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Ghobashi AH, Lanzloth R, Ladaika CA, Masood A, O’Hagan HM. Single-Cell Profiling Reveals the Impact of Genetic Alterations on the Differentiation of Inflammation-Induced Murine Colon Tumors. Cancers (Basel) 2024; 16:2040. [PMID: 38893159 PMCID: PMC11171101 DOI: 10.3390/cancers16112040] [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: 04/25/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Genetic mutations and chronic inflammation of the colon contribute to the development of colorectal cancer (CRC). Using a murine model of inflammation-induced colon tumorigenesis, we determined how genetic mutations alter colon tumor cell differentiation. Inflammation induced by enterotoxigenic Bacteroides fragilis (ETBF) colonization of multiple intestinal neoplasia (MinApcΔ716/+) mice triggers loss of heterozygosity of Apc causing colon tumor formation. Here, we report that the addition of BRAFV600E mutation (BRAFF-V600ELgr5tm1(Cre/ERT2)CleMinApcΔ716/+, BLM) or knocking out Msh2 (Msh2LoxP/LoxPVil1-creMinApcΔ716/+, MSH2KO) in the Min model altered colon tumor differentiation. Using single-cell RNA sequencing, we uncovered the differences between BLM, Min, and MSH2KO tumors at a single-cell resolution. BLM tumors showed an increase in differentiated tumor epithelial cell lineages and a reduction in the tumor stem cell population. Interestingly, the tumor stem cell population of BLM tumors had revival colon stem cell characteristics with low WNT signaling and an increase in RevCSC marker gene expression. In contrast, MSH2KO tumors were characterized by an increased tumor stem cell population that had higher WNT signaling activity compared to Min tumors. Furthermore, overall BLM tumors had higher expression of transcription factors that drive differentiation, such as Cdx2, than Min tumors. Using RNA velocity, we identified additional potential regulators of BLM tumor differentiation such as NDRG1. The role of CDX2 and NDRG1 as putative regulators for BLM tumor cell differentiation was verified using organoids derived from BLM tumors. Our results demonstrate the critical connections between genetic mutations and cell differentiation in inflammation-induced colon tumorigenesis. Understanding such roles will deepen our understanding of inflammation-associated colon cancer.
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Affiliation(s)
- Ahmed H. Ghobashi
- Genome, Cell, and Developmental Biology Graduate Program, Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
| | - Rosie Lanzloth
- Genome, Cell, and Developmental Biology Graduate Program, Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Christopher A. Ladaika
- Genome, Cell, and Developmental Biology Graduate Program, Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
| | - Ashiq Masood
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Heather M. O’Hagan
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Normanno N, Caridi V, Fassan M, Avallone A, Ciardiello F, Pinto C. Resistance to immune checkpoint inhibitors in colorectal cancer with deficient mismatch repair/microsatellite instability: misdiagnosis, pseudoprogression and/or tumor heterogeneity? EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2024; 5:495-507. [PMID: 38966168 PMCID: PMC11220308 DOI: 10.37349/etat.2024.00231] [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: 01/09/2024] [Accepted: 03/19/2024] [Indexed: 07/06/2024] Open
Abstract
Colorectal carcinoma (CRC) with deficiency of the deficient mismatch repair (dMMR) pathway/microsatellite instability (MSI) is characterized by a high mutation load and infiltration of immune cells in the tumor microenvironment. In agreement with these findings, clinical trials have demonstrated a significant activity of immune checkpoint inhibitors (ICIs) in dMMR/MSI metastatic CRC (mCRC) patients and, more recently, in CRC patients with early disease undergoing neoadjuvant therapy. However, despite high response rates and durable clinical benefits, a fraction of mCRC patients, up to 30%, showed progressive disease when treated with single agent anti-programmed cell death 1 (PD-1) antibody. This article discusses the three main causes that have been associated with early progression of dMMR/MSI mCRC patients while on treatment with ICIs, i.e., misdiagnosis, pseudoprogression and tumor heterogeneity. While pseudoprogression probably does not play a relevant role, data from clinical studies demonstrate that some dMMR/MSI CRC cases with rapid progression on ICIs may be misdiagnosed, underlining the importance of correct diagnostics. More importantly, evidence suggests that dMMR/MSI mCRC is a heterogeneous group of tumors with different sensitivity to ICIs. Therefore, we propose novel diagnostic and therapeutic strategies to improve the outcome of dMMR/MSI CRC patients.
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Affiliation(s)
- Nicola Normanno
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Vincenza Caridi
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, 35100 Padua, Italy
- Veneto Institute of Oncology, IOV-IRCCS, 35100 Padua, Italy
| | - Antonio Avallone
- Medical Oncology, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Fortunato Ciardiello
- Department of Precision Medicine, The University of Campania Luigi Vanvitelli, 80138 Naples, Italy
| | - Carmine Pinto
- Medical Oncology, Comprehensive Cancer Centre IRCCS-AUSL Reggio Emilia, 42121 Reggio Emilia, Italy
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53
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Li Y, Wu X, Sheng C, Liu H, Liu H, Tang Y, Liu C, Ding Q, Xie B, Xiao X, Zheng R, Yu Q, Guo Z, Ma J, Wang J, Gao J, Tian M, Wang W, Zhou J, Jiang L, Gu M, Shi S, Paull M, Yang G, Yang W, Landau S, Bao X, Hu X, Liu XS, Xiao T. IGSF8 is an innate immune checkpoint and cancer immunotherapy target. Cell 2024; 187:2703-2716.e23. [PMID: 38657602 DOI: 10.1016/j.cell.2024.03.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/18/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
Antigen presentation defects in tumors are prevalent mechanisms of adaptive immune evasion and resistance to cancer immunotherapy, whereas how tumors evade innate immunity is less clear. Using CRISPR screens, we discovered that IGSF8 expressed on tumors suppresses NK cell function by interacting with human KIR3DL2 and mouse Klra9 receptors on NK cells. IGSF8 is normally expressed in neuronal tissues and is not required for cell survival in vitro or in vivo. It is overexpressed and associated with low antigen presentation, low immune infiltration, and worse clinical outcomes in many tumors. An antibody that blocks IGSF8-NK receptor interaction enhances NK cell killing of malignant cells in vitro and upregulates antigen presentation, NK cell-mediated cytotoxicity, and T cell signaling in vivo. In syngeneic tumor models, anti-IGSF8 alone, or in combination with anti-PD1, inhibits tumor growth. Our results indicate that IGSF8 is an innate immune checkpoint that could be exploited as a therapeutic target.
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Affiliation(s)
- Yulong Li
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Xiangyang Wu
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Caibin Sheng
- GV20 Therapeutics LLC, 237 Putnam Avenue, Cambridge, MA 02139, USA
| | - Hailing Liu
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Huizhu Liu
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Yixuan Tang
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Chao Liu
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Qingyang Ding
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Bin Xie
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Xi Xiao
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Rongbin Zheng
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Quan Yu
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Zengdan Guo
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Jian Ma
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Jin Wang
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Jinghong Gao
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Mei Tian
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Wei Wang
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Jia Zhou
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Li Jiang
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Mengmeng Gu
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Sailing Shi
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Michael Paull
- GV20 Therapeutics LLC, 237 Putnam Avenue, Cambridge, MA 02139, USA
| | - Guanhua Yang
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China
| | - Wei Yang
- GV20 Therapeutics LLC, 237 Putnam Avenue, Cambridge, MA 02139, USA
| | - Steve Landau
- GV20 Therapeutics LLC, 237 Putnam Avenue, Cambridge, MA 02139, USA
| | - Xingfeng Bao
- GV20 Therapeutics LLC, 237 Putnam Avenue, Cambridge, MA 02139, USA
| | - Xihao Hu
- GV20 Therapeutics LLC, 237 Putnam Avenue, Cambridge, MA 02139, USA.
| | - X Shirley Liu
- GV20 Therapeutics LLC, 237 Putnam Avenue, Cambridge, MA 02139, USA.
| | - Tengfei Xiao
- Shanghai Xunbaihui Biotechnology Co., Ltd., 3rd floor of Building 4, No. 3728, Jinke Road, Pudong New Area, Shanghai, 201203, China.
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54
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Putro E, Carnevale A, Marangio C, Fulci V, Paolini R, Molfetta R. New Insight into Intestinal Mast Cells Revealed by Single-Cell RNA Sequencing. Int J Mol Sci 2024; 25:5594. [PMID: 38891782 PMCID: PMC11171657 DOI: 10.3390/ijms25115594] [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: 04/04/2024] [Revised: 05/14/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
Mast cells (MCs) are tissue-resident immune cells distributed in all tissues and strategically located close to blood and lymphatic vessels and nerves. Thanks to the expression of a wide array of receptors, MCs act as tissue sentinels, able to detect the presence of bacteria and parasites and to respond to different environmental stimuli. MCs originate from bone marrow (BM) progenitors that enter the circulation and mature in peripheral organs under the influence of microenvironment factors, thus differentiating into heterogeneous tissue-specific subsets. Even though MC activation has been traditionally linked to IgE-mediated allergic reactions, a role for these cells in other pathological conditions including tumor progression has recently emerged. However, several aspects of MC biology remain to be clarified. The advent of single-cell RNA sequencing platforms has provided the opportunity to understand MCs' origin and differentiation as well as their phenotype and functions within different tissues, including the gut. This review recapitulates how single-cell transcriptomic studies provided insight into MC development as well as into the functional role of intestinal MC subsets in health and disease.
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Affiliation(s)
| | | | | | | | - Rossella Paolini
- Department of Molecular Medicine, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (E.P.); (A.C.); (C.M.); (V.F.); (R.M.)
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55
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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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56
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Ryan AT, Kim M, Lim K. Immune Cell Migration to Cancer. Cells 2024; 13:844. [PMID: 38786066 PMCID: PMC11120175 DOI: 10.3390/cells13100844] [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: 03/23/2024] [Revised: 04/27/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Immune cell migration is required for the development of an effective and robust immune response. This elegant process is regulated by both cellular and environmental factors, with variables such as immune cell state, anatomical location, and disease state that govern differences in migration patterns. In all cases, a major factor is the expression of cell surface receptors and their cognate ligands. Rapid adaptation to environmental conditions partly depends on intrinsic cellular immune factors that affect a cell's ability to adjust to new environment. In this review, we discuss both myeloid and lymphoid cells and outline key determinants that govern immune cell migration, including molecules required for immune cell adhesion, modes of migration, chemotaxis, and specific chemokine signaling. Furthermore, we summarize tumor-specific elements that contribute to immune cell trafficking to cancer, while also exploring microenvironment factors that can alter these cellular dynamics within the tumor in both a pro and antitumor fashion. Specifically, we highlight the importance of the secretome in these later aspects. This review considers a myriad of factors that impact immune cell trajectory in cancer. We aim to highlight the immunotherapeutic targets that can be harnessed to achieve controlled immune trafficking to and within tumors.
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Affiliation(s)
- Allison T. Ryan
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA; (A.T.R.); (M.K.)
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, NY 14642, USA
| | - Minsoo Kim
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA; (A.T.R.); (M.K.)
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, NY 14642, USA
| | - Kihong Lim
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA; (A.T.R.); (M.K.)
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, NY 14642, USA
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57
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Ma J, Wu Y, Ma L, Yang X, Zhang T, Song G, Li T, Gao K, Shen X, Lin J, Chen Y, Liu X, Fu Y, Gu X, Chen Z, Jiang S, Rao D, Pan J, Zhang S, Zhou J, Huang C, Shi S, Fan J, Guo G, Zhang X, Gao Q. A blueprint for tumor-infiltrating B cells across human cancers. Science 2024; 384:eadj4857. [PMID: 38696569 DOI: 10.1126/science.adj4857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 03/06/2024] [Indexed: 05/04/2024]
Abstract
B lymphocytes are essential mediators of humoral immunity and play multiple roles in human cancer. To decode the functions of tumor-infiltrating B cells, we generated a B cell blueprint encompassing single-cell transcriptome, B cell-receptor repertoire, and chromatin accessibility data across 20 different cancer types (477 samples, 269 patients). B cells harbored extraordinary heterogeneity and comprised 15 subsets, which could be grouped into two independent developmental paths (extrafollicular versus germinal center). Tumor types grouped into the extrafollicular pathway were linked with worse clinical outcomes and resistance to immunotherapy. The dysfunctional extrafollicular program was associated with glutamine-derived metabolites through epigenetic-metabolic cross-talk, which promoted a T cell-driven immunosuppressive program. These data suggest an intratumor B cell balance between extrafollicular and germinal-center responses and suggest that humoral immunity could possibly be harnessed for B cell-targeting immunotherapy.
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Affiliation(s)
- Jiaqiang Ma
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yingcheng Wu
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lifeng Ma
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Xupeng Yang
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Tiancheng Zhang
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Guohe Song
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Teng Li
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ke Gao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xia Shen
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian Lin
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yamin Chen
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoshan Liu
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuting Fu
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Xixi Gu
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zechuan Chen
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shan Jiang
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dongning Rao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiaomeng Pan
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shu Zhang
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chen Huang
- Department of Gastrointestinal Surgery, Shanghai General Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200080, China
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiaoming Zhang
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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Tian J, Ashique AM, Weeks S, Lan T, Yang H, Chen HIH, Song C, Koyano K, Mondal K, Tsai D, Cheung I, Moshrefi M, Kekatpure A, Fan B, Li B, Qurashi S, Rocha L, Aguayo J, Rodgers C, Meza M, Heeke D, Medfisch SM, Chu C, Starck S, Basak NP, Sankaran S, Malhotra M, Crawley S, Tran TT, Duey DY, Ho C, Mikaelian I, Liu W, Rivera LB, Huang J, Paavola KJ, O'Hollaren K, Blum LK, Lin VY, Chen P, Iyer A, He S, Roda JM, Wang Y, Sissons J, Kutach AK, Kaplan DD, Stone GW. ILT2 and ILT4 Drive Myeloid Suppression via Both Overlapping and Distinct Mechanisms. Cancer Immunol Res 2024; 12:592-613. [PMID: 38393969 DOI: 10.1158/2326-6066.cir-23-0568] [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: 07/16/2023] [Revised: 10/28/2023] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
Solid tumors are dense three-dimensional (3D) multicellular structures that enable efficient receptor-ligand trans interactions via close cell-cell contact. Immunoglobulin-like transcript (ILT)2 and ILT4 are related immune-suppressive receptors that play a role in the inhibition of myeloid cells within the tumor microenvironment. The relative contribution of ILT2 and ILT4 to immune inhibition in the context of solid tumor tissue has not been fully explored. We present evidence that both ILT2 and ILT4 contribute to myeloid inhibition. We found that although ILT2 inhibits myeloid cell activation in the context of trans-engagement by MHC-I, ILT4 efficiently inhibits myeloid cells in the presence of either cis- or trans-engagement. In a 3D spheroid tumor model, dual ILT2/ILT4 blockade was required for the optimal activation of myeloid cells, including the secretion of CXCL9 and CCL5, upregulation of CD86 on dendritic cells, and downregulation of CD163 on macrophages. Humanized mouse tumor models showed increased immune activation and cytolytic T-cell activity with combined ILT2 and ILT4 blockade, including evidence of the generation of immune niches, which have been shown to correlate with clinical response to immune-checkpoint blockade. In a human tumor explant histoculture system, dual ILT2/ILT4 blockade increased CXCL9 secretion, downregulated CD163 expression, and increased the expression of M1 macrophage, IFNγ, and cytolytic T-cell gene signatures. Thus, we have revealed distinct contributions of ILT2 and ILT4 to myeloid cell biology and provide proof-of-concept data supporting the combined blockade of ILT2 and ILT4 to therapeutically induce optimal myeloid cell reprogramming in the tumor microenvironment.
