvironment and regulate the mechanisms of tumor advancement, immune evasion, and sensitivity to standard chemotherapy. More comprehensive research is needed to demonstrate these results and turn them into new therapeutic outlooks.
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Affiliation(s)
| | - Sogand Vahidi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Trauma Institute, Guilan University of Medical Sciences, Rasht, Iran
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36
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Knapen DG, Hone Lopez S, de Groot DJA, de Haan JJ, de Vries EGE, Dienstmann R, de Jong S, Bhattacharya A, Fehrmann RSN. Independent transcriptional patterns reveal biological processes associated with disease-free survival in early colorectal cancer. COMMUNICATIONS MEDICINE 2024; 4:79. [PMID: 38702451 PMCID: PMC11068726 DOI: 10.1038/s43856-024-00504-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 04/19/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Bulk transcriptional profiles of early colorectal cancer (CRC) can fail to detect biological processes associated with disease-free survival (DFS) if the transcriptional patterns are subtle and/or obscured by other processes' patterns. Consensus-independent component analysis (c-ICA) can dissect such transcriptomes into statistically independent transcriptional components (TCs), capturing both pronounced and subtle biological processes. METHODS In this study we (1) integrated transcriptomes (n = 4228) from multiple early CRC studies, (2) performed c-ICA to define the TC landscape within this integrated data set, 3) determined the biological processes captured by these TCs, (4) performed Cox regression to identify DFS-associated TCs, (5) performed random survival forest (RSF) analyses with activity of DFS-associated TCs as classifiers to identify subgroups of patients, and 6) performed a sensitivity analysis to determine the robustness of our results RESULTS: We identify 191 TCs, 43 of which are associated with DFS, revealing transcriptional diversity among DFS-associated biological processes. A prominent example is the epithelial-mesenchymal transition (EMT), for which we identify an association with nine independent DFS-associated TCs, each with coordinated upregulation or downregulation of various sets of genes. CONCLUSIONS This finding indicates that early CRC may have nine distinct routes to achieve EMT, each requiring a specific peri-operative treatment strategy. Finally, we stratify patients into DFS patient subgroups with distinct transcriptional patterns associated with stage 2 and stage 3 CRC.
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Affiliation(s)
- Daan G Knapen
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sara Hone Lopez
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Derk Jan A de Groot
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jacco-Juri de Haan
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Elisabeth G E de Vries
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Rodrigo Dienstmann
- Oncology Data Science (ODysSey) Group, Vall d'Hebron Institute of Oncology, Universitat Autónoma de Barcelona, Barcelona, Spain
| | - Steven de Jong
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Arkajyoti Bhattacharya
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
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Yap DRY, Lui RN, Samol J, Ngeow J, Sung JJ, Wong SH. Beyond a vestigial organ: effects of the appendix on gut microbiome and colorectal cancer. J Gastroenterol Hepatol 2024; 39:826-835. [PMID: 38303116 DOI: 10.1111/jgh.16497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/11/2023] [Accepted: 01/07/2024] [Indexed: 02/03/2024]
Abstract
The role of appendectomy in the pathogenesis of colorectal cancer (CRC) is a recent topic of contention. Given that appendectomy remains one of the most commonly performed operations and a first-line management strategy of acute appendicitis, it is inherently crucial to elucidate the association between prior appendectomy and subsequent development of CRC, as there may be long-term health repercussions. In this review, we summarize the data behind the relationship of CRC in post-appendectomy patients, discuss the role of the microbiome in relation to appendectomy and CRC pathogenesis, and provide an appraisal of our current understanding of the function of the appendix. We seek to piece together the current landscape surrounding the microbiome and immunological changes in the colon post-appendectomy and suggest a direction for future research involving molecular, transcriptomic, and immunologic analysis to complement our current understanding of the alterations in gut microbiome.
