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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Xu Z, Li W, Dong X, Chen Y, Zhang D, Wang J, Zhou L, He G. Precision medicine in colorectal cancer: Leveraging multi-omics, spatial omics, and artificial intelligence. Clin Chim Acta 2024; 559:119686. [PMID: 38663471 DOI: 10.1016/j.cca.2024.119686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related deaths. Recent advancements in genomic technologies and analytical approaches have revolutionized CRC research, enabling precision medicine. This review highlights the integration of multi-omics, spatial omics, and artificial intelligence (AI) in advancing precision medicine for CRC. Multi-omics approaches have uncovered molecular mechanisms driving CRC progression, while spatial omics have provided insights into the spatial heterogeneity of gene expression in CRC tissues. AI techniques have been utilized to analyze complex datasets, identify new treatment targets, and enhance diagnosis and prognosis. Despite the tumor's heterogeneity and genetic and epigenetic complexity, the fusion of multi-omics, spatial omics, and AI shows the potential to overcome these challenges and advance precision medicine in CRC. The future lies in integrating these technologies to provide deeper insights and enable personalized therapies for CRC patients.
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Affiliation(s)
- Zishan Xu
- Department of Pathology, Xinxiang Medical University, Xinxiang 453000, China
| | - Wei Li
- School of Forensic Medicine, Xinxiang Medical University, Xinxiang 453000, China
| | - Xiangyang Dong
- Department of Pathology, Xinxiang Medical University, Xinxiang 453000, China
| | - Yingying Chen
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453000, China
| | - Dan Zhang
- Department of Pathology, Xinxiang Medical University, Xinxiang 453000, China
| | - Jingnan Wang
- Xinxiang Medical University SanQuan Medical College, Xinxiang 453003, China
| | - Lin Zhou
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Guoyang He
- Department of Pathology, Xinxiang Medical University, Xinxiang 453000, China.
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Hashimoto M, Kojima Y, Sakamoto T, Ozato Y, Nakano Y, Abe T, Hosoda K, Saito H, Higuchi S, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Hata T, Nagayama S, Kagawa K, Goto Y, Utou M, Gamachi A, Imamura K, Kuze Y, Zenkoh J, Suzuki A, Takahashi K, Niida A, Hirose H, Hayashi S, Koseki J, Fukuchi S, Murakami K, Yoshizumi T, Kadomatsu K, Tobo T, Oda Y, Uemura M, Eguchi H, Doki Y, Mori M, Oshima M, Shibata T, Suzuki Y, Shimamura T, Mimori K. Spatial and single-cell colocalisation analysis reveals MDK-mediated immunosuppressive environment with regulatory T cells in colorectal carcinogenesis. EBioMedicine 2024:105102. [PMID: 38614865 DOI: 10.1016/j.ebiom.2024.105102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/15/2024] Open
Abstract
BACKGROUND Cell-cell interaction factors that facilitate the progression of adenoma to sporadic colorectal cancer (CRC) remain unclear, thereby hindering patient survival. METHODS We performed spatial transcriptomics on five early CRC cases, which included adenoma and carcinoma, and one advanced CRC. To elucidate cell-cell interactions within the tumour microenvironment (TME), we investigated the colocalisation network at single-cell resolution using a deep generative model for colocalisation analysis, combined with a single-cell transcriptome, and assessed the clinical significance in CRC patients. FINDINGS CRC cells colocalised with regulatory T cells (Tregs) at the adenoma-carcinoma interface. At early-stage carcinogenesis, cell-cell interaction inference between colocalised adenoma and cancer epithelial cells and Tregs based on the spatial distribution of single cells highlighted midkine (MDK) as a prominent signalling molecule sent from tumour epithelial cells to Tregs. Interaction between MDK-high CRC cells and SPP1+ macrophages and stromal cells proved to be the mechanism underlying immunosuppression in the TME. Additionally, we identified syndecan4 (SDC4) as a receptor for MDK associated with Treg colocalisation. Finally, clinical analysis using CRC datasets indicated that increased MDK/SDC4 levels correlated with poor overall survival in CRC patients. INTERPRETATION MDK is involved in the immune tolerance shown by Tregs to tumour growth. MDK-mediated formation of the TME could be a potential target for early diagnosis and treatment of CRC. FUNDING Japan Society for the Promotion of Science (JSPS) Grant-in-Aid for Science Research; OITA Cancer Research Foundation; AMED under Grant Number; Japan Science and Technology Agency (JST); Takeda Science Foundation; The Princess Takamatsu Cancer Research Fund.