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Affiliation(s)
- Jane Tian
- NGM Biopharmaceuticals, South San Francisco, California
| | | | - Sabrina Weeks
- NGM Biopharmaceuticals, South San Francisco, California
| | - Tian Lan
- NGM Biopharmaceuticals, South San Francisco, California
| | - Hong Yang
- NGM Biopharmaceuticals, South San Francisco, California
| | | | | | - Kikuye Koyano
- NGM Biopharmaceuticals, South San Francisco, California
| | | | - Daniel Tsai
- NGM Biopharmaceuticals, South San Francisco, California
| | - Isla Cheung
- NGM Biopharmaceuticals, South San Francisco, California
| | | | | | - Bin Fan
- NGM Biopharmaceuticals, South San Francisco, California
| | - Betty Li
- NGM Biopharmaceuticals, South San Francisco, California
| | - Samir Qurashi
- NGM Biopharmaceuticals, South San Francisco, California
| | - Lauren Rocha
- NGM Biopharmaceuticals, South San Francisco, California
| | | | - Col Rodgers
- NGM Biopharmaceuticals, South San Francisco, California
| | | | - Darren Heeke
- NGM Biopharmaceuticals, South San Francisco, California
| | | | - Chun Chu
- NGM Biopharmaceuticals, South San Francisco, California
| | | | | | | | | | | | | | - Dana Y Duey
- NGM Biopharmaceuticals, South San Francisco, California
| | - Carmence Ho
- NGM Biopharmaceuticals, South San Francisco, California
| | | | - Wenhui Liu
- NGM Biopharmaceuticals, South San Francisco, California
| | - Lee B Rivera
- NGM Biopharmaceuticals, South San Francisco, California
| | - Jiawei Huang
- NGM Biopharmaceuticals, South San Francisco, California
| | | | | | - Lisa K Blum
- NGM Biopharmaceuticals, South San Francisco, California
| | - Vicky Y Lin
- NGM Biopharmaceuticals, South San Francisco, California
| | - Peirong Chen
- NGM Biopharmaceuticals, South San Francisco, California
| | | | - Sisi He
- NGM Biopharmaceuticals, South San Francisco, California
| | - Julie M Roda
- NGM Biopharmaceuticals, South San Francisco, California
| | - Yan Wang
- NGM Biopharmaceuticals, South San Francisco, California
| | - James Sissons
- NGM Biopharmaceuticals, South San Francisco, California
| | - Alan K Kutach
- NGM Biopharmaceuticals, South San Francisco, California
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59
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Hisano K, Mizuuchi Y, Ohuchida K, Kawata J, Torata N, Zhang J, Katayama N, Tsutsumi C, Nakamura S, Okuda S, Otsubo Y, Tamura K, Nagayoshi K, Ikenaga N, Shindo K, Nakata K, Oda Y, Nakamura M. Microenvironmental changes in familial adenomatous polyposis during colorectal cancer carcinogenesis. Cancer Lett 2024; 589:216822. [PMID: 38521200 DOI: 10.1016/j.canlet.2024.216822] [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: 12/18/2023] [Revised: 02/28/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024]
Abstract
Familial adenomatous polyposis (FAP) is a heritable disease that increases the risk of colorectal cancer (CRC) development because of heterozygous mutations in APC. Little is known about the microenvironment of FAP. Here, single-cell RNA sequencing was performed on matched normal tissues, adenomas, and carcinomas from four patients with FAP. We analyzed the transcriptomes of 56,225 unsorted single cells, revealing the heterogeneity of each cell type, and compared gene expression among tissues. Then we compared the gene expression with that of sporadic CRC. Furthermore, we analyzed specimens of 26 FAP patients and 40 sporadic CRC patients by immunohistochemistry. Immunosuppressiveness of myeloid cells, fibroblasts, and regulatory T cells was upregulated even in the early stages of carcinogenesis. CD8+ T cells became exhausted only in carcinoma, although the cytotoxicity of CD8+ T cells was gradually increased according to the carcinogenic step. When compared with those in the sporadic CRC microenvironment, the composition and function of each cell type in the FAP-derived CRC microenvironment had differences. Our findings indicate that an immunosuppressive microenvironment is constructed from a precancerous stage in FAP.
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Affiliation(s)
- Kyoko Hisano
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yusuke Mizuuchi
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Kenoki Ohuchida
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Advanced Medical Initiatives, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Jun Kawata
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Anatomical Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Nobuhiro Torata
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jinghui Zhang
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naoki Katayama
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Chikanori Tsutsumi
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shoichi Nakamura
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Sho Okuda
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshiki Otsubo
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koji Tamura
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kinuko Nagayoshi
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naoki Ikenaga
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koji Shindo
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kohei Nakata
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshinao Oda
- Department of Anatomical Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masafumi Nakamura
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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60
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Xu J, Guo P, Hao S, Shangguan S, Shi Q, Volpe G, Huang K, Zuo J, An J, Yuan Y, Cheng M, Deng Q, Zhang X, Lai G, Nan H, Wu B, Shentu X, Wu L, Wei X, Jiang Y, Huang X, Pan F, Song Y, Li R, Wang Z, Liu C, Liu S, Li Y, Yang T, Xu Z, Du W, Li L, Ahmed T, You K, Dai Z, Li L, Qin B, Li Y, Lai L, Qin D, Chen J, Fan R, Li Y, Hou J, Ott M, Sharma AD, Cantz T, Schambach A, Kristiansen K, Hutchins AP, Göttgens B, Maxwell PH, Hui L, Xu X, Liu L, Chen A, Lai Y, Esteban MA. A spatiotemporal atlas of mouse liver homeostasis and regeneration. Nat Genet 2024; 56:953-969. [PMID: 38627598 DOI: 10.1038/s41588-024-01709-7] [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: 01/08/2023] [Accepted: 03/06/2024] [Indexed: 05/09/2024]
Abstract
The mechanism by which mammalian liver cell responses are coordinated during tissue homeostasis and perturbation is poorly understood, representing a major obstacle in our understanding of many diseases. This knowledge gap is caused by the difficulty involved with studying multiple cell types in different states and locations, particularly when these are transient. We have combined Stereo-seq (spatiotemporal enhanced resolution omics-sequencing) with single-cell transcriptomic profiling of 473,290 cells to generate a high-definition spatiotemporal atlas of mouse liver homeostasis and regeneration at the whole-lobe scale. Our integrative study dissects in detail the molecular gradients controlling liver cell function, systematically defining how gene networks are dynamically modulated through intercellular communication to promote regeneration. Among other important regulators, we identified the transcriptional cofactor TBL1XR1 as a rheostat linking inflammation to Wnt/β-catenin signaling for facilitating hepatocyte proliferation. Our data and analytical pipelines lay the foundation for future high-definition tissue-scale atlases of organ physiology and malfunction.
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Affiliation(s)
- Jiangshan Xu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Pengcheng Guo
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China.
- 3DC STAR, Spatiotemporal Campus at BGI Shenzhen, Shenzhen, China.
| | - Shijie Hao
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuncheng Shangguan
- BGI Research, Shenzhen, China
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou, China
| | - Quan Shi
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Giacomo Volpe
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Keke Huang
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jing Zuo
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Juan An
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yue Yuan
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Mengnan Cheng
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Qiuting Deng
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Guangyao Lai
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Haitao Nan
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Baihua Wu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xinyi Shentu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Liang Wu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoyu Wei
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Yujia Jiang
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Xin Huang
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fengyu Pan
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Yumo Song
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Ronghai Li
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Zhifeng Wang
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Chuanyu Liu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China
| | - Shiping Liu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | | | - Tao Yang
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Provincial Genomics Data Center, BGI Research, Shenzhen, China
| | - Zhicheng Xu
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Provincial Genomics Data Center, BGI Research, Shenzhen, China
| | - Wensi Du
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Provincial Genomics Data Center, BGI Research, Shenzhen, China
| | - Ling Li
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Provincial Genomics Data Center, BGI Research, Shenzhen, China
| | - Tanveer Ahmed
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Kai You
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhen Dai
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Li Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Baoming Qin
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yinxiong Li
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Liangxue Lai
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Dajiang Qin
- The Fifth Affiliated Hospital of Guangzhou Medical University-BGI Research Center for Integrative Biology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Junling Chen
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China
| | - Rong Fan
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China
| | - Yongyin Li
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China
| | - Jinlin Hou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China
| | - Michael Ott
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Amar Deep Sharma
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Tobias Cantz
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | | | - Andrew P Hutchins
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Berthold Göttgens
- Department of Haematology and Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Patrick H Maxwell
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Lijian Hui
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xun Xu
- BGI Research, Hangzhou, China.
- BGI Research, Shenzhen, China.
- BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China.
| | - Longqi Liu
- BGI Research, Hangzhou, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China.
| | - Ao Chen
- BGI Research, Shenzhen, China.
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- BGI Research, Chongqing, China.
- JFL-BGI STOmics Center, BGI-Shenzhen, Chongqing, China.
| | - Yiwei Lai
- BGI Research, Hangzhou, China.
- BGI Research, Shenzhen, China.
- 3DC STAR, Spatiotemporal Campus at BGI Shenzhen, Shenzhen, China.
- BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China.
| | - Miguel A Esteban
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China.
- 3DC STAR, Spatiotemporal Campus at BGI Shenzhen, Shenzhen, China.
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- The Fifth Affiliated Hospital of Guangzhou Medical University-BGI Research Center for Integrative Biology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.
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61
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Liu S, Liu Y, Qiu X, Suhail Y, Kshitiz. Tissue-of-origin for cancers determines HIF-1 activation induced phenotypic heterogeneity. Mol Carcinog 2024; 63:834-848. [PMID: 38372346 PMCID: PMC11013563 DOI: 10.1002/mc.23691] [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: 10/21/2023] [Revised: 01/02/2024] [Accepted: 01/16/2024] [Indexed: 02/20/2024]
Abstract
Hypoxia-inducible factor-1 (HIF-1) is the master regulator of cellular response to hypoxia, and is activated in many cancers contributing to many steps in the metastatic cascade by acting as a key transcription co-regulator for a large number of downstream genes. Presence of hypoxia within a tumor is spatially nonuniform, and can also by dynamic. Further, although HIF-1 is primarily stabilized and activated by lack of molecular O2, its stability is also affected by other factors present in the tumor microenvironment. HIF-1 also crosstalks with other transcription factors in co-regulating gene expression. Consequently, it is nontrivial to predict the gene expression patterns in cells in response to hypoxia, or HIF-1 activation. Additionally, cancers originating from tissue origins with different basal level of partial oxygen tension may activate HIF-1 at different threshold of hypoxia. We analyzed large published single cell RNAseq data for colorectal, lung, and pancreatic cancers to investigate the phenotypic outcome of HIF-1 activation in cancer cells. We found that cancers from tissues with different partial O2 tension levels exhibit HIF-1 activation at different stages of metastasis, and phenotypically respond differently to HIF-1 activation, likely by contextual co-option of different transcription factors. We experimentally confirmed these predictions by using cell lines representative of colorectal, lung, and pancreatic cancers, finding that while hypoxia enhances growth of colorectal cancer, it induces increased invasion of lung, and pancreatic cancers. Our analysis suggest that HIF-1 activation may act as a rheostat regulating downstream gene expression towards phenotypic outcomes differently in various cancers.
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Affiliation(s)
- Shaofei Liu
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, Connecticut, USA
| | - Yamin Liu
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, Connecticut, USA
| | - Xihua Qiu
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, Connecticut, USA
| | - Yasir Suhail
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, Connecticut, USA
| | - Kshitiz
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, Connecticut, USA
- Center for Cell Analysis and Modeling, University of Connecticut Health, Farmington, Connecticut, USA
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62
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An M, Mehta A, Min BH, Heo YJ, Wright SJ, Parikh M, Bi L, Lee H, Kim TJ, Lee SY, Moon J, Park RJ, Strickland MR, Park WY, Kang WK, Kim KM, Kim ST, Klempner SJ, Lee J. Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer. Cancer Discov 2024; 14:766-785. [PMID: 38319303 PMCID: PMC11061611 DOI: 10.1158/2159-8290.cd-23-0857] [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: 08/01/2023] [Revised: 11/28/2023] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Adding anti-programmed cell death protein 1 (anti-PD-1) to 5-fluorouracil (5-FU)/platinum improves survival in some advanced gastroesophageal adenocarcinomas (GEA). To understand the effects of chemotherapy and immunotherapy, we conducted a phase II first-line trial (n = 47) sequentially adding pembrolizumab to 5-FU/platinum in advanced GEA. Using serial biopsy of the primary tumor at baseline, after one cycle of 5-FU/platinum, and after the addition of pembrolizumab, we transcriptionally profiled 358,067 single cells to identify evolving multicellular tumor microenvironment (TME) networks. Chemotherapy induced early on-treatment multicellular hubs with tumor-reactive T-cell and M1-like macrophage interactions in slow progressors. Faster progression featured increased MUC5A and MSLN containing treatment resistance programs in tumor cells and M2-like macrophages with immunosuppressive stromal interactions. After pembrolizumab, we observed increased CD8 T-cell infiltration and development of an immunity hub involving tumor-reactive CXCL13 T-cell program and epithelial interferon-stimulated gene programs. Strategies to drive increases in antitumor immune hub formation could expand the portion of patients benefiting from anti-PD-1 approaches. SIGNIFICANCE The benefit of 5-FU/platinum with anti-PD-1 in first-line advanced gastric cancer is limited to patient subgroups. Using a trial with sequential anti-PD-1, we show coordinated induction of multicellular TME hubs informs the ability of anti-PD-1 to potentiate T cell-driven responses. Differential TME hub development highlights features that underlie clinical outcomes. This article is featured in Selected Articles from This Issue, p. 695.
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Affiliation(s)
- Minae An
- Experimental Therapeutics Development Center, Samsung Medical Center, Seoul, Korea
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Arnav Mehta
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Byung Hoon Min
- Department of Medicine, Division of Gastroenterology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Samuel J. Wright
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Milan Parikh
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Lynn Bi
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Hyuk Lee
- Department of Medicine, Division of Gastroenterology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae Jun Kim
- Department of Medicine, Division of Gastroenterology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Song-Yi Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeonghyeon Moon
- Departments of Neurology and Immunology, Yale School of Medicine, New Haven, Connecticut
| | - Ryan J. Park
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Division of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Matthew R. Strickland
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | | | - Won Ki Kang
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Samuel J. Klempner
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Muyas F, Sauer CM, Valle-Inclán JE, Li R, Rahbari R, Mitchell TJ, Hormoz S, Cortés-Ciriano I. De novo detection of somatic mutations in high-throughput single-cell profiling data sets. Nat Biotechnol 2024; 42:758-767. [PMID: 37414936 PMCID: PMC11098751 DOI: 10.1038/s41587-023-01863-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/07/2023] [Indexed: 07/08/2023]
Abstract
Characterization of somatic mutations at single-cell resolution is essential to study cancer evolution, clonal mosaicism and cell plasticity. Here, we describe SComatic, an algorithm designed for the detection of somatic mutations in single-cell transcriptomic and ATAC-seq (assay for transposase-accessible chromatin sequence) data sets directly without requiring matched bulk or single-cell DNA sequencing data. SComatic distinguishes somatic mutations from polymorphisms, RNA-editing events and artefacts using filters and statistical tests parameterized on non-neoplastic samples. Using >2.6 million single cells from 688 single-cell RNA-seq (scRNA-seq) and single-cell ATAC-seq (scATAC-seq) data sets spanning cancer and non-neoplastic samples, we show that SComatic detects mutations in single cells accurately, even in differentiated cells from polyclonal tissues that are not amenable to mutation detection using existing methods. Validated against matched genome sequencing and scRNA-seq data, SComatic achieves F1 scores between 0.6 and 0.7 across diverse data sets, in comparison to 0.2-0.4 for the second-best performing method. In summary, SComatic permits de novo mutational signature analysis, and the study of clonal heterogeneity and mutational burdens at single-cell resolution.
