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Huart C, Gupta MS, Van Ginderachter JA. The role of RNA modifications in disease-associated macrophages. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102315. [PMID: 39296330 PMCID: PMC11408368 DOI: 10.1016/j.omtn.2024.102315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
In recent years, the field of epitranscriptomics has witnessed significant breakthroughs with the identification of more than 150 different chemical modifications in different RNA species. It has become increasingly clear that these chemical modifications play an important role in the regulation of fundamental processes linked to cell fate and development. Further interest was sparked by the ability of the epitranscriptome to regulate pathogenesis. However, despite the involvement of macrophages in a multitude of diseases, a clear knowledge gap exists in the understanding of how RNA modifications regulate the phenotype of these cells. Here, we provide a comprehensive overview of the known roles of macrophage RNA modifications in the context of different diseases.
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Affiliation(s)
- Camille Huart
- Lab of Cellular and Molecular Immunology, Brussels Center for Immunology (BCIM), Vrije Universiteit Brussel, Brussels, Belgium
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium
| | - Mayuk Saibal Gupta
- Lab of Cellular and Molecular Immunology, Brussels Center for Immunology (BCIM), Vrije Universiteit Brussel, Brussels, Belgium
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium
| | - Jo A Van Ginderachter
- Lab of Cellular and Molecular Immunology, Brussels Center for Immunology (BCIM), Vrije Universiteit Brussel, Brussels, Belgium
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium
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2
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Li D, Mei Q, Li G. scQA: A dual-perspective cell type identification model for single cell transcriptome data. Comput Struct Biotechnol J 2024; 23:520-536. [PMID: 38235363 PMCID: PMC10791572 DOI: 10.1016/j.csbj.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024] Open
Abstract
Single-cell RNA sequencing technologies have been pivotal in advancing the development of algorithms for clustering heterogeneous cell populations. Existing methods for utilizing scRNA-seq data to identify cell types tend to neglect the beneficial impact of dropout events and perform clustering focusing solely on quantitative perspective. Here, we introduce a novel method named scQA, notable for its ability to concurrently identify cell types and cell type-specific key genes from both qualitative and quantitative perspectives. In contrast to other methods, scQA not only identifies cell types but also extracts key genes associated with these cell types, enabling bidirectional clustering for scRNA-seq data. Through an iterative process, our approach aims to minimize the number of landmarks to approximately a dozen while maximizing the inclusion of quasi-trend-preserved genes with dropouts both qualitatively and quantitatively. It then clusters cells by employing an ingenious label propagation strategy, obviating the requirement for a predetermined number of cell types. Validated on 20 publicly available scRNA-seq datasets, scQA consistently outperforms other salient tools. Furthermore, we confirm the effectiveness and potential biological significance of the identified key genes through both external and internal validation. In conclusion, scQA emerges as a valuable tool for investigating cell heterogeneity due to its distinctive fusion of qualitative and quantitative facets, along with bidirectional clustering capabilities. Furthermore, it can be seamlessly integrated into border scRNA-seq analyses. The source codes are publicly available at https://github.com/LD-Lyndee/scQA.
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Affiliation(s)
- Di Li
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China
| | - Qinglin Mei
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Guojun Li
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China
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3
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Ozakinci H, Song X, Nazario GS, Lila T, Chen B, Simpson T, Nguyen JV, Moran Segura CM, Thompson ZJ, Thapa R, Rose TA, Haura EB, Pellini B, Yu X, Ruffell BH, Chen DT, Boyle TA, Beg AA. Rapid Autopsy to Define Dendritic Cell Spatial Distribution and T Cell Association in Lung Adenocarcinoma. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:1033-1041. [PMID: 39120462 PMCID: PMC11404669 DOI: 10.4049/jimmunol.2400234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024]
Abstract
Immunotherapy response is associated with the presence of conventional dendritic cells (cDCs). cDC type 1 (cDC1) is critically important for CD8+ T cell activation, cDC type 2 (cDC2) regulates CD4+ T cell responses, and mature regulatory cDCs may dampen T cell responses in the tumor microenvironment (TME). However, we lack a clear understanding of cDC distribution in the human TME, cDC prevalence in metastatic sites, and cDC differences in early- versus late-stage disease. Rapid autopsy specimens of 10 patients with lung adenocarcinoma were evaluated to detect cDCs and immune cells via multiplex immunofluorescence using 18 markers and 42 tumors. First, we found that T cells, cDC1, and cDC2 were confined to stroma, whereas mature regulatory DCs were enriched in tumor, suggesting unique localization-specific functions. Second, lung and lymph node tumors were more enriched in T cells and cDCs than liver tumors, underscoring differences in the TME of metastatic sites. Third, although the proportion of T cells and cDC1 did not differ in different stages, an increase in the proportion of cDC2 and macrophages in late stage suggests potential differences in regulation of T cell responses in different stages. Collectively, these findings provide new, to our knowledge, insights into cDC biology in human cancer that may have important therapeutic implications.
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Affiliation(s)
- Hilal Ozakinci
- Thoracic Oncology Department, Moffitt Cancer Center, Tampa, FL
| | - Xiaofei Song
- Biostatistics and Bioinformatics Department, Moffitt Cancer Center, Tampa, FL
| | - Gina S Nazario
- Thoracic Oncology Department, Moffitt Cancer Center, Tampa, FL
| | - Thomas Lila
- Solid Tumor Translational Medicine, Bristol Myers Squibb, Cambridge, MA
| | - Benjamin Chen
- Solid Tumor Translational Medicine, Bristol Myers Squibb, Cambridge, MA
| | - Tyler Simpson
- Solid Tumor Translational Medicine, Bristol Myers Squibb, Cambridge, MA
| | - Jonathan V Nguyen
- Advanced Analytical and Digital Laboratory, Moffitt Cancer Center, Tampa, FL
| | | | - Zachary J Thompson
- Biostatistics and Bioinformatics Department, Moffitt Cancer Center, Tampa, FL
| | - Ram Thapa
- Biostatistics and Bioinformatics Department, Moffitt Cancer Center, Tampa, FL
| | - Trevor A Rose
- Diagnostic Imaging and Interventional Radiology, Moffitt Cancer Center, Tampa, FL
| | - Eric B Haura
- Thoracic Oncology Department, Moffitt Cancer Center, Tampa, FL
| | - Bruna Pellini
- Thoracic Oncology Department, Moffitt Cancer Center, Tampa, FL
| | - Xiaoqing Yu
- Biostatistics and Bioinformatics Department, Moffitt Cancer Center, Tampa, FL
| | | | - Dung-Tsa Chen
- Biostatistics and Bioinformatics Department, Moffitt Cancer Center, Tampa, FL
| | - Theresa A Boyle
- Thoracic Oncology Department, Moffitt Cancer Center, Tampa, FL
- Pathology Department, Moffitt Cancer Center, Tampa, FL
| | - Amer A Beg
- Thoracic Oncology Department, Moffitt Cancer Center, Tampa, FL
- Immunology Department, Moffitt Cancer Center, Tampa, FL
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4
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Bosteels V, Janssens S. Striking a balance: new perspectives on homeostatic dendritic cell maturation. Nat Rev Immunol 2024:10.1038/s41577-024-01079-5. [PMID: 39289483 DOI: 10.1038/s41577-024-01079-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2024] [Indexed: 09/19/2024]
Abstract
Dendritic cells (DCs) are crucial gatekeepers of the balance between immunity and tolerance. They exist in two functional states, immature or mature, that refer to an information-sensing versus an information-transmitting state, respectively. Historically, the term DC maturation was used to describe the acquisition of immunostimulatory capacity by DCs following their triggering by pathogens or tissue damage signals. As such, immature DCs were proposed to mediate tolerance, whereas mature DCs were associated with the induction of protective T cell immunity. Later studies have challenged this view and unequivocally demonstrated that two distinct modes of DC maturation exist, homeostatic and immunogenic DC maturation, each with a distinct functional outcome. Therefore, the mere expression of maturation markers cannot be used to predict immunogenicity. How DCs become activated in homeostatic conditions and maintain tolerance remains an area of intense debate. Several recent studies have shed light on the signals driving the homeostatic maturation programme, especially in the conventional type 1 DC (cDC1) compartment. Here, we highlight our growing understanding of homeostatic DC maturation and the relevance of this process for immune tolerance.
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Affiliation(s)
- Victor Bosteels
- Laboratory for ER Stress and Inflammation, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Sophie Janssens
- Laboratory for ER Stress and Inflammation, VIB Center for Inflammation Research, Ghent, Belgium.
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.
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5
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Morali K, Giacomello G, Vuono M, Gregori S. Leveraging current insights on IL-10-producing dendritic cells for developing effective immunotherapeutic approaches. FEBS Lett 2024. [PMID: 39266465 DOI: 10.1002/1873-3468.15017] [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: 03/28/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 09/14/2024]
Abstract
Dendritic cells (DC) are professional antigen-presenting cells involved in promoting and controlling immune responses. Different subsets of DC, named tolerogenic (tol)DC, play a critical role in the maintenance of tissue homeostasis and in fostering tolerance. These unique skills make tolDC especially attractive for strategies aimed at re-establishing/inducing tolerance in immune-mediated conditions. The generation of potent tolDC in vitro from peripheral blood monocytes has seen remarkable advancements. TolDC modulate T cell dynamics by favoring regulatory T cells (Tregs) and curbing effector/pathogenic T cells. Among the several methods developed for in vitro tolDC generation, IL-10 conditioning has been proven to be the most efficient, as IL-10-modulated tolDC were demonstrated to promote Tregs with the strongest suppressive activities. Investigating the molecular, metabolic, and functional profiles of tolDC uncovers essential pathways that facilitate their immunoregulatory functions. This Review provides an overview of current knowledge on the role of tolDC in health and disease, focusing on IL-10 production, functional characterization of in vitro generated tolDC, molecular and metabolic changes occurring in tolDC induced by tolerogenic agents, clinical applications of tolDC-based therapy, and finally new perspectives in the generation of effective tolDC.
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Affiliation(s)
- Konstantina Morali
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Gloria Giacomello
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- PhD Course in Medicina Traslazionale e Molecolare (DIMET), University of Milano Bicocca, Italy
| | - Michela Vuono
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- PhD Course in Molecular Medicine, University Vita-Salute San Raffaele, Milan, Italy
| | - Silvia Gregori
- Mechanisms of Peripheral Tolerance Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
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6
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Hayashi Y, Kamimura-Aoyagi Y, Nishikawa S, Noka R, Iwata R, Iwabuchi A, Watanabe Y, Matsunuma N, Yuki K, Kobayashi H, Harada Y, Harada H. IL36G-producing neutrophil-like monocytes promote cachexia in cancer. Nat Commun 2024; 15:7662. [PMID: 39266531 PMCID: PMC11393454 DOI: 10.1038/s41467-024-51873-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 08/19/2024] [Indexed: 09/14/2024] Open
Abstract
Most patients with advanced cancer develop cachexia, a multifactorial syndrome characterized by progressive skeletal muscle wasting. Despite its catastrophic impact on survival, the critical mediators responsible for cancer cachexia development remain poorly defined. Here, we show that a distinct subset of neutrophil-like monocytes, which we term cachexia-inducible monocytes (CiMs), emerges in the advanced cancer milieu and promotes skeletal muscle loss. Unbiased transcriptome analysis reveals that interleukin 36 gamma (IL36G)-producing CD38+ CiMs are induced in chronic monocytic blood cancer characterized by prominent cachexia. Notably, the emergence of CiMs and the activation of CiM-related gene signatures in monocytes are confirmed in various advanced solid cancers. Stimuli of toll-like receptor 4 signaling are responsible for the induction of CiMs. Genetic inhibition of IL36G-mediated signaling attenuates skeletal muscle loss and rescues cachexia phenotypes in advanced cancer models. These findings indicate that the IL36G-producing subset of neutrophil-like monocytes could be a potential therapeutic target in cancer cachexia.
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Affiliation(s)
- Yoshihiro Hayashi
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan.
- Laboratory of Cancer Pathobiology and Therapeutics, College of Pharmaceutical Sciences, Ritsumeikan University, Shiga, Japan.
| | - Yasushige Kamimura-Aoyagi
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Sayuri Nishikawa
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Rena Noka
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Rika Iwata
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Asami Iwabuchi
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Yushin Watanabe
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Natsumi Matsunuma
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Kanako Yuki
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Hiroki Kobayashi
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Yuka Harada
- Clinical Research Support Center, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Hironori Harada
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan.