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Affiliation(s)
- Masahiro Hashimoto
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yasuhiro Kojima
- Division of Computational Bioscience, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Takeharu Sakamoto
- Department of Cancer Biology, Institute of Biomedical Science, Kansai Medical University, Hirakata, 573-1010, Japan.
| | - Yuki Ozato
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yusuke Nakano
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Tadashi Abe
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Kiyotaka Hosoda
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Hideyuki Saito
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of General Surgical Science, Gastroenterological Surgery, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Satoshi Higuchi
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yuichi Hisamatsu
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Takeo Toshima
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Yusuke Yonemura
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Tsuyoshi Hata
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Satoshi Nagayama
- Department of Surgery, Uji-Tokushukai Medical Center, Uji, 611-0041, Japan
| | - Koichi Kagawa
- Department of Gastroenterology, Shin Beppu Hospital, Beppu, 874-8538, Japan
| | - Yasuhiro Goto
- Department of Gastroenterology, Shin Beppu Hospital, Beppu, 874-8538, Japan
| | - Mitsuaki Utou
- Department of Pathology, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Ayako Gamachi
- Department of Pathology, Oita Oka Hospital, Oita, 870-0192, Japan
| | - Kiyomi Imamura
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Yuta Kuze
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Junko Zenkoh
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Ayako Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Kazuki Takahashi
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Atsushi Niida
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Haruka Hirose
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Shuto Hayashi
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Jun Koseki
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Satoshi Fukuchi
- Department of Gastroenterological Medicine, Almeida Memorial Hospital, Oita, 870-1195, Japan
| | - Kazunari Murakami
- Department of Gastroenterology, Oita University Hospital, Yufu, 879-5593, Japan
| | - Tomoharu Yoshizumi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kenji Kadomatsu
- Department of Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Taro Tobo
- Department of Pathology, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Kyushu University Hospital, Fukuoka, 812-8582, Japan
| | - Mamoru Uemura
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Masaki Mori
- Tokai University School of Medicine, Isehara, 259-1193, Japan
| | - Masanobu Oshima
- Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Tatsuhiro Shibata
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan; Department of Computational and Systems Biology, Medical Research Insitute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-0034, Japan.
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan.
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Gan Q, Li Y, Li Y, Liu H, Chen D, Liu L, Peng C. Pathways and molecules for overcoming immunotolerance in metastatic gastrointestinal tumors. Front Immunol 2024; 15:1359914. [PMID: 38646539 PMCID: PMC11026648 DOI: 10.3389/fimmu.2024.1359914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Worldwide, gastrointestinal (GI) cancer is recognized as one of the leading malignancies diagnosed in both genders, with mortality largely attributed to metastatic dissemination. It has been identified that in GI cancer, a variety of signaling pathways and key molecules are modified, leading to the emergence of an immunotolerance phenotype. Such modifications are pivotal in the malignancy's evasion of immune detection. Thus, a thorough analysis of the pathways and molecules contributing to GI cancer's immunotolerance is vital for advancing our comprehension and propelling the creation of efficacious pharmacological treatments. In response to this necessity, our review illuminates a selection of groundbreaking cellular signaling pathways associated with immunotolerance in GI cancer, including the Phosphoinositide 3-kinases/Akt, Janus kinase/Signal Transducer and Activator of Transcription 3, Nuclear Factor kappa-light-chain-enhancer of activated B cells, Transforming Growth Factor-beta/Smad, Notch, Programmed Death-1/Programmed Death-Ligand 1, and Wingless and INT-1/beta-catenin-Interleukin 10. Additionally, we examine an array of pertinent molecules like Indoleamine-pyrrole 2,3-dioxygenase, Human Leukocyte Antigen G/E, Glycoprotein A Repetitions Predominant, Clever-1, Interferon regulatory factor 8/Osteopontin, T-cell immunoglobulin and mucin-domain containing-3, Carcinoembryonic antigen-related cell adhesion molecule 1, Cell division control protein 42 homolog, and caspases-1 and -12.
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Affiliation(s)
- Qixin Gan
- 1Department of Radiology, First Affiliated Hospital of Hunan College of TCM (Hunan Province Directly Affiliated TCM Hospital), Zhuzhou, Hunan, China
| | - Yue Li
- Department of Cardiovascular Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yuejun Li
- Department of Oncology, First Affiliated Hospital of Hunan College of TCM (Hunan Province Directly Affiliated TCM Hospital), Zhuzhou, Hunan, China
| | - Haifen Liu
- 1Department of Radiology, First Affiliated Hospital of Hunan College of TCM (Hunan Province Directly Affiliated TCM Hospital), Zhuzhou, Hunan, China
| | - Daochuan Chen
- 1Department of Radiology, First Affiliated Hospital of Hunan College of TCM (Hunan Province Directly Affiliated TCM Hospital), Zhuzhou, Hunan, China
| | - Lanxiang Liu
- 1Department of Radiology, First Affiliated Hospital of Hunan College of TCM (Hunan Province Directly Affiliated TCM Hospital), Zhuzhou, Hunan, China
| | - Churan Peng
- 1Department of Radiology, First Affiliated Hospital of Hunan College of TCM (Hunan Province Directly Affiliated TCM Hospital), Zhuzhou, Hunan, China
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Wang S, Wang J, Xia Y, Zhang L, Jiang Y, Liu M, Gao Q, Zhang C. Harnessing the potential of HLA-G in cancer therapy: advances, challenges, and prospects. J Transl Med 2024; 22:130. [PMID: 38310272 PMCID: PMC10838004 DOI: 10.1186/s12967-024-04938-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/27/2024] [Indexed: 02/05/2024] Open
Abstract
Immune checkpoint blockades have been prized in circumventing and ablating the impediments posed by immunosuppressive receptors, reaching an exciting juncture to be an innovator in anticancer therapy beyond traditional therapeutics. Thus far, approved immune checkpoint blockades have principally targeted PD-1/PD-L1 and CTLA-4 with exciting success in a plethora of tumors and yet are still trapped in dilemmas of limited response rates and adverse effects. Hence, unveiling new immunotherapeutic targets has aroused immense scientific interest in the hope of expanding the clinical application of immune checkpoint blockades to scale new heights. Human leukocyte antigen-G (HLA-G), a non-classical major histocompatibility complex (MHC) class I molecule, is enriched on various malignant cells and is involved in the hindrance of immune effector cells and the facilitation of immunosuppressive cells. HLA-G stands out as a crucial next-generation immune checkpoint showing great promise for the benefit of cancer patients. Here, we provide an overview of the current understanding of the expression pattern and immunological functions of HLA-G, as well as its interaction with well-characterized immune checkpoints. Since HLA-G can be shed from the cell surface or released by various cells as free soluble HLA-G (sHLA-G) or as part of extracellular vesicles (EVs), namely HLA-G-bearing EVs (HLA-GEV), we discuss the potential of sHLA-G and HLA-GEV as predictive biomarkers. This review also addresses the advancement of HLA-G-based therapies in preclinical and clinical settings, with a focus on their clinical application in cancer.