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Affiliation(s)
- Francesc Muyas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Carolin M Sauer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Jose Espejo Valle-Inclán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Ruoyan Li
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Raheleh Rahbari
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Thomas J Mitchell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Sahand Hormoz
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.
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Thomas MF, Slowikowski K, Manakongtreecheep K, Sen P, Samanta N, Tantivit J, Nasrallah M, Zubiri L, Smith NP, Tirard A, Ramesh S, Arnold BY, Nieman LT, Chen JH, Eisenhaure T, Pelka K, Song Y, Xu KH, Jorgji V, Pinto CJ, Sharova T, Glasser R, Chan P, Sullivan RJ, Khalili H, Juric D, Boland GM, Dougan M, Hacohen N, Li B, Reynolds KL, Villani AC. Single-cell transcriptomic analyses reveal distinct immune cell contributions to epithelial barrier dysfunction in checkpoint inhibitor colitis. Nat Med 2024; 30:1349-1362. [PMID: 38724705 DOI: 10.1038/s41591-024-02895-x] [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: 06/06/2022] [Accepted: 03/01/2024] [Indexed: 05/23/2024]
Abstract
Immune checkpoint inhibitor (ICI) therapy has revolutionized oncology, but treatments are limited by immune-related adverse events, including checkpoint inhibitor colitis (irColitis). Little is understood about the pathogenic mechanisms driving irColitis, which does not readily occur in model organisms, such as mice. To define molecular drivers of irColitis, we used single-cell multi-omics to profile approximately 300,000 cells from the colon mucosa and blood of 13 patients with cancer who developed irColitis (nine on anti-PD-1 or anti-CTLA-4 monotherapy and four on dual ICI therapy; most patients had skin or lung cancer), eight controls on ICI therapy and eight healthy controls. Patients with irColitis showed expanded mucosal Tregs, ITGAEHi CD8 tissue-resident memory T cells expressing CXCL13 and Th17 gene programs and recirculating ITGB2Hi CD8 T cells. Cytotoxic GNLYHi CD4 T cells, recirculating ITGB2Hi CD8 T cells and endothelial cells expressing hypoxia gene programs were further expanded in colitis associated with anti-PD-1/CTLA-4 therapy compared to anti-PD-1 therapy. Luminal epithelial cells in patients with irColitis expressed PCSK9, PD-L1 and interferon-induced signatures associated with apoptosis, increased cell turnover and malabsorption. Together, these data suggest roles for circulating T cells and epithelial-immune crosstalk critical to PD-1/CTLA-4-dependent tolerance and barrier function and identify potential therapeutic targets for irColitis.
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Affiliation(s)
- Molly Fisher Thomas
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Division of Gastroenterology, Department of Medicine, Oregon Health and Sciences University, Portland, OR, USA.
- Department of Cell, Developmental, and Cancer Biology, Oregon Health and Sciences University, Portland, OR, USA.
| | - Kamil Slowikowski
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Kasidet Manakongtreecheep
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Pritha Sen
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Transplant, Oncology, and Immunocompromised Host Group, Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nandini Samanta
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Jessica Tantivit
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Mazen Nasrallah
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Department of Medicine, North Shore Physicians Group, Mass General Brigham Healthcare Center, Lynn, MA, USA
| | - Leyre Zubiri
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Neal P Smith
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Alice Tirard
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Swetha Ramesh
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Benjamin Y Arnold
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Linda T Nieman
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jonathan H Chen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas Eisenhaure
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Karin Pelka
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Yuhui Song
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Katherine H Xu
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Vjola Jorgji
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Tatyana Sharova
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Rachel Glasser
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - PuiYee Chan
- Harvard Medical School, Boston, MA, USA
- Clinical Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Ryan J Sullivan
- Harvard Medical School, Boston, MA, USA
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Hamed Khalili
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Dejan Juric
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Genevieve M Boland
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Dougan
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nir Hacohen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bo Li
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Kerry L Reynolds
- Harvard Medical School, Boston, MA, USA
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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Zhai X, Chen B, Hu H, Deng Y, Chen Y, Hong Y, Ren X, Jiang C. Identification of the molecular subtypes and signatures to predict the prognosis, biological functions, and therapeutic response based on the anoikis-related genes in colorectal cancer. Cancer Med 2024; 13:e7315. [PMID: 38785271 PMCID: PMC11117457 DOI: 10.1002/cam4.7315] [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: 08/28/2023] [Revised: 04/25/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Tumors that resist anoikis, a programmed cell death triggered by detachment from the extracellular matrix, promote metastasis; however, the role of anoikis-related genes (ARGs) in colorectal cancer (CRC) stratification, prognosis, and biological functions remains unclear. METHODS We obtained transcriptomic profiles of CRC and 27 ARGs from The Cancer Genome Atlas, the Gene Expression Omnibus, and MSigDB databases, respectively. CRC tissue samples were classified into two clusters based on the expression pattern of ARGs, and their functional differences were explored. Hub genes were screened using weighted gene co-expression network analysis, univariate analysis, and least absolute selection and shrinkage operator analysis, and validated in cell lines, tissues, or the Human Protein Atlas database. We constructed an ARG-risk model and nomogram to predict prognosis in patients with CRC, which was validated using an external cohort. Multifaceted landscapes, including stemness, tumor microenvironment (TME), immune landscape, and drug sensitivity, between high- and low-risk groups were examined. RESULTS Patients with CRC were divided into C1 and C2 clusters. Cluster C1 exhibited higher TME scores, whereas cluster C2 had favorable outcomes and a higher stemness index. Eight upregulated hub ARGs (TIMP1, P3H1, SPP1, HAMP, IFI30, ADAM8, ITGAX, and APOC1) were utilized to construct the risk model. The qRT-PCR, Western blotting, and immunohistochemistry results were consistent with those of the bioinformatics analysis. Patients with high risk exhibited worse overall survival (p < 0.01), increased stemness, TME, immune checkpoint expression, immune infiltration, tumor mutation burden, and drug susceptibility compared with the patients with low risk. CONCLUSION Our results offer a novel CRC stratification based on ARGs and a risk-scoring system that could predict the prognosis, stemness, TME, immunophenotypes, and drug susceptibility of patients with CRC, thereby improving their prognosis. This stratification may facilitate personalized therapies.
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Affiliation(s)
- Xiang Zhai
- Department of Colorectal and Anal SurgeryZhongnan Hospital of Wuhan UniversityWuhanChina
- Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University)WuhanChina
- Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University)WuhanChina
| | - Baoxiang Chen
- Department of Colorectal and Anal SurgeryZhongnan Hospital of Wuhan UniversityWuhanChina
- Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University)WuhanChina
- Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University)WuhanChina
| | - Heng Hu
- Department of Colorectal and Anal SurgeryZhongnan Hospital of Wuhan UniversityWuhanChina
- Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University)WuhanChina
- Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University)WuhanChina
| | - Yanrong Deng
- Department of Colorectal and Anal SurgeryZhongnan Hospital of Wuhan UniversityWuhanChina
- Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University)WuhanChina
- Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University)WuhanChina
| | - Yazhu Chen
- West China Hospital of Sichuan universityChengduChina
| | - Yuntian Hong
- Department of Colorectal and Anal SurgeryZhongnan Hospital of Wuhan UniversityWuhanChina
- Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University)WuhanChina
- Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University)WuhanChina
| | - Xianghai Ren
- Department of Colorectal and Anal SurgeryZhongnan Hospital of Wuhan UniversityWuhanChina
- Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University)WuhanChina
- Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University)WuhanChina
| | - Congqing Jiang
- Department of Colorectal and Anal SurgeryZhongnan Hospital of Wuhan UniversityWuhanChina
- Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University)WuhanChina
- Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University)WuhanChina
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Domblides C, Crampton S, Liu H, Bartleson JM, Nguyen A, Champagne C, Landy EE, Spiker L, Proffitt C, Bhattarai S, Grawe AP, Fuentealba Valenzuela M, Lartigue L, Mahouche I, Dupaul-Chicoine J, Nishimura K, Lefort F, Decraecker M, Velasco V, Netzer S, Pitard V, Roy C, Soubeyran I, Racine V, Blanco P, Déchanet-Merville J, Saleh M, Canna SW, Furman D, Faustin B. Human NLRC4 expression promotes cancer survival and associates with type I interferon signaling and immune infiltration. J Clin Invest 2024; 134:e166085. [PMID: 38652550 PMCID: PMC11142746 DOI: 10.1172/jci166085] [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: 10/10/2022] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
The immune system can control cancer progression. However, even though some innate immune sensors of cellular stress are expressed intrinsically in epithelial cells, their potential role in cancer aggressiveness and subsequent overall survival in humans is mainly unknown. Here, we show that nucleotide-binding oligomerization domain-like receptor (NLR) family CARD domain-containing 4 (NLRC4) is downregulated in epithelial tumor cells of patients with colorectal cancer (CRC) by using spatial tissue imaging. Strikingly, only the loss of tumor NLRC4, but not stromal NLRC4, was associated with poor immune infiltration (mainly DCs and CD4+ and CD8+ T cells) and accurately predicted progression to metastatic stage IV and decrease in overall survival. By combining multiomics approaches, we show that restoring NLRC4 expression in human CRC cells triggered a broad inflammasome-independent immune reprogramming consisting of type I interferon (IFN) signaling genes and the release of chemokines and myeloid growth factors involved in the tumor infiltration and activation of DCs and T cells. Consistently, such reprogramming in cancer cells was sufficient to directly induce maturation of human DCs toward a Th1 antitumor immune response through IL-12 production in vitro. In multiple human carcinomas (colorectal, lung, and skin), we confirmed that NLRC4 expression in patient tumors was strongly associated with type I IFN genes, immune infiltrates, and high microsatellite instability. Thus, we shed light on the epithelial innate immune sensor NLRC4 as a therapeutic target to promote an efficient antitumor immune response against the aggressiveness of various carcinomas.
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Affiliation(s)
- Charlotte Domblides
- University of Bordeaux, Bordeaux, France
- ImmunoConcEpt, CNRS UMR 5164, INSERM ERL 1303, Bordeaux University, Bordeaux, France
- Department of Medical Oncology, University Hospital of Bordeaux, Bordeaux, France
| | - Steven Crampton
- Discovery Immunology, Johnson & Johnson Innovative Medicine, San Diego, California, USA
| | - Hong Liu
- GI and Immune-Oncology DDUs, Takeda Pharmaceuticals, San Diego, California, and Cambridge, Massachusetts, USA
| | | | - Annie Nguyen
- Discovery Immunology, Johnson & Johnson Innovative Medicine, San Diego, California, USA
| | | | - Emily E. Landy
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lindsey Spiker
- Department of Genetics, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Christopher Proffitt
- GI and Immune-Oncology DDUs, Takeda Pharmaceuticals, San Diego, California, and Cambridge, Massachusetts, USA
| | - Sunil Bhattarai
- Discovery Immunology, Johnson & Johnson Innovative Medicine, San Diego, California, USA
| | - Anissa P. Grawe
- Buck Institute for Research on Aging, Novato, California, USA
| | | | | | | | | | - Kazuho Nishimura
- GI and Immune-Oncology DDUs, Takeda Pharmaceuticals, San Diego, California, and Cambridge, Massachusetts, USA
| | - Félix Lefort
- ImmunoConcEpt, CNRS UMR 5164, INSERM ERL 1303, Bordeaux University, Bordeaux, France
- Department of Medical Oncology, University Hospital of Bordeaux, Bordeaux, France
| | - Marie Decraecker
- ImmunoConcEpt, CNRS UMR 5164, INSERM ERL 1303, Bordeaux University, Bordeaux, France
| | - Valérie Velasco
- Comprehensive Cancer Center, Department of Biopathology, Institut Bergonié, Bordeaux, France
| | - Sonia Netzer
- University of Bordeaux, Bordeaux, France
- ImmunoConcEpt, CNRS UMR 5164, INSERM ERL 1303, Bordeaux University, Bordeaux, France
| | - Vincent Pitard
- University of Bordeaux, Bordeaux, France
- ImmunoConcEpt, CNRS UMR 5164, INSERM ERL 1303, Bordeaux University, Bordeaux, France
| | - Christian Roy
- GI and Immune-Oncology DDUs, Takeda Pharmaceuticals, San Diego, California, and Cambridge, Massachusetts, USA
| | - Isabelle Soubeyran
- Comprehensive Cancer Center, Department of Biopathology, Institut Bergonié, Bordeaux, France
| | - Victor Racine
- QuantaCell, Hôpital Saint Eloi, IRMB, Montpellier, France
| | - Patrick Blanco
- University of Bordeaux, Bordeaux, France
- ImmunoConcEpt, CNRS UMR 5164, INSERM ERL 1303, Bordeaux University, Bordeaux, France
| | - Julie Déchanet-Merville
- University of Bordeaux, Bordeaux, France
- ImmunoConcEpt, CNRS UMR 5164, INSERM ERL 1303, Bordeaux University, Bordeaux, France
| | - Maya Saleh
- INRS Santé Biotechnologie, Laval, Québec, Canada
| | - Scott W. Canna
- Pediatric Rheumatology, The Children’s Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - David Furman
- Buck Institute for Research on Aging, Novato, California, USA
- Stanford 1000 Immunomes Project, Stanford School of Medicine, Stanford, California, USA
| | - Benjamin Faustin
- University of Bordeaux, Bordeaux, France
- ImmunoConcEpt, CNRS UMR 5164, INSERM ERL 1303, Bordeaux University, Bordeaux, France
- Discovery Immunology, Johnson & Johnson Innovative Medicine, San Diego, California, USA
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Xu AM, Haro M, Walts AE, Hu Y, John J, Karlan BY, Merchant A, Orsulic S. Spatiotemporal architecture of immune cells and cancer-associated fibroblasts in high-grade serous ovarian carcinoma. SCIENCE ADVANCES 2024; 10:eadk8805. [PMID: 38630822 PMCID: PMC11023532 DOI: 10.1126/sciadv.adk8805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
High-grade serous ovarian carcinoma (HGSOC), the deadliest form of ovarian cancer, is typically diagnosed after it has metastasized and often relapses after standard-of-care platinum-based chemotherapy, likely due to advanced tumor stage, heterogeneity, and immune evasion and tumor-promoting signaling from the tumor microenvironment. To understand how spatial heterogeneity contributes to HGSOC progression and early relapse, we profiled an HGSOC tissue microarray of patient-matched longitudinal samples from 42 patients. We found spatial patterns associated with early relapse, including changes in T cell localization, malformed tertiary lymphoid structure (TLS)-like aggregates, and increased podoplanin-positive cancer-associated fibroblasts (CAFs). Using spatial features to compartmentalize the tissue, we found that plasma cells distribute in two different compartments associated with TLS-like aggregates and CAFs, and these distinct microenvironments may account for the conflicting reports about the role of plasma cells in HGSOC prognosis.
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Affiliation(s)
- Alexander M. Xu
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Marcela Haro
- Department of Obstetrics and Gynecology and Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ann E. Walts
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ye Hu
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Joshi John
- Department of Veterans Affairs, Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
- Department of Medicine, Division of Geriatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Beth Y. Karlan
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Akil Merchant
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sandra Orsulic
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Veterans Affairs, Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA 90095, USA
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68
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Patel A, Gulhati P. Molecular Landscape and Therapeutic Strategies against Colorectal Cancer. Cancers (Basel) 2024; 16:1551. [PMID: 38672633 PMCID: PMC11049251 DOI: 10.3390/cancers16081551] [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: 03/07/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer deaths worldwide. Although the overall incidence of CRC is decreasing, the incidence of young-onset CRC, characterized by a diagnosis of CRC before age 50, is increasing. Outcomes for CRC patients are improving, partly due to comprehensive molecular characterization of tumors and novel therapeutic strategies. Advances in genomic and transcriptomic analyses using blood- and tumor-tissue-based sequencing have facilitated identification of distinct tumor subtypes harboring unique biological characteristics and therapeutic vulnerabilities. These insights have led to the development and incorporation of targeted therapies and immunotherapy in CRC treatment. In this review, we discuss the molecular landscape and key oncogenes/tumor suppressors contributing to CRC tumorigenesis, metastasis, and therapeutic resistance. We also discuss personalized therapeutic strategies for subsets of CRC patients and provide an overview of evolving novel treatments being evaluated in clinical trials.