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7
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Chiffelle J, Barras D, Pétremand R, Orcurto A, Bobisse S, Arnaud M, Auger A, Rodrigo BN, Ghisoni E, Sauvage C, Saugy D, Michel A, Murgues B, Fahr N, Imbimbo M, Ochoa de Olza M, Latifyan S, Crespo I, Benedetti F, Genolet R, Queiroz L, Schmidt J, Homicsko K, Zimmermann S, Michielin O, Bassani-Sternberg M, Kandalaft LE, Dafni U, Corria-Osorio J, Trueb L, Dangaj Laniti D, Harari A, Coukos G. Tumor-reactive T cell clonotype dynamics underlying clinical response to TIL therapy in melanoma. Immunity 2024:S1074-7613(24)00413-8. [PMID: 39276771 DOI: 10.1016/j.immuni.2024.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 04/12/2024] [Accepted: 08/22/2024] [Indexed: 09/17/2024]
Abstract
Adoptive cell therapy (ACT) using in vitro expanded tumor-infiltrating lymphocytes (TILs) has inconsistent clinical responses. To better understand determinants of therapeutic success, we tracked TIL clonotypes from baseline tumors to ACT products and post-ACT blood and tumor samples in melanoma patients using single-cell RNA and T cell receptor (TCR) sequencing. Patients with clinical responses had baseline tumors enriched in tumor-reactive TILs, and these were more effectively mobilized upon in vitro expansion, yielding products enriched in tumor-specific CD8+ cells that preferentially infiltrated tumors post-ACT. Conversely, lack of clinical responses was associated with tumors devoid of tumor-reactive resident clonotypes and with cell products mostly composed of blood-borne clonotypes that persisted in blood but not in tumors post-ACT. Upon expansion, tumor-specific TILs lost tumor-associated transcriptional signatures, including exhaustion, and responders exhibited an intermediate exhausted effector state after TIL engraftment in the tumor, suggesting functional reinvigoration. Our findings provide insight into the nature and dynamics of tumor-specific clonotypes associated with clinical response to TIL-ACT, with implications for treatment optimization.
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Affiliation(s)
- Johanna Chiffelle
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - David Barras
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Rémy Pétremand
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Angela Orcurto
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland; Immuno-oncology Service, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Sara Bobisse
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Marion Arnaud
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Aymeric Auger
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Blanca Navarro Rodrigo
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland; Immuno-oncology Service, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Eleonora Ghisoni
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland; Immuno-oncology Service, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Christophe Sauvage
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Damien Saugy
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Alexandra Michel
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Baptiste Murgues
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Noémie Fahr
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Martina Imbimbo
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland; Immuno-oncology Service, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Maria Ochoa de Olza
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland; Immuno-oncology Service, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Sofiya Latifyan
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Medical Oncology Service, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Isaac Crespo
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Fabrizio Benedetti
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Raphael Genolet
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Lise Queiroz
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Julien Schmidt
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Krisztian Homicsko
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland; Immuno-oncology Service, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland; Medical Oncology Service, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Stefan Zimmermann
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland; Immuno-oncology Service, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Olivier Michielin
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Medical Oncology Service, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Lana E Kandalaft
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Urania Dafni
- Faculty of Nursing, National and Kapodistrian University of Athens, Athens, Greece
| | - Jesus Corria-Osorio
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Lionel Trueb
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland; Immuno-oncology Service, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Denarda Dangaj Laniti
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland.
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland; Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland; Immuno-oncology Service, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland.
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8
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Dong H, Hu F, Hao B, Jin X, Zheng Q, Su Y. Single-cell analysis reveals the disparities in immune profiles between younger and elder patients. Eur Geriatr Med 2024:10.1007/s41999-024-01032-8. [PMID: 39244673 DOI: 10.1007/s41999-024-01032-8] [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: 11/01/2023] [Accepted: 07/26/2024] [Indexed: 09/10/2024]
Abstract
PURPOSE The immune profiles of elder patients with non-small cell lung cancer (NSCLC) differ significantly from those of younger patients. The tumor microenvironment (TME) is a crucial factor in cancer progression and therapeutic responses. The present study aims to decipher the difference in TME between younger and elderly patients with lung cancers. METHODS We downloaded single-cell RNA data from public databases. The algorithm of uniform manifold approximation and projection (UMAP) was applied to cluster and visualize single-cell sequencing data. Gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) analysis were performed to evaluate the physiological functional characteristics in sub-group cells. CellPhoneDB was used to identify cell-cell interactions between immune cells within TME. RESULTS We conducted single-cell RNA sequencing on 96,491 cells from elderly patients and 169,207 cells from younger patients, respectively. We observed that epithelial cells were the predominant component of the TME in younger patients, whereas T/NK cells were the predominant cell type in the TME of elderly patients. We also found that there was a higher proportion of Tregs and a lower proportion of NK, effector CD8+T and γδT cells in elder patients compared with younger patients. In addition, a comparative GSEA analysis of NK cells between older and younger patients revealed that the pathways of Parkinson's disease, Alzheimer's disease, mismatch repair, and base excision repair were up-regulated in NK cells from elderly patients, while the pathways related to natural killer cell-mediated cytotoxicity and allograft rejection were downregulated. Furthermore, we identified tumor-associated neutrophils (TANs) in elder patients, and GSVA analysis demonstrated that the pathway of angiogenesis was upregulated, and the pathway of interferon_γ_response, inflammatory_response, TNFα_signaling_via_NFκB pathways were downregulated. Importantly, the pro-inflammatory response scores of complement C1q C chain positive (C1QC+) macrophages, tissue-resident macrophages (TRM), non-classical monocytes (NCM), secreted phosphoprotein 1 positive (SPP1+) macrophages, and classical monocytes (CM) in elder patients were significantly lower compared to those in younger patients. Finally, cell-to-cell communication analyses unveiled the disparities in regulatory patterns between elder and younger patients, namely the pairs of CXCL13-ACKR4 and CSF1-SIRPA in elder patients and the pairs of CTLA4-CD86 and TIGIT-NECTIN2 in younger patients. CONCLUSION This study reveals the distinct immune profiles between younger and elder NSCLC patients, and the elder patients were likely to exhibit a more immunosuppressive TME and attenuated tumor-killing capability compared with younger patients.
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Affiliation(s)
- Huixing Dong
- Department of Pulmonary and Critical Care Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai, 200336, China
| | - Feng Hu
- Department of Pulmonary and Critical Care Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai, 200336, China
| | - Bo Hao
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan University, 238 Jiefang Road, Wuhan, 430060, China
| | - Xiaoyan Jin
- Department of Pulmonary and Critical Care Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai, 200336, China
| | - Qi Zheng
- Department of Respiratory and Critical Care Medicine, Huangpu Branch, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, No.58, Pu Yu Dong Road, Shanghai, 200011, China.
| | - Yiliang Su
- Department of Pulmonary and Critical Care Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai, 200336, China.
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9
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Protti G, Spreafico R. A primer on single-cell RNA-seq analysis using dendritic cells as a case study. FEBS Lett 2024. [PMID: 39245787 DOI: 10.1002/1873-3468.15009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/18/2024] [Accepted: 08/12/2024] [Indexed: 09/10/2024]
Abstract
Recent advances in single-cell (sc) transcriptomics have revolutionized our understanding of dendritic cells (DCs), pivotal players of the immune system. ScRNA-sequencing (scRNA-seq) has unraveled a previously unrecognized complexity and heterogeneity of DC subsets, shedding light on their ontogeny and specialized roles. However, navigating the rapid technological progress and computational methods can be daunting for researchers unfamiliar with the field. This review aims to provide immunologists with a comprehensive introduction to sc transcriptomic analysis, offering insights into recent developments in DC biology. Addressing common analytical queries, we guide readers through popular tools and methodologies, supplemented with references to benchmarks and tutorials for in-depth understanding. By examining findings from pioneering studies, we illustrate how computational techniques have expanded our knowledge of DC biology. Through this synthesis, we aim to equip researchers with the necessary tools and knowledge to navigate and leverage scRNA-seq for unraveling the intricacies of DC biology and advancing immunological research.
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Affiliation(s)
- Giulia Protti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Roberto Spreafico
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA
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10
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Huang S, Tan C, Zheng J, Huang Z, Li Z, Lv Z, Chen W, Chen M, Yuan X, Chen C, Yan Q. Identification of RNMT as an immunotherapeutic and prognostic biomarker: From pan-cancer analysis to lung squamous cell carcinoma validation. Immunobiology 2024; 229:152836. [PMID: 39018675 DOI: 10.1016/j.imbio.2024.152836] [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: 04/05/2024] [Revised: 06/23/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024]
Abstract
BACKGROUND Dysregulation of RNA guanine-7 methyltransferase (RNMT) plays a crucial role in the tumor progression and immune responses. However, the detailed role of RNMT in pan-cancer is still unknown. METHODS Bulk transcriptomic data of pan-cancer were obtained from the Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Cancer Cell Line Encyclopedia (CCLE) databases. Single-cell transcriptomic and proteomics data of lung squamous cell carcinoma (LUSC) were analyzed in the Tumor Immune Single-cell Hub 2 (TISCH2) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) databases, respectively. The correlation between RNMT expression and cancer prognosis was analyzed by Cox proportional hazards regression and Kaplan-Meier analyses. The correlation of RNMT expression with common immunoregulators, tumor mutation burden (TMB), microsatellite instability (MSI), mismatch repair (MMR), and DNA methyltransferase (DNMT) was analyzed. Additionally, the correlation between RNMT expression and immune infiltration level was evaluated. A total of 1287 machine learning combinations were used to construct prognostic models for LUSC. qRT-PCR and Western blot were used to validate the bioinformatics findings of RNMT upregulation in LUSC. RESULTS RNMT was widely expressed across different cancers, with significant correlation to prognosis in cancers such as kidney chromophobe (KICH) (p = 0.0033, HR = 7.12), liver hepatocellular carcinoma (LIHC) (p = 0.01, HR = 1.41), and others. Notably, RNMT participates in the regulation of the tumor microenvironment. RNMT expression positively correlated with immune cell expression (Spearman's rank correlation, p < 0.05). Moreover, RNMT expression was strongly associated with immunoregulators, TMB, MSI, MMR, and DNMT in most cancer types. Notably, RNMT expression displayed excellent prognostic and immunological performance in LUSC. The expression of RNMT was mainly enriched in B cells of LUSC tissues. qRT-PCR and Western blot verified the high expression of RNMT in LUSC. CONCLUSION RNMT expression widely correlated with prognosis and immune infiltration in various tumors, especially LUSC. The RNMT detection may provide a new idea for future tumor immune studies and treatment strategies.
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Affiliation(s)
- Shuqiang Huang
- Center for Reproductive Medicine, the Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, Guangdong 511518, China
| | - Cuiyu Tan
- Center for Reproductive Medicine, the Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, Guangdong 511518, China
| | - Jinzhen Zheng
- Center for Reproductive Medicine, the Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, Guangdong 511518, China
| | - Zhugu Huang
- School of Pediatrics, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Zhihong Li
- Center for Reproductive Medicine, the Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, Guangdong 511518, China
| | - Ziyin Lv
- The First School of Clinical Medicine, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Wanru Chen
- The Third School of Clinical Medicine, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Miaoqi Chen
- Center for Reproductive Medicine, the Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, Guangdong 511518, China
| | - Xiaojun Yuan
- Center for Reproductive Medicine, the Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, Guangdong 511518, China
| | - Cairong Chen
- Center for Reproductive Medicine, the Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, Guangdong 511518, China; Guangdong Engineering Technology Research Center of Urinary Continence and Reproductive Medicine, the Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, Guangdong 511518, China.
| | - Qiuxia Yan
- Center for Reproductive Medicine, the Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, Guangdong 511518, China; Guangdong Engineering Technology Research Center of Urinary Continence and Reproductive Medicine, the Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan, Guangdong 511518, China.
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11
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Chen J, Larsson L, Swarbrick A, Lundeberg J. Spatial landscapes of cancers: insights and opportunities. Nat Rev Clin Oncol 2024; 21:660-674. [PMID: 39043872 DOI: 10.1038/s41571-024-00926-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2024] [Indexed: 07/25/2024]
Abstract
Solid tumours comprise many different cell types organized in spatially structured arrangements, with substantial intratumour and intertumour heterogeneity. Advances in spatial profiling technologies over the past decade hold promise to capture the complexity of these cellular architectures to build a holistic view of the intricate molecular mechanisms that shape the tumour ecosystem. Some of these mechanisms act at the cellular scale and are controlled by cell-autonomous programmes or communication between nearby cells, whereas other mechanisms result from coordinated efforts between large networks of cells and extracellular molecules organized into tissues and organs. In this Review we provide insights into the application of single-cell and spatial profiling tools, with a focus on spatially resolved transcriptomic tools developed to understand the cellular architecture of the tumour microenvironment and identify opportunities to use them to improve clinical management of cancers.
