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Zhou S, Lin N, Yu L, Su X, Liu Z, Yu X, Gao H, Lin S, Zeng Y. Single-cell multi-omics in the study of digestive system cancers. Comput Struct Biotechnol J 2024; 23:431-445. [PMID: 38223343 PMCID: PMC10787224 DOI: 10.1016/j.csbj.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024] Open
Abstract
Digestive system cancers are prevalent diseases with a high mortality rate, posing a significant threat to public health and economic burden. The diagnosis and treatment of digestive system cancer confront conventional cancer problems, such as tumor heterogeneity and drug resistance. Single-cell sequencing (SCS) emerged at times required and has developed from single-cell RNA-seq (scRNA-seq) to the single-cell multi-omics era represented by single-cell spatial transcriptomics (ST). This article comprehensively reviews the advances of single-cell omics technology in the study of digestive system tumors. While analyzing and summarizing the research cases, vital details on the sequencing platform, sample information, sampling method, and key findings are provided. Meanwhile, we summarize the commonly used SCS platforms and their features, as well as the advantages of multi-omics technologies in combination. Finally, the development trends and prospects of the application of single-cell multi-omics technology in digestive system cancer research are prospected.
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Affiliation(s)
- Shuang Zhou
- The Second Clinical Medical School of Fujian Medical University, Quanzhou, Fujian Province, China
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Nanfei Lin
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Liying Yu
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Xiaoshan Su
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
| | - Zhenlong Liu
- Lady Davis Institute for Medical Research, Jewish General Hospital, & Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC, Canada
| | - Xiaowan Yu
- Clinical Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Hongzhi Gao
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Shu Lin
- Centre of Neurological and Metabolic Research, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia
| | - Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
- Fujian Provincial Key Laboratory of Lung Stem Cells, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong Province, China
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Fu C, Wang J, Ma T, Yin C, Zhou L, Clausen BE, Mi QS, Jiang A. β-Catenin in Dendritic Cells Negatively Regulates CD8 T Cell Immune Responses through the Immune Checkpoint Molecule Tim-3. Vaccines (Basel) 2024; 12:460. [PMID: 38793711 PMCID: PMC11125945 DOI: 10.3390/vaccines12050460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Recent studies have demonstrated that β-catenin in dendritic cells (DCs) serves as a key mediator in promoting both CD4 and CD8 T cell tolerance, although the mechanisms underlying how β-catenin exerts its functions remain incompletely understood. Here, we report that activation of β-catenin leads to the up-regulation of inhibitory molecule T-cell immunoglobulin and mucin domain 3 (Tim-3) in type 1 conventional DCs (cDC1s). Using a cDC1-targeted vaccine model with anti-DEC-205 engineered to express the melanoma antigen human gp100 (anti-DEC-205-hgp100), we demonstrated that CD11c-β-cateninactive mice exhibited impaired cross-priming and memory responses of gp100-specific CD8 T (Pmel-1) cells upon immunization with anti-DEC-205-hgp100. Single-cell RNA sequencing (scRNA-seq) analysis revealed that β-catenin in DCs negatively regulated transcription programs for effector function and proliferation of primed Pmel-1 cells, correlating with suppressed CD8 T cell immunity in CD11c-β-cateninactive mice. Further experiments showed that treating CD11c-β-cateninactive mice with an anti-Tim-3 antibody upon anti-DEC-205-hgp100 vaccination led to restored cross-priming and memory responses of gp100-specific CD8 T cells, suggesting that anti-Tim-3 treatment likely synergizes with DC vaccines to improve their efficacy. Indeed, treating B16F10-bearing mice with DC vaccines using anti-DEC-205-hgp100 in combination with anti-Tim-3 treatment resulted in significantly reduced tumor growth compared with treatment with the DC vaccine alone. Taken together, we identified the β-catenin/Tim-3 axis as a potentially novel mechanism to inhibit anti-tumor CD8 T cell immunity and that combination immunotherapy of a DC-targeted vaccine with anti-Tim-3 treatment leads to improved anti-tumor efficacy.
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Affiliation(s)
- Chunmei Fu
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI 48202, USA; (C.F.); (J.W.); (C.Y.); (L.Z.)
- Immunology Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI 48202, USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Jie Wang
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI 48202, USA; (C.F.); (J.W.); (C.Y.); (L.Z.)
- Immunology Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI 48202, USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Tianle Ma
- Department of Computer Science and Engineering, School of Engineering and Computer Science, Oakland University, Rochester, MI 48309, USA;
| | - Congcong Yin
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI 48202, USA; (C.F.); (J.W.); (C.Y.); (L.Z.)
- Immunology Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI 48202, USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Li Zhou
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI 48202, USA; (C.F.); (J.W.); (C.Y.); (L.Z.)
- Immunology Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI 48202, USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
- Department of Internal Medicine, Henry Ford Health, Detroit, MI 48202, USA
| | - Björn E. Clausen
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany;
| | - Qing-Sheng Mi
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI 48202, USA; (C.F.); (J.W.); (C.Y.); (L.Z.)