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Affiliation(s)
- Aakash Patel
- Division of Medical Oncology, Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA
| | - Pat Gulhati
- Division of Medical Oncology, Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA
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69
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Wang L, Ma L, Song Z, Zhou L, Chen K, Wang X, Liu Z, Wang B, Shen C, Guo X, Jia X. Single-cell transcriptome analysis profiling lymphatic invasion-related TME in colorectal cancer. Sci Rep 2024; 14:8911. [PMID: 38632387 PMCID: PMC11024122 DOI: 10.1038/s41598-024-59656-6] [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: 01/18/2024] [Accepted: 04/12/2024] [Indexed: 04/19/2024] Open
Abstract
Lymphatic invasion (LI) is extremely aggressive and induces worse prognosis among patients with colorectal cancer (CRC). Thus, it is critical to characterize the cellular and molecular mechanisms underlying LI in order to establish novel and efficacious therapeutic targets that enhance the prognosis of CRC patients. RNA-seq data, clinical and survival information of colon adenocarcinoma (COAD) patients were obtained from the TCGA database. In addition, three scRNA-seq datasets of CRC patients were acquired from the GEO database. Data analyses were conducted with the R packages. We assessed the tumor microenvironment (TME) differences between LI+ and LI- based scRNA-seq data, LI+ cells exhibited augmented abundance of immunosuppression and invasive subset. Marked extracellular matrix network activation was also observed in LI+ cells within SPP1+ macrophages. We revealed that an immunosuppressive and pro-angiogenic TME strongly enhanced LI, as was evidenced by the CD4+ Tregs, CD8+ GZMK+, SPP1+ macrophages, e-myCAFs, and w-myCAFs subcluster infiltrations. Furthermore, we identified potential LI targets that influenced tumor development, metastasis, and immunotherapeutic response. Finally, a novel LIRS model was established based on the expression of 14 LI-related signatures, and in the two testing cohorts, LIRS was also proved to have accurate prognostic predictive ability. In this report, we provided a valuable resource and extensive insights into the LI of CRC. Our conclusions can potentially benefit the establishment of highly efficacious therapeutic targets as well as diagnostic biomarkers that improve patient outcomes.
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Affiliation(s)
- Liping Wang
- Department of Geriatrics, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, China
| | - Liming Ma
- Harbin Inji Technology Co., Ltd., Harbin, 150060, Heilongjiang, China
| | - Zhaona Song
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, China
| | - Li Zhou
- Beijing Easyresearch Technology Limited, Beijing, 100049, China
| | - Kexin Chen
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, China
| | - Xizi Wang
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, China
| | - Zhen Liu
- Harbin Inji Technology Co., Ltd., Harbin, 150060, Heilongjiang, China
| | - Baozhong Wang
- Department of Oncology, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, China
| | - Chen Shen
- Department of Data and Information, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, Zhejiang, China
| | - Xianchao Guo
- Harbin Inji Technology Co., Ltd., Harbin, 150060, Heilongjiang, China.
| | - Xiaodong Jia
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, China.
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Liu X, Wang X, Yang Q, Luo L, Liu Z, Ren X, Lei K, Li S, Xie Z, Zheng G, Zhang Y, Hao Y, Zhou Q, Hou Y, Fang F, Song W, Cui J, Ma J, Xie W, Shen S, Tang C, Peng S, Yu J, Kuang M, Song X, Wang F, Xu L. Th17 Cells Secrete TWEAK to Trigger Epithelial-Mesenchymal Transition and Promote Colorectal Cancer Liver Metastasis. Cancer Res 2024; 84:1352-1371. [PMID: 38335276 DOI: 10.1158/0008-5472.can-23-2123] [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: 07/16/2023] [Revised: 11/28/2023] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Liver metastasis is the leading cause of mortality in patients with colorectal cancer. Given the significance of both epithelial-mesenchymal transition (EMT) of tumor cells and the immune microenvironment in colorectal cancer liver metastasis (CRLM), the interplay between them could hold the key for developing improved treatment options. We employed multiomics analysis of 130 samples from 18 patients with synchronous CRLM integrated with external datasets to comprehensively evaluate the interaction between immune cells and EMT of tumor cells in liver metastasis. Single-cell RNA sequencing analysis revealed distinct distributions of nonmalignant cells between primary tumors from patients with metastatic colorectal cancer (mCRC) and non-metastatic colorectal cancer, showing that Th17 cells were predominantly enriched in the primary lesion of mCRC. TWEAK, a cytokine secreted by Th17 cells, promoted EMT by binding to receptor Fn14 on tumor cells, and the TWEAK-Fn14 interaction enhanced tumor migration and invasion. In mouse models, targeting Fn14 using CRISPR-induced knockout or lipid nanoparticle-encapsulated siRNA alleviated metastasis and prolonged survival. Mice lacking Il17a or Tnfsf12 (encoding TWEAK) exhibited fewer metastases compared with wild-type mice, while cotransfer of Th17 with tumor cells promoted liver metastasis. Higher TWEAK expression was associated with a worse prognosis in patients with colorectal cancer. In addition, CD163L1+ macrophages interacted with Th17 cells, recruiting Th17 via the CCL4-CCR5 axis. Collectively, this study unveils the role of immune cells in the EMT process and identifies TWEAK secreted by Th17 as a driver of CRLM. SIGNIFICANCE TWEAK secreted by Th17 cells promotes EMT by binding to Fn14 on colorectal cancer cells, suggesting that blocking the TWEAK-Fn14 interaction may be a promising therapeutic approach to inhibit liver metastasis.
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Affiliation(s)
- Xin Liu
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xin Wang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Qingxia Yang
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Li Luo
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Ziqin Liu
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xiaoxue Ren
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Kai Lei
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Shangru Li
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Zonglin Xie
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Gaomin Zheng
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yifan Zhang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yijie Hao
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Qianying Zhou
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yingdong Hou
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Fei Fang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Wu Song
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Ji Cui
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Jinping Ma
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Wenxuan Xie
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Shunli Shen
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Ce Tang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Sui Peng
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Clinical Trial Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Jun Yu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
| | - Ming Kuang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xinming Song
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Fang Wang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Lixia Xu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
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Zhu X, Huang X, Hu M, Sun R, Li J, Wang H, Pan X, Ma Y, Ning L, Tong T, Zhou Y, Ding J, Zhao Y, Xuan B, Fang JY, Hong J, Hon Wong JW, Zhang Y, Chen H. A specific enterotype derived from gut microbiome of older individuals enables favorable responses to immune checkpoint blockade therapy. Cell Host Microbe 2024; 32:489-505.e5. [PMID: 38513657 DOI: 10.1016/j.chom.2024.03.002] [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: 09/28/2023] [Revised: 12/15/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Immunotherapy has revolutionized cancer treatment, but inconsistent responses persist. Our study delves into the intriguing phenomenon of enhanced immunotherapy sensitivity in older individuals with cancers. Through a meta-analysis encompassing 25 small-to-mid-sized trials of immune checkpoint blockade (ICB), we demonstrate that older individuals exhibit heightened responsiveness to ICB therapy. To understand the underlying mechanism, we reanalyze single-cell RNA sequencing (scRNA-seq) data from multiple studies and unveil distinct upregulation of exhausted and cytotoxic T cell markers within the tumor microenvironment (TME) of older patients. Recognizing the potential role of gut microbiota in modulating the efficacy of immunotherapy, we identify an aging-enriched enterotype linked to improved immunotherapy outcomes in older patients. Fecal microbiota transplantation experiments in mice confirm the therapeutic potential of the aging-enriched enterotype, enhancing treatment sensitivity and reshaping the TME. Our discoveries confront the prevailing paradox and provide encouraging paths for tailoring cancer immunotherapy strategies according to an individual's gut microbiome profile.
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Affiliation(s)
- Xiaoqiang Zhu
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Centre for Oncology and Immunology, Hong Kong Science Park. Hong Kong, Hong Kong SAR, China; Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowen Huang
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Muni Hu
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Rongrong Sun
- Department of Medical Oncology, Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Jiantao Li
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University
| | - Hai Wang
- Department of Endoscopy, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Xuefeng Pan
- Department of Medical Oncology, Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Yanru Ma
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lijun Ning
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tianying Tong
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yilu Zhou
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jinmei Ding
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Zhao
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Baoqin Xuan
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing-Yuan Fang
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Hong
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jason Wing Hon Wong
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Centre for Oncology and Immunology, Hong Kong Science Park. Hong Kong, Hong Kong SAR, China.
| | - Youwei Zhang
- Department of Medical Oncology, Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou, China.
| | - Haoyan Chen
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Ke S, Lei Y, Guo Y, Xie F, Yu Y, Geng H, Zhong Y, Xu D, Liu X, Yu F, Xia X, Zhang Z, Zhu C, Ling W, Li B, Zhao W. CD177 drives the transendothelial migration of Treg cells enriched in human colorectal cancer. Clin Transl Immunology 2024; 13:e1506. [PMID: 38596253 PMCID: PMC11003710 DOI: 10.1002/cti2.1506] [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: 05/31/2023] [Revised: 01/27/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
Objectives Regulatory T (Treg) cells regulate immunity in autoimmune diseases and cancers. However, immunotherapies that target tumor-infiltrating Treg cells often induce unwanted immune responses and tissue inflammation. Our research focussed on exploring the expression pattern of CD177 in tumor-infiltrating Treg cells with the aim of identifying a potential target that can enhance immunotherapy effectiveness. Methods Single-cell RNA sequencing (scRNA-seq) data and survival data were obtained from public databases. Twenty-one colorectal cancer patient samples, including fresh tumor tissues, peritumoral tissues and peripheral blood mononuclear cells (PBMCs), were analysed using flow cytometry. The transendothelial activity of CD177+ Treg cells was substantiated using in vitro experiments. Results ScRNA-seq and flow cytometry results indicated that CD177 was exclusively expressed in intratumoral Treg cells. CD177+ Treg cells exhibited greater activation status and expressed elevated Treg cell canonical markers and immune checkpoint molecules than CD177- Treg cells. We further discovered that both intratumoral CD177+ Treg cells and CD177-overexpressing induced Treg (iTreg) cells had lower levels of PD-1 than their CD177- counterparts. Moreover, CD177 overexpression significantly enhanced the transendothelial migration of Treg cells in vitro. Conclusions These results demonstrated that Treg cells with higher CD177 levels exhibited an enhanced activation status and transendothelial migration capacity. Our findings suggest that CD177 may serve as an immunotherapeutic target and that overexpression of CD177 may improve the efficacy of chimeric antigen receptor T (CAR-T) cell therapy.
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Affiliation(s)
- Shouyu Ke
- Department of Gastrointestinal Surgery, Ren Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yi Lei
- Center for Immune‐Related Diseases at Shanghai Institute of Immunology, Department of Respiratory and Critical Care Medicine of Ruijin Hospital, Department of Thoracic Surgery of Ruijin Hospital, Department of Immunology and MicrobiologyShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yixian Guo
- Department of Gastrointestinal Surgery, Ren Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Feng Xie
- Center for Immune‐Related Diseases at Shanghai Institute of Immunology, Department of Respiratory and Critical Care Medicine of Ruijin Hospital, Department of Thoracic Surgery of Ruijin Hospital, Department of Immunology and MicrobiologyShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yimeng Yu
- Center for Immune‐Related Diseases at Shanghai Institute of Immunology, Department of Respiratory and Critical Care Medicine of Ruijin Hospital, Department of Thoracic Surgery of Ruijin Hospital, Department of Immunology and MicrobiologyShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Haigang Geng
- Department of Gastrointestinal Surgery, Ren Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yiqing Zhong
- Department of Gastrointestinal Surgery, Ren Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Danhua Xu
- Department of Gastrointestinal Surgery, Ren Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xu Liu
- Department of Gastrointestinal Surgery, Ren Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Fengrong Yu
- Department of Gastrointestinal Surgery, Ren Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiang Xia
- Department of Gastrointestinal Surgery, Ren Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Zizhen Zhang
- Department of Gastrointestinal Surgery, Ren Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Chunchao Zhu
- Department of Gastrointestinal Surgery, Ren Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Wei Ling
- Department of Gastrointestinal Surgery, Ren Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Bin Li
- Center for Immune‐Related Diseases at Shanghai Institute of Immunology, Department of Respiratory and Critical Care Medicine of Ruijin Hospital, Department of Thoracic Surgery of Ruijin Hospital, Department of Immunology and MicrobiologyShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Wenyi Zhao
- Department of Gastrointestinal Surgery, Ren Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
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Ali AM, Raza A. scRNAseq and High-Throughput Spatial Analysis of Tumor and Normal Microenvironment in Solid Tumors Reveal a Possible Origin of Circulating Tumor Hybrid Cells. Cancers (Basel) 2024; 16:1444. [PMID: 38611120 PMCID: PMC11010995 DOI: 10.3390/cancers16071444] [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: 03/01/2024] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Metastatic cancer is a leading cause of death in cancer patients worldwide. While circulating hybrid cells (CHCs) are implicated in metastatic spread, studies documenting their tissue origin remain sparse, with limited candidate approaches using one-two markers. Utilizing high-throughput single-cell and spatial transcriptomics, we identified tumor hybrid cells (THCs) co-expressing epithelial and macrophage markers and expressing a distinct transcriptome. Rarely, normal tissue showed these cells (NHCs), but their transcriptome was easily distinguishable from THCs. THCs with unique transcriptomes were observed in breast and colon cancers, suggesting this to be a generalizable phenomenon across cancer types. This study establishes a framework for HC identification in large datasets, providing compelling evidence for their tissue residence and offering comprehensive transcriptomic characterization. Furthermore, it sheds light on their differential function and identifies pathways that could explain their newly acquired invasive capabilities. THCs should be considered as potential therapeutic targets.
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Affiliation(s)
- Abdullah Mahmood Ali
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Edward P Evans MDS Center, Herbert Irving Comprehensive Cancer Center, New York, NY 10032, USA
| | - Azra Raza
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Edward P Evans MDS Center, Herbert Irving Comprehensive Cancer Center, New York, NY 10032, USA
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Sharma S, Singh N, Turk AA, Wan I, Guttikonda A, Dong JL, Zhang X, Opyrchal M. Molecular insights into clinical trials for immune checkpoint inhibitors in colorectal cancer: Unravelling challenges and future directions. World J Gastroenterol 2024; 30:1815-1835. [PMID: 38659481 PMCID: PMC11036501 DOI: 10.3748/wjg.v30.i13.1815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/22/2024] [Accepted: 03/13/2024] [Indexed: 04/03/2024] Open
Abstract
Colorectal cancer (CRC) is a complex disease with diverse etiologies and clinical outcomes. Despite considerable progress in development of CRC therapeutics, challenges remain regarding the diagnosis and management of advanced stage metastatic CRC (mCRC). In particular, the five-year survival rate is very low since mCRC is currently rarely curable. Over the past decade, cancer treatment has significantly improved with the introduction of cancer immunotherapies, specifically immune checkpoint inhibitors. Therapies aimed at blocking immune checkpoints such as PD-1, PD-L1, and CTLA-4 target inhibitory pathways of the immune system, and thereby enhance anti-tumor immunity. These therapies thus have shown promising results in many clinical trials alone or in combination. The efficacy and safety of immunotherapy, either alone or in combination with CRC, have been investigated in several clinical trials. Clinical trials, including KEYNOTE-164 and CheckMate 142, have led to Food and Drug Administration approval of the PD-1 inhibitors pembrolizumab and nivolumab, respectively, for the treatment of patients with unresectable or metastatic microsatellite instability-high or deficient mismatch repair CRC. Unfortunately, these drugs benefit only a small percentage of patients, with the benefits of immunotherapy remaining elusive for the vast majority of CRC patients. To this end, primary and secondary resistance to immunotherapy remains a significant issue, and further research is necessary to optimize the use of immunotherapy in CRC and identify biomarkers to predict the response. This review provides a comprehensive overview of the clinical trials involving immune checkpoint inhibitors in CRC. The underlying rationale, challenges faced, and potential future steps to improve the prognosis and enhance the likelihood of successful trials in this field are discussed.