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Affiliation(s)
- Julia Chen
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Department of Medical Oncology, St George Hospital, Sydney, New South Wales, Australia
| | - Ludvig Larsson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.
| | - Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
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12
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Abo KM, Merritt C, Basil MC, Lin SM, Cantu E, Morley MP, Bawa P, Gallagher M, Byers DE, Morrisey EE, Wilson AA. Pulmonary Cellular Toxicity in Alpha-1 Antitrypsin Deficiency. Chest 2024; 166:472-479. [PMID: 38360172 DOI: 10.1016/j.chest.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/09/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024] Open
Affiliation(s)
- Kristine M Abo
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Carly Merritt
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Maria C Basil
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Susan M Lin
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Edward Cantu
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Division of Cardiovascular Surgery, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Michael P Morley
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Pushpinder Bawa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Marissa Gallagher
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA
| | - Derek E Byers
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St Louis, MO
| | - Edward E Morrisey
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA.
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13
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Aktar T, Modak S, Majumder D, Maiti D. A detailed insight into macrophages' role in shaping lung carcinogenesis. Life Sci 2024; 352:122896. [PMID: 38972632 DOI: 10.1016/j.lfs.2024.122896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/24/2024] [Accepted: 07/03/2024] [Indexed: 07/09/2024]
Abstract
Despite significant advancements in cancer treatment in recent decades, the high mortality rate associated with lung cancer remains a significant concern. The development and proper execution of new targeted therapies needs more deep knowledge regarding the lung cancer associated tumour microenvironment. One of the key component of that tumour microenvironment is the lung resident macrophages. Although in normal physiological condition the lung resident macrophages are believed to maintain lung homeostasis, but they may also initiate a vicious inflammatory response in abnormal conditions which is linked to lung cancer development. Depending on the activation pathway, the lung resident macrophages are either of M1 or M2 sub-type. The M1 and M2 sub-types differ significantly in various prospectuses, from phenotypic markers to metabolic pathways. In addition to this generalized classification, the recent advancement of the multiomics technology is able to identify some other sub-types of lung resident macrophages. Researchers have also observed that these different sub-types can manipulate the pathogenesis of lung carcinogenesis in a context dependent manner and can either promote or inhibit the development of lung carcinogenesis upon receiving proper activation. As proper knowledge about the role played by the lung resident macrophages' in shaping the lung carcinogenesis is limited, so the main purpose of this review is to bring all the available information under the same roof. We also elaborated the different mechanisms involved in maintenance of the plasticity of M1/M2 sub-type, as this plasticity can be a good target for lung cancer treatment.
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Affiliation(s)
- Tamanna Aktar
- Immunology Microbiology Lab, Department of Human Physiology, Tripura University, Suryamaninagar, Tripura 799022, India
| | - Snehashish Modak
- Immunology Microbiology Lab, Department of Human Physiology, Tripura University, Suryamaninagar, Tripura 799022, India
| | - Debabrata Majumder
- Immunology Microbiology Lab, Department of Human Physiology, Tripura University, Suryamaninagar, Tripura 799022, India; Department of Integrative Immunobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Debasish Maiti
- Immunology Microbiology Lab, Department of Human Physiology, Tripura University, Suryamaninagar, Tripura 799022, India.
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14
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Li H, Xiao H, Mai X, Huang S, Chen J, Xiao X. A great diversity of ROBO4 expression and regulations identified by data mining and transgene mice. Gene Expr Patterns 2024; 53:119375. [PMID: 39181524 DOI: 10.1016/j.gep.2024.119375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/31/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
ROBO4 involves in the stabilization of blood vessel and mediates the migration of hematopoietic stem cell and newborn neuron. However, the patterns of expression and regulation are not quite clear. To resolve this, we analyzed the single cell sequence data, and confirmed that Robo4 mainly expresses in various endothelial cells, but also in epithelial cells, pericytes, and stem or progenitor cells of bone marrow, fibroblast cells/mesenchymal stem cell of adipose tissues, muscle cells and neuron. Robo4 expressions in endothelial cells derived from capillary vessel, tip/stalk/activated endothelial cells were higher than that in artery and large vein (matured endothelial cells). On the other hand, via mining the gene expression data deposited in the NCBI Gene Expression Omnibus database as well as National Genomics Data Center (NGDC), we uncovered that the expression of Robo4 were regulated by different stimulus and variable in diseases' condition.Moreover, we constructed enhanced GFP (eGFP) transgene mouse controlled by Robo4 promoter using CRISPR/CAS9 system. We found GFP signals in many cell types from the embryonic section, confirming a widely expression of Robo4. Together, Robo4 widely and dynamically express in multiple cell types, and can be regulated by diverse factors.
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Affiliation(s)
- Huiping Li
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Huiyan Xiao
- Shantou Jinshan Middle School, Shantou, China
| | - Xiaoting Mai
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Shaofeng Huang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Jiongyu Chen
- Central Laboratory, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Xiaoqiang Xiao
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China.
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15
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Ono Y, Fujino N, Saito T, Matsumoto S, Konno S, Endo T, Suzuki M, Yamada M, Okada Y, Sugiura H. Characterization of IL-6R-expressing monocytes in the lung of patients with chronic obstructive pulmonary disease. Respir Investig 2024; 62:856-866. [PMID: 39068895 DOI: 10.1016/j.resinv.2024.07.013] [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: 04/30/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Monocytes play a crucial role in innate immune responses for host defense, however, their involvement in chronic obstructive pulmonary disease (COPD) remains poorly understood. We previously identified a subset of monocytes in COPD lung tissues characterized by high interleukin-6 receptor (IL-6R) expression. This study aimed to characterize the phenotypes of IL-6Rhi monocytes in the lungs of COPD patients. METHODS Using flow cytometry, we assessed the abundance of pulmonary CD14+IL-6Rhi cells in never smokers (CNS), control ex-smokers (CES) and COPD patients. IL-6 expression in CD14+ monocytes isolated from the peripheral blood of patients with COPD was also examined. CD45+CD206-CD14+IL-6Rhi and CD45+CD206-CD14+IL-6R-/lo cells were isolated from COPD lung tissues for transcriptome analysis. A monocyte line THP1 cell with constitutive IL-6R expression was stimulated with recombinant IL-6, followed by RNA sequencing to evaluate the IL-6 responsiveness of IL-6R+ monocytes. RESULTS The number of pulmonary CD14+IL-6Rhi monocytes was elevated in COPD patients compared to CNS, whereas CD14+ monocytes in the peripheral blood of COPD patients did not express IL-6R. Upregulated mRNA expression in CD14+IL-6Rhi monocytes was associated with chemotaxis, monocyte differentiation, fatty acid metabolism and integrin-mediated signaling pathway. Stimulation of THP1 cells with recombinant IL-6 induced changes in the expression of genes linked to chemotaxis and organism development. CONCLUSION In patients with COPD, CD14+IL-6Rhi monocytes are increased in lung tissues compared to those in CNS. They exhibit a transcriptome profile different from that of CD14+IL-6R-/lo monocytes.
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Affiliation(s)
- Yoshinao Ono
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, 1-1 Seiryocho, Aoba-ku, Sendai, Miyagi, 980 8574, Japan
| | - Naoya Fujino
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, 1-1 Seiryocho, Aoba-ku, Sendai, Miyagi, 980 8574, Japan.
| | - Takuya Saito
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, 1-1 Seiryocho, Aoba-ku, Sendai, Miyagi, 980 8574, Japan
| | - Shuichiro Matsumoto
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, 1-1 Seiryocho, Aoba-ku, Sendai, Miyagi, 980 8574, Japan
| | - Shuichi Konno
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, 1-1 Seiryocho, Aoba-ku, Sendai, Miyagi, 980 8574, Japan
| | - Takuto Endo
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, 1-1 Seiryocho, Aoba-ku, Sendai, Miyagi, 980 8574, Japan
| | - Manami Suzuki
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, 1-1 Seiryocho, Aoba-ku, Sendai, Miyagi, 980 8574, Japan
| | - Mitsuhiro Yamada
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, 1-1 Seiryocho, Aoba-ku, Sendai, Miyagi, 980 8574, Japan
| | - Yoshinori Okada
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryocho, Aoba-ku, Sendai, Miyagi, 980 8575, Japan
| | - Hisatoshi Sugiura
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, 1-1 Seiryocho, Aoba-ku, Sendai, Miyagi, 980 8574, Japan
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Moghaddam SJ, Savai R, Salehi-Rad R, Sengupta S, Kammer MN, Massion P, Beane JE, Ostrin EJ, Priolo C, Tennis MA, Stabile LP, Bauer AK, Sears CR, Szabo E, Rivera MP, Powell CA, Kadara H, Jenkins BJ, Dubinett SM, Houghton AM, Kim CF, Keith RL. Premalignant Progression in the Lung: Knowledge Gaps and Novel Opportunities for Interception of Non-Small Cell Lung Cancer. An Official American Thoracic Society Research Statement. Am J Respir Crit Care Med 2024; 210:548-571. [PMID: 39115548 PMCID: PMC11389570 DOI: 10.1164/rccm.202406-1168st] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Indexed: 08/13/2024] Open
Abstract
Rationale: Despite significant advances in precision treatments and immunotherapy, lung cancer is the most common cause of cancer death worldwide. To reduce incidence and improve survival rates, a deeper understanding of lung premalignancy and the multistep process of tumorigenesis is essential, allowing timely and effective intervention before cancer development. Objectives: To summarize existing information, identify knowledge gaps, formulate research questions, prioritize potential research topics, and propose strategies for future investigations into the premalignant progression in the lung. Methods: An international multidisciplinary team of basic, translational, and clinical scientists reviewed available data to develop and refine research questions pertaining to the transformation of premalignant lung lesions to advanced lung cancer. Results: This research statement identifies significant gaps in knowledge and proposes potential research questions aimed at expanding our understanding of the mechanisms underlying the progression of premalignant lung lesions to lung cancer in an effort to explore potential innovative modalities to intercept lung cancer at its nascent stages. Conclusions: The identified gaps in knowledge about the biological mechanisms of premalignant progression in the lung, together with ongoing challenges in screening, detection, and early intervention, highlight the critical need to prioritize research in this domain. Such focused investigations are essential to devise effective preventive strategies that may ultimately decrease lung cancer incidence and improve patient outcomes.
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Fan G, Xie T, Tang L, Li L, Han X, Shi Y. The co-location of CD14+APOE+ cells and MMP7+ tumour cells contributed to worse immunotherapy response in non-small cell lung cancer. Clin Transl Med 2024; 14:e70009. [PMID: 39187937 PMCID: PMC11347392 DOI: 10.1002/ctm2.70009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 08/13/2024] [Accepted: 08/15/2024] [Indexed: 08/28/2024] Open
Abstract
Intra-tumour immune infiltration is a crucial determinant affecting immunotherapy response in non-small cell lung cancer (NSCLC). However, its phenotype and related spatial structure have remained elusive. To overcome these restrictions, we undertook a comprehensive study comprising spatial transcriptomic (ST) data (28 712 spots from six samples). We identified two distinct intra-tumour infiltration patterns: immune exclusion (characterised by myeloid cells) and immune activation (characterised by plasma cells). The immune exclusion and immune activation signatures showed adverse and favourable roles in NSCLC patients' survival, respectively. Notably, CD14+APOE+ cells were recognised as the main cell type in immune exclusion samples, with increased epithelial‒mesenchymal transition and decreased immune activities. The co-location of CD14+APOE+ cells and MMP7+ tumour cells was observed in both ST and bulk transcriptomics data, validated by multiplex immunofluorescence performed on 20 NSCLC samples. The co-location area exhibited the upregulation of proliferation-related pathways and hypoxia activities. This co-localisation inhibited T-cell infiltration and the formation of tertiary lymphoid structures. Both CD14+APOE+ cells and MMP7+ tumour cells were associated with worse survival. In an immunotherapy cohort from the ORIENT-3 clinical trial, NSCLC patients who responded unfavourably exhibited higher infiltration of CD14+APOE+ cells and MMP7+ tumour cells. Within the co-location area, the MK, SEMA3 and Macrophage migration inhibitory factor (MIF) signalling pathway was most active in cell‒cell communication. This study identified immune exclusion and activation patterns in NSCLC and the co-location of CD14+APOE+ cells and MMP7+ tumour cells as contributors to immune resistance.