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Affiliation(s)
- Siyuan Wang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Jiaxin Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Yu Xia
- Cancer Biology Research Center (Key Laboratory of Chinese Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Le Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Yueqiang Jiang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Man Liu
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Qinglei Gao
- Cancer Biology Research Center (Key Laboratory of Chinese Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, China.
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.
| | - Cuntai Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.
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Wang J, Zhu N, Su X, Gao Y, Yang R. Novel tumor-associated macrophage populations and subpopulations by single cell RNA sequencing. Front Immunol 2024; 14:1264774. [PMID: 38347955 PMCID: PMC10859433 DOI: 10.3389/fimmu.2023.1264774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/30/2023] [Indexed: 02/15/2024] Open
Abstract
Tumor-associated macrophages (TAMs) are present in almost all solid tumor tissues. 16They play critical roles in immune regulation, tumor angiogenesis, tumor stem cell activation, tumor invasion and metastasis, and resistance to therapy. However, it is unclear how TAMs perform these functions. With the application of single-cell RNA sequencing (scRNA-seq), it has become possible to identify TAM subpopulations associated with distinct functions. In this review, we discuss four novel TAM subpopulations in distinct solid tumors based on core gene signatures by scRNA-seq, including FCN1 +, SPP1 +, C1Q + and CCL18 + TAMs. Functional enrichment and gene expression in scRNA-seq data from different solid tumor tissues found that FCN1 + TAMs may induce inflammation; SPP1 + TAMs are potentially involved in metastasis, angiogenesis, and cancer cell stem cell activation, whereas C1Q + TAMs participate in immune regulation and suppression; And CCL18 + cells are terminal immunosuppressive macrophages that not only have a stronger immunosuppressive function but also enhance tumor metastasis. SPP1 + and C1Q + TAM subpopulations can be further divided into distinct populations with different functions. Meanwhile, we will also present emerging evidence highlighting the separating macrophage subpopulations associated with distinct functions. However, there exist the potential disconnects between cell types and subpopulations identified by scRNA-seq and their actual function.
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Affiliation(s)
- Juanjuan Wang
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Ningning Zhu
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Xiaomin Su
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Yunhuan Gao
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Rongcun Yang
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
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Xu K, Yu D, Zhang S, Chen L, Liu Z, Xie L. Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data. Genes (Basel) 2024; 15:100. [PMID: 38254989 PMCID: PMC10815467 DOI: 10.3390/genes15010100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
The heterogeneity and intricate cellular architecture of complex cellular ecosystems play a crucial role in the progression and therapeutic response of cancer. Understanding the regulatory relationships of malignant cells at the invasive front of the tumor microenvironment (TME) is important to explore the heterogeneity of the TME and its role in disease progression. In this study, we inferred malignant cells at the invasion front by analyzing single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) data of ER-positive (ER+) breast cancer patients. In addition, we developed a software pipeline for constructing intercellular gene regulatory networks (IGRNs), which help to reduce errors generated by single-cell communication analysis and increase the confidence of selected cell communication signals. Based on the constructed IGRN between malignant cells at the invasive front of the TME and the immune cells of ER+ breast cancer patients, we found that a high expression of the transcription factors FOXA1 and EZH2 played a key role in driving tumor progression. Meanwhile, elevated levels of their downstream target genes (ESR1 and CDKN1A) were associated with poor prognosis of breast cancer patients. This study demonstrates a bioinformatics workflow of combining scRNA-seq and ST data; in addition, the study provides the software pipelines for constructing IGRNs automatically (cIGRN). This strategy will help decipher cancer progression by revealing bidirectional signaling between invasive frontline malignant tumor cells and immune cells, and the selected signaling molecules in the regulatory network may serve as biomarkers for mechanism studies or therapeutic targets.
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Affiliation(s)
- Kun Xu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China;
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, The Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (D.Y.); (S.Z.)
| | - Dongshuo Yu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, The Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (D.Y.); (S.Z.)
| | - Siwen Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, The Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (D.Y.); (S.Z.)
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China;
| | - Zhenhao Liu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, The Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (D.Y.); (S.Z.)
| | - Lu Xie
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China;
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, The Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (D.Y.); (S.Z.)