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Affiliation(s)
- Daniel Ren Yi Yap
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Rashid N Lui
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Faculty of Medicine, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Department of Clinical Oncology, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Jens Samol
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Medical Oncology, Tan Tock Seng Hospital, National Healthcare Group, Singapore, Singapore
- Johns Hospital University, Baltimore, Maryland, USA
| | - Joanne Ngeow
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Cancer Centre Singapore, Singapore Health Services, Singapore, Singapore
| | - Joseph Jy Sung
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Gastroenterology and Hepatology, Tan Tock Seng Hospital, National Healthcare Group, Singapore, Singapore
| | - Sunny H Wong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Gastroenterology and Hepatology, Tan Tock Seng Hospital, National Healthcare Group, Singapore, Singapore
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38
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Lorenzo-Martín LF, Hübscher T, Bowler AD, Broguiere N, Langer J, Tillard L, Nikolaev M, Radtke F, Lutolf MP. Spatiotemporally resolved colorectal oncogenesis in mini-colons ex vivo. Nature 2024; 629:450-457. [PMID: 38658753 PMCID: PMC11078756 DOI: 10.1038/s41586-024-07330-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/18/2024] [Indexed: 04/26/2024]
Abstract
Three-dimensional organoid culture technologies have revolutionized cancer research by allowing for more realistic and scalable reproductions of both tumour and microenvironmental structures1-3. This has enabled better modelling of low-complexity cancer cell behaviours that occur over relatively short periods of time4. However, available organoid systems do not capture the intricate evolutionary process of cancer development in terms of tissue architecture, cell diversity, homeostasis and lifespan. As a consequence, oncogenesis and tumour formation studies are not possible in vitro and instead require the extensive use of animal models, which provide limited spatiotemporal resolution of cellular dynamics and come at a considerable cost in terms of resources and animal lives. Here we developed topobiologically complex mini-colons that are able to undergo tumorigenesis ex vivo by integrating microfabrication, optogenetic and tissue engineering approaches. With this system, tumorigenic transformation can be spatiotemporally controlled by directing oncogenic activation through blue-light exposure, and emergent colon tumours can be tracked in real-time at the single-cell resolution for several weeks without breaking the culture. These induced mini-colons display rich intratumoural and intertumoural diversity and recapitulate key pathophysiological hallmarks displayed by colorectal tumours in vivo. By fine-tuning cell-intrinsic and cell-extrinsic parameters, mini-colons can be used to identify tumorigenic determinants and pharmacological opportunities. As a whole, our study paves the way for cancer initiation research outside living organisms.
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Affiliation(s)
- L Francisco Lorenzo-Martín
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Tania Hübscher
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Amber D Bowler
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Nicolas Broguiere
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jakob Langer
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lucie Tillard
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Mikhail Nikolaev
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Freddy Radtke
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Matthias P Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
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39
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Hosohama L, Tifrea DF, Nee K, Park SY, Wu J, Habowski AN, Van C, Seldin MM, Edwards RA, Waterman ML. Colorectal Cancer Stem Cell Subtypes Orchestrate Distinct Tumor Microenvironments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591144. [PMID: 38712298 PMCID: PMC11071458 DOI: 10.1101/2024.04.25.591144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Several classification systems have been developed to define tumor subtypes in colorectal cancer (CRC). One system proposes that tumor heterogeneity derives in part from distinct cancer stem cell populations that co-exist as admixtures of varying proportions. However, the lack of single cell resolution has prohibited a definitive identification of these types of stem cells and therefore any understanding of how each influence tumor phenotypes. Here were report the isolation and characterization of two cancer stem cell subtypes from the SW480 CRC cell line. We find these cancer stem cells are oncogenic versions of the normal Crypt Base Columnar (CBC) and Regenerative Stem Cell (RSC) populations from intestinal crypts and that their gene signatures are consistent with the "Admixture" and other CRC classification systems. Using publicly available single cell RNA sequencing (scRNAseq) data from CRC patients, we determine that RSC and CBC cancer stem cells are commonly co-present in human CRC. To characterize influences on the tumor microenvironment, we develop subtype-specific xenograft models and we define their tumor microenvironments at high resolution via scRNAseq. RSCs create differentiated, inflammatory, slow growing tumors. CBCs create proliferative, undifferentiated, invasive tumors. With this enhanced resolution, we unify current CRC patient classification schema with TME phenotypes and organization.