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Affiliation(s)
- Guangyu Fan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted DrugsBeijingChina
| | - Tongji Xie
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted DrugsBeijingChina
| | - Le Tang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted DrugsBeijingChina
| | - Lin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Xiaohong Han
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe and Rare Diseases, NMPA Key Laboratory for Clinical Research and Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative DrugsChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Yuankai Shi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted DrugsBeijingChina
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Han Y, Ye M, Ye S, Liu B. Comparison of Lung Tissue-Derived Extracellular Vesicles Using Multiple Dissociation Methods for Profiling Protein Biomarkers. Biotechnol J 2024; 19:e202400329. [PMID: 39295555 DOI: 10.1002/biot.202400329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 08/29/2024] [Accepted: 09/02/2024] [Indexed: 09/21/2024]
Abstract
Extracellular vesicles (EVs) operate as chemical messengers that facilitate intercellular communication. Emerging evidence has demonstrated that lung tissue-derived EVs play pivotal roles in pulmonary physiological processes and have potential as biomarkers and therapeutics for lung diseases. Multiple methods have been proposed for the isolation of lung tissue-derived EVs. However, the effects of different tissue pre-treatments on lung EV isolation and subsequent disease biomarker discovery have not yet been comprehensively investigated. In this study, we compared the physical characteristics, recovery yields, and protein compositions of EVs isolated from lung tissues using three methods based on different tissue dissociation principles. Methodologically, the beneficial roles of blood perfusion and gentle meshing were emphasized based on their impact on EV yield and purity. These results demonstrate that different methods enrich distinct subpopulations of EVs that exhibit significant differences in their protein cargo and surface properties. These disparities directly affect the diagnostic detection of marker proteins related to lung diseases, including lung tumors, asthma, and pulmonary fibrosis. Collectively, these findings highlight the variations in EV characteristics resulting from the applied approaches and offer compelling suggestions for guiding researchers in selecting a suitable isolation method based on downstream functional studies and clinical applications.
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Affiliation(s)
- Yue Han
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Meng Ye
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Sheng Ye
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Bowen Liu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
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19
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Meng Z, Zhang R, Wu X, Piao Z, Zhang M, Jin T. LncRNA HAGLROS promotes breast cancer evolution through miR-135b-3p/COL10A1 axis and exosome-mediated macrophage M2 polarization. Cell Death Dis 2024; 15:633. [PMID: 39198393 PMCID: PMC11358487 DOI: 10.1038/s41419-024-07020-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024]
Abstract
Long non-coding RNAs (lncRNAs) play an important role in breast cancer progression, but the function of lncRNAs in regulating tumor-associated macrophages (TAMs) remains unclear. As carriers of lncRNAs, exosomes play an important role as mediators in the communication between cancer cells and the tumor microenvironment. In this study, we found that lncRNA HAGLROS was highly expressed in breast cancer tissues and plasma exosomes, and its high expression was related to the poor prognosis of breast cancer patients. Functionally, breast cancer cell-derived exosomal lncRNA HAGLROS promotes breast cancer cell proliferation, migration, epithelial-mesenchymal transition (EMT) process and angiogenesis by inducing TAM/M2 polarization. Mechanistically, lncRNA HAGLROS competitively binds to miR-135-3p to prevent the degradation of its target gene COL10A1. Collectively, these results indicated that the lncRNA HAGLROS/miR-135b-3p/COL10A1 axis promoted breast cancer progression, and revealed the interactive communication mechanism between breast cancer cells and TAMs, suggesting that lncRNA HAGLROS may be a potential biomarker and therapeutic target for breast cancer.
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Affiliation(s)
- Ziqi Meng
- Department of Central Laboratory, Yanbian University Hospital, Yanji, China
- Department of Pathology and Cancer Research Center, Yanbian University, Yanji, China
| | - Rui Zhang
- Department of Pathology and Cancer Research Center, Yanbian University, Yanji, China
| | - Xuwei Wu
- Department of Pathology, Chifeng Municipal Hospital, Chifeng, China
| | - Zhengri Piao
- Department of Radiology, Yanbian University Hospital, Yanji, Jilin, China
| | - Meihua Zhang
- Department of Health Examination Centre, Yanbian University Hospital, Yanji, China.
| | - Tiefeng Jin
- Department of Central Laboratory, Yanbian University Hospital, Yanji, China.
- Department of Pathology and Cancer Research Center, Yanbian University, Yanji, China.
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20
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Zhang YH, Xie R, Dai CS, Gao HW, Zhou G, Qi TT, Wang WY, Wang H, Cui YM. Thyroid hormone receptor-beta agonist HSK31679 alleviates MASLD by modulating gut microbial sphingolipids. J Hepatol 2024:S0168-8278(24)02486-3. [PMID: 39181210 DOI: 10.1016/j.jhep.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 08/02/2024] [Accepted: 08/05/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND & AIMS As the first approved medication for metabolic dysfunction-associated steatohepatitis (MASH), thyroid hormone receptor-beta (THR-β) agonist MGL-3196 (Resmetirom) is highly spotlighted as the liver-directed, bioactive oral drug. However, it was also identified with remarkable heterogeneity of individual clinical efficacy and its interference with gut microbiota in host hepatoenteral circulation was still undocumented. METHODS We compared MASH attenuation by MGL-3196 and its derivative drug HSK31679 between germ-free (GF) and specific-pathogen free (SPF) mice to evaluate the role of gut microbiota. Then cross-omics analyses of microbial metagenome, metabolome and single-cell RNA-sequencing were applied into the randomized, double-blind, placebo-controlled multiple-ascending-dose (MAD) cohort of HSK31679 treatment (n = 40), to comprehensively investigate the altered gut microbiota metabolism and circulating immune signatures. RESULTS HSK31679 outperformed MGL-3196 in ameliorating MASH diet-induced steatohepatitis of SPF mice but not GF mice. In the MAD cohort of HSK31679, relative abundance of B. thetaiotaomicron was significantly enriched to impair glucosylceramide synthase (GCS)-catalyzed monoglucosylation of microbial Cer(d18:1/16:0) and Cer(d18:1/24:1). In stark contrast to the non-inferiority MASH resolution between MGL-3196 and HSK31679 for GFBTΔGCS mice, HSK31679 manifested superior steatohepatitis alleviation than MGL-3196 for GFBTWT mice, due to its steric hindrance with R123 and Y401 of gut microbial GCS. For participants with high fecal GCS activity, the administration of 160 mg HSK31679 induced a shift in peripheral compartments towards an immunosuppressive niche, characterized by decreased CD8α+ dendritic cells and MINCLE+ macrophages. CONCLUSIONS This study provided novel insights into the indispensable gut microbiota for HSK31679 treatment, which revealed microbial GCS may serve as its prognostic biomarker of MASH treatment, as well as the new target for further strategies of microbiota-based MASH therapeutics. IMPACT AND IMPLICATIONS Remarkable heterogeneity of individual clinical efficacy of THR-β agonists and their interferences with microbiome in host hepatoenteral circulation are poorly understood. In our current germ-free mice models and randomized, double-blind multiple-dose cohort study, we identified microbial GCS as the prognostic biomarker of HSK31679 treatment, as well as the new target for further strategies of microbiota-based MASLD therapeutics.
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Affiliation(s)
- Yu-Hang Zhang
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China, 100191; Department of Pharmacy, Peking University First Hospital, Beijing, China, 100034
| | - Ran Xie
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China, 100191; Department of Pharmacy, Peking University First Hospital, Beijing, China, 100034
| | - Chen-Shu Dai
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China, 100191; Department of Pharmacy, Wenzhou Medical University, Wenzhou, China, 325035
| | - Hong-Wei Gao
- Biomarker Technologies Corporation, Beijing, China, 101300
| | - Gan Zhou
- Department of Pharmacy, Xiangya Hospital of Central South University, Changsha, China, 410008
| | - Tian-Tian Qi
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China, 100191
| | - Wen-Yu Wang
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China, 100029
| | - Hua Wang
- Department of Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei, China, 230022; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China, 230032.
| | - Yi-Min Cui
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China, 100191; Department of Pharmacy, Peking University First Hospital, Beijing, China, 100034.
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21
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Yu J, Yan Y, Li S, Xu Y, Parolia A, Rizvi S, Wang W, Zhai Y, Xiao R, Li X, Liao P, Zhou J, Okla K, Lin H, Lin X, Grove S, Wei S, Vatan L, Hu J, Szumilo J, Kotarski J, Freeman ZT, Skala S, Wicha M, Cho KR, Chinnaiyan AM, Schon S, Wen F, Kryczek I, Wang S, Chen L, Zou W. Progestogen-driven B7-H4 contributes to onco-fetal immune tolerance. Cell 2024; 187:4713-4732.e19. [PMID: 38968937 PMCID: PMC11344674 DOI: 10.1016/j.cell.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/09/2024] [Accepted: 06/09/2024] [Indexed: 07/07/2024]
Abstract
Immune tolerance mechanisms are shared in cancer and pregnancy. Through cross-analyzing single-cell RNA-sequencing data from multiple human cancer types and the maternal-fetal interface, we found B7-H4 (VTCN1) is an onco-fetal immune tolerance checkpoint. We showed that genetic deficiency of B7-H4 resulted in immune activation and fetal resorption in allogeneic pregnancy models. Analogously, B7-H4 contributed to MPA/DMBA-induced breast cancer progression, accompanied by CD8+ T cell exhaustion. Female hormone screening revealed that progesterone stimulated B7-H4 expression in placental and breast cancer cells. Mechanistically, progesterone receptor (PR) bound to a newly identified -58 kb enhancer, thereby mediating B7-H4 transcription via the PR-P300-BRD4 axis. PR antagonist or BRD4 degrader potentiated immunotherapy in a murine B7-H4+ breast cancer model. Thus, our work unravels a mechanistic and biological connection of a female sex hormone (progesterone) to onco-fetal immune tolerance via B7-H4 and suggests that the PR-P300-BRD4 axis is targetable for treating B7-H4+ cancer.
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Affiliation(s)
- Jiali Yu
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Yijian Yan
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Shasha Li
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Ying Xu
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Abhijit Parolia
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Syed Rizvi
- Department of Chemical Engineering, University of Michigan School of Engineering, Ann Arbor, MI, USA
| | - Weichao Wang
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Yiwen Zhai
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Rongxin Xiao
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Xiong Li
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Peng Liao
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Jiajia Zhou
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Karolina Okla
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Department of Oncological Gynecology and Gynecology, Medical University of Lublin, Lublin, Poland
| | - Heng Lin
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Xun Lin
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Sara Grove
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Shuang Wei
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Linda Vatan
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Jiantao Hu
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Justyna Szumilo
- Department of Clinical Pathomorphology, Medical University of Lublin, Lublin, Poland
| | - Jan Kotarski
- Department of Oncological Gynecology and Gynecology, Medical University of Lublin, Lublin, Poland
| | - Zachary T Freeman
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie Skala
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Max Wicha
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kathleen R Cho
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Samantha Schon
- Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan School of Engineering, Ann Arbor, MI, USA
| | - Ilona Kryczek
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Shaomeng Wang
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lieping Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Weiping Zou
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Graduate Program in Immunology, University of Michigan, Ann Arbor, MI, USA; Graduate Program in Cancer Biology, University of Michigan, Ann Arbor, MI, USA.
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22
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Lapuente-Santana Ó, Sturm G, Kant J, Ausserhofer M, Zackl C, Zopoglou M, McGranahan N, Rieder D, Trajanoski Z, da Cunha Carvalho de Miranda NF, Eduati F, Finotello F. Multimodal analysis unveils tumor microenvironment heterogeneity linked to immune activity and evasion. iScience 2024; 27:110529. [PMID: 39161957 PMCID: PMC11331718 DOI: 10.1016/j.isci.2024.110529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 06/03/2024] [Accepted: 07/13/2024] [Indexed: 08/21/2024] Open
Abstract
The cellular and molecular heterogeneity of tumors is a major obstacle to cancer immunotherapy. Here, we use a systems biology approach to derive a signature of the main sources of heterogeneity in the tumor microenvironment (TME) from lung cancer transcriptomics. We demonstrate that this signature, which we called iHet, is conserved in different cancers and associated with antitumor immunity. Through analysis of single-cell and spatial transcriptomics data, we trace back the cellular origin of the variability explaining the iHet signature. Finally, we demonstrate that iHet has predictive value for cancer immunotherapy, which can be further improved by disentangling three major determinants of anticancer immune responses: activity of immune cells, immune infiltration or exclusion, and cancer-cell foreignness. This work shows how transcriptomics data can be integrated to derive a holistic representation of the phenotypic heterogeneity of the TME and to predict its unfolding and fate during immunotherapy with immune checkpoint blockers.