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8
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Jing R, Bai S, Zhang P, Ren H, Jia L, Li W, Zheng G. IDO-1 impairs antitumor immunity of natural killer cells in triple-negative breast cancer via up-regulation of HLA-G. Breast Cancer 2024; 31:135-147. [PMID: 37981615 PMCID: PMC10764509 DOI: 10.1007/s12282-023-01522-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/28/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND Triple-negative breast cancers (TNBC) are highly aggressive malignancies with poor prognosis. As an essential enzyme in the tryptophan-kynurenine metabolic pathway, indoleamine 2,3 dioxygenase-1 (IDO-1) has been reported to facilitate immune escape of various tumors. However, the mechanism underlying the immunosuppressive role of IDO-1 in TNBC remains largely uncharacterized. METHODS We examined the IDO-1 expression in 93 clinical TNBC tissues and paired adjacent normal tissues, and analyzed the regulation role of environmental cytokines like IFN-γ in IDO-1 expression. The effect of IDO-1 expression in TNBC cells on the function of NK cells were then evaluated and the underlying mechanisms were exploited. RESULTS IDO-1 expressed in 50 of 93 (54.1%) TNBC patients. TNBC patients with high IDO-1 expression tended to have more infiltrated immune cells including NK cells, which are less active than patients with low IDO-1 expression. NK cells could produce IFN-γ, which induced IDO-1 expression in TNBC cells, whereas IDO-1 impaired the cytotoxicity of co-cultured NK cells by upregulation of HLA-G. Blockade of HLA-G improved the antitumor activity of NK cells to TNBC in vivo. CONCLUSION TNBC cells induce dysfunction of NK cells through an IFN-γ/IDO-1/HLA-G pathway, which provide novel insights into the mechanisms of TNBC progression and demonstrate the applicability of IDO-1 and HLA-G targeting in the treatment of TNBC.
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Affiliation(s)
- Rui Jing
- College of Life Sciences, Northwest University, Xi'an, 710069, China
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Shukun Bai
- College of Life Sciences, Northwest University, Xi'an, 710069, China
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Peipei Zhang
- College of Life Sciences, Northwest University, Xi'an, 710069, China
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Hao Ren
- Department of Urology, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710038, China
| | - Lintao Jia
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Weimiao Li
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, 710004, China.
| | - Guoxu Zheng
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Immunology, Fourth Military Medical University, 169 Changle West Road, Xi'an, 710032, China.
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9
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Ding K, Mou P, Wang Z, Liu S, Liu J, Lu H, Yu G. The next bastion to be conquered in immunotherapy: microsatellite stable colorectal cancer. Front Immunol 2023; 14:1298524. [PMID: 38187388 PMCID: PMC10770832 DOI: 10.3389/fimmu.2023.1298524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer-related deaths worldwide, and its incidence continues to rise, particularly in developing countries. The advent of immune checkpoint inhibitors (ICIs) has represented a significant advancement in CRC treatment. Deficient mismatch repair (dMMR) or high microsatellite instability (MSI-H) serves as a biomarker for immunotherapy, with dMMR/MSI-H CRC exhibiting significantly better response rates to immunotherapy compared to proficient mismatch repair (pMMR)or microsatellite stable (MSS) CRC. While some progress has been made in the treatment of pMMR/MSS CRC in recent years, it remains a challenging issue in clinical practice. The tumor microenvironment (TME) plays a crucial role not only in the development and progression of CRC but also in determining the response to immunotherapy. Understanding the characteristics of the TME in pMMR/MSS CRC could offer new insights to enhance the efficacy of immunotherapy. In this review, we provide an overview of the current research progress on the TME characteristics and advancements in immunotherapy for pMMR/MSS CRC.
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Affiliation(s)
- Kai Ding
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Pei Mou
- Department of Ophthalmology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Zhe Wang
- Department of General Surgery, Pudong New Area People’s Hospital, Shanghai, China
| | - Shuqing Liu
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - JinPei Liu
- Department of Gastroenterology, Gongli Hospital of Shanghai Pudong New Area, Shanghai, China
| | - Hao Lu
- Department of General Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Ganjun Yu
- Department of Immunology, College of Basic Medicine & National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai, China
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10
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Nasir I, McGuinness C, Poh AR, Ernst M, Darcy PK, Britt KL. Tumor macrophage functional heterogeneity can inform the development of novel cancer therapies. Trends Immunol 2023; 44:971-985. [PMID: 37995659 DOI: 10.1016/j.it.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/25/2023]
Abstract
Macrophages represent a key component of the tumor microenvironment (TME) and are largely associated with poor prognosis. Therapeutic targeting of macrophages has historically focused on inhibiting their recruitment or reprogramming their phenotype from a protumor (M2-like) to an antitumor (M1-like) one. Unfortunately, this approach has not provided clinical breakthroughs that have changed practice. Emerging studies utilizing single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics have improved our understanding of the ontogeny, phenotype, and functional plasticity of macrophages. Overlaying the wealth of current information regarding macrophage molecular subtypes and functions has also identified novel therapeutic vulnerabilities that might drive better control of tumor-associated macrophages (TAMs). Here, we discuss the functional profiling of macrophages and provide an update of novel macrophage-targeted therapies in development.