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Affiliation(s)
- Linzi Hosohama
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, California
| | - Delia F. Tifrea
- Department of Pathology & Laboratory Medicine, School of Medicine, University of California, Irvine, California
- Chao Family Comprehensive Cancer Center, University of California, Irvine, California
| | - Kevin Nee
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California
| | - Sung Yun Park
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, California
| | - Jie Wu
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California
- Chao Family Comprehensive Cancer Center, University of California, Irvine, California
| | - Amber N. Habowski
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, California
| | - Cassandra Van
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California
| | - Marcus M. Seldin
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California
- Chao Family Comprehensive Cancer Center, University of California, Irvine, California
- Cancer Research Institute, University of California, Irvine, California
| | - Robert A. Edwards
- Department of Pathology & Laboratory Medicine, School of Medicine, University of California, Irvine, California
- Chao Family Comprehensive Cancer Center, University of California, Irvine, California
- Cancer Research Institute, University of California, Irvine, California
| | - Marian L. Waterman
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, California
- Chao Family Comprehensive Cancer Center, University of California, Irvine, California
- Cancer Research Institute, University of California, Irvine, California
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40
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Ran R, Muñoz Briones J, Jena S, Anderson NL, Olson MR, Green LN, Brubaker DK. Detailed survey of an in vitro intestinal epithelium model by single-cell transcriptomics. iScience 2024; 27:109383. [PMID: 38523788 PMCID: PMC10959667 DOI: 10.1016/j.isci.2024.109383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 12/01/2023] [Accepted: 02/27/2024] [Indexed: 03/26/2024] Open
Abstract
The co-culture of two adult human colorectal cancer cell lines, Caco-2 and HT29, on Transwell is commonly used as an in vitro gut mimic, yet the translatability of insights from such a system to adult human physiological contexts is not fully characterized. Here, we used single-cell RNA sequencing on the co-culture to obtain a detailed survey of cell type heterogeneity in the system and conducted a holistic comparison with human physiology. We identified the intestinal stem cell-, transit amplifying-, enterocyte-, goblet cell-, and enteroendocrine-like cells in the system. In general, the co-culture was fetal intestine-like, with less variety of gene expression compared to the adult human gut. Transporters for major types of nutrients were found in the majority of the enterocytes-like cells in the system. TLR 4 was not expressed in the sample, indicating that the co-culture model is incapable of mimicking the innate immune aspect of the human epithelium.
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Affiliation(s)
- Ran Ran
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Javier Muñoz Briones
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Purdue Interdisciplinary Life Science Program, West Lafayette, IN, USA
| | - Smrutiti Jena
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Nicole L. Anderson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Matthew R. Olson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Leopold N. Green
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Douglas K. Brubaker
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- The Blood, Heart, Lung, and Immunology Research Center, Case Western Reserve University, University Hospitals of Cleveland, Cleveland, OH, USA
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41
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Li K, Zhang C, Zhou R, Cheng M, Ling R, Xiong G, Ma J, Zhu Y, Chen S, Chen J, Chen D, Peng L. Single cell analysis unveils B cell-dominated immune subtypes in HNSCC for enhanced prognostic and therapeutic stratification. Int J Oral Sci 2024; 16:29. [PMID: 38622125 PMCID: PMC11018606 DOI: 10.1038/s41368-024-00292-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/17/2024] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is characterized by high recurrence or distant metastases rate and the prognosis is challenging. There is mounting evidence that tumor-infiltrating B cells (TIL-Bs) have a crucial, synergistic role in tumor control. However, little is known about the role TIL-Bs play in immune microenvironment and the way TIL-Bs affect the outcome of immune checkpoint blockade. Using single-cell RNA sequencing (scRNA-seq) data from the Gene Expression Omnibus (GEO) database, the study identified distinct gene expression patterns in TIL-Bs. HNSCC samples were categorized into TIL-Bs inhibition and TIL-Bs activation groups using unsupervised clustering. This classification was further validated with TCGA HNSCC data, correlating with patient prognosis, immune cell infiltration, and response to immunotherapy. We found that the B cells activation group exhibited a better prognosis, higher immune cell infiltration, and distinct immune checkpoint levels, including elevated PD-L1. A prognostic model was also developed and validated, highlighting four genes as potential biomarkers for predicting survival outcomes in HNSCC patients. Overall, this study provides a foundational approach for B cells-based tumor classification in HNSCC, offering insights into targeted treatment and immunotherapy strategies.
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Affiliation(s)
- Kang Li
- State Key Laboratory of Oncology in South China, Department of Oral and Maxillofacial Surgery; Institute of Precision Medicine; Center for Translational Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Caihua Zhang
- State Key Laboratory of Oncology in South China, Department of Oral and Maxillofacial Surgery; Institute of Precision Medicine; Center for Translational Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ruoxing Zhou
- State Key Laboratory of Oncology in South China, Department of Oral and Maxillofacial Surgery; Institute of Precision Medicine; Center for Translational Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Maosheng Cheng
- State Key Laboratory of Oncology in South China, Department of Oral and Maxillofacial Surgery; Institute of Precision Medicine; Center for Translational Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Rongsong Ling
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Gan Xiong
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Jieyi Ma
- State Key Laboratory of Oncology in South China, Department of Oral and Maxillofacial Surgery; Institute of Precision Medicine; Center for Translational Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yan Zhu
- State Key Laboratory of Oncology in South China, Department of Oral and Maxillofacial Surgery; Institute of Precision Medicine; Center for Translational Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shuang Chen
- State Key Laboratory of Oncology in South China, Department of Oral and Maxillofacial Surgery; Institute of Precision Medicine; Center for Translational Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jie Chen
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, China.
| | - Demeng Chen
- State Key Laboratory of Oncology in South China, Department of Oral and Maxillofacial Surgery; Institute of Precision Medicine; Center for Translational Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Liang Peng
- Senior Department of Oncology, The Fifth Medical Center of PLA General Hospital, Beijing, China.