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Affiliation(s)
- Samantha Sharma
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Naresh Singh
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Anita Ahmed Turk
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Isabella Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Akshay Guttikonda
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Julia Lily Dong
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Xinna Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Mateusz Opyrchal
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, United States
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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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Marmarelis MG, Littman R, Battaglin F, Niedzwiecki D, Venook A, Ambite JL, Galstyan A, Lenz HJ, Ver Steeg G. q-Diffusion leverages the full dimensionality of gene coexpression in single-cell transcriptomics. Commun Biol 2024; 7:400. [PMID: 38565955 PMCID: PMC11255321 DOI: 10.1038/s42003-024-06104-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: 06/23/2023] [Accepted: 03/25/2024] [Indexed: 04/04/2024] Open
Abstract
Unlocking the full dimensionality of single-cell RNA sequencing data (scRNAseq) is the next frontier to a richer, fuller understanding of cell biology. We introduce q-diffusion, a framework for capturing the coexpression structure of an entire library of genes, improving on state-of-the-art analysis tools. The method is demonstrated via three case studies. In the first, q-diffusion helps gain statistical significance for differential effects on patient outcomes when analyzing the CALGB/SWOG 80405 randomized phase III clinical trial, suggesting precision guidance for the treatment of metastatic colorectal cancer. Secondly, q-diffusion is benchmarked against existing scRNAseq classification methods using an in vitro PBMC dataset, in which the proposed method discriminates IFN-γ stimulation more accurately. The same case study demonstrates improvements in unsupervised cell clustering with the recent Tabula Sapiens human atlas. Finally, a local distributional segmentation approach for spatial scRNAseq, driven by q-diffusion, yields interpretable structures of human cortical tissue.
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Affiliation(s)
- Myrl G Marmarelis
- Information Sciences Institute, University of Southern California, 4676 Admiralty Way, Marina del Rey, CA, 90292, USA.
| | - Russell Littman
- University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Francesca Battaglin
- Keck School of Medicine, University of Southern California, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | | | - Alan Venook
- University of California San Francisco, San Francisco, CA, 94143, USA
| | - Jose-Luis Ambite
- Information Sciences Institute, University of Southern California, 4676 Admiralty Way, Marina del Rey, CA, 90292, USA
| | - Aram Galstyan
- Information Sciences Institute, University of Southern California, 4676 Admiralty Way, Marina del Rey, CA, 90292, USA
| | - Heinz-Josef Lenz
- Keck School of Medicine, University of Southern California, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | - Greg Ver Steeg
- Information Sciences Institute, University of Southern California, 4676 Admiralty Way, Marina del Rey, CA, 90292, USA
- University of California Riverside, Riverside, CA, 92521, USA
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Bui TM, Yalom LK, Ning E, Urbanczyk JM, Ren X, Herrnreiter CJ, Disario JA, Wray B, Schipma MJ, Velichko YS, Sullivan DP, Abe K, Lauberth SM, Yang GY, Dulai PS, Hanauer SB, Sumagin R. Tissue-specific reprogramming leads to angiogenic neutrophil specialization and tumor vascularization in colorectal cancer. J Clin Invest 2024; 134:e174545. [PMID: 38329810 PMCID: PMC10977994 DOI: 10.1172/jci174545] [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: 08/04/2023] [Accepted: 02/06/2024] [Indexed: 02/10/2024] Open
Abstract
Neutrophil (PMN) tissue accumulation is an established feature of ulcerative colitis (UC) lesions and colorectal cancer (CRC). To assess the PMN phenotypic and functional diversification during the transition from inflammatory ulceration to CRC we analyzed the transcriptomic landscape of blood and tissue PMNs. Transcriptional programs effectively separated PMNs based on their proximity to peripheral blood, inflamed colon, and tumors. In silico pathway overrepresentation analysis, protein-network mapping, gene signature identification, and gene-ontology scoring revealed unique enrichment of angiogenic and vasculature development pathways in tumor-associated neutrophils (TANs). Functional studies utilizing ex vivo cultures, colitis-induced murine CRC, and patient-derived xenograft models demonstrated a critical role for TANs in promoting tumor vascularization. Spp1 (OPN) and Mmp14 (MT1-MMP) were identified by unbiased -omics and mechanistic studies to be highly induced in TANs, acting to critically regulate endothelial cell chemotaxis and branching. TCGA data set and clinical specimens confirmed enrichment of SPP1 and MMP14 in high-grade CRC but not in patients with UC. Pharmacological inhibition of TAN trafficking or MMP14 activity effectively reduced tumor vascular density, leading to CRC regression. Our findings demonstrate a niche-directed PMN functional specialization and identify TAN contributions to tumor vascularization, delineating what we believe to be a new therapeutic framework for CRC treatment focused on TAN angiogenic properties.
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Affiliation(s)
- Triet M. Bui
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lenore K. Yalom
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Edward Ning
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jessica M. Urbanczyk
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Xingsheng Ren
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Caroline J. Herrnreiter
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jackson A. Disario
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Brian Wray
- Quantitative Data Science Core, Lurie Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Matthew J. Schipma
- Quantitative Data Science Core, Lurie Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Yuri S. Velichko
- Department of Radiology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - David P. Sullivan
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kouki Abe
- Simpson Querrey Institute for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shannon M. Lauberth
- Simpson Querrey Institute for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Guang-Yu Yang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Parambir S. Dulai
- Department of Medicine, Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, Illinois, USA
| | - Stephen B. Hanauer
- Department of Medicine, Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, Illinois, USA
| | - Ronen Sumagin
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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78
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Chen JH, Nieman LT, Spurrell M, Jorgji V, Elmelech L, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Van Raay K, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee MJ, Mino-Kenudson M, Gainor JF, Korsunsky I, Hacohen N. Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy. Nat Immunol 2024; 25:644-658. [PMID: 38503922 DOI: 10.1038/s41590-024-01792-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 02/15/2024] [Indexed: 03/21/2024]
Abstract
The organization of immune cells in human tumors is not well understood. Immunogenic tumors harbor spatially localized multicellular 'immunity hubs' defined by expression of the T cell-attracting chemokines CXCL10/CXCL11 and abundant T cells. Here, we examined immunity hubs in human pre-immunotherapy lung cancer specimens and found an association with beneficial response to PD-1 blockade. Critically, we discovered the stem-immunity hub, a subtype of immunity hub strongly associated with favorable PD-1-blockade outcome. This hub is distinct from mature tertiary lymphoid structures and is enriched for stem-like TCF7+PD-1+CD8+ T cells, activated CCR7+LAMP3+ dendritic cells and CCL19+ fibroblasts as well as chemokines that organize these cells. Within the stem-immunity hub, we find preferential interactions between CXCL10+ macrophages and TCF7-CD8+ T cells as well as between mature regulatory dendritic cells and TCF7+CD4+ and regulatory T cells. These results provide a picture of the spatial organization of the human intratumoral immune response and its relevance to patient immunotherapy outcomes.
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Affiliation(s)
- Jonathan H Chen
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA.
- Department of Pathology, MGH, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Linda T Nieman
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Maxwell Spurrell
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Vjola Jorgji
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Liad Elmelech
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Peter Richieri
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Katherine H Xu
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Roopa Madhu
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Division of Genetics, Boston, MA, USA
| | - Milan Parikh
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Izabella Zamora
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Arnav Mehta
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Christopher S Nabel
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA
| | - Samuel S Freeman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Joshua D Pirl
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Chenyue Lu
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Catherine B Meador
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Division of Hematology/Oncology, MGH, HMS, Boston, MA, USA
| | | | | | - Alexander L Tang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Siranush Sarkizova
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | | | | | | | | | | | - Keren Yizhak
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Matan Hofree
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Lautenberg Center for Immunology and Cancer Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Angela Shih
- Department of Pathology, MGH, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Moshe Sade-Feldman
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Genevieve M Boland
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Surgery, MGH, Boston, MA, USA
| | - Karin Pelka
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Gladstone-UCSF Institute of Genomic Immunology, Gladstone Institutes, San Francisco, CA, USA
| | - Martin J Aryee
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mari Mino-Kenudson
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Justin F Gainor
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Center for Thoracic Cancers, MGH, Boston, MA, USA.
| | - Ilya Korsunsky
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Brigham and Women's Hospital, Division of Genetics, Boston, MA, USA.
| | - Nir Hacohen
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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79
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Hao J, Liu C, Gu Z, Yang X, Lan X, Guo X. Dysregulation of Wnt/β-catenin signaling contributes to intestinal inflammation through regulation of group 3 innate lymphoid cells. Nat Commun 2024; 15:2820. [PMID: 38561332 PMCID: PMC10985070 DOI: 10.1038/s41467-024-45616-1] [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: 06/14/2023] [Accepted: 01/30/2024] [Indexed: 04/04/2024] Open
Abstract
RORγt+ group 3 innate lymphoid cells (ILC3s) are essential for intestinal homeostasis. Dysregulation of ILC3s has been found in the gut of patients with inflammatory bowel disease and colorectal cancer, yet the specific mechanisms still require more investigation. Here we observe increased β-catenin in intestinal ILC3s from inflammatory bowel disease and colon cancer patients compared with healthy donors. In contrast to promoting RORγt expression in T cells, activation of Wnt/β-catenin signaling in ILC3s suppresses RORγt expression, inhibits its proliferation and function, and leads to a deficiency of ILC3s and subsequent intestinal inflammation in mice. Activated β-catenin and its interacting transcription factor, TCF-1, cannot directly suppress RORγt expression, but rather alters global chromatin accessibility and inhibits JunB expression, which is essential for RORγt expression in ILC3s. Together, our findings suggest that dysregulated Wnt/β-catenin signaling impairs intestinal ILC3s through TCF-1/JunB/RORγt regulation, further disrupting intestinal homeostasis, and promoting inflammation and cancer.
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Affiliation(s)
- Jiacheng Hao
- Institute for Immunology, Tsinghua University, 100084, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Chang Liu
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Zhijie Gu
- Institute for Immunology, Tsinghua University, 100084, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xuanming Yang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, 200240, Shanghai, China
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Xun Lan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohuan Guo
- Institute for Immunology, Tsinghua University, 100084, Beijing, China.
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China.
- Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, 100084, Beijing, China.
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80
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Didriksen BJ, Eshleman EM, Alenghat T. Epithelial regulation of microbiota-immune cell dynamics. Mucosal Immunol 2024; 17:303-313. [PMID: 38428738 DOI: 10.1016/j.mucimm.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/09/2024] [Accepted: 02/23/2024] [Indexed: 03/03/2024]
Abstract
The mammalian gastrointestinal tract hosts a diverse community of trillions of microorganisms, collectively termed the microbiota, which play a fundamental role in regulating tissue physiology and immunity. Recent studies have sought to dissect the cellular and molecular mechanisms mediating communication between the microbiota and host immune system. Epithelial cells line the intestine and form an initial barrier separating the microbiota from underlying immune cells, and disruption of epithelial function has been associated with various conditions ranging from infection to inflammatory bowel diseases and cancer. From several studies, it is now clear that epithelial cells integrate signals from commensal microbes. Importantly, these non-hematopoietic cells also direct regulatory mechanisms that instruct the recruitment and function of microbiota-sensitive immune cells. In this review, we discuss the central role that has emerged for epithelial cells in orchestrating intestinal immunity and highlight epithelial pathways through which the microbiota can calibrate tissue-intrinsic immune responses.
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Affiliation(s)
- Bailey J Didriksen
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA; Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Emily M Eshleman
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.
| | - Theresa Alenghat
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.
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81
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Hu A, Nussbaum YI, Mitchem J, Yoo J. Colorectal Cancer-Associated Myofibroblasts Exhibit Enhanced Angiogenin Expression and Signaling via the PLXNB2 Receptor. J Surg Res 2024; 296:273-280. [PMID: 38295715 DOI: 10.1016/j.jss.2023.12.036] [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: 05/24/2023] [Revised: 12/11/2023] [Accepted: 12/30/2023] [Indexed: 03/19/2024]
Abstract
INTRODUCTION Dynamic cell-cell interactions shape the tumor microenvironment to regulate tumor growth and invasiveness. Myofibroblasts are gastrointestinal stromal cells that are upregulated in the setting of colorectal cancer (CRC) and may play an important role in tumor-stromal cell communication. Angiogenin is a 14-kDa ribonuclease that regulates myofibroblast function and has been implicated in myofibroblast-CRC cell communication in mouse models. However, its role in human patients has not been well established. METHODS Open access, annotated single-cell RNA sequencing data of paired normal human colon and CRC tissue were available in the National Center for Biotechnology Information Gene Expression Omnibus Database. We supplemented and verified these data by analyzing scRNA-seq data from an independent set of paired normal human colon and CRC tissue. CellChat was used to quantitatively infer biologically meaningful cell-cell communication networks from scRNA-seq data. PLXNB2 and α-2 actin (ACTA2) are cell surface angiogenin receptors that regulate angiogenin signaling. Ligand-receptor interactions involving angiogenin, PLXNB2, and ACTA2 were analyzed between cell populations in each sample. RESULTS We found no difference in overall angiogenin expression comparing normal colon and CRC tissue. In normal colon tissue, myofibroblasts do not express angiogenin or the PLXNB2 receptor. In the presence of CRC, there was a striking increase in the number of myofibroblast cells within the surrounding stroma. CRC-associated myofibroblasts were characterized by a significant upregulation of both angiogenin and PLXNB2 receptor expression (P < 0.05), while no difference was seen in ACTA2. CRC cells not only use angiogenin for autocrine signaling but also communicate with myofibroblasts via the PLXNB2 receptor. CONCLUSIONS Compared to normal human colon tissue, CRC tissue is associated with an enrichment of myofibroblasts that exhibit upregulated expression of angiogenin and the angiogenin receptor PLXNB2. CRC cells engage in autocrine signaling via angiogenin and paracrine signaling with myofibroblasts via PLXNB2. Angiogenin appears to be directly involved in tumor-stromal cell communication in human CRC tissue and may play an important role in disease progression.
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Affiliation(s)
- Alexander Hu
- Department of Surgery, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts
| | - Yulia I Nussbaum
- Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri
| | - Jonathan Mitchem
- Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri; Department of Surgery, Cleveland Clinic, Cleveland, Ohio
| | - James Yoo
- Department of Surgery, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts.