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Affiliation(s)
- Óscar Lapuente-Santana
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
- Boehringer Ingelheim International Pharma GmbH & Co KG, 55216 Ingelheim am Rhein, Germany
| | - Joan Kant
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Markus Ausserhofer
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, 6020 Innsbruck, Austria
| | - Constantin Zackl
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, 6020 Innsbruck, Austria
| | - Maria Zopoglou
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, 6020 Innsbruck, Austria
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London WC1E 6DD, UK
| | - Dietmar Rieder
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | | | - Federica Eduati
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
| | - Francesca Finotello
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, 6020 Innsbruck, Austria
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23
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Yao X, Redekar NR, Keeran KJ, Qu X, Jeffries KR, Soria-Florido M, Saxena A, Dagur PK, Lin WC, McCoy JP, Levine SJ. Neutrophil Heterogeneity Is Modified during Acute Lung Inflammation in Apoa1-/- Mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:456-468. [PMID: 38912868 PMCID: PMC11300144 DOI: 10.4049/jimmunol.2300459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 06/01/2024] [Indexed: 06/25/2024]
Abstract
Neutrophils play important roles in inflammatory airway diseases. In this study, we assessed whether apolipoprotein A-I modifies neutrophil heterogeneity as part of the mechanism by which it attenuates acute airway inflammation. Neutrophilic airway inflammation was induced by daily intranasal administration of LPS plus house dust mite (LPS+HDM) to Apoa1-/- and Apoa1+/+ mice for 3 d. Single-cell RNA sequencing was performed on cells recovered from bronchoalveolar lavage fluid on day 4. Unsupervised profiling identified 10 clusters of neutrophils in bronchoalveolar lavage fluid from Apoa1-/- and Apoa1+/+ mice. LPS+HDM-challenged Apoa1-/- mice had an increased proportion of the Neu4 neutrophil cluster that expressed S100a8, S100a9, and Mmp8 and had high maturation, aggregation, and TLR4 binding scores. There was also an increase in the Neu6 cluster of immature neutrophils, whereas neutrophil clusters expressing IFN-stimulated genes were decreased. An unsupervised trajectory analysis showed that Neu4 represented a distinct lineage in Apoa1-/- mice. LPS+HDM-challenged Apoa1-/- mice also had an increased proportion of recruited airspace macrophages, which was associated with a reciprocal reduction in resident airspace macrophages. Increased expression of a common set of proinflammatory genes, S100a8, S100a9, and Lcn2, was present in all neutrophils and airspace macrophages from LPS+HDM-challenged Apoa1-/- mice. These findings show that Apoa1-/- mice have increases in specific neutrophil and macrophage clusters in the lung during acute inflammation mediated by LPS+HDM, as well as enhanced expression of a common set of proinflammatory genes. This suggests that modifications in neutrophil and macrophage heterogeneity contribute to the mechanism by which apolipoprotein A-I attenuates acute airway inflammation.
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Affiliation(s)
- Xianglan Yao
- Laboratory of Asthma and Lung Inflammation, Critical Care Medicine and Pulmonary Branch, Division of Intramural Research, NHLBI, NIH, Bethesda, Maryland
| | - Neelam R. Redekar
- NIAID Collaborative Bioinformatics Resource, Integrated Data Sciences Section, Research Technologies Branch, Division of Intramural Research, NIAID, NIH, Bethesda, Maryland
| | - Karen J. Keeran
- Animal Surgery and Resources Core Facility, Division of Intramural Research, NHLBI, NIH, Bethesda, Maryland
| | - Xuan Qu
- Laboratory of Asthma and Lung Inflammation, Critical Care Medicine and Pulmonary Branch, Division of Intramural Research, NHLBI, NIH, Bethesda, Maryland
| | - Kenneth R. Jeffries
- Animal Surgery and Resources Core Facility, Division of Intramural Research, NHLBI, NIH, Bethesda, Maryland
| | - M.T. Soria-Florido
- Laboratory of Asthma and Lung Inflammation, Critical Care Medicine and Pulmonary Branch, Division of Intramural Research, NHLBI, NIH, Bethesda, Maryland
| | - Ankit Saxena
- Flow Cytometry Core Facility, Division of Intramural Research, NHLBI, NIH, Bethesda, Maryland
| | - Pradeep K. Dagur
- Flow Cytometry Core Facility, Division of Intramural Research, NHLBI, NIH, Bethesda, Maryland
| | - Wan-Chi Lin
- Flow Cytometry Core Facility, Division of Intramural Research, NHLBI, NIH, Bethesda, Maryland
| | - J. Philip McCoy
- Flow Cytometry Core Facility, Division of Intramural Research, NHLBI, NIH, Bethesda, Maryland
| | - Stewart J. Levine
- Laboratory of Asthma and Lung Inflammation, Critical Care Medicine and Pulmonary Branch, Division of Intramural Research, NHLBI, NIH, Bethesda, Maryland
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24
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You S, Li S, Zeng L, Song J, Li Z, Li W, Ni H, Xiao X, Deng W, Li H, Lin W, Liang C, Zheng Y, Cheng SC, Xiao N, Tong M, Yu R, Huang J, Huang H, Xu H, Han J, Ren J, Mao K. Lymphatic-localized Treg-mregDC crosstalk limits antigen trafficking and restrains anti-tumor immunity. Cancer Cell 2024; 42:1415-1433.e12. [PMID: 39029466 DOI: 10.1016/j.ccell.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/29/2024] [Accepted: 06/23/2024] [Indexed: 07/21/2024]
Abstract
The tumor microenvironment (TME) has a significant impact on tumor growth and immunotherapy efficacies. However, the precise cellular interactions and spatial organizations within the TME that drive these effects remain elusive. Using advanced multiplex imaging techniques, we have discovered that regulatory T cells (Tregs) accumulate around lymphatic vessels in the peripheral tumor stroma. This localized accumulation is facilitated by mature dendritic cells enriched in immunoregulatory molecules (mregDCs), which promote chemotaxis of Tregs, establishing a peri-lymphatic Treg-mregDC niche. Within this niche, mregDCs facilitate Treg activation, which in turn restrains the trafficking of tumor antigens to the draining mesenteric lymph nodes, thereby impeding the initiation of anti-tumor adaptive immune responses. Disrupting Treg recruitment to mregDCs inhibits tumor progression. Our study provides valuable insights into the organization of TME and how local crosstalk between lymphoid and myeloid cells suppresses anti-tumor immune responses.
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Affiliation(s)
- Siyuan You
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China
| | - Shuqin Li
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China
| | - Lingsu Zeng
- Department of Gastroenterology, The National Key Clinical Specialty, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361004, China; Clinical Research Center for Gut Microbiota and Digestive Diseases of Fujian Province, Xiamen Key Laboratory of Intestinal Microbiome and Human Health, Xiamen, Fujian 361004, China; The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian 350001, China
| | - Jinsheng Song
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China
| | - Zifeng Li
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China
| | - Weiyun Li
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China
| | - Hengxiao Ni
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China
| | - Xu Xiao
- School of Informatics, Xiamen University, Xiamen, Fujian 361005, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Wenbo Deng
- Key Laboratory of Reproductive Health Research, Fujian Province University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Hongye Li
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China
| | - Wenbo Lin
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China
| | - Chenyu Liang
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China
| | - Yanfei Zheng
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China
| | - Shih-Chin Cheng
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China; Department of Gastroenterology, The National Key Clinical Specialty, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361004, China; Department of Digestive Diseases, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Nengming Xiao
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China
| | - Mengsha Tong
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Rongshan Yu
- School of Informatics, Xiamen University, Xiamen, Fujian 361005, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Jialiang Huang
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China
| | - Hongling Huang
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China
| | - Hongzhi Xu
- Department of Gastroenterology, The National Key Clinical Specialty, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361004, China; Clinical Research Center for Gut Microbiota and Digestive Diseases of Fujian Province, Xiamen Key Laboratory of Intestinal Microbiome and Human Health, Xiamen, Fujian 361004, China; Department of Digestive Diseases, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China
| | - Jianlin Ren
- Department of Gastroenterology, The National Key Clinical Specialty, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361004, China; Clinical Research Center for Gut Microbiota and Digestive Diseases of Fujian Province, Xiamen Key Laboratory of Intestinal Microbiome and Human Health, Xiamen, Fujian 361004, China; Department of Digestive Diseases, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Kairui Mao
- State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; Xiamen, Fujian 361102, China; Department of Gastroenterology, The National Key Clinical Specialty, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361004, China; Department of Digestive Diseases, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China.
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Wu W, Chen Z, Wen H, Zhang H. Unveiling potential drug targets for lung squamous cell carcinoma through the integration of druggable genome and genome-wide association data. Front Genet 2024; 15:1431684. [PMID: 39175755 PMCID: PMC11338847 DOI: 10.3389/fgene.2024.1431684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 07/29/2024] [Indexed: 08/24/2024] Open
Abstract
Background: Lung squamous cell carcinoma (LSCC) is a major subtype of lung cancer with poor prognosis and low survival rate. Compared with lung adenocarcinoma, yet no FDA-approved targeted-therapy has been found for lung squamous cell carcinoma. Methods: To identify potential drug targets for LSCC, Summary-data-based Mendelian randomization (SMR) analysis was used to examine the potential association between 4,543 druggable genes and LSCC, followed by colocalization analysis and HEIDI tests to confirm the robustness of the result. Phenome-wide association study (PheWAS) explored potential side effects of candidate drug targets. Enrichment analysis and protein-protein interaction networks revealed the function and significance of therapeutic targets. Single-cell expression analysis was used to examine cell types with enrichment expression of druggable genes in LSCC tissue. Drug prediction included screening potential drug candidates and evaluating their interactions with targets through molecular docking. Results: This research has identified ten significant drug targets for LSCC through a comprehensive SMR analysis. These targets included (COPA, PKD2L1, CCR1, C2, CYP21A2, and NCSTN as risk factors, and CCNA2, C4A, APOM, and LPAR2 as protective factors). PheWAS demonstrated that C2, CCNA2, LPAR2, and NCSTN exhibited associations with other phenotypes at the genetic level. Then, we found four potentially effective drugs with the Dsigdb database. Subsequently, molecular docking indicated that favorable binding interactions between drug candidates and potential target molecules. In the druggability evaluation, five out of ten drug target genes have been used in drug development (APOM, C4A, CCNA2, COPA, and PKD2L1). Six out of ten druggable genes showed significant expression in LSCC tissues (COPA, PKD2L1, CCR1, C2, NCSTN, LPAR2). Besides, Single-cell expression analysis revealed that C2 and CCNA2 were primarily enriched in macrophages, while COPA and NCSTN were enriched in both macrophages and epithelial cells. Conclusion: Our research revealed ten potential druggable genes for LSCC treatment, which might help to advance the precise and efficient therapeutic approaches of LSCC.
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Affiliation(s)
- Wenhua Wu
- The Second Clinical Medical College, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhengrui Chen
- The Second Clinical Medical College, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Haiteng Wen
- The Second Clinical Medical College, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Haiyun Zhang
- Department of Pulmonary and Critical Care Medicine, Zhujiang Hosptial, Southern Medical University, Guangzhou, Guangdong, China
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Tran MA, Youssef D, Shroff S, Chowhan D, Beaumont KG, Sebra R, Mehrazin R, Wiklund P, Lin JJ, Horowitz A, Farkas AM, Galsky MD, Sfakianos JP, Bhardwaj N. Urine scRNAseq reveals new insights into the bladder tumor immune microenvironment. J Exp Med 2024; 221:e20240045. [PMID: 38847806 PMCID: PMC11157455 DOI: 10.1084/jem.20240045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/04/2024] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
Due to bladder tumors' contact with urine, urine-derived cells (UDCs) may serve as a surrogate for monitoring the tumor microenvironment (TME) in bladder cancer (BC). However, the composition of UDCs and the extent to which they mirror the tumor remain poorly characterized. We generated the first single-cell RNA-sequencing of BC patient UDCs with matched tumor and peripheral blood mononuclear cells (PBMC). BC urine was more cellular than healthy donor (HD) urine, containing multiple immune populations including myeloid cells, CD4+ and CD8+ T cells, natural killer (NK) cells, B cells, and dendritic cells (DCs) in addition to tumor and stromal cells. Immune UDCs were transcriptionally more similar to tumor than blood. UDCs encompassed cytotoxic and activated CD4+ T cells, exhausted and tissue-resident memory CD8+ T cells, macrophages, germinal-center-like B cells, tissue-resident and adaptive NK cells, and regulatory DCs found in tumor but lacking or absent in blood. Our findings suggest BC UDCs may be surrogates for the TME and serve as therapeutic biomarkers.