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42
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Shin JH, Park J, Lim J, Jeong J, Dinesh RK, Maher SE, Hong JY, Wysolmerski J, Choi J, Bothwell ALM. Metastasis of colon cancer requires Dickkopf-2 to generate cancer cells with Paneth cell properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589235. [PMID: 38659853 PMCID: PMC11042192 DOI: 10.1101/2024.04.12.589235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Metastasis is the leading cause of cancer-related mortality. Paneth cells provide stem cell niche factors in homeostatic conditions, but the underlying mechanisms of cancer stem cell niche development are unclear. Here we report that Dickkopf-2 (DKK2) is essential for the generation of cancer cells with Paneth cell properties during colon cancer metastasis. Splenic injection of Dkk2-knockout (KO) cancer organoids into C57BL/6 mice resulted in a significant reduction of liver metastases. Transcriptome analysis showed reduction of Paneth cell markers such as lysozymes in KO organoids. Single cell RNA sequencing analyses of murine metastasized colon cancer cells and patient samples identified the presence of lysozyme positive cells with Paneth cell properties including enhanced glycolysis. Further analyses of transcriptome and chromatin accessibility suggested Hepatocyte nuclear factor 4-alpha (HNF4A) as a downstream target of DKK2. Chromatin immunoprecipitation followed by sequencing analysis revealed that HNF4A binds to the promoter region of Sox9, a well-known transcription factor for Paneth cell differentiation. In the liver metastatic foci, DKK2 knockout rescued HNF4A protein levels followed by reduction of lysozyme positive cancer cells. Taken together, DKK2-mediated reduction of HNF4A protein promotes the generation of lysozyme positive cancer cells with Paneth cell properties in the metastasized colon cancers.
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Affiliation(s)
- Jae Hun Shin
- Integrative Science and Engineering Division, Underwood International College, Yonsei University, Incheon 21983, Korea
| | - Jooyoung Park
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Jaechul Lim
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Jaekwang Jeong
- Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520, U.S
| | - Ravi K. Dinesh
- Department of Pathology, Stanford University, Stanford, California 94305, U.S
| | - Stephen E. Maher
- Department of Urology, Yale University School of Medicine, New Haven, Connecticut 06520, U.S
| | - Jun Young Hong
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - John Wysolmerski
- Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520, U.S
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Alfred L. M. Bothwell
- Dept. of Pathology, Microbiology and Immunology, University of Nebraska Medical Center, 505 S. 45 Street., Omaha, NE 68198, U.S
- Dept. of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, U.S
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43
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Lafarge MW, Domingo E, Sirinukunwattana K, Wood R, Samuel L, Murray G, Richman SD, Blake A, Sebag-Montefiore D, Gollins S, Klieser E, Neureiter D, Huemer F, Greil R, Dunne P, Quirke P, Weiss L, Rittscher J, Maughan T, Koelzer VH. Image-based consensus molecular subtyping in rectal cancer biopsies and response to neoadjuvant chemoradiotherapy. NPJ Precis Oncol 2024; 8:89. [PMID: 38594327 PMCID: PMC11003957 DOI: 10.1038/s41698-024-00580-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
The development of deep learning (DL) models to predict the consensus molecular subtypes (CMS) from histopathology images (imCMS) is a promising and cost-effective strategy to support patient stratification. Here, we investigate whether imCMS calls generated from whole slide histopathology images (WSIs) of rectal cancer (RC) pre-treatment biopsies are associated with pathological complete response (pCR) to neoadjuvant long course chemoradiotherapy (LCRT) with single agent fluoropyrimidine. DL models were trained to classify WSIs of colorectal cancers stained with hematoxylin and eosin into one of the four CMS classes using a multi-centric dataset of resection and biopsy specimens (n = 1057 WSIs) with paired transcriptional data. Classifiers were tested on a held out RC biopsy cohort (ARISTOTLE) and correlated with pCR to LCRT in an independent dataset merging two RC cohorts (ARISTOTLE, n = 114 and SALZBURG, n = 55 patients). DL models predicted CMS with high classification performance in multiple comparative analyses. In the independent cohorts (ARISTOTLE, SALZBURG), cases with WSIs classified as imCMS1 had a significantly higher likelihood of achieving pCR (OR = 2.69, 95% CI 1.01-7.17, p = 0.048). Conversely, imCMS4 was associated with lack of pCR (OR = 0.25, 95% CI 0.07-0.88, p = 0.031). Classification maps demonstrated pathologist-interpretable associations with high stromal content in imCMS4 cases, associated with poor outcome. No significant association was found in imCMS2 or imCMS3. imCMS classification of pre-treatment biopsies is a fast and inexpensive solution to identify patient groups that could benefit from neoadjuvant LCRT. The significant associations between imCMS1/imCMS4 with pCR suggest the existence of predictive morphological features that could enhance standard pathological assessment.