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Affiliation(s)
- Ibraheem Nasir
- Breast Cancer Risk and Prevention Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Conor McGuinness
- Breast Cancer Risk and Prevention Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Melbourne, VIC 3000, Australia
| | - Ashleigh R Poh
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia; La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia; La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Phillip K Darcy
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Melbourne, VIC 3000, Australia; Cancer Immunology Research Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Kara L Britt
- Breast Cancer Risk and Prevention Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Melbourne, VIC 3000, Australia.
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11
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Alzamami A. Implications of single-cell immune landscape of tumor microenvironment for the colorectal cancer diagnostics and therapy. Med Oncol 2023; 40:352. [PMID: 37950801 DOI: 10.1007/s12032-023-02226-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/18/2023] [Indexed: 11/13/2023]
Abstract
Colorectal cancer (CRC) originates from the polyps lining the colon and is among the most common types of cancer. With the increasing popularity of single-cell sequencing technologies, researchers have been able to better understand the immune landscape of colorectal cancer, by analyzing their expression and interactions in detail with the tumor microenvironment (TME) at single-cell level. Since the tumor-immune cell interactions play a critical part in the advancement as well as treatment response in colorectal cancer, the release of inhibitory factors such as T cells are important for recognizing and destroying cancer cells. Such information is vital to identify immunotherapeutic targets for cure and monitoring response to treatments. Therefore, a comprehensive single-cell studies-based overview of key immunogenic agents regulating the TME of CRC is provided in this review. Tumor-associated macrophages can promote tumor growth and resistance to treatment by releasing factors that inhibit the function of other immune cells. Additionally, colorectal cancer cells can express programmed cell death protein 1 and its ligand, which can also inhibit T-cell function. Researchers have found that certain types of immune cells, prominently T cells, natural killer, and dendritic cells, can have a positive impact on the prognosis of colorectal cancer patients. Treatments like immune checkpoint inhibitors and CAR-T therapies that help to release the inhibitory signals from the cancer cells allow the immune cells to function more effectively.
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Affiliation(s)
- Ahmad Alzamami
- Clinical Laboratory Science Department, College of Applied Medical Sciences, Shaqra University, 11961, Al-Quwayiyah, Saudi Arabia.
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12
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Wang Q, Zhi Y, Zi M, Mo Y, Wang Y, Liao Q, Zhang S, Gong Z, Wang F, Zeng Z, Guo C, Xiong W. Spatially Resolved Transcriptomics Technology Facilitates Cancer Research. Adv Sci (Weinh) 2023; 10:e2302558. [PMID: 37632718 PMCID: PMC10602551 DOI: 10.1002/advs.202302558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/16/2023] [Indexed: 08/28/2023]
Abstract
Single cell RNA sequencing (scRNA-seq) provides a great convenience for studying tumor occurrence and development for its ability to study gene expression at the individual cell level. However, patient-derived tumor tissues are composed of multiple types of cells including tumor cells and adjacent non-malignant cells such as stromal cells and immune cells. The spatial locations of various cells in situ tissues plays a pivotal role in the occurrence and development of tumors, which cannot be elucidated by scRNA-seq alone. Spatially resolved transcriptomics (SRT) technology emerges timely to explore the unrecognized relationship between the spatial background of a particular cell and its functions, and is increasingly used in cancer research. This review provides a systematic overview of the SRT technologies that are developed, in particular the more widely used cutting-edge SRT technologies based on next-generation sequencing (NGS). In addition, the main achievements by SRT technologies in precisely unveiling the underappreciated spatial locations on gene expression and cell function with unprecedented high-resolution in cancer research are emphasized, with the aim of developing more effective clinical therapeutics oriented to a deeper understanding of the interaction between tumor cells and surrounding non-malignant cells.
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Affiliation(s)
- Qian Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Yuan Zhi
- Department of Oral and Maxillofacial SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaHunan410012P. R. China
| | - Moxin Zi
- Department of Oral and Maxillofacial SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaHunan410012P. R. China
| | - Yongzhen Mo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
- Department of Otolaryngology Head and Neck SurgeryXiangya HospitalCentral South UniversityChangshaHunan410008P. R. China
| | - Yumin Wang
- Department of Otolaryngology Head and Neck SurgeryXiangya HospitalCentral South UniversityChangshaHunan410008P. R. China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
| | - Shanshan Zhang
- Department of Otolaryngology Head and Neck SurgeryXiangya HospitalCentral South UniversityChangshaHunan410008P. R. China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaHunan410012P. R. China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Can Guo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
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13
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Ozer M, Vegivinti CTR, Syed M, Ferrell ME, Gonzalez Gomez C, Cheng S, Holder-Murray J, Bruno T, Saeed A, Sahin IH. Neoadjuvant Immunotherapy for Patients with dMMR/MSI-High Gastrointestinal Cancers: A Changing Paradigm. Cancers (Basel) 2023; 15:3833. [PMID: 37568648 PMCID: PMC10417711 DOI: 10.3390/cancers15153833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Immune checkpoint inhibitors have revolutionized the management of mismatch repair-deficient (MMR-D)/microsatellite instability-high (MSI-H) gastrointestinal cancers, particularly colorectal cancer. Cancers with the MMR-D/MSI-H genotype often carry a higher tumor mutation burden with frameshift alterations, leading to increased mutation-associated neoantigen (MANA) generation. The dramatic response seen with immune checkpoint inhibitors (ICIs), which are orchestrated by MANA-primed effector T cells, resulted in the rapid development of these novel therapeutics within the landscape of MSI-H gastrointestinal cancers. Recently, several clinical trials have utilized ICIs as potential neoadjuvant therapies for MSI-H gastrointestinal cancers and demonstrated deep clinical and pathological responses, creating opportunities for organ preservation. However, there are potential challenges to the neoadjuvant use of ICIs for certain disease types due to the clinical risk of overtreatment for a disease that can be cured through a surgery-only approach. In this review article, we discuss neoadjuvant management approaches with ICI therapy for patients with MSI-H gastrointestinal cancers, including those with oligometastatic disease. We also elaborate on potential challenges and opportunities for the neoadjuvant utilization of ICIs and provide further insight into the changing treatment paradigm of MMR-D/MSI-H gastrointestinal cancers.