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Affiliation(s)
- Michelle A. Tran
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dina Youssef
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sanjana Shroff
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Disha Chowhan
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristin G. Beaumont
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Reza Mehrazin
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peter Wiklund
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jenny J. Lin
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amir Horowitz
- Department of Immunology and Immunotherapy, The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam M. Farkas
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D. Galsky
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John P. Sfakianos
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nina Bhardwaj
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Extramural Member, Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
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Wang D, Li S, Yang Z, Yu C, Wu P, Yang Y, Zhang R, Li Q, Yang J, Li H, Ji G, Wang Y, Xie K, Liu Y, Wang K, Zhu D, Zhang W, Liu D, Chen B, Li W. Single-cell transcriptome analysis deciphers the CD74-mediated immune evasion and tumour growth in lung squamous cell carcinoma with chronic obstructive pulmonary disease. Clin Transl Med 2024; 14:e1786. [PMID: 39113235 PMCID: PMC11306293 DOI: 10.1002/ctm2.1786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/08/2024] [Accepted: 07/18/2024] [Indexed: 08/11/2024] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) contributes to the incidence and prognosis of lung cancer. The presence of COPD significantly increases the risk of lung squamous cell carcinoma (LSCC). COPD may promote an immunosuppressive microenvironment in LSCC by regulating the expression of immune-inhibitory factors in T cells, although the mechanisms remain unclear. In this study, we aimed to decipher the tumour microenvironment signature for LSCC with COPD at a single-cell level. METHODS We performed single-cell RNA sequencing on tumour tissues from LSCC with or without COPD, then investigated the features of the immune and tumour cells. We employed multiple techniques, including multispectral imaging, flow cytometry, tissue microarray analysis, survival analysis, co-culture systems and in vitro and in vivo treatment experiments, to validate the findings obtained from single-cell analyses. RESULTS LSCC with COPD showed increased proportions of tumour-associated macrophages (TAMs) and higher levels of CD8+ T cell exhaustion molecules, which contributed to an immunosuppressive microenvironment. Further analysis revealed a critical cluster of CD74+ tumour cells that expressed both epithelial and immune cell signatures, exhibited a stronger capacity for tumorigenesis and predicted worse overall survival. Notably, migration inhibitory factor (MIF) secreted by TAMs from LSCC with COPD may promote the activation of CD74. MIF-CD74 may interact with CD8+ T cells and impair their anti-tumour activity by regulating the PI3K-STAT3-programmed cell death-1 ligand 1 signalling pathway, facilitating tumour proliferation and immune evasion. CONCLUSIONS Our comprehensive picture of the tumour ecosystem in LSCC with COPD provides deeper insights into relevant immune evasion mechanisms and potential targets for immunotherapy. HIGHLIGHT Our results demonstrated higher proportions of tumour-associated macrophages (TAMs) and higher levels of exhaustion molecules in CD8+ T cells in the microenvironment of LSCC with COPD. CD74+tumour cells were associated with poor disease prognosis. Migration inhibitory factor (MIF)-CD74 may interact with CD8+ T cells and impair their anti-tumour activity by regulating the PI3K-STAT3-PD-L1 signalling pathway, facilitating immune evasion.
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Affiliation(s)
- Denian Wang
- Precision Medicine Research CenterPrecision Medicine Key Laboratory of Sichuan ProvinceState Key Laboratory of Respiratory Health and MultimorbidityWest China HospitalSichuan UniversityChengduSichuanChina
- Department of Respiratory and Critical Care MedicinePrecision Medicine CenterFrontiers Science Center for Disease‐Related Molecular NetworkWest China HospitalSichuan UniversityChengduSichuanChina
- Research Units of West ChinaChinese Academy of Medical SciencesWest China HospitalChengduSichuanChina
| | - Sixiang Li
- Department of Respiratory and Critical Care MedicinePrecision Medicine CenterFrontiers Science Center for Disease‐Related Molecular NetworkWest China HospitalSichuan UniversityChengduSichuanChina
- Department of Respiratory and Critical Care MedicineNational Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Zhi Yang
- Department of NephrologyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Chunyan Yu
- Frontiers Science Center for Disease‐Related Molecular NetworkLaboratory of Omics Technology and BioinformaticsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Pengfei Wu
- Department of Respiratory HealthFrontiers Science Center for Disease‐Related Molecular NetworkWest China HospitalSichuan UniversityChengduSichuanChina
| | - Ying Yang
- Department of Respiratory HealthFrontiers Science Center for Disease‐Related Molecular NetworkWest China HospitalSichuan UniversityChengduSichuanChina
| | - Rui Zhang
- Department of Respiratory and Critical Care MedicinePrecision Medicine CenterFrontiers Science Center for Disease‐Related Molecular NetworkWest China HospitalSichuan UniversityChengduSichuanChina
| | - Qingyan Li
- Department of Respiratory HealthFrontiers Science Center for Disease‐Related Molecular NetworkWest China HospitalSichuan UniversityChengduSichuanChina
| | - Jian Yang
- Center of GrowthMetabolism, and AgingKey Laboratory of Bio‐Resources and Eco‐EnvironmentCollege of Life SciencesSichuan UniversityChengduSichuanChina
| | - Hongchun Li
- National Chengdu Center for Safety Evaluation of DrugsState Key Laboratory of Biotherapy/Collaborative Innovation Center for BiotherapyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Guiyi Ji
- Health Management CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Yan Wang
- Department of Thoracic SurgeryWest China HospitalSichuan UniversityChengduSichuanChina
| | - Kang Xie
- Precision Medicine Research CenterPrecision Medicine Key Laboratory of Sichuan ProvinceState Key Laboratory of Respiratory Health and MultimorbidityWest China HospitalSichuan UniversityChengduSichuanChina
| | - Yanyan Liu
- Lung Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Kaige Wang
- Department of Respiratory and Critical Care MedicinePrecision Medicine CenterFrontiers Science Center for Disease‐Related Molecular NetworkWest China HospitalSichuan UniversityChengduSichuanChina
| | - Daxing Zhu
- Lung Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Wengeng Zhang
- Precision Medicine Research CenterPrecision Medicine Key Laboratory of Sichuan ProvinceState Key Laboratory of Respiratory Health and MultimorbidityWest China HospitalSichuan UniversityChengduSichuanChina
| | - Dan Liu
- Department of Respiratory and Critical Care MedicinePrecision Medicine CenterFrontiers Science Center for Disease‐Related Molecular NetworkWest China HospitalSichuan UniversityChengduSichuanChina
| | - Bojiang Chen
- Precision Medicine Research CenterPrecision Medicine Key Laboratory of Sichuan ProvinceState Key Laboratory of Respiratory Health and MultimorbidityWest China HospitalSichuan UniversityChengduSichuanChina
| | - Weimin Li
- Precision Medicine Research CenterPrecision Medicine Key Laboratory of Sichuan ProvinceState Key Laboratory of Respiratory Health and MultimorbidityWest China HospitalSichuan UniversityChengduSichuanChina
- Department of Respiratory and Critical Care MedicinePrecision Medicine CenterFrontiers Science Center for Disease‐Related Molecular NetworkWest China HospitalSichuan UniversityChengduSichuanChina
- Research Units of West ChinaChinese Academy of Medical SciencesWest China HospitalChengduSichuanChina
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Li Y, Xun Z, Long J, Sun H, Yang X, Wang Y, Wang Y, Xue J, Zhang N, Zhang J, Bian J, Shi J, Yang X, Wang H, Zhao H. Immunosuppression and phenotypic plasticity in an atlas of human hepatocholangiocarcinoma. Hepatobiliary Surg Nutr 2024; 13:586-603. [PMID: 39175731 PMCID: PMC11336540 DOI: 10.21037/hbsn-23-400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/30/2023] [Indexed: 08/24/2024]
Abstract
Background Hepatocholangiocarcinoma (H-ChC) has the clinicopathological features of both hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA) and is a more aggressive subtype of primary hepatic carcinoma than HCC or iCCA. Methods We sequenced 91,112 single-cell transcriptomes from 16 human samples to elucidate the molecular mechanisms underlying the coexistence of HCC and iCCA components in H-ChC. Results We observed two molecular subtypes of H-ChC at the whole-transcriptome level (CHP and CIP), where a metabolically active tumour cell subpopulation enriched in CHP was characterized by a cellular pre-differentiation property. To define the heterogeneity of tumours and their associated microenvironments, we observe greater tumour diversity in H-ChC than HCC and iCCA. H-ChC exhibits weaker immune cell infiltration and greater CD8+ exhausted T cell (Tex) dysfunction than HCC and iCCA. Then we defined two broad cell states of 6,852 CD8+ Tex cells: GZMK+ CD8+ Tex cells and terminal CD8+ Tex cells. GZMK+ CD8+ Tex cells exhibited higher infiltration of after treatment in H-ChC, the effector scores and expression of the immune checkpoints of them greatly increased after immunotherapy, which indicated that H-ChC might be more sensitive than HCC or iCCA to immunotherapy. Conclusions In this paper, H-ChC was explored, hoping to contribute to the study of mixed tumours in other cancers.
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Affiliation(s)
- Yiran Li
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Ziyu Xun
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Junyu Long
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Huishan Sun
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xu Yang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Yanyu Wang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Yunchao Wang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Jingnan Xue
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Nan Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Junwei Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Jin Bian
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Jie Shi
- Division of Pulmonary and Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xiaobo Yang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Hanping Wang
- Division of Pulmonary and Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Haitao Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
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Yan L, Wang J, Cai X, Liou Y, Shen H, Hao J, Huang C, Luo G, He W. Macrophage plasticity: signaling pathways, tissue repair, and regeneration. MedComm (Beijing) 2024; 5:e658. [PMID: 39092292 PMCID: PMC11292402 DOI: 10.1002/mco2.658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
Macrophages are versatile immune cells with remarkable plasticity, enabling them to adapt to diverse tissue microenvironments and perform various functions. Traditionally categorized into classically activated (M1) and alternatively activated (M2) phenotypes, recent advances have revealed a spectrum of macrophage activation states that extend beyond this dichotomy. The complex interplay of signaling pathways, transcriptional regulators, and epigenetic modifications orchestrates macrophage polarization, allowing them to respond to various stimuli dynamically. Here, we provide a comprehensive overview of the signaling cascades governing macrophage plasticity, focusing on the roles of Toll-like receptors, signal transducer and activator of transcription proteins, nuclear receptors, and microRNAs. We also discuss the emerging concepts of macrophage metabolic reprogramming and trained immunity, contributing to their functional adaptability. Macrophage plasticity plays a pivotal role in tissue repair and regeneration, with macrophages coordinating inflammation, angiogenesis, and matrix remodeling to restore tissue homeostasis. By harnessing the potential of macrophage plasticity, novel therapeutic strategies targeting macrophage polarization could be developed for various diseases, including chronic wounds, fibrotic disorders, and inflammatory conditions. Ultimately, a deeper understanding of the molecular mechanisms underpinning macrophage plasticity will pave the way for innovative regenerative medicine and tissue engineering approaches.
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Affiliation(s)
- Lingfeng Yan
- Institute of Burn ResearchState Key Laboratory of Trauma and Chemical Poisoningthe First Affiliated Hospital of Army Medical University (the Third Military Medical University)ChongqingChina
- Chongqing Key Laboratory for Wound Damage Repair and RegenerationChongqingChina
| | - Jue Wang
- Institute of Burn ResearchState Key Laboratory of Trauma and Chemical Poisoningthe First Affiliated Hospital of Army Medical University (the Third Military Medical University)ChongqingChina
- Chongqing Key Laboratory for Wound Damage Repair and RegenerationChongqingChina
| | - Xin Cai
- Institute of Burn ResearchState Key Laboratory of Trauma and Chemical Poisoningthe First Affiliated Hospital of Army Medical University (the Third Military Medical University)ChongqingChina
- Chongqing Key Laboratory for Wound Damage Repair and RegenerationChongqingChina
| | - Yih‐Cherng Liou
- Department of Biological SciencesFaculty of ScienceNational University of SingaporeSingaporeSingapore
- National University of Singapore (NUS) Graduate School for Integrative Sciences and EngineeringNational University of SingaporeSingaporeSingapore
| | - Han‐Ming Shen
- Faculty of Health SciencesUniversity of MacauMacauChina
| | - Jianlei Hao
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and TreatmentZhuhai Institute of Translational MedicineZhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University)Jinan UniversityZhuhaiGuangdongChina
- The Biomedical Translational Research InstituteFaculty of Medical ScienceJinan UniversityGuangzhouGuangdongChina
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer CenterWest China Hospitaland West China School of Basic Medical Sciences and Forensic MedicineSichuan University, and Collaborative Innovation Center for BiotherapyChengduChina
| | - Gaoxing Luo
- Institute of Burn ResearchState Key Laboratory of Trauma and Chemical Poisoningthe First Affiliated Hospital of Army Medical University (the Third Military Medical University)ChongqingChina
- Chongqing Key Laboratory for Wound Damage Repair and RegenerationChongqingChina
| | - Weifeng He
- Institute of Burn ResearchState Key Laboratory of Trauma and Chemical Poisoningthe First Affiliated Hospital of Army Medical University (the Third Military Medical University)ChongqingChina
- Chongqing Key Laboratory for Wound Damage Repair and RegenerationChongqingChina
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Calderon-Espinosa E, De Ridder K, Benoot T, Jansen Y, Vanhonacker D, Heestermans R, De Becker A, Van Riet I, Decoster L, Goyvaerts C. The crosstalk between lung cancer and the bone marrow niche fuels emergency myelopoiesis. Front Immunol 2024; 15:1397469. [PMID: 39148724 PMCID: PMC11324509 DOI: 10.3389/fimmu.2024.1397469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 07/15/2024] [Indexed: 08/17/2024] Open
Abstract
Modest response rates to immunotherapy observed in advanced lung cancer patients underscore the need to identify reliable biomarkers and targets, enhancing both treatment decision-making and efficacy. Factors such as PD-L1 expression, tumor mutation burden, and a 'hot' tumor microenvironment with heightened effector T cell infiltration have consistently been associated with positive responses. In contrast, the predictive role of the abundantly present tumor-infiltrating myeloid cell (TIMs) fraction remains somewhat uncertain, partly explained by their towering variety in terms of ontogeny, phenotype, location, and function. Nevertheless, numerous preclinical and clinical studies established a clear link between lung cancer progression and alterations in intra- and extramedullary hematopoiesis, leading to emergency myelopoiesis at the expense of megakaryocyte/erythroid and lymphoid differentiation. These observations affirm that a continuous crosstalk between solid cancers such as lung cancer and the bone marrow niche (BMN) must take place. However, the BMN, encompassing hematopoietic stem and progenitor cells, differentiated immune and stromal cells, remains inadequately explored in solid cancer patients. Subsequently, no clear consensus has been reached on the exact breadth of tumor installed hematopoiesis perturbing cues nor their predictive power for immunotherapy. As the current era of single-cell omics is reshaping our understanding of the hematopoietic process and the subcluster landscape of lung TIMs, we aim to present an updated overview of the hierarchical differentiation process of TIMs within the BMN of solid cancer bearing subjects. Our comprehensive overview underscores that lung cancer should be regarded as a systemic disease in which the cues governing the lung tumor-BMN crosstalk might bolster the definition of new biomarkers and druggable targets, potentially mitigating the high attrition rate of leading immunotherapies for NSCLC.