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Affiliation(s)
- Maxime W Lafarge
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Enric Domingo
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Korsuk Sirinukunwattana
- Ground Truth Labs, Oxford, UK
- Department of Engineering Science, Institute of Biomedical Engineering (IBME), University of Oxford, Oxford, UK
| | - Ruby Wood
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Leslie Samuel
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Graeme Murray
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Susan D Richman
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Andrew Blake
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | | | - Simon Gollins
- North Wales Cancer Treatment Centre, Besti Cadwaladr University Health Board, Bodelwyddan, UK
| | - Eckhard Klieser
- Institute of Pathology, Paracelsus Medical University, Salzburg, Austria
| | - Daniel Neureiter
- Institute of Pathology, Paracelsus Medical University, Salzburg, Austria
| | - Florian Huemer
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute-Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Richard Greil
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute-Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Philip Dunne
- The Patrick G Johnston Centre for Cancer Research, Queens University Belfast, Belfast, UK
| | - Philip Quirke
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Lukas Weiss
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute-Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Jens Rittscher
- Department of Engineering Science, Institute of Biomedical Engineering (IBME), University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tim Maughan
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Viktor H Koelzer
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
- Department of Oncology and Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.
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44
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Lin K, Chowdhury S, Zeineddine MA, Zeineddine FA, Hornstein NJ, Villarreal OE, Maru DM, Haymaker CL, Vauthey JN, Chang GJ, Bogatenkova E, Menter D, Kopetz S, Shen JP. Identification of Colorectal Cancer Cell Stemness from Single-Cell RNA Sequencing. Mol Cancer Res 2024; 22:337-346. [PMID: 38156967 PMCID: PMC10987274 DOI: 10.1158/1541-7786.mcr-23-0468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/12/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Cancer stem cells (CSC) play a critical role in metastasis, relapse, and therapy resistance in colorectal cancer. While characterization of the normal lineage of cell development in the intestine has led to the identification of many genes involved in the induction and maintenance of pluripotency, recent studies suggest significant heterogeneity in CSC populations. Moreover, while many canonical colorectal cancer CSC marker genes have been identified, the ability to use these classical markers to annotate stemness at the single-cell level is limited. In this study, we performed single-cell RNA sequencing on a cohort of 6 primary colon, 9 liver metastatic tumors, and 11 normal (nontumor) controls to identify colorectal CSCs at the single-cell level. Finding poor alignment of the 11 genes most used to identify colorectal CSC, we instead extracted a single-cell stemness signature (SCS_sig) that robustly identified "gold-standard" colorectal CSCs that expressed all marker genes. Using this SCS_sig to quantify stemness, we found that while normal epithelial cells show a bimodal distribution, indicating distinct stem and differentiated states, in tumor epithelial cells stemness is a continuum, suggesting greater plasticity in these cells. The SCS_sig score was quite variable between different tumors, reflective of the known transcriptomic heterogeneity of CRC. Notably, patients with higher SCS_sig scores had significantly shorter disease-free survival time after curative intent surgical resection, suggesting stemness is associated with relapse. IMPLICATIONS This study reveals significant heterogeneity of expression of genes commonly used to identify colorectal CSCs, and identifies a novel stemness signature to identify these cells from scRNA-seq data.