- Immunology Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI 48202, USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
- Department of Internal Medicine, Henry Ford Health, Detroit, MI 48202, USA
| | - Aimin Jiang
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI 48202, USA; (C.F.); (J.W.); (C.Y.); (L.Z.)
- Immunology Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI 48202, USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
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Pei XZ, Cai M, Jiang DW, Chen SH, Wang QQ, Lu HM, Lu YF. FAM53B promotes pancreatic ductal adenocarcinoma metastasis by regulating macrophage M2 polarization. World J Gastrointest Oncol 2024; 16:1479-1499. [PMID: 38660645 PMCID: PMC11037046 DOI: 10.4251/wjgo.v16.i4.1479] [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: 11/20/2023] [Revised: 01/08/2024] [Accepted: 03/01/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Our study investigated the role of FAM53B in regulating macrophage M2 polarization and its potential mechanisms in promoting pancreatic ductal adenocarcinoma (PDAC) metastasis. AIM To further investigate the role of FAM53B in regulating macrophage M2 polarization and its potential mechanism in promoting PDAC metastasis. Our goal is to determine how FAM53B affects macrophage M2 polarization and to define its underlying mechanism in PDAC metastasis. METHODS Cell culture and various experiments, including protein analysis, immunohistochemistry, and animal model experiments, were conducted. We compared FAM53B expression between PDAC tissues and healthy tissues and assessed the correlation of FAM53B expression with clinical features. Our study analyzed the role of FAM53B in macrophage M2 polarization in vitro by examining the expression of relevant markers. Finally, we used a murine model to study the role of FAM53B in PDAC metastasis and analyzed the potential underlying mechanisms. RESULTS Our research showed that there was a significant increase in FAM53B levels in PDAC tissues, which was linked to adverse tumor features. Experimental findings indicated that FAM53B can enhance macrophage M2 polarization, leading to increased anti-inflammatory factor release. The results from the mouse model further supported the role of FAM53B in PDAC metastasis, as blocking FAM53B prevented tumor cell invasion and metastasis. CONCLUSION FAM53B promotes PDAC metastasis by regulating macrophage M2 polarization. This discovery could lead to the development of new strategies for treating PDAC. For example, interfering with the FAM53B signaling pathway may prevent cancer spread. Our research findings also provide important information for expanding our understanding of PDAC pathogenesis.
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Affiliation(s)
- Xuan-Zeng Pei
- Department of Hepatological Surgery, The First Hospital of Jiaxing, Jiaxing 314000, Zhejiang Province, China
| | - Min Cai
- Department of Hepatological Surgery, The First Hospital of Jiaxing, Jiaxing 314000, Zhejiang Province, China
| | - Da-Wei Jiang
- Department of Hepatological Surgery, The First Hospital of Jiaxing, Jiaxing 314000, Zhejiang Province, China
| | - Song-Hai Chen
- Department of Hepatological Surgery, The First Hospital of Jiaxing, Jiaxing 314000, Zhejiang Province, China
| | - Qing-Qing Wang
- Department of Hepatological Surgery, The First Hospital of Jiaxing, Jiaxing 314000, Zhejiang Province, China
| | - Hui-Min Lu
- Department of General Surgery, West China Hospital of Sichuan University, Chengdu 610044, Sichuan Province, China
| | - Yi-Fan Lu
- Department of Hepatological Surgery, The First Hospital of Jiaxing, Jiaxing 314000, Zhejiang Province, China
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Guo D, Sheng K, Zhang Q, Li P, Sun H, Wang Y, Lyu X, Jia Y, Wang C, Wu J, Zhang X, Wang D, Sun Y, Huang S, Yu J, Zhang J. Single-cell transcriptomic analysis reveals the landscape of epithelial-mesenchymal transition molecular heterogeneity in esophageal squamous cell carcinoma. Cancer Lett 2024; 587:216723. [PMID: 38342234 DOI: 10.1016/j.canlet.2024.216723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/13/2024]
Abstract
Esophageal squamous cell carcinoma (ESCC) is a prevalent and highly lethal malignant disease. The epithelial-mesenchymal transition (EMT) is crucial in promoting ESCC development. However, the molecular heterogeneity of ESCC and the potential inhibitory strategies targeting EMT remain poorly understood. In this study, we analyzed high-resolution single-cell transcriptome data encompassing 209,231 ESCC cells from 39 tumor samples and 16 adjacent samples obtained from 44 individuals. We identified distinct cell populations exhibiting heterogeneous EMT characteristics and identified 87 EMT-associated molecules. The expression profiles of these EMT-associated molecules showed heterogeneity across different stages of ESCC progression. Moreover, we observed that EMT primarily occurred in early-stage tumors, before lymph node metastasis, and significantly promoted the rapid deterioration of ESCC. Notably, we identified SERPINH1 as a potential novel marker for ESCC EMT. By classifying ESCC patients based on EMT gene sets, we found that those with high EMT exhibited poorer prognosis. Furthermore, we predicted and experimentally validated drugs targeting ESCC EMT, including dactolisib, docetaxel, and nutlin, which demonstrated efficacy in inhibiting EMT and metastasis in ESCC. Through the integration of scRNA-seq, RNA-seq, and TCGA data with experimental validation, our comprehensive analysis elucidated the landscape of EMT during the entire course of ESCC development and metastasis. These findings provide valuable insights and a reference for refining ESCC clinical treatment strategies.