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Affiliation(s)
- Evelyn Calderon-Espinosa
- Laboratory for Molecular and Cellular Therapy (LMCT), Translational Oncology Research Center (TORC), Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory for Molecular Imaging and Therapy (MITH), Vrije Universiteit Brussel, Brussels, Belgium
- Department of Chemistry, University of Warwick, Warwick, United Kingdom
| | - Kirsten De Ridder
- Laboratory for Molecular and Cellular Therapy (LMCT), Translational Oncology Research Center (TORC), Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory for Molecular Imaging and Therapy (MITH), Vrije Universiteit Brussel, Brussels, Belgium
| | - Thomas Benoot
- Laboratory for Molecular and Cellular Therapy (LMCT), Translational Oncology Research Center (TORC), Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory for Molecular Imaging and Therapy (MITH), Vrije Universiteit Brussel, Brussels, Belgium
| | - Yanina Jansen
- Department of Thoracic Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Domien Vanhonacker
- Department of Anesthesiology, Perioperative and Pain Medicine, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Robbe Heestermans
- Department of Hematology, Team Hematology and Immunology (HEIM), Translational Oncology Research Center (TORC), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Ann De Becker
- Department of Hematology, Team Hematology and Immunology (HEIM), Translational Oncology Research Center (TORC), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Ivan Van Riet
- Department of Hematology, Team Hematology and Immunology (HEIM), Translational Oncology Research Center (TORC), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Lore Decoster
- Department of Medical Oncology, Team Laboratory for Medical and Molecular Oncology (LMMO), Translational Oncology Research Center (TORC), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Cleo Goyvaerts
- Laboratory for Molecular and Cellular Therapy (LMCT), Translational Oncology Research Center (TORC), Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory for Molecular Imaging and Therapy (MITH), Vrije Universiteit Brussel, Brussels, Belgium
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Shah FH, Lee HW. Endothelial and macrophage interactions in the angiogenic niche. Cytokine Growth Factor Rev 2024; 78:64-76. [PMID: 39019663 DOI: 10.1016/j.cytogfr.2024.07.005] [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: 06/28/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/19/2024]
Abstract
The interactions between vascular cells, especially endothelial cells, and macrophages play a pivotal role in maintaining the subtle balance of vascular biology, which is crucial for angiogenesis in both healthy and diseased states. These cells are central to ensuring a harmonious balance between tissue repair and preventing excessive angiogenic activity, which could lead to pathological conditions. Recent advances in sophisticated genetic engineering vivo models and novel sequencing approaches, such as single-cell RNA-sequencing, in immunobiology have significantly enhanced our understanding of the gene expression and behavior of macrophages. These insights offer new perspectives on the role macrophages play not only in development but also across various health conditions. In this review, we explore the complex interactions between multiple types of macrophages and endothelium, focusing on their impact on new blood vessel formation. By understanding these intricate interactions, we aim to provide insights into new methods for managing angiogenesis in various diseases, thereby offering hope for the development of novel therapeutic approaches.
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Affiliation(s)
- Fahad Hassan Shah
- College of Pharmacy, Chosun University, Gwangju 61452, Republic of Korea
| | - Heon-Woo Lee
- College of Pharmacy, Chosun University, Gwangju 61452, Republic of Korea.
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Kwak JW, Nguyen HQ, Camai A, Huffman GM, Mekvanich S, Kenney NN, Zhu X, Randolph TW, Houghton AM. CXCR1/2 antagonism inhibits neutrophil function and not recruitment in cancer. Oncoimmunology 2024; 13:2384674. [PMID: 39076249 PMCID: PMC11285219 DOI: 10.1080/2162402x.2024.2384674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/10/2024] [Accepted: 07/22/2024] [Indexed: 07/31/2024] Open
Abstract
The level of tumor and circulating CXCR1/2-expressing neutrophils and CXCR1/2 ligands correlate with poor patient outcomes, inversely correlate with tumoral lymphocyte content, and predict immune checkpoint inhibitor (ICI) treatment failure. Accordingly, CXCR2-selective and CXCR1/2 dual inhibitors exhibit activity both as single agents and in combination with ICI treatment in mouse tumor models. Based on such reports, clinical trials combining CXCR1/2 axis antagonists with ICI treatment for cancer patients are underway. It has been assumed that CXCR1/2 blockade impacts tumors by blocking neutrophil chemotaxis and reducing neutrophil content in tumors. Here, we show that while CXCR2 antagonism does slow tumor growth, it does not preclude neutrophil recruitment into tumor. Instead, CXCR1/2 inhibition alters neutrophil function by blocking the polarization of transcriptional programs toward immune suppressive phenotypes and rendering neutrophils incapable of suppressing lymphocyte proliferation. This is associated with decreased release of reactive oxygen species and Arginase-1 into the extracellular milieu. Remarkably, these therapeutics do not impact the ability of neutrophils to phagocytose and kill ingested bacteria. Taken together, these results mechanistically explain why CXCR1/2 inhibition has been active in cancer but without infectious complications.
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Affiliation(s)
- Jeff W. Kwak
- Translational Science & Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Helena Q. Nguyen
- Translational Science & Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Alex Camai
- Translational Science & Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Grace M. Huffman
- Translational Science & Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Surapat Mekvanich
- Translational Science & Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Naia N. Kenney
- Translational Science & Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Xiaodong Zhu
- Translational Science & Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, USA
| | | | - A. McGarry Houghton
- Translational Science & Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, USA
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, WA, USA
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Adapa SR, Sami A, Meshram P, Ferreira GC, Jiang RHY. Uncovering Porphyrin Accumulation in the Tumor Microenvironment. Genes (Basel) 2024; 15:961. [PMID: 39062740 PMCID: PMC11275590 DOI: 10.3390/genes15070961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Heme, an iron-containing tetrapyrrole, is essential in almost all organisms. Heme biosynthesis needs to be precisely regulated particularly given the potential cytotoxicity of protoporphyrin IX, the intermediate preceding heme formation. Here, we report on the porphyrin intermediate accumulation within the tumor microenvironment (TME), which we propose to result from dysregulation of heme biosynthesis concomitant with an enhanced cancer survival dependence on mid-step genes, a process we recently termed "Porphyrin Overdrive". Specifically, porphyrins build up in both lung cancer cells and stromal cells in the TME. Within the TME's stromal cells, evidence supports cancer-associated fibroblasts (CAFs) actively producing porphyrins through an imbalanced pathway. Conversely, normal tissues exhibit no porphyrin accumulation, and CAFs deprived of tumor cease porphyrin overproduction, indicating that both cancer and tumor-stromal porphyrin overproduction is confined to the cancer-specific tissue niche. The clinical relevance of our findings is implied by establishing a correlation between imbalanced porphyrin production and overall poorer survival in more aggressive cancers. These findings illuminate the anomalous porphyrin dynamics specifically within the tumor microenvironment, suggesting a potential target for therapeutic intervention.
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Affiliation(s)
- Swamy R. Adapa
- USF Genomics Program, Center for Global Health and Infectious Diseases, College of Public Health, University of South Florida, Tampa, FL 33612, USA;
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA;
| | - Abdus Sami
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; (A.S.); (G.C.F.)
| | - Pravin Meshram
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA;
| | - Gloria C. Ferreira
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; (A.S.); (G.C.F.)
- Department of Chemistry, College of Arts and Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Rays H. Y. Jiang
- USF Genomics Program, Center for Global Health and Infectious Diseases, College of Public Health, University of South Florida, Tampa, FL 33612, USA;
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA;
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Liang Y, Wu G, Tan J, Xiao X, Yang L, Saw PE. Targeting NETosis: nature's alarm system in cancer progression. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2024; 7:28. [PMID: 39143953 PMCID: PMC11322967 DOI: 10.20517/cdr.2024.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/30/2024] [Accepted: 07/15/2024] [Indexed: 08/16/2024]
Abstract
Neutrophils are recognized active participants in inflammatory responses and are intricately linked to cancer progression. In response to inflammatory stimuli, neutrophils become activated, releasing neutrophils extracellular traps (NETs) for the capture and eradication of pathogens, a phenomenon termed NETosis. With a deeper understanding of NETs, there is growing evidence supporting their role in cancer progression and their involvement in conferring resistance to various cancer therapies, especially concerning tumor reactions to chemotherapy, radiation therapy (RT), and immunotherapy. This review summarizes the roles of NETs in the tumor microenvironment (TME) and their mechanisms of neutrophil involvement in the host defense. Additionally, it elucidates the mechanisms through which NETs promote tumor progression and their role in cancer treatment resistance, highlighting their potential as promising therapeutic targets in cancer treatment and their clinical applicability.
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Affiliation(s)
- Yixia Liang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, China
- Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-Sen Memorial Hospital, Foshan 528200, Guangdong, China
- Authors contributed equally
| | - Guo Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, China
- Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-Sen Memorial Hospital, Foshan 528200, Guangdong, China
- Authors contributed equally
| | - Jiabao Tan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, China
- Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-Sen Memorial Hospital, Foshan 528200, Guangdong, China
| | - Xiaoyun Xiao
- Department of Ultrasound, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, Guangdong, China
| | - Linbin Yang
- Breast Tumor Center, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, Guangdong, China
| | - Phei Er Saw
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, China
- Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-Sen Memorial Hospital, Foshan 528200, Guangdong, China
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Du W, Zhou B, Forjaz A, Shin SM, Wu F, Crawford AJ, Nair PR, Johnston AC, West-Foyle H, Tang A, Kim D, Fan R, Kiemen AL, Wu PH, Phillip JM, Ho WJ, Sanin DE, Wirtz D. High-motility pro-tumorigenic monocytes drive macrophage enrichment in the tumor microenvironment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603739. [PMID: 39071324 PMCID: PMC11275814 DOI: 10.1101/2024.07.16.603739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Enrichment of tumor-associated macrophages (TAMΦs) in the tumor microenvironment correlates with worse clinical outcomes in triple-negative breast cancer (TNBC) patients, prompting the development of therapies to inhibit TAMΦ infiltration. However, the lackluster efficacy of CCL2-based chemotaxis blockade in clinical trials suggests that a new understanding of monocyte/macrophage infiltration may be necessary. Here we demonstrate that random migration, and not only chemotaxis, drives macrophage tumor infiltration. We identified tumor- associated monocytes (TAMos) that display a dramatically enhanced migration capability, induced rapidly by the tumor microenvironment, that drives effective tumor infiltration, in contrast to low-motility differentiated macrophages. TAMo, not TAMΦ, promotes cancer cell proliferation through activation of the MAPK pathway. IL-6 secreted both by cancer cells and TAMo themselves enhances TAMo migration by increasing dendritic protrusion dynamics and myosin- based contractility via the JAK2/STAT3 signaling pathway. Independent from CCL2 mediated chemotaxis, IL-6 driven enhanced migration and pro-proliferative effect of TAMo were validated in a syngeneic TNBC mouse model. Depletion of IL-6 in cancer cells significantly attenuated monocyte infiltration and reversed TAMo-induced cancer cell proliferation. This work reveals the critical role random migration plays in monocyte driven TAMΦ enrichment in a tumor and pinpoints IL-6 as a potential therapeutic target in combination with CCL2 to ameliorate current strategies against TAMΦ infiltration.