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Affiliation(s)
- Kangyu Lin
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Saikat Chowdhury
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mohammad A. Zeineddine
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Fadl A. Zeineddine
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Nicholas J. Hornstein
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Oscar E. Villarreal
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dipen M. Maru
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cara L. Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jean-Nicolas Vauthey
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - George J. Chang
- Department of Colon and Rectal Surgery, The University of Texas-MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elena Bogatenkova
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
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45
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Sadien ID, Davies RJ, Wheeler JMD. The genomics of sporadic and hereditary colorectal cancer. Ann R Coll Surg Engl 2024; 106:313-320. [PMID: 38555871 PMCID: PMC10981993 DOI: 10.1308/rcsann.2024.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2024] [Indexed: 04/02/2024] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer deaths worldwide. Over the past three decades, extensive efforts have sought to elucidate the genomic landscape of CRC. These studies reveal that CRC is highly heterogeneous at the molecular level, with different subtypes characterised by distinct somatic mutational profiles, epigenetic aberrations and transcriptomic signatures. This review summarises our current understanding of the genomic and epigenomic alterations implicated in CRC development and progression. Particular focus is given to how characterisation of CRC genomes is leading to more personalised approaches to diagnosis and treatment.
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Affiliation(s)
| | | | - JMD Wheeler
- Cambridge University Hospitals NHS Foundation Trust, UK
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46
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Johnson D, Chee CE, Wong W, Lam RCT, Tan IBH, Ma BBY. Current advances in targeted therapy for metastatic colorectal cancer - Clinical translation and future directions. Cancer Treat Rev 2024; 125:102700. [PMID: 38422896 DOI: 10.1016/j.ctrv.2024.102700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/02/2024]
Abstract
The last two decades have witnessed major breakthroughs in the development of targeted therapy for patients with metastatic colorectal cancer (mCRC), an achievement which stems largely from advances in translational research. Precision medicine is now widely practiced in routine oncological care, where systemic therapy is individualized based on clinical factors such as primary tumor sidedness, location and number of metastases, as well as molecular factors such as the RAS and BRAF mutation status, mismatch repair / microsatellite status and presence of other actionable genomic alterations in the tumor. The optimal selection of patients with RAS and BRAF-wild type (WT), left-sided primary tumor for treatment with epidermal growth factor receptor (EGFR) and chemotherapy (chemo) has markedly improved survival in the first-line setting. The pivotal trials of cetuximab in combination with BRAF/ MEK inhibitor for BRAF V600E mutant mCRC, and panitumumab with KRAS G12C inhibitor in KRAS(G12C)-mutant mCRC have been practice-changing. Anti-HER2 small molecular inhibitor, antibodies and antibody-drug conjugates have significantly improved the treatment outcome of patients with HER2 amplified mCRC. Anti-angiogenesis agents are now used across all lines of treatment and novel combinations with immune-checkpoint inhibitors are under active investigation in MSS mCRC. The non-invasive monitoring of molecular resistance to targeted therapies using Next Generation Sequencing analysis of circulating tumor-derived DNA (ctDNA) and captured sequencing of tumors have improved patient selection for targeted therapies. This review will focus on how latest advances, challenges and future directions in the development of targeted therapies in mCRC.
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Affiliation(s)
- David Johnson
- Department of Clinical Oncology, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region
| | - Cheng Ean Chee
- Department of Hematology-Oncology, National University Cancer Institute, Singapore.
| | - Wesley Wong
- Department of Clinical Oncology, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region
| | - Rachel C T Lam
- Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region.
| | - Iain Bee Huat Tan
- National Cancer Centre Singapore and Duke NUS, Graduate Medical School and Genome Institute of Singapore, Singapore.
| | - Brigette B Y Ma
- State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region.
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Ogasawara N, Kano Y, Yoneyama Y, Kobayashi S, Watanabe S, Kirino S, Velez-Bravo FD, Hong Y, Ostapiuk A, Lutsik P, Onishi I, Yamauchi S, Hiraguri Y, Ito G, Kinugasa Y, Ohashi K, Watanabe M, Okamoto R, Tejpar S, Yui S. Discovery of non-genomic drivers of YAP signaling modulating the cell plasticity in CRC tumor lines. iScience 2024; 27:109247. [PMID: 38439969 PMCID: PMC10910304 DOI: 10.1016/j.isci.2024.109247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 03/06/2024] Open
Abstract
In normal intestines, a fetal/regenerative/revival cell state can be induced upon inflammation. This plasticity in cell fate is also one of the current topics in human colorectal cancer (CRC). To dissect the underlying mechanisms, we generated human CRC organoids with naturally selected genetic mutation profiles and exposed them to two different conditions by modulating the extracellular matrix (ECM). Among tested mutation profiles, a fetal/regenerative/revival state was induced following YAP activation via a collagen type I-enriched microenvironment. Mechanistically, YAP transcription was promoted by activating AP-1 and TEAD-dependent transcription and suppressing intestinal lineage-determining transcription via mechanotransduction. The phenotypic conversion was also involved in chemoresistance, which could be potentially resolved by targeting the underlying YAP regulatory elements, a potential target of CRC treatment.