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82
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Elomaa H, Härkönen J, Väyrynen SA, Ahtiainen M, Ogino S, Nowak JA, Lau MC, Helminen O, Wirta EV, Seppälä TT, Böhm J, Mecklin JP, Kuopio T, Väyrynen JP. Quantitative Multiplexed Analysis of Indoleamine 2,3-Dioxygenase (IDO) and Arginase-1 (ARG1) Expression and Myeloid Cell Infiltration in Colorectal Cancer. Mod Pathol 2024; 37:100450. [PMID: 38369188 DOI: 10.1016/j.modpat.2024.100450] [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: 10/19/2023] [Revised: 01/12/2024] [Accepted: 02/04/2024] [Indexed: 02/20/2024]
Abstract
Indoleamine 2,3-dioxygenase (IDO) and arginase-1 (ARG1) are amino acid-metabolizing enzymes, frequently highly expressed in cancer. Their expression may deplete essential amino acids, lead to immunosuppression, and promote cancer growth. Still, their expression patterns, prognostic significance, and spatial localization in the colorectal cancer microenvironment are incompletely understood. Using a custom 10-plex immunohistochemistry assay and supervised machine learning-based digital image analysis, we characterized IDO and ARG1 expression in monocytic cells, granulocytes, mast cells, and tumor cells in 833 colorectal cancer patients. We evaluated the prognostic value and spatial arrangement of IDO- and ARG1-expressing myeloid and tumor cells. IDO was mainly expressed not only by monocytic cells but also by some tumor cells, whereas ARG1 was predominantly expressed by granulocytes. Higher density of IDO+ monocytic cells was an independent prognostic factor for improved cancer-specific survival both in the tumor center (Ptrend = .0002; hazard ratio [HR] for the highest ordinal category Q4 [vs Q1], 0.51; 95% CI, 0.33-0.79) and the invasive margin (Ptrend = .0015). Higher density of granulocytes was associated with prolonged cancer-specific survival in univariable models, and higher FCGR3+ARG1+ neutrophil density in the tumor center also in multivariable analysis (Ptrend = .0020). Granulocytes were, on average, located closer to tumor cells than monocytic cells. Furthermore, IDO+ monocytic cells and ARG1- granulocytes were closer than IDO- monocytic cells and ARG1+ granulocytes, respectively. The mRNA expression of the IDO1 gene was assessed in myeloid and tumor cells using publicly available single-cell RNA sequencing data for 62 colorectal cancers. IDO1 was mainly expressed in monocytes and dendritic cells, and high IDO1 activity in monocytes was associated with enriched immunostimulatory pathways. Our findings provided in-depth information about the infiltration patterns and prognostic value of cells expressing IDO and/or ARG1 in the colorectal cancer microenvironment, highlighting the significance of host immune response in tumor progression.
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Affiliation(s)
- Hanna Elomaa
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland; Department of Education and Research, Hospital Nova of Central Finland, Well Being Services County of Central Finland, Jyväskylä, Finland
| | - Jouni Härkönen
- Department of Pathology, Hospital Nova of Central Finland, Well Being Services County of Central Finland, Jyväskylä, Finland; Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Sara A Väyrynen
- Department of Internal Medicine, Oulu University Hospital, Oulu, Finland
| | - Maarit Ahtiainen
- Department of Pathology, Hospital Nova of Central Finland, Well Being Services County of Central Finland, Jyväskylä, Finland
| | - Shuji Ogino
- Program in Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Cancer Immunology and Cancer Epidemiology Programs, Dana-Farber Harvard Cancer Center, Boston, Massachusetts
| | - Jonathan A Nowak
- Program in Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Mai Chan Lau
- Bioinformatics Institute (BII), Agency of Science, Technology and Research (A∗STAR), Singapore, Singapore; Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Olli Helminen
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Erkki-Ville Wirta
- Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland; Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Toni T Seppälä
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland; Department of Gastrointestinal Surgery, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics, Research Program Unit, University of Helsinki, Helsinki, Finland; Abdominal Center, Helsinki University Hospital, Helsinki, Finland
| | - Jan Böhm
- Department of Pathology, Hospital Nova of Central Finland, Well Being Services County of Central Finland, Jyväskylä, Finland
| | - Jukka-Pekka Mecklin
- Department of Education and Research, Hospital Nova of Central Finland, Well Being Services County of Central Finland, Jyväskylä, Finland; Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Teijo Kuopio
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland; Department of Pathology, Hospital Nova of Central Finland, Well Being Services County of Central Finland, Jyväskylä, Finland
| | - Juha P Väyrynen
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland.
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Park SS, Lee YK, Choi YW, Lim SB, Park SH, Kim HK, Shin JS, Kim YH, Lee DH, Kim JH, Park TJ. Cellular senescence is associated with the spatial evolution toward a higher metastatic phenotype in colorectal cancer. Cell Rep 2024; 43:113912. [PMID: 38446659 DOI: 10.1016/j.celrep.2024.113912] [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: 08/03/2023] [Revised: 12/21/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
In this study, we explore the dynamic process of colorectal cancer progression, emphasizing the evolution toward a more metastatic phenotype. The term "evolution" as used in this study specifically denotes the phenotypic transition toward a higher metastatic potency from well-formed glandular structures to collective invasion, ultimately resulting in the development of cancer cell buddings at the invasive front. Our findings highlight the spatial correlation of this evolution with tumor cell senescence, revealing distinct types of senescent tumor cells (types I and II) that play different roles in the overall cancer progression. Type I senescent tumor cells (p16INK4A+/CXCL12+/LAMC2-/MMP7-) are identified in the collective invasion region, whereas type II senescent tumor cells (p16INK4A+/CXCL12+/LAMC2+/MMP7+), representing the final evolved form, are prominently located in the partial-EMT region. Importantly, type II senescent tumor cells associate with local invasion and lymph node metastasis in colorectal cancer, potentially affecting patient prognosis.
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Affiliation(s)
- Soon Sang Park
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon 16499, Korea; Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Korea; Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon 16499, Korea
| | - Young-Kyoung Lee
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon 16499, Korea; Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon 16499, Korea
| | - Yong Won Choi
- Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon 16499, Korea; Department of Hematology and Oncology, Ajou University School of Medicine, Suwon 16499, Korea
| | - Su Bin Lim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon 16499, Korea; Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Korea; Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon 16499, Korea
| | - So Hyun Park
- Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon 16499, Korea; Department of Pathology, Ajou University School of Medicine, Suwon 16499, Korea
| | - Han Ki Kim
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Korea; Department of Brain Science and Neurology, Ajou University School of Medicine, Suwon 16499, Korea
| | - Jun Sang Shin
- Department of Surgery, Ajou University School of Medicine, Suwon 16499, Korea
| | - Young Hwa Kim
- Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon 16499, Korea; Department of Pathology, Ajou University School of Medicine, Suwon 16499, Korea
| | - Dong Hyun Lee
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon 16499, Korea; Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Korea; Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon 16499, Korea
| | - Jang-Hee Kim
- Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon 16499, Korea; Department of Pathology, Ajou University School of Medicine, Suwon 16499, Korea.
| | - Tae Jun Park
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon 16499, Korea; Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Korea; Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon 16499, Korea.
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84
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Sweet-Cordero E, Marini K, Champion E, Lee A, Young I, Leung S, Mathey-Andrews N, Jacks T, Jackson P, Cochran J. The CLCF1-CNTFR axis drives an immunosuppressive tumor microenvironment and blockade enhances the effects of established cancer therapies. RESEARCH SQUARE 2024:rs.3.rs-4046823. [PMID: 38562778 PMCID: PMC10984090 DOI: 10.21203/rs.3.rs-4046823/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Tumors comprise a complex ecosystem consisting of many cell types that communicate through secreted factors. Targeting these intercellular signaling networks remains an important challenge in cancer research. Cardiotrophin-like cytokine factor 1 (CLCF1) is an interleukin-6 (IL-6) family member secreted by cancer-associated fibroblasts (CAFs) that binds to ciliary neurotrophic factor receptor (CNTFR), promoting tumor growth in lung and liver cancer1,2. A high-affinity soluble receptor (eCNTFR-Fc) that sequesters CLCF1 has anti-oncogenic effects3. However, the role of CLCF1 in mediating cell-cell interactions in cancer has remained unclear. We demonstrate that eCNTFR-Fc has widespread effects on both tumor cells and the tumor microenvironment and can sensitize cancer cells to KRAS inhibitors or immune checkpoint blockade. After three weeks of treatment with eCNTFR-Fc, there is a shift from an immunosuppressive to an immunostimulatory macrophage phenotype as well as an increase in activated T, NKT, and NK cells. Combination of eCNTFR-Fc and αPD1 was significantly more effective than single-agent therapy in a syngeneic allograft model, and eCNTFR-Fc sensitizes tumor cells to αPD1 in a non-responsive GEM model of lung adenocarcinoma. These data suggest that combining eCNTFR-Fc with KRAS inhibition or with αPD1 is a novel therapeutic strategy for lung cancer and potentially other cancers in which these therapies have been used but to date with only modest effect. Overall, we demonstrate the potential of cancer therapies that target cytokines to alter the immune microenvironment.
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Affiliation(s)
| | - Kieren Marini
- Division of Oncology, Department of Pediatrics, University of California San Francisco
| | - Emma Champion
- Division of Oncology, Department of Pediatrics, University of California San Francisco
| | - Alex Lee
- University of California, San Francisco
| | - Isabelle Young
- Division of Oncology, Department of Pediatrics, University of California San Francisco
| | - Stanley Leung
- Division of Oncology, Department of Pediatrics, University of California San Francisco
| | | | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research
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85
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Scheuermann S, Kristmann B, Engelmann F, Nuernbergk A, Scheuermann D, Koloseus M, Abed T, Solass W, Seitz CM. Unveiling spatial complexity in solid tumor immune microenvironments through multiplexed imaging. Front Immunol 2024; 15:1383932. [PMID: 38566984 PMCID: PMC10985204 DOI: 10.3389/fimmu.2024.1383932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Deciphering cellular components and the spatial interaction network of the tumor immune microenvironment (TIME) of solid tumors is pivotal for understanding biologically relevant cross-talks and, ultimately, advancing therapies. Multiplexed tissue imaging provides a powerful tool to elucidate spatial complexity in a holistic manner. We established and cross-validated a comprehensive immunophenotyping panel comprising over 121 markers for multiplexed tissue imaging using MACSima™ imaging cyclic staining (MICS) alongside an end-to-end analysis workflow. Applying this panel and workflow to primary cancer tissues, we characterized tumor heterogeneity, investigated potential therapeutical targets, conducted in-depth profiling of cell types and states, sub-phenotyped T cells within the TIME, and scrutinized cellular neighborhoods of diverse T cell subsets. Our findings highlight the advantage of spatial profiling, revealing immunosuppressive molecular signatures of tumor-associated myeloid cells interacting with neighboring exhausted, PD1high T cells in the TIME of hepatocellular carcinoma (HCC). This study establishes a robust framework for spatial exploration of TIMEs in solid tumors and underscores the potency of multiplexed tissue imaging and ultra-deep cell phenotyping in unraveling clinically relevant tumor components.
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Affiliation(s)
- Sophia Scheuermann
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
- iFIT Cluster of Excellence EXC 2180 ‘Image-Guided and Functionally Instructed Tumor Therapies’, University of Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK), partner site Tuebingen, a partnership between German Cancer Research Center (DKFZ) and University Hospital Tuebingen, Tuebingen, Germany
| | - Beate Kristmann
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
| | - Fabienne Engelmann
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
| | - Alice Nuernbergk
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
| | - David Scheuermann
- School of Business and Economics, Faculty of Economics and Social Sciences, University of Tuebingen, Tuebingen, Germany
| | - Marie Koloseus
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
| | - Tayeb Abed
- Institute of Pathology and Neuropathology, University Hospital Tuebingen and Comprehensive Cancer Center, Tuebingen, Germany
| | - Wiebke Solass
- Institute of Tissue Medicine and Pathology (ITMP), University of Bern, Bern, Switzerland
| | - Christian M. Seitz
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
- iFIT Cluster of Excellence EXC 2180 ‘Image-Guided and Functionally Instructed Tumor Therapies’, University of Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK), partner site Tuebingen, a partnership between German Cancer Research Center (DKFZ) and University Hospital Tuebingen, Tuebingen, Germany
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86
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Liu W, You W, Lan Z, Ren Y, Gao S, Li S, Chen WW, Huang C, Zeng Y, Xiao N, Wang Z, Xie H, Ma H, Chen Y, Wang G, Chen C, Li H. An immune cell map of human lung adenocarcinoma development reveals an anti-tumoral role of the Tfh-dependent tertiary lymphoid structure. Cell Rep Med 2024; 5:101448. [PMID: 38458196 PMCID: PMC10983046 DOI: 10.1016/j.xcrm.2024.101448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/10/2023] [Accepted: 02/08/2024] [Indexed: 03/10/2024]
Abstract
The immune responses during the initiation and invasion stages of human lung adenocarcinoma (LUAD) development are largely unknown. Here, we generated a single-cell RNA sequencing map to decipher the immune dynamics during human LUAD development. We found that T follicular helper (Tfh)-like cells, germinal center B cells, and dysfunctional CD8+ T cells increase during tumor initiation/invasion and form a tertiary lymphoid structure (TLS) inside the tumor. This TLS starts with an aggregation of CD4+ T cells and the generation of CXCL13-expressing Tfh-like cells, followed by an accumulation of B cells, and then forms a CD4+ T and B cell aggregate. TLS and its associated cells are correlated with better patient survival. Inhibiting TLS formation by Tfh or B cell depletion promotes tumor growth in mouse models. The anti-tumoral effect of the Tfh-dependent TLS is mediated through interleukin-21 (IL-21)-IL-21 receptor signaling. Our study establishes an anti-tumoral role of the Tfh-dependent TLS in the development of LUAD.
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Affiliation(s)
- Wei Liu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproductive Medicine and Genetics, Shenzhen Zhongshan Obstetrics & Gynecology Hospital, Shenzhen, China
| | - Wenhua You
- Department of Immunology, School of Basic Medical Sciences, Wuxi Medical Center, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing 211166, Jiangsu, China; School of Chemistry and Chemical Engineering, Southeast University, Nanjing, China
| | - Zhenwei Lan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yijiu Ren
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shuangshu Gao
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Shuchao Li
- Department of Automation, Xiamen University, Xiamen, Fujian, China
| | - Wei-Wei Chen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chunyu Huang
- Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproductive Medicine and Genetics, Shenzhen Zhongshan Obstetrics & Gynecology Hospital, Shenzhen, China; Guangdong Engineering Technology Research Center of Reproductive Immunology for Peri-implantation, Shenzhen, Guangdong, China
| | - Yong Zeng
- Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproductive Medicine and Genetics, Shenzhen Zhongshan Obstetrics & Gynecology Hospital, Shenzhen, China; Guangdong Engineering Technology Research Center of Reproductive Immunology for Peri-implantation, Shenzhen, Guangdong, China
| | - Nengming Xiao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Zeshuai Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Huikang Xie
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huan Ma
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Yun Chen
- Department of Immunology, School of Basic Medical Sciences, Wuxi Medical Center, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing 211166, Jiangsu, China.
| | - Guangsuo Wang
- The Department of Thoracic Surgery, Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China.
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Hanjie Li
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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87
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Zhou X, Seow WY, Ha N, Cheng TH, Jiang L, Boonruangkan J, Goh JJL, Prabhakar S, Chou N, Chen KH. Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes. Nat Commun 2024; 15:2342. [PMID: 38491027 PMCID: PMC10943009 DOI: 10.1038/s41467-024-46669-y] [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: 08/11/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
High-dimensional, spatially resolved analysis of intact tissue samples promises to transform biomedical research and diagnostics, but existing spatial omics technologies are costly and labor-intensive. We present Fluorescence In Situ Hybridization of Cellular HeterogeneIty and gene expression Programs (FISHnCHIPs) for highly sensitive in situ profiling of cell types and gene expression programs. FISHnCHIPs achieves this by simultaneously imaging ~2-35 co-expressed genes (clustered into modules) that are spatially co-localized in tissues, resulting in similar spatial information as single-gene Fluorescence In Situ Hybridization (FISH), but with ~2-20-fold higher sensitivity. Using FISHnCHIPs, we image up to 53 modules from the mouse kidney and mouse brain, and demonstrate high-speed, large field-of-view profiling of a whole tissue section. FISHnCHIPs also reveals spatially restricted localizations of cancer-associated fibroblasts in a human colorectal cancer biopsy. Overall, FISHnCHIPs enables fast, robust, and scalable cell typing of tissues with normal physiology or undergoing pathogenesis.
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Affiliation(s)
- Xinrui Zhou
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Wan Yi Seow
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Norbert Ha
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Teh How Cheng
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Lingfan Jiang
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Jeeranan Boonruangkan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Jolene Jie Lin Goh
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Shyam Prabhakar
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Nigel Chou
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore.
| | - Kok Hao Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore.