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Karimova AF, Ketkar A, Suezov R, Khalitova AR, Gomzikova M, Mukhamedshina Y, Lauth M, Huber M, Simon HU, Brichkina A. In vitro functional assays to assess the reciprocal interplay between tumor cells and macrophages. FASEB J 2024; 38:e23730. [PMID: 38900063 DOI: 10.1096/fj.202400240r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/03/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024]
Abstract
Tumor-associated macrophages (TAMs) are integral components of the tumor microenvironment. They are involved in various aspects of tumor cell biology, driving pathological processes such as tumor cell proliferation, metastasis, immunosuppression, and resistance to therapy. TAMs exert their tumorigenic effects by secreting growth factors, cytokines/chemokines, metabolites, and other soluble bioactive molecules. These mediators directly promote tumor cell proliferation and modulate interactions with immune and stromal cells, facilitating further tumor growth. As research into therapies targeting TAMs intensifies, there is a growing need for reliable methods to comprehend the impact of TAMs on cancer progression and to validate novel therapeutics directed at TAMs. The traditional "M1-M2" macrophage classification based on transcriptional profiles of TAMs is not only too simplistic to describe their physiological roles, it also does not explain differences observed between mouse and human macrophages. In this context, methods that assess how TAMs influence tumor or immune cells, either through direct contact or the release of soluble factors, offer a more promising approach. We describe here comprehensive protocols for in vitro functional assays to study TAMs, specifically regarding their impact on the growth of lung cancer cells. We have applied these methods to both mouse and human macrophages, achieving similar outcomes in promoting the proliferation of cancer cells. This methodology can serve as a standardized approach for testing novel therapeutic approaches, targeting TAMs with novel immunotherapeutic compounds, or utilizing gene-editing techniques. Taken together, the described methodology may contribute to our understanding of complex macrophage-tumor interactions and support the development of innovative therapeutic strategies.
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Affiliation(s)
- Adelya F Karimova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Avanee Ketkar
- Institute of Systems Immunology, Center for Tumor- and Immune Biology, Philipps University of Marburg, Marburg, Germany
- German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), Marburg, Germany
| | - Roman Suezov
- Institute of Systems Immunology, Center for Tumor- and Immune Biology, Philipps University of Marburg, Marburg, Germany
- German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), Marburg, Germany
- Department of Gastroenterology, Endocrinology and Metabolism, Center for Tumor- and Immune Biology, Philipps University of Marburg, Marburg, Germany
| | - Adelya R Khalitova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Marina Gomzikova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Yana Mukhamedshina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Matthias Lauth
- Department of Gastroenterology, Endocrinology and Metabolism, Center for Tumor- and Immune Biology, Philipps University of Marburg, Marburg, Germany
| | - Magdalena Huber
- Institute of Systems Immunology, Center for Tumor- and Immune Biology, Philipps University of Marburg, Marburg, Germany
- German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), Marburg, Germany
| | - Hans-Uwe Simon
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Institute of Pharmacology, University of Bern, Bern, Switzerland
- Institute of Biochemistry, Brandenburg Medical School, Neuruppin, Germany
| | - Anna Brichkina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Institute of Systems Immunology, Center for Tumor- and Immune Biology, Philipps University of Marburg, Marburg, Germany
- German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), Marburg, Germany
- Department of Gastroenterology, Endocrinology and Metabolism, Center for Tumor- and Immune Biology, Philipps University of Marburg, Marburg, Germany
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37
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Coulton A, Murai J, Qian D, Thakkar K, Lewis CE, Litchfield K. Using a pan-cancer atlas to investigate tumour associated macrophages as regulators of immunotherapy response. Nat Commun 2024; 15:5665. [PMID: 38969631 PMCID: PMC11226649 DOI: 10.1038/s41467-024-49885-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/24/2024] [Indexed: 07/07/2024] Open
Abstract
The paradigm for macrophage characterization has evolved from the simple M1/M2 dichotomy to a more complex model that encompasses the broad spectrum of macrophage phenotypic diversity, due to differences in ontogeny and/or local stimuli. We currently lack an in-depth pan-cancer single cell RNA-seq (scRNAseq) atlas of tumour-associated macrophages (TAMs) that fully captures this complexity. In addition, an increased understanding of macrophage diversity could help to explain the variable responses of cancer patients to immunotherapy. Our atlas includes well established macrophage subsets as well as a number of additional ones. We associate macrophage composition with tumour phenotype and show macrophage subsets can vary between primary and metastatic tumours growing in sites like the liver. We also examine macrophage-T cell functional cross talk and identify two subsets of TAMs associated with T cell activation. Analysis of TAM signatures in a large cohort of immune checkpoint inhibitor-treated patients (CPI1000 + ) identify multiple TAM subsets associated with response, including the presence of a subset of TAMs that upregulate collagen-related genes. Finally, we demonstrate the utility of our data as a resource and reference atlas for mapping of novel macrophage datasets using projection. Overall, these advances represent an important step in both macrophage classification and overcoming resistance to immunotherapies in cancer.
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Affiliation(s)
- Alexander Coulton
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK
| | - Jun Murai
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK
| | - Danwen Qian
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK
| | - Krupa Thakkar
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK
| | - Claire E Lewis
- Department of Oncology and Metabolism, University of Sheffield Medical School, Beech Hill Road, Sheffield, Yorkshire, S10 2RX, UK.
| | - Kevin Litchfield
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK.
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38
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Perdiguero P, Jiménez-Barrios P, Morel E, Abós B, Tafalla C. Single-cell atlas of rainbow trout peripheral blood leukocytes and profiling of their early response to infectious pancreatic necrosis virus. Front Immunol 2024; 15:1404209. [PMID: 39035000 PMCID: PMC11258392 DOI: 10.3389/fimmu.2024.1404209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/21/2024] [Indexed: 07/23/2024] Open
Abstract
The recent development of single cell sequencing technologies has revolutionized the state-of-art of cell biology, allowing the simultaneous measurement of thousands of genes in single cells. This technology has been applied to study the transcriptome of single cells in homeostasis and also in response to pathogenic exposure, greatly increasing our knowledge of the immune response to infectious agents. Yet the number of these studies performed in aquacultured fish species is still very limited. Thus, in the current study, we have used the 10x Genomics single cell RNA sequencing technology to study the response of rainbow trout (Oncorhynchus mykiss) peripheral blood leukocytes (PBLs) to infectious pancreatic necrosis virus (IPNV), an important trout pathogen. The study allowed us to obtain a transcriptomic profile of 12 transcriptionally distinct leukocyte cell subpopulations that included four different subsets of B cells, T cells, monocytes, two populations of dendritic-like cells (DCs), hematopoietic progenitor cells, non-specific cytotoxic cells (NCC), neutrophils and thrombocytes. The transcriptional pattern of these leukocyte subpopulations was compared in PBL cultures that had been exposed in vitro to IPNV for 24 h and mock-infected cultures. Our results revealed that monocytes and neutrophils showed the highest number of upregulated protein-coding genes in response to IPNV. Interestingly, IgM+IgD+ and IgT+ B cells also upregulated an important number of genes to the virus, but a much fainter response was observed in ccl4 + or plasma-like cells (irf4 + cells). A substantial number of protein-coding genes and genes coding for ribosomal proteins were also transcriptionally upregulated in response to IPNV in T cells and thrombocytes. Interestingly, although genes coding for ribosomal proteins were regulated in all affected PBL subpopulations, the number of such genes transcriptionally regulated was higher in IgM+IgD+ and IgT+ B cells. A further analysis dissected which of the regulated genes were common and which were specific to the different cell clusters, identifying eight genes that were transcriptionally upregulated in all the affected groups. The data provided constitutes a comprehensive transcriptional perspective of how the different leukocyte populations present in blood respond to an early viral encounter in fish.
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Affiliation(s)
- Pedro Perdiguero
- Fish Immunology and Pathology Group, Animal Health Research Center (CISA-INIA), Valdeolmos, Madrid, Spain
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), Madrid, Spain
| | - Pablo Jiménez-Barrios
- Fish Immunology and Pathology Group, Animal Health Research Center (CISA-INIA), Valdeolmos, Madrid, Spain
| | - Esther Morel
- Fish Immunology and Pathology Group, Animal Health Research Center (CISA-INIA), Valdeolmos, Madrid, Spain
| | - Beatriz Abós
- Fish Immunology and Pathology Group, Animal Health Research Center (CISA-INIA), Valdeolmos, Madrid, Spain
| | - Carolina Tafalla
- Fish Immunology and Pathology Group, Animal Health Research Center (CISA-INIA), Valdeolmos, Madrid, Spain
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van der Meijs NL, Travecedo MA, Marcelo F, van Vliet SJ. The pleiotropic CLEC10A: implications for harnessing this receptor in the tumor microenvironment. Expert Opin Ther Targets 2024; 28:601-612. [PMID: 38946482 DOI: 10.1080/14728222.2024.2374743] [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: 02/06/2024] [Accepted: 06/27/2024] [Indexed: 07/02/2024]
Abstract
INTRODUCTION CLEC10A is a C-type lectin receptor that specifically marks the conventional dendritic cell subsets two and three (cDC2 and DC3). It has a unique recognition profile of glycan antigens, with terminal N-Acetylgalactosamine residues that are frequently present in the tumor microenvironment. Even though CLEC10A expression allows for precise targeting of cDC2 and DC3 for the treatment of cancer, CLEC10A signaling has also been associated with anti-inflammatory responses that would promote tumor growth. AREAS COVERED Here, we review the potential benefits and drawbacks of CLEC10A engagement in the tumor microenvironment. We discuss the CLEC10A-mediated effects in different cell types and incorporate the pleiotropic effects of IL-10, the main anti-inflammatory response upon CLEC10A binding. EXPERT OPINION To translate this to a successful CLEC10A-mediated immunotherapy with limited tumor-promoting capacities, finding the right ligand presentation and adjuvant combination will be key.
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Affiliation(s)
- Nadia L van der Meijs
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunology, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Maria Alejandra Travecedo
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Filipa Marcelo
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Sandra J van Vliet
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunology, Inflammatory Diseases, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
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40
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Zhang M, Xia L, Peng W, Xie G, Li F, Zhang C, Syeda MZ, Hu Y, Lan F, Yan F, Jin Z, Du X, Han Y, Lv B, Wang Y, Li M, Fei X, Zhao Y, Chen K, Chen Y, Li W, Chen Z, Zhou Q, Zhang M, Ying S, Shen H. CCL11/CCR3-dependent eosinophilia alleviates malignant pleural effusions and improves prognosis. NPJ Precis Oncol 2024; 8:138. [PMID: 38951159 PMCID: PMC11217290 DOI: 10.1038/s41698-024-00608-8] [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: 07/03/2023] [Accepted: 05/09/2024] [Indexed: 07/03/2024] Open
Abstract
Malignant pleural effusion (MPE) is a common occurrence in advanced cancer and is often linked with a poor prognosis. Eosinophils were reported to involve in the development of MPE. However, the role of eosinophils in MPE remains unclear. To investigate this, we conducted studies using both human samples and mouse models. Increased eosinophil counts were observed in patients with MPE, indicating that the higher the number of eosinophils is, the lower the LENT score is. In our animal models, eosinophils were found to migrate to pleural cavity actively upon exposure to tumor cells. Intriguingly, we discovered that a deficiency in eosinophils exacerbated MPE, possibly due to their anti-tumor effects generated by modifying the microenvironment of MPE. Furthermore, our experiments explored the role of the C-C motif chemokine ligand 11 (CCL11) and its receptor C-C motif chemokine receptor 3 (CCR3) in MPE pathology. As a conclusion, our study underscores the protective potential of eosinophils against the development of MPE, and that an increase in eosinophils through adoptive transfer of eosinophils or increasing their numbers improved MPE.
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Affiliation(s)
- Min Zhang
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Lixia Xia
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Wenbei Peng
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Guogang Xie
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Fei Li
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Chao Zhang
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Madiha Zahra Syeda
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yue Hu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Fen Lan
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Fugui Yan
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Zhangchu Jin
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Xufei Du
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yinling Han
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Baihui Lv
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yuejue Wang
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Miao Li
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Xia Fei
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yun Zhao
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Kaijun Chen
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yan Chen
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, 322000, China
| | - Wen Li
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Zhihua Chen
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Qiong Zhou
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Min Zhang
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
| | - Songmin Ying
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, 322000, China.
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Huahao Shen
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
- State Key Lab for Respiratory Diseases, National Clinical Research Centre for Respiratory Disease, Guangzhou, 510120, Guangdong, China.
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Zvirblyte J, Nainys J, Juzenas S, Goda K, Kubiliute R, Dasevicius D, Kincius M, Ulys A, Jarmalaite S, Mazutis L. Single-cell transcriptional profiling of clear cell renal cell carcinoma reveals a tumor-associated endothelial tip cell phenotype. Commun Biol 2024; 7:780. [PMID: 38942917 PMCID: PMC11213875 DOI: 10.1038/s42003-024-06478-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 06/21/2024] [Indexed: 06/30/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most prevalent form of renal cancer, accounting for over 75% of cases. The asymptomatic nature of the disease contributes to late-stage diagnoses and poor survival. Highly vascularized and immune infiltrated microenvironment are prominent features of ccRCC, yet the interplay between vasculature and immune cells, disease progression and response to therapy remains poorly