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Affiliation(s)
- Muhammet Ozer
- Department of Gastrointestinal Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Masood Syed
- Department of Medicine, University of Pittsburg School of Medicine, Pittsburgh, PA 15213, USA
| | - Morgan E. Ferrell
- Department of Medicine, University of Pittsburg School of Medicine, Pittsburgh, PA 15213, USA
| | - Cyndi Gonzalez Gomez
- Department of Medicine, University of Pittsburg School of Medicine, Pittsburgh, PA 15213, USA
| | - Svea Cheng
- Department of Medicine, University of Pittsburg School of Medicine, Pittsburgh, PA 15213, USA
| | - Jennifer Holder-Murray
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Tullia Bruno
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Anwaar Saeed
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ibrahim Halil Sahin
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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14
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Ledford H. Cell 'atlases' offer unprecedented view of placenta, intestines and kidneys. Nature 2023:10.1038/d41586-023-02348-4. [PMID: 37468819 DOI: 10.1038/d41586-023-02348-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
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15
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Li C, Guan R, Li W, Wei D, Cao S, Xu C, Chang F, Wang P, Chen L, Lei D. Single-cell RNA sequencing reveals tumor immune microenvironment in human hypopharygeal squamous cell carcinoma and lymphatic metastasis. Front Immunol 2023; 14:1168191. [PMID: 37503341 PMCID: PMC10369788 DOI: 10.3389/fimmu.2023.1168191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023] Open
Abstract
Background Human hypopharygeal squamous cell carcinoma (HSCC) is a common head and neck cancer with a poor prognosis in advanced stages. The occurrence and development of tumor is the result of mutual influence and co-evolution between tumor cells and tumor microenvironment (TME). Tumor immune microenvironment (TIME) refers to the immune microenvironment surrounding tumor cells. Studying TIME in HSCC could provide new targets and therapeutic strategies for HSCC. Methods We performed single-cell RNA sequencing (scRNA-seq) and analysis of hypopharyngeal carcinoma, paracancerous, and lymphoid tissues from five HSCC patients. Subdivide of B cells, T cells, macrophages cells, and monocytes and their distribution in three kinds of tissues as well as marker genes were analyzed. Different genes of IGHG1 plasma cells and SPP1+ macrophages between HSCC tissues, adjacent normal tissues and lymphatic tissues were analyzed. Additionally, we studied proliferating lymphocytes, T cells exhaustion, and T cell receptor (TCR) repertoire in three kinds of tissues. Results Transcriptome profiles of 132,869 single cells were obtained and grouped into seven cell clusters, including epithelial cells, lymphocytes, mononuclear phagocytics system (MPs), fibroblasts, endothelial cells (ECs), plasmacytoid dendritic cells (pDCs), and mast cells. Tumor metastasis occurred in three lymphoid tissues. Four distinct populations were identified from lymphocytes, including B cells, plasma cells, T cells and proliferating lymphocytes. We found IGHA1 and IGHG1 specific plasma cells significantly overexpressed in HSCC tissues compared with normal hypopharygeal tissues and lymphatic tissues. Five distinct populations from MPs were identified, including macrophages, monocytes, mature dendritic cells (DCs), Type 1 conventional dendritic cells (cDC1) and Type 2 conventional dendritic cells (cDC2). SPP1+ macrophages were significantly overexpressed in HSCC tissues and lymphatic tissues compared with normal hypopharygeal tissues, which are thought to be M2-type macrophages. Exhaustion of CD8+ Teff cells occurred in HSCC tissues. At last, we verified that IgA and IgG1 protein expression levels were significantly up-regulated in HSCC tissues compared to adjacent normal tissues. Conclusion Overall, this study revealed TIME in HSCC and lymphatic metastasis, and provided potential therapeutic targets for HSCC.