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Affiliation(s)
- Dianhao Guo
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Kaiwen Sheng
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Qi Zhang
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Pin Li
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Haoqiang Sun
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Yongjie Wang
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Xinxing Lyu
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Yang Jia
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250117, China.
| | - Caifan Wang
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Jing Wu
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Xiaohang Zhang
- Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau.
| | - Dandan Wang
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Yawen Sun
- Department of Clinical Epidemiology and Biostatistics, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Shuhong Huang
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Jinming Yu
- Department of Radiation Oncology and Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China; Research Unit of Radiation Oncology, Chinese Academy of Medical Sciences, Jinan, Shandong, China.
| | - Jingze Zhang
- Department of Radiation Oncology and Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
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Tognarelli EI, Gutiérrez-Vera C, Palacios PA, Pasten-Ferrada IA, Aguirre-Muñoz F, Cornejo DA, González PA, Carreño LJ. Natural Killer T Cell Diversity and Immunotherapy. Cancers (Basel) 2023; 15:5737. [PMID: 38136283 PMCID: PMC10742272 DOI: 10.3390/cancers15245737] [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: 11/03/2023] [Revised: 11/28/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
Invariant natural killer T cells (iNKTs), a type of unconventional T cells, share features with NK cells and have an invariant T cell receptor (TCR), which recognizes lipid antigens loaded on CD1d molecules, a major histocompatibility complex class I (MHC-I)-like protein. This interaction produces the secretion of a wide array of cytokines by these cells, including interferon gamma (IFN-γ) and interleukin 4 (IL-4), allowing iNKTs to link innate with adaptive responses. Interestingly, molecules that bind CD1d have been identified that enable the modulation of these cells, highlighting their potential pro-inflammatory and immunosuppressive capacities, as required in different clinical settings. In this review, we summarize key features of iNKTs and current understandings of modulatory α-galactosylceramide (α-GalCer) variants, a model iNKT cell activator that can shift the outcome of adaptive immune responses. Furthermore, we discuss advances in the development of strategies that modulate these cells to target pathologies that are considerable healthcare burdens. Finally, we recapitulate findings supporting a role for iNKTs in infectious diseases and tumor immunotherapy.
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Affiliation(s)
- Eduardo I. Tognarelli
- Millennium Institute on Immunology and Immunotherapy, Santiago 8330025, Chile; (E.I.T.); (C.G.-V.); (P.A.P.); (I.A.P.-F.); (F.A.-M.); (D.A.C.)
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Cristián Gutiérrez-Vera
- Millennium Institute on Immunology and Immunotherapy, Santiago 8330025, Chile; (E.I.T.); (C.G.-V.); (P.A.P.); (I.A.P.-F.); (F.A.-M.); (D.A.C.)
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
| | - Pablo A. Palacios
- Millennium Institute on Immunology and Immunotherapy, Santiago 8330025, Chile; (E.I.T.); (C.G.-V.); (P.A.P.); (I.A.P.-F.); (F.A.-M.); (D.A.C.)
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
| | - Ignacio A. Pasten-Ferrada
- Millennium Institute on Immunology and Immunotherapy, Santiago 8330025, Chile; (E.I.T.); (C.G.-V.); (P.A.P.); (I.A.P.-F.); (F.A.-M.); (D.A.C.)
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Fernanda Aguirre-Muñoz
- Millennium Institute on Immunology and Immunotherapy, Santiago 8330025, Chile; (E.I.T.); (C.G.-V.); (P.A.P.); (I.A.P.-F.); (F.A.-M.); (D.A.C.)
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
| | - Daniel A. Cornejo
- Millennium Institute on Immunology and Immunotherapy, Santiago 8330025, Chile; (E.I.T.); (C.G.-V.); (P.A.P.); (I.A.P.-F.); (F.A.-M.); (D.A.C.)
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Pablo A. González
- Millennium Institute on Immunology and Immunotherapy, Santiago 8330025, Chile; (E.I.T.); (C.G.-V.); (P.A.P.); (I.A.P.-F.); (F.A.-M.); (D.A.C.)
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Leandro J. Carreño
- Millennium Institute on Immunology and Immunotherapy, Santiago 8330025, Chile; (E.I.T.); (C.G.-V.); (P.A.P.); (I.A.P.-F.); (F.A.-M.); (D.A.C.)
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
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