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88
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Lv H, Mu Y, Zhang C, Zhao M, Jiang P, Xiao S, Sun H, Wu N, Sun D, Jin Y. Comparative analysis of single-cell transcriptome reveals heterogeneity and commonality in the immune microenvironment of colorectal cancer and inflammatory bowel disease. Front Immunol 2024; 15:1356075. [PMID: 38529274 PMCID: PMC10961339 DOI: 10.3389/fimmu.2024.1356075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024] Open
Abstract
Background During aging, chronic inflammation can promote tumor development and metastasis. Patients with chronic inflammatory bowel diseases (IBD) are at an increased risk of developing colorectal cancer (CRC). However, the molecular mechanism underlying is still unclear. Methods We conducted a large-scale single-cell sequencing analysis comprising 432,314 single cells from 92 CRC and 24 IBD patients. The analysis focused on the heterogeneity and commonality of CRC and IBD with respect to immune cell landscape, cellular communication, aging and inflammatory response, and Meta programs. Results The CRC and IBD had significantly different propensities in terms of cell proportions, differential genes and their functions, and cellular communication. The progression of CRC was mainly associated with epithelial cells, fibroblasts, and monocyte-macrophages, which displayed pronounced metabolic functions. In particular, monocyte-macrophages were enriched for the aging and inflammation-associated NF-κB pathway. And IBD was enriched in immune-related functions with B cells and T cells. Cellular communication analysis in CRC samples displayed an increase in MIF signaling from epithelial cells to T cells, and an increase in the efferent signal of senescence-associated SPP1 signaling from monocyte-macrophages. Notably, we also found some commonalities between CRC and IBD. The efferent and afferent signals showed that the pro-inflammatory cytokine played an important role. And the activity of aging and inflammatory response with AUCell analysis also showed a high degree of commonality. Furthermore, using the Meta programs (MPs) with the NMF algorithm, we found that the CRC non-malignant cells shared a substantial proportion of the MP genes with CRC malignant cells (68% overlap) and IBD epithelial cells (52% overlap), respectively. And it was extensively involved in functions of cell cycle and immune response, revealing its dual properties of inflammation and cancer. In addition, CRC malignant and non-malignant cells were enriched for the senescence-related cell cycle G2M phase transition and the p53 signaling pathway. Conclusion Our study highlights the characteristics of aging, inflammation and tumor in CRC and IBD at the single-cell level, and the dual property of inflammation-cancer in CRC non-malignant cells may provide a more up-to-date understanding of disease transformation.
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Affiliation(s)
- Hongchao Lv
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, Heilongjiang, China
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yu Mu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, Heilongjiang, China
| | - Chen Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Meiqi Zhao
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, Heilongjiang, China
| | - Ping Jiang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, Heilongjiang, China
| | - Shan Xiao
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, Heilongjiang, China
| | - Haiming Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, Heilongjiang, China
| | - Nan Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, Heilongjiang, China
| | - Donglin Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, Heilongjiang, China
| | - Yan Jin
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, Heilongjiang, China
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
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89
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Ren J, Lyu X, Guo J, Shi X, Zhou Y, Li Q. CDSKNN XMBD: a novel clustering framework for large-scale single-cell data based on a stable graph structure. J Transl Med 2024; 22:233. [PMID: 38433205 PMCID: PMC10910752 DOI: 10.1186/s12967-024-05009-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: 11/09/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Accurate and efficient cell grouping is essential for analyzing single-cell transcriptome sequencing (scRNA-seq) data. However, the existing clustering techniques often struggle to provide timely and accurate cell type groupings when dealing with datasets with large-scale or imbalanced cell types. Therefore, there is a need for improved methods that can handle the increasing size of scRNA-seq datasets while maintaining high accuracy and efficiency. METHODS We propose CDSKNNXMBD (Community Detection based on a Stable K-Nearest Neighbor Graph Structure), a novel single-cell clustering framework integrating partition clustering algorithm and community detection algorithm, which achieves accurate and fast cell type grouping by finding a stable graph structure. RESULTS We evaluated the effectiveness of our approach by analyzing 15 tissues from the human fetal atlas. Compared to existing methods, CDSKNN effectively counteracts the high imbalance in single-cell data, enabling effective clustering. Furthermore, we conducted comparisons across multiple single-cell datasets from different studies and sequencing techniques. CDSKNN is of high applicability and robustness, and capable of balancing the complexities of across diverse types of data. Most importantly, CDSKNN exhibits higher operational efficiency on datasets at the million-cell scale, requiring an average of only 6.33 min for clustering 1.46 million single cells, saving 33.3% to 99% of running time compared to those of existing methods. CONCLUSIONS The CDSKNN is a flexible, resilient, and promising clustering tool that is particularly suitable for clustering imbalanced data and demonstrates high efficiency on large-scale scRNA-seq datasets.
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Affiliation(s)
- Jun Ren
- School of Informatics, Xiamen University, Xiamen, 361105, China
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361102, China
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, 361102, China
| | - Xuejing Lyu
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, 361102, China
| | - Jintao Guo
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, 361102, China
| | - Xiaodong Shi
- School of Informatics, Xiamen University, Xiamen, 361105, China
| | - Ying Zhou
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361102, China.
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, 361102, China.
| | - Qiyuan Li
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361102, China.
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, 361102, China.
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90
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Wang Y, Huang M, Mu X, Song W, Guo Q, Zhang M, Liu Y, Chen YG, Ge L. TMED10-mediated unconventional secretion of IL-33 regulates intestinal epithelium differentiation and homeostasis. Cell Res 2024; 34:258-261. [PMID: 38185700 PMCID: PMC10907340 DOI: 10.1038/s41422-023-00891-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/13/2023] [Indexed: 01/09/2024] Open
Affiliation(s)
- Yang Wang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Meimei Huang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiangyue Mu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wanlu Song
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qing Guo
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Min Zhang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Yuan Liu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Ye-Guang Chen
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing, China.
- School of Basic Medicine, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China.
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing, China.
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
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91
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Goto N, Westcott PMK, Goto S, Imada S, Taylor MS, Eng G, Braverman J, Deshpande V, Jacks T, Agudo J, Yilmaz ÖH. SOX17 enables immune evasion of early colorectal adenomas and cancers. Nature 2024; 627:636-645. [PMID: 38418875 DOI: 10.1038/s41586-024-07135-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
A hallmark of cancer is the avoidance of immune destruction. This process has been primarily investigated in locally advanced or metastatic cancer1-3; however, much less is known about how pre-malignant or early invasive tumours evade immune detection. Here, to understand this process in early colorectal cancers (CRCs), we investigated how naive colon cancer organoids that were engineered in vitro to harbour Apc-null, KrasG12D and Trp53-null (AKP) mutations adapted to the in vivo native colonic environment. Comprehensive transcriptomic and chromatin analyses revealed that the endoderm-specifying transcription factor SOX17 became strongly upregulated in vivo. Notably, whereas SOX17 loss did not affect AKP organoid propagation in vitro, its loss markedly reduced the ability of AKP tumours to persist in vivo. The small fraction of SOX17-null tumours that grew displayed notable interferon-γ (IFNγ)-producing effector-like CD8+ T cell infiltrates in contrast to the immune-suppressive microenvironment in wild-type counterparts. Mechanistically, in both endogenous Apc-null pre-malignant adenomas and transplanted organoid-derived AKP CRCs, SOX17 suppresses the ability of tumour cells to sense and respond to IFNγ, preventing anti-tumour T cell responses. Finally, SOX17 engages a fetal intestinal programme that drives differentiation away from LGR5+ tumour cells to produce immune-evasive LGR5- tumour cells with lower expression of major histocompatibility complex class I (MHC-I). We propose that SOX17 is a transcription factor that is engaged during the early steps of colon cancer to orchestrate an immune-evasive programme that permits CRC initiation and progression.
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Affiliation(s)
- Norihiro Goto
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter M K Westcott
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Saori Goto
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shinya Imada
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - George Eng
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jonathan Braverman
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Hospital and Harvard Medical School, Boston, MA, USA
| | - Tyler Jacks
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Judith Agudo
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Immunology, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Boston, MA, USA.
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA, USA.
- New York Stem Cell Foundation-Robertson Investigator, New York, NY, USA.
| | - Ömer H Yilmaz
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Beth Israel Deaconess Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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92
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Huang C, Wang X, Wang Y, Feng Y, Wang X, Chen S, Yan P, Liao J, Zhang Q, Mao C, Li Y, Wang L, Wang X, Yi W, Cai W, Chen S, Hong N, He W, Chen J, Jin W. Sirpα on tumor-associated myeloid cells restrains antitumor immunity in colorectal cancer independent of its interaction with CD47. NATURE CANCER 2024; 5:500-516. [PMID: 38200243 DOI: 10.1038/s43018-023-00691-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 11/15/2023] [Indexed: 01/12/2024]
Abstract
Immunosuppressive myeloid cells hinder immunotherapeutic efficacy in tumors, but the precise mechanisms remain undefined. Here, by performing single-cell RNA sequencing in colorectal cancer tissues, we found tumor-associated macrophages and granulocytic myeloid-derived suppressor cells increased most compared to their counterparts in normal tissue and displayed the highest immune-inhibitory signatures among all immunocytes. These cells exhibited significantly increased expression of immunoreceptor tyrosine-based inhibitory motif-bearing receptors, including SIRPA. Notably, Sirpa-/- mice were more resistant to tumor progression than wild-type mice. Moreover, Sirpα deficiency reprogramed the tumor microenvironment through expansion of TAM_Ccl8hi and gMDSC_H2-Q10hi subsets showing strong antitumor activity. Sirpa-/- macrophages presented strong phagocytosis and antigen presentation to enhance T cell activation and proliferation. Furthermore, Sirpa-/- macrophages facilitated T cell recruitment via Syk/Btk-dependent Ccl8 secretion. Therefore, Sirpα deficiency enhances innate and adaptive immune activation independent of expression of CD47 and Sirpα blockade could be a promising strategy to improve cancer immunotherapy efficacy.
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Affiliation(s)
- Chunliu Huang
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xuefei Wang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yingzhao Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yongyi Feng
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiumei Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shan Chen
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Peidong Yan
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jing Liao
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Qi Zhang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Chengzhou Mao
- Department of Anatomy and Histology, Shenzhen University Health Science Center, Shenzhen, China
| | - Yang Li
- Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Lixiang Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xinyu Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wei Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Weibin Cai
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shoudeng Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China
| | - Ni Hong
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
| | - Weiling He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Department of Gastrointestinal Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China.
| | - Jun Chen
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-sen University, Guangzhou, China.
- Jinfeng Laboratory, Chongqing, China.
| | - Wenfei Jin
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
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93
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Singhal V, Chou N, Lee J, Yue Y, Liu J, Chock WK, Lin L, Chang YC, Teo EML, Aow J, Lee HK, Chen KH, Prabhakar S. BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis. Nat Genet 2024; 56:431-441. [PMID: 38413725 PMCID: PMC10937399 DOI: 10.1038/s41588-024-01664-3] [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: 04/03/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Spatial omics data are clustered to define both cell types and tissue domains. We present Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an algorithm that unifies these two spatial clustering problems by embedding cells in a product space of their own and the local neighborhood transcriptome, representing cell state and microenvironment, respectively. BANKSY's spatial feature augmentation strategy improved performance on both tasks when tested on diverse RNA (imaging, sequencing) and protein (imaging) datasets. BANKSY revealed unexpected niche-dependent cell states in the mouse brain and outperformed competing methods on domain segmentation and cell typing benchmarks. BANKSY can also be used for quality control of spatial transcriptomics data and for spatially aware batch effect correction. Importantly, it is substantially faster and more scalable than existing methods, enabling the processing of millions of cell datasets. In summary, BANKSY provides an accurate, biologically motivated, scalable and versatile framework for analyzing spatially resolved omics data.
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Affiliation(s)
- Vipul Singhal
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Nigel Chou
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Joseph Lee
- Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
| | - Yifei Yue
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Republic of Singapore
| | - Jinyue Liu
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Wan Kee Chock
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Li Lin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | | | | | - Jonathan Aow
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Hwee Kuan Lee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- School of Computing, National University of Singapore, Singapore, Republic of Singapore
- Singapore Eye Research Institute, Singapore, Republic of Singapore
- International Research Laboratory on Artificial Intelligence, Singapore, Republic of Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Kok Hao Chen
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
| | - Shyam Prabhakar
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Population and Global Health, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Republic of Singapore.
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94
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Kim J, Kim TJ, Chae S, Ha H, Park Y, Park S, Yoon CJ, Lim SA, Lee H, Kim J, Kim J, Im K, Lee K, Kim J, Kim D, Lee E, Shin MH, Park SI, Rhee I, Jung K, Lee J, Lee KH, Hwang D, Lee KM. Targeted deletion of CD244 on monocytes promotes differentiation into anti-tumorigenic macrophages and potentiates PD-L1 blockade in melanoma. Mol Cancer 2024; 23:45. [PMID: 38424542 PMCID: PMC10903025 DOI: 10.1186/s12943-024-01936-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: 09/28/2023] [Accepted: 01/07/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND In the myeloid compartment of the tumor microenvironment, CD244 signaling has been implicated in immunosuppressive phenotype of monocytes. However, the precise molecular mechanism and contribution of CD244 to tumor immunity in monocytes/macrophages remains elusive due to the co-existing lymphoid cells expressing CD244. METHODS To directly assess the role of CD244 in tumor-associated macrophages, monocyte-lineage-specific CD244-deficient mice were generated using cre-lox recombination and challenged with B16F10 melanoma. The phenotype and function of tumor-infiltrating macrophages along with antigen-specific CD8 T cells were analyzed by flow cytometry and single cell RNA sequencing data analysis, and the molecular mechanism underlying anti-tumorigenic macrophage differentiation, antigen presentation, phagocytosis was investigated ex vivo. Finally, the clinical feasibility of CD244-negative monocytes as a therapeutic modality in melanoma was confirmed by adoptive transfer experiments. RESULTS CD244fl/flLysMcre mice demonstrated a significant reduction in tumor volume (61% relative to that of the CD244fl/fl control group) 14 days after tumor implantation. Within tumor mass, CD244fl/flLysMcre mice also showed higher percentages of Ly6Clow macrophages, along with elevated gp100+IFN-γ+ CD8 T cells. Flow cytometry and RNA sequencing data demonstrated that ER stress resulted in increased CD244 expression on monocytes. This, in turn, impeded the generation of anti-tumorigenic Ly6Clow macrophages, phagocytosis and MHC-I antigen presentation by suppressing autophagy pathways. Combining anti-PD-L1 antibody with CD244-/- bone marrow-derived macrophages markedly improved tumor rejection compared to the anti-PD-L1 antibody alone or in combination with wild-type macrophages. Consistent with the murine data, transcriptome analysis of human melanoma tissue single-cell RNA-sequencing dataset revealed close association between CD244 and the inhibition of macrophage maturation and function. Furthermore, the presence of CD244-negative monocytes/macrophages significantly increased patient survival in primary and metastatic tumors. CONCLUSION Our study highlights the novel role of CD244 on monocytes/macrophages in restraining anti-tumorigenic macrophage generation and tumor antigen-specific T cell response in melanoma. Importantly, our findings suggest that CD244-deficient macrophages could potentially be used as a therapeutic agent in combination with immune checkpoint inhibitors. Furthermore, CD244 expression in monocyte-lineage cells serve as a prognostic marker in cancer patients.