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16
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Mestrallet G, Brown M, Bozkus CC, Bhardwaj N. Immune escape and resistance to immunotherapy in mismatch repair deficient tumors. Front Immunol 2023; 14:1210164. [PMID: 37492581 PMCID: PMC10363668 DOI: 10.3389/fimmu.2023.1210164] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/21/2023] [Indexed: 07/27/2023] Open
Abstract
Up to 30% of colorectal, endometrial and gastric cancers have a deficiency in mismatch repair (MMR) protein expression due to either germline or epigenetic inactivation. Patients with Lynch Syndrome who inherit an inactive MMR allele have an up to 80% risk for developing a mismatch repair deficient (MMRd) cancer. Due to an inability to repair DNA, MMRd tumors present with genomic instability in microsatellite regions (MS). Tumors with high MS instability (MSI-H) are characterized by an increased frequency of insertion/deletions (indels) that can encode novel neoantigens if they occur in coding regions. The high tumor antigen burden for MMRd cancers is accompanied by an inflamed tumor microenvironment (TME) that contributes to the clinical effectiveness of anti-PD-1 therapy in this patient population. However, between 40 and 70% of MMRd cancer patients do not respond to treatment with PD-1 blockade, suggesting that tumor-intrinsic and -extrinsic resistance mechanisms may affect the success of checkpoint blockade. Immune evasion mechanisms that occur during early tumorigenesis and persist through cancer development may provide a window into resistance pathways that limit the effectiveness of anti-PD-1 therapy. Here, we review the mechanisms of immune escape in MMRd tumors during development and checkpoint blockade treatment, including T cell dysregulation and myeloid cell-mediated immunosuppression in the TME. Finally, we discuss the development of new therapeutic approaches to tackle resistance in MMRd tumors, including cancer vaccines, therapies targeting immunosuppressive myeloid programs, and immune checkpoint combination strategies.
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Affiliation(s)
- Guillaume Mestrallet
- Division of Hematology and Oncology, Hess Center for Science & Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Matthew Brown
- Division of Hematology and Oncology, Hess Center for Science & Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Cansu Cimen Bozkus
- Division of Hematology and Oncology, Hess Center for Science & Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Nina Bhardwaj
- Division of Hematology and Oncology, Hess Center for Science & Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Extramural member, Parker Institute for Cancer Immunotherapy, San Francisco, CA, United States
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17
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Leung LL, Myles T, Morser J. Thrombin Cleavage of Osteopontin and the Host Anti-Tumor Immune Response. Cancers (Basel) 2023; 15:3480. [PMID: 37444590 DOI: 10.3390/cancers15133480] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023] Open
Abstract
Osteopontin (OPN) is a multi-functional protein that is involved in various cellular processes such as cell adhesion, migration, and signaling. There is a single conserved thrombin cleavage site in OPN that, when cleaved, yields two fragments with different properties from full-length OPN. In cancer, OPN has tumor-promoting activity and plays a role in tumor growth and metastasis. High levels of OPN expression in cancer cells and tumor tissue are found in various types of cancer, including breast, lung, prostate, ovarian, colorectal, and pancreatic cancer, and are associated with poor prognosis and decreased survival rates. OPN promotes tumor progression and invasion by stimulating cell proliferation and angiogenesis and also facilitates the metastasis of cancer cells to other parts of the body by promoting cell adhesion and migration. Furthermore, OPN contributes to immune evasion by inhibiting the activity of immune cells. Thrombin cleavage of OPN initiates OPN's tumor-promoting activity, and thrombin cleavage fragments of OPN down-regulate the host immune anti-tumor response.
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Affiliation(s)
- Lawrence L Leung
- Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA
| | - Timothy Myles
- Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA
| | - John Morser
- Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA
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18
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Egan H, Treacy O, Lynch K, Leonard NA, O'Malley G, Reidy E, O'Neill A, Corry SM, De Veirman K, Vanderkerken K, Egan LJ, Ritter T, Hogan AM, Redmond K, Peng L, Che J, Gatlin W, Jayaraman P, Sheehan M, Canney A, Hynes SO, Kerr EM, Dunne PD, O'Dwyer ME, Ryan AE. Targeting stromal cell sialylation reverses T cell-mediated immunosuppression in the tumor microenvironment. Cell Rep 2023; 42:112475. [PMID: 37167967 DOI: 10.1016/j.celrep.2023.112475] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 02/03/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023] Open
Abstract
Immunosuppressive tumor microenvironments (TMEs) reduce the effectiveness of immune responses in cancer. Mesenchymal stromal cells (MSCs), precursors to cancer-associated fibroblasts (CAFs), promote tumor progression by enhancing immune cell suppression in colorectal cancer (CRC). Hyper-sialylation of glycans promotes immune evasion in cancer through binding of sialic acids to their receptors, Siglecs, expressed on immune cells, which results in inhibition of effector functions. The role of sialylation in shaping MSC/CAF immunosuppression in the TME is not well characterized. In this study, we show that tumor-conditioned stromal cells have increased sialyltransferase expression, α2,3/6-linked sialic acid, and Siglec ligands. Tumor-conditioned stromal cells and CAFs induce exhausted immunomodulatory CD8+ PD1+ and CD8+ Siglec-7+/Siglec-9+ T cell phenotypes. In vivo, targeting stromal cell sialylation reverses stromal cell-mediated immunosuppression, as shown by infiltration of CD25 and granzyme B-expressing CD8+ T cells in the tumor and draining lymph node. Targeting stromal cell sialylation may overcome immunosuppression in the CRC TME.
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Affiliation(s)
- Hannah Egan
- Discipline of Pharmacology and Therapeutics, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Regenerative Medicine Institute (REMEDI), School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland
| | - Oliver Treacy
- Discipline of Pharmacology and Therapeutics, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Regenerative Medicine Institute (REMEDI), School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland
| | - Kevin Lynch
- Discipline of Pharmacology and Therapeutics, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Regenerative Medicine Institute (REMEDI), School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland
| | - Niamh A Leonard
- Discipline of Pharmacology and Therapeutics, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Regenerative Medicine Institute (REMEDI), School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland
| | - Grace O'Malley
- Discipline of Pharmacology and Therapeutics, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Regenerative Medicine Institute (REMEDI), School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland
| | - Eileen Reidy
- Discipline of Pharmacology and Therapeutics, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Regenerative Medicine Institute (REMEDI), School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland
| | - Aoise O'Neill
- Discipline of Pharmacology and Therapeutics, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Regenerative Medicine Institute (REMEDI), School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland
| | - Shania M Corry
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Kim De Veirman
- Laboratory for Haematology and Immunology (HEIM), Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Karin Vanderkerken
- Laboratory for Haematology and Immunology (HEIM), Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Laurence J Egan
- Discipline of Pharmacology and Therapeutics, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland
| | - Thomas Ritter
- Regenerative Medicine Institute (REMEDI), School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland
| | - Aisling M Hogan
- Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Department of Colorectal Surgery, Galway University Hospital, Galway, Ireland
| | - Keara Redmond
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Li Peng
- Palleon Pharmaceuticals, Waltham, MA 02451, USA
| | - Jenny Che
- Palleon Pharmaceuticals, Waltham, MA 02451, USA
| | | | | | - Margaret Sheehan
- Division of Anatomical Pathology, Galway University Hospital, Galway, Ireland
| | - Aoife Canney
- Division of Anatomical Pathology, Galway University Hospital, Galway, Ireland
| | - Sean O Hynes
- Division of Anatomical Pathology, Galway University Hospital, Galway, Ireland; Discipline of Pathology, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland
| | - Emma M Kerr
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Philip D Dunne
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK; Cancer Research UK Beatson Institute, Glasgow, UK
| | - Michael E O'Dwyer
- Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Blood Cancer Network of Ireland (BCNI), Galway, Ireland; Department of Hematology, Galway University Hospital, Galway, Ireland
| | - Aideen E Ryan
- Discipline of Pharmacology and Therapeutics, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Regenerative Medicine Institute (REMEDI), School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland; CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland.
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Jia X, Zhang T, Lv X, Du H, Sun Y, Guan Y. Identification of the six-hormone secretion-related gene signature as a prognostic biomarker for colon adenocarcinoma. Cancer Biomark 2023; 38:523-535. [PMID: 38143338 DOI: 10.3233/cbm-230126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
BACKGROUND Colon adenocarcinoma (COAD) is a globally prevalent cancer, with hormone secretion playing a crucial role in its progression. Despite this, there is limited understanding of the impact of hormone secretion on COAD prognosis. This study aimed to establish a prognostic signature based on hormone secretion-related genes and to elucidate the potential functional mechanisms of these genes in COAD. METHODS Using data from The Cancer Genome Atlas COAD cohort (TCGA-COAD), six hormone secretion-related genes were identified (CYP19A1, FOXD1, GRP, INHBB, SPP1, and UCN). These genes were used to develop a Hormone secretion score (HSS), which was then evaluated using the Kaplan-Meier curve and multivariable Cox analysis. The HSS model was further validated with external GEO cohorts (GSE41258, GSE39582, and GSE87211). Functional enrichment analyses were performed, and the CIBERSORT and TIDE algorithms were used to assess tumor infiltration. RESULTS The study developed a prognostic signature, dividing patients into HSS-high and HSS-low groups. The HSS-high group showed a notably worse prognosis within the TCGA-COAD dataset and in three independent datasets: GSE41258, GSE39582, and GSE87211. Moreover, the HSS-high group predicted a shorter overall survival rate in patients maintaining microsatellite stability (MSS). The functional analysis associated HSS-high with the hypoxic, epithelial-mesenchymal transition (EMT), and TGF-β signaling pathways and correlated with distant and lymph node metastases. The tumor immune microenvironment analysis revealed an elevated CIBERSORT score in the HSS-high group, suggesting an association with tumor metastasis. Further, the HSS-high group showed a higher TIDE score, indicating that patients with high HSS scores are less likely to benefit from Immune Checkpoint Inhibitor (ICI) therapy. CONCLUSIONS This study demonstrated the prognostic significance of a HSS signature based on six hormone secretion-related genes in COAD. The findings suggest that this gene signature may serve as a reliable biomarker for predicting survival outcomes in COAD patients.
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Affiliation(s)
- Xiongjie Jia
- Department of Gastrointestinal Surgery, Affiliated Hospital of Hebei University, Baoding, Heibei, China
- Department of Gastrointestinal Surgery, Affiliated Hospital of Hebei University, Baoding, Heibei, China
| | - Tao Zhang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Hebei University, Baoding, Heibei, China
- Department of Gastrointestinal Surgery, Affiliated Hospital of Hebei University, Baoding, Heibei, China
| | - Xinze Lv
- Burning Rock Biotech, Guangzhou, Guangdong, China
| | - Haiwei Du
- Burning Rock Biotech, Guangzhou, Guangdong, China
| | - Yongkun Sun
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yin Guan
- Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
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