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Affiliation(s)
- Nobuhiko Ogasawara
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yoshihito Kano
- Department of Clinical Oncology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yosuke Yoneyama
- Institute of Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Sakurako Kobayashi
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Satoshi Watanabe
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Sakura Kirino
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | | | - Yourae Hong
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | | | - Pavlo Lutsik
- Computational Cancer Biology and Epigenomics, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Iichiroh Onishi
- Department of Diagnostic Pathology, Tokyo Medical and Dental University Hospital, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Shinichi Yamauchi
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yui Hiraguri
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Go Ito
- Advanced Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yusuke Kinugasa
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Kenichi Ohashi
- Department of Human Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Mamoru Watanabe
- Advanced Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Ryuichi Okamoto
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Sabine Tejpar
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Shiro Yui
- Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
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48
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Wu Z, Park J, Steiner PR, Zhu B, Zhang JXJ. Generative Adversarial Network Model to Classify Human Induced Pluripotent Stem Cell-Cardiomyocytes based on Maturation Level. RESEARCH SQUARE 2024:rs.3.rs-4061531. [PMID: 38559233 PMCID: PMC10980104 DOI: 10.21203/rs.3.rs-4061531/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Objective Our study develops a generative adversarial network (GAN)-based method that generates faithful synthetic image data of human cardiomyocytes at varying stages in their maturation process, as a tool to significantly enhance the classification accuracy of cells and ultimately assist the throughput of computational analysis of cellular structure and functions. Methods Human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) were cultured on micropatterned collagen coated hydrogels of physiological stiffnesses to facilitate maturation and optical measurements were performed for their structural and functional analyses. Control groups were cultured on collagen coated glass well plates. These image recordings were used as the real data to train the GAN model. Results The results show the GAN approach is able to replicate true features from the real data, and inclusion of such synthetic data significantly improves the classification accuracy compared to usage of only real experimental data that is often limited in scale and diversity. Conclusion The proposed model outperformed four conventional machine learning algorithms with respect to improved data generalization ability and data classification accuracy by incorporating synthetic data. Significance This work demonstrates the importance of integrating synthetic data in situations where there are limited sample sizes and thus, effectively addresses the challenges imposed by data availability.
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Affiliation(s)
- Ziqian Wu
- Thayer School of Engineering, Dartmouth College, Hanover, NH USA
| | - Jiyoon Park
- Thayer School of Engineering, Dartmouth College, Hanover, NH USA
| | | | - Bo Zhu
- Department of Computer Science, Dartmouth College, Hanover, NH USA. He is now with the School of Interactive Computing, Georgia Institute of Technology, GA USA
| | - John X J Zhang
- Thayer School of Engineering, Dartmouth College, Hanover, NH USA
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Liu W, Luo X, Zhang Z, Chen Y, Dai Y, Deng J, Yang C, Liu H. Construction of an immune predictive model and identification of TRIP6 as a prognostic marker and therapeutic target of CRC by integration of single-cell and bulk RNA-seq data. Cancer Immunol Immunother 2024; 73:69. [PMID: 38430268 PMCID: PMC10908634 DOI: 10.1007/s00262-024-03658-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 02/19/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND Investigations elucidating the complex immunological mechanisms involved in colorectal cancer (CRC) and accurately predicting patient outcomes via bulk RNA-Seq analysis have been notably limited. This study aimed to identify the immune status of CRC patients, construct a prognostic model, and identify prognostic signatures via bulk RNA sequencing (RNA-seq) and single-cell RNA-seq (scRNA-seq). METHODS The scRNA-seq data of CRC were downloaded from Gene Expression Omnibus (GEO). The UCSC Xena database was used to obtain bulk RNA-seq data. Differentially expressed gene (DEG), functional enrichment, and random forest analyses were conducted in order to identify core genes associated with colorectal cancer (CRC) that were relevant to prognosis. A molecular immune prediction model was developed using logistic regression after screening features using the least absolute shrinkage and selection operator (LASSO). The differences in immune cell infiltration, mutation, chemotherapeutic drug sensitivity, cellular senescence, and communication between patients who were at high and low risk of CRC according to the predictive model were investigated. The prognostic genes that were closely associated with CRC were identified by random survival forest (RSF) analysis. The expression levels and clinical significance of the hub genes were analyzed in vitro. The LoVo cell line was employed to ascertain the biological role of thyroid hormone receptor-interacting protein 6 (TRIP6). RESULTS A total of seven main cell subtypes were identified by scRNA-seq analysis. A molecular immune predictive model was constructed based on the risk scores. The risk score was significantly associated with OS, stage, mutation burden, immune cell infiltration, response to immunotherapy, key pathways, and cell-cell communication. The functions of the six hub genes were determined and further utilized to establish a regulatory network. Our findings unequivocally confirmed that TRIP6 upregulation was verified in the CRC samples. After knocking down TRIP6, cell proliferation, migration, and invasion of LoVo cells were inhibited, and apoptosis was promoted. CONCLUSIONS The molecular predictive model reliably distinguished the immune status of CRC patients. We further revealed that TRIP6 may act as an oncogene in CRC, making it a promising candidate for targeted therapy and as a prognostic marker for CRC.
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Affiliation(s)
- Wenjun Liu
- The First Department of General Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China
| | - Xitu Luo
- The First Department of General Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China
| | - Zilang Zhang
- Department of Anorectal Surgery, The First People's Hospital of Foshan, Guangdong, 528010, China
| | - Yepeng Chen
- The First Department of General Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China
| | - Yongliang Dai
- The First Department of General Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China
| | - Jianzhong Deng
- Department of Anorectal Surgery, The First People's Hospital of Foshan, Guangdong, 528010, China
| | - Chengyu Yang
- The First Department of General Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China
| | - Hao Liu
- Division of Vascular and Interventional Radiology, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510000, Guangdong, China.
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50
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Malla SB, Byrne RM, Lafarge MW, Corry SM, Fisher NC, Tsantoulis PK, Mills ML, Ridgway RA, Lannagan TRM, Najumudeen AK, Gilroy KL, Amirkhah R, Maguire SL, Mulholland EJ, Belnoue-Davis HL, Grassi E, Viviani M, Rogan E, Redmond KL, Sakhnevych S, McCooey AJ, Bull C, Hoey E, Sinevici N, Hall H, Ahmaderaghi B, Domingo E, Blake A, Richman SD, Isella C, Miller C, Bertotti A, Trusolino L, Loughrey MB, Kerr EM, Tejpar S, Maughan TS, Lawler M, Campbell AD, Leedham SJ, Koelzer VH, Sansom OJ, Dunne PD. Pathway level subtyping identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer. Nat Genet 2024; 56:458-472. [PMID: 38351382 PMCID: PMC10937375 DOI: 10.1038/s41588-024-01654-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/03/2024] [Indexed: 02/29/2024]
Abstract
Molecular stratification using gene-level transcriptional data has identified subtypes with distinctive genotypic and phenotypic traits, as exemplified by the consensus molecular subtypes (CMS) in colorectal cancer (CRC). Here, rather than gene-level data, we make use of gene ontology and biological activation state information for initial molecular class discovery. In doing so, we defined three pathway-derived subtypes (PDS) in CRC: PDS1 tumors, which are canonical/LGR5+ stem-rich, highly proliferative and display good prognosis; PDS2 tumors, which are regenerative/ANXA1+ stem-rich, with elevated stromal and immune tumor microenvironmental lineages; and PDS3 tumors, which represent a previously overlooked slow-cycling subset of tumors within CMS2 with reduced stem populations and increased differentiated lineages, particularly enterocytes and enteroendocrine cells, yet display the worst prognosis in locally advanced disease. These PDS3 phenotypic traits are evident across numerous bulk and single-cell datasets, and demark a series of subtle biological states that are currently under-represented in pre-clinical models and are not identified using existing subtyping classifiers.
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Affiliation(s)
- Sudhir B Malla
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Ryan M Byrne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Maxime W Lafarge
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Shania M Corry
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Natalie C Fisher
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | | | | | | | | | | | - Raheleh Amirkhah
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Sarah L Maguire
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | | | - Elena Grassi
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Marco Viviani
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Emily Rogan
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Keara L Redmond
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Svetlana Sakhnevych
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Aoife J McCooey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Courtney Bull
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Emily Hoey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Nicoleta Sinevici
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Holly Hall
- Cancer Research UK Scotland Institute, Glasgow, UK
| | - Baharak Ahmaderaghi
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, UK
| | - Enric Domingo
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Andrew Blake
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Susan D Richman
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Claudio Isella
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Crispin Miller
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Andrea Bertotti
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Livio Trusolino
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Maurice B Loughrey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Department of Cellular Pathology, Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, UK
| | - Emma M Kerr
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Sabine Tejpar
- Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Timothy S Maughan
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Mark Lawler
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | | | - Viktor H Koelzer
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Owen J Sansom
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Philip D Dunne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK.
- Cancer Research UK Scotland Institute, Glasgow, UK.
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