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Affiliation(s)
- Jeongsoo Kim
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - Tae-Jin Kim
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, South Korea
| | - Sehyun Chae
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University, Chuncheon, 24341, South Korea
| | - Hyojeong Ha
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - Yejin Park
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - Sunghee Park
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - Chul Joo Yoon
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, 02841, South Korea
| | - Seon Ah Lim
- Department of Life Science, Ewha Womans University, Seoul, 03760, South Korea
| | - Hyemin Lee
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - Jiyoung Kim
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - Jungwon Kim
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - Kyungtaek Im
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - Kyunghye Lee
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - Jeongmin Kim
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - Daham Kim
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, South Korea
| | - Eunju Lee
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, South Korea
| | - Min Hwa Shin
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
- Immune Research Institute, Seegene Medical Foundation, Seoul, 04805, South Korea
| | - Serk In Park
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - Inmoo Rhee
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul, 05006, South Korea
| | - Keehoon Jung
- Department of Biomedical Sciences, Department of Anatomy and Cell Biology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jeewon Lee
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, 02841, South Korea
| | - Keun Hwa Lee
- Department of Microbiology, College of Medicine, Hanyang University, Seoul, 04763, South Korea.
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea.
| | - Kyung-Mi Lee
- Department of Biochemistry and Molecular biology, College of Medicine, Korea University, Seoul, 02841, South Korea.
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95
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Ash SL, Orha R, Mole H, Dinesh-Kumar M, Lee SP, Turrell FK, Isacke CM. Targeting the activated microenvironment with endosialin (CD248)-directed CAR-T cells ablates perivascular cells to impair tumor growth and metastasis. J Immunother Cancer 2024; 12:e008608. [PMID: 38413223 PMCID: PMC10900351 DOI: 10.1136/jitc-2023-008608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Targeting of solid cancers with chimeric antigen receptor (CAR)-T cells is limited by the lack of suitable tumor-specific antigens and the immunosuppressive, desmoplastic tumor microenvironment that impedes CAR-T cell infiltration, activity and persistence. We hypothesized that targeting the endosialin (CD248) receptor, strongly expressed by tumor-associated pericytes and perivascular cancer-associated fibroblasts, would circumvent these challenges and offer an exciting antigen for CAR-T cell therapy due to the close proximity of target cells to the tumor vasculature, the limited endosialin expression in normal tissues and the lack of phenotype observed in endosialin knockout mice. METHODS We generated endosialin-directed E3K CAR-T cells from three immunocompetent mouse strains, BALB/c, FVB/N and C57BL/6. E3K CAR-T cell composition (CD4+/CD8+ ratio), activity in vitro against endosialin+ and endosialin- cells, and expansion and activity in vivo in syngeneic tumor models as well as in tumor-naive healthy and wounded mice and tumor-bearing endosialin knockout mice was assessed. RESULTS E3K CAR-T cells were active in vitro against both mouse and human endosialin+, but not endosialin-, cells. Adoptively transferred E3K CAR-T cells exhibited no activity in endosialin knockout mice, tumor-naive endosialin wildtype mice or in wound healing models, demonstrating an absence of off-target and on-target/off-tumor activity. By contrast, adoptive transfer of E3K CAR-T cells into BALB/c, FVB/N or C57BL/6 mice bearing syngeneic breast or lung cancer lines depleted target cells in the tumor stroma resulting in increased tumor necrosis, reduced tumor growth and a substantial impairment in metastatic outgrowth. CONCLUSIONS Together these data highlight endosialin as a viable antigen for CAR-T cell therapy and that targeting stromal cells closely associated with the tumor vasculature avoids CAR-T cells having to navigate the harsh immunosuppressive tumor microenvironment. Further, the ability of E3K CAR-T cells to recognize and target both mouse and human endosialin+ cells makes a humanized and optimized E3K CAR a promising candidate for clinical development applicable to a broad range of solid tumor types.
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Affiliation(s)
- Sarah L Ash
- The Institute of Cancer Research, London, UK
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | | | - Holly Mole
- University of Birmingham, Birmingham, UK
| | | | | | - Frances K Turrell
- The Institute of Cancer Research, London, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
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96
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Zhu LH, Yang J, Zhang YF, Yan L, Lin WR, Liu WQ. Identification and validation of a pyroptosis-related prognostic model for colorectal cancer based on bulk and single-cell RNA sequencing data. World J Clin Oncol 2024; 15:329-355. [PMID: 38455135 PMCID: PMC10915942 DOI: 10.5306/wjco.v15.i2.329] [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: 10/01/2023] [Revised: 12/24/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Pyroptosis impacts the development of malignant tumors, yet its role in colorectal cancer (CRC) prognosis remains uncertain. AIM To assess the prognostic significance of pyroptosis-related genes and their association with CRC immune infiltration. METHODS Gene expression data were obtained from The Cancer Genome Atlas (TCGA) and single-cell RNA sequencing dataset GSE178341 from the Gene Expression Omnibus (GEO). Pyroptosis-related gene expression in cell clusters was analyzed, and enrichment analysis was conducted. A pyroptosis-related risk model was developed using the LASSO regression algorithm, with prediction accuracy assessed through K-M and receiver operating characteristic analyses. A nomogram predicting survival was created, and the correlation between the risk model and immune infiltration was analyzed using CIBERSORTx calculations. Finally, the differential expression of the 8 prognostic genes between CRC and normal samples was verified by analyzing TCGA-COADREAD data from the UCSC database. RESULTS An effective pyroptosis-related risk model was constructed using 8 genes-CHMP2B, SDHB, BST2, UBE2D2, GJA1, AIM2, PDCD6IP, and SEZ6L2 (P < 0.05). Seven of these genes exhibited differential expression between CRC and normal samples based on TCGA database analysis (P < 0.05). Patients with higher risk scores demonstrated increased death risk and reduced overall survival (P < 0.05). Significant differences in immune infiltration were observed between low- and high-risk groups, correlating with pyroptosis-related gene expression. CONCLUSION We developed a pyroptosis-related prognostic model for CRC, affirming its correlation with immune infiltration. This model may prove useful for CRC prognostic evaluation.
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Affiliation(s)
- Li-Hua Zhu
- Department of Surgical Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, China
| | - Jun Yang
- Department of Surgical Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, China
| | - Yun-Fei Zhang
- Department of Surgical Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, China
| | - Li Yan
- Department of Internal Medicine-Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, China
| | - Wan-Rong Lin
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, China
| | - Wei-Qing Liu
- Department of Internal Medicine-Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, China
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97
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Qu H, Liang Y, Guo Q, Lu L, Yang Y, Xu W, Zhang Y, Qin Y. Identifying CTH and MAP1LC3B as ferroptosis biomarkers for prognostic indication in gastric cancer decoding. Sci Rep 2024; 14:4352. [PMID: 38388661 PMCID: PMC10883967 DOI: 10.1038/s41598-024-54837-9] [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: 11/10/2023] [Accepted: 02/17/2024] [Indexed: 02/24/2024] Open
Abstract
Gastric cancer (GC), known for its high incidence and poor prognosis, urgently necessitates the identification of reliable prognostic biomarkers to enhance patient outcomes. We scrutinized data from 375 GC patients alongside 32 non-cancer controls, sourced from the TCGA database. A univariate Cox Proportional Hazards Model (COX) regression was employed to evaluate expressions of ferroptosis-related genes. This was followed by the application of Least Absolute Shrinkage and Selection Operator (LASSO) and multivariate COX regression for the development of prognostic models. The composition of immune cell subtypes was quantified utilizing CIBERSORT, with their distribution in GC versus control samples being comparatively analyzed. Furthermore, the correlation between the expressions of Cystathionine Gamma-Lyase (CTH) and Microtubule Associated Protein 1 Light Chain 3 Beta (MAP1LC3B) and the abundance of immune cell subtypes was explored. Our bioinformatics findings underwent validation through immunohistochemical analysis. Our prognostic models integrated CTH and MAP1LC3B. Survival analysis indicated that patients categorized as high-risk, as defined by the model, exhibited significantly lower survival rates compared to their low-risk counterparts. Notably, CTH expression inversely correlated with monocyte levels, while MAP1LC3B expression showed an inverse relationship with the abundance of M2 macrophages. Immunohistochemical validation corroborated lower expressions of CTH and MAP1LC3B in GC tissues relative to control samples, in concordance with our bioinformatics predictions. Our study suggests that the dysregulation of CTH, MAP1LC3B, and the accompanying monocyte-macrophage dynamics could be pivotal in the prognosis of GC. These elements present potential targets for prognostic assessment and therapeutic intervention.
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Affiliation(s)
- Haishun Qu
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yunxiao Liang
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Quan Guo
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Ling Lu
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yanwei Yang
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Weicheng Xu
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yitian Zhang
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yijue Qin
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
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98
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Hattangady NG, Carter K, Maroni-Rana B, Wang T, Ayers JL, Yu M, Grady WM. Mapping the core senescence phenotype of primary human colon fibroblasts. Aging (Albany NY) 2024; 16:3068-3087. [PMID: 38385965 PMCID: PMC10929841 DOI: 10.18632/aging.205577] [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: 05/16/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024]
Abstract
Advanced age is the largest risk factor for many diseases and several types of cancer, including colorectal cancer (CRC). Senescent cells are known to accumulate with age in various tissues, where they can modulate the surrounding tissue microenvironment through their senescence associated secretory phenotype (SASP). Recently, we showed that there is an increased number of senescent cells in the colons of CRC patients and demonstrated that senescent fibroblasts and their SASP create microniches in the colon that are conducive to CRC onset and progression. However, the composition of the SASP is heterogenous and cell-specific, and the precise senescence profile of colon fibroblasts has not been well-defined. To generate a SASP atlas of human colon fibroblasts, we induced senescence in primary human colon fibroblasts using various in vitro methods and assessed the resulting transcriptome. Using RNASequencing and further validation by quantitative RT-PCR and Luminex assays, we define and validate a 'core senescent profile' that might play a significant role in shaping the colon microenvironment. We also performed KEGG analysis and GO analyses to identify key pathways and biological processes that are differentially regulated in colon fibroblast senescence. These studies provide insights into potential driver proteins involved in senescence-associated diseases, like CRC, which may lead to therapies to improve overall health in the elderly and to prevent CRC.
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Affiliation(s)
- Namita Ganesh Hattangady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Kelly Carter
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Brett Maroni-Rana
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ting Wang
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jessica Lee Ayers
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ming Yu
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - William M. Grady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA 98195, USA
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99
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Saeed A, Park R, Pathak H, Al-Bzour AN, Dai J, Phadnis M, Al-Rajabi R, Kasi A, Baranda J, Sun W, Williamson S, Chiu YC, Osmanbeyoglu HU, Madan R, Abushukair H, Mulvaney K, Godwin AK, Saeed A. Clinical and biomarker results from a phase II trial of combined cabozantinib and durvalumab in patients with chemotherapy-refractory colorectal cancer (CRC): CAMILLA CRC cohort. Nat Commun 2024; 15:1533. [PMID: 38378868 PMCID: PMC10879200 DOI: 10.1038/s41467-024-45960-2] [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: 10/17/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
CAMILLA is a basket trial (NCT03539822) evaluating cabozantinib plus the ICI durvalumab in chemorefractory gastrointestinal cancer. Herein, are the phase II colorectal cohort results. 29 patients were evaluable. 100% had confirmed pMMR/MSS tumors. Primary endpoint was met with ORR of 27.6% (95% CI 12.7-47.2%). Secondary endpoints of 4-month PFS rate was 44.83% (95% CI 26.5-64.3%); and median OS was 9.1 months (95% CI 5.8-20.2). Grade≥3 TRAE occurred in 39%. In post-hoc analysis of patients with RAS wild type tumors, ORR was 50% and median PFS and OS were 6.3 and 21.5 months respectively. Exploratory spatial transcriptomic profiling of pretreatment tumors showed upregulation of VEGF and MET signaling, increased extracellular matrix activity and preexisting anti-tumor immune responses coexisting with immune suppressive features like T cell migration barriers in responders versus non-responders. Cabozantinib plus durvalumab demonstrated anti-tumor activity, manageable toxicity, and have led to the activation of the phase III STELLAR-303 trial.
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Affiliation(s)
- Anwaar Saeed
- Department of Medicine, Division of Hematology & Oncology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, USA.
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Robin Park
- Division of Hematology and Medical Oncology, Moffitt Cancer Cente, Tampa, FL, USA
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Ayah Nedal Al-Bzour
- Department of Medicine, Division of Hematology & Oncology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, USA
| | - Junqiang Dai
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA
| | - Milind Phadnis
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA
| | - Raed Al-Rajabi
- Department of Medicine, Division of Medical Oncology, University of Kansas Medical Center, Kansas City, Ks, USA
- University of Kansas Cancer Center, Kansas City, KS, USA
| | - Anup Kasi
- Department of Medicine, Division of Medical Oncology, University of Kansas Medical Center, Kansas City, Ks, USA
- University of Kansas Cancer Center, Kansas City, KS, USA
| | - Joaquina Baranda
- Department of Medicine, Division of Medical Oncology, University of Kansas Medical Center, Kansas City, Ks, USA
- University of Kansas Cancer Center, Kansas City, KS, USA
| | - Weijing Sun
- Department of Medicine, Division of Medical Oncology, University of Kansas Medical Center, Kansas City, Ks, USA
- University of Kansas Cancer Center, Kansas City, KS, USA
| | - Stephen Williamson
- Department of Medicine, Division of Medical Oncology, University of Kansas Medical Center, Kansas City, Ks, USA
- University of Kansas Cancer Center, Kansas City, KS, USA
| | | | | | - Rashna Madan
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Hassan Abushukair
- Department of Medicine, Division of Hematology & Oncology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, USA
| | - Kelly Mulvaney
- University of Kansas Cancer Center, Kansas City, KS, USA
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
- University of Kansas Cancer Center, Kansas City, KS, USA
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Azhar Saeed
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, USA
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100
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Bao X, Li Q, Chen D, Dai X, Liu C, Tian W, Zhang H, Jin Y, Wang Y, Cheng J, Lai C, Ye C, Xin S, Li X, Su G, Ding Y, Xiong Y, Xie J, Tano V, Wang Y, Fu W, Deng S, Fang W, Sheng J, Ruan J, Zhao P. A multiomics analysis-assisted deep learning model identifies a macrophage-oriented module as a potential therapeutic target in colorectal cancer. Cell Rep Med 2024; 5:101399. [PMID: 38307032 PMCID: PMC10897549 DOI: 10.1016/j.xcrm.2024.101399] [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: 03/06/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 02/04/2024]
Abstract
Colorectal cancer (CRC) is a common malignancy involving multiple cellular components. The CRC tumor microenvironment (TME) has been characterized well at single-cell resolution. However, a spatial interaction map of the CRC TME is still elusive. Here, we integrate multiomics analyses and establish a spatial interaction map to improve the prognosis, prediction, and therapeutic development for CRC. We construct a CRC immune module (CCIM) that comprises FOLR2+ macrophages, exhausted CD8+ T cells, tolerant CD8+ T cells, exhausted CD4+ T cells, and regulatory T cells. Multiplex immunohistochemistry is performed to depict the CCIM. Based on this, we utilize advanced deep learning technology to establish a spatial interaction map and predict chemotherapy response. CCIM-Net is constructed, which demonstrates good predictive performance for chemotherapy response in both the training and testing cohorts. Lastly, targeting FOLR2+ macrophage therapeutics is used to disrupt the immunosuppressive CCIM and enhance the chemotherapy response in vivo.
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Affiliation(s)
- Xuanwen Bao
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China.
| | - Qiong Li
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Dong Chen
- Department of Colorectal Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Xiaomeng Dai
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Chuan Liu
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Weihong Tian
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Hangyu Zhang
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Yuzhi Jin
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Yin Wang
- College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Jinlin Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Chunyu Lai
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Chanqi Ye
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Shan Xin
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Xin Li
- Department of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ge Su
- College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Yangyang Xiong
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Jindong Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Vincent Tano
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | - Yanfang Wang
- Ludwig-Maximilians-Universität München (LMU), 80539 Munich, Germany
| | - Wenguang Fu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Shuiguang Deng
- College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Weijia Fang
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Jianpeng Sheng
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China.
| | - Jian Ruan
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China; Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province 646000, China.
| | - Peng Zhao
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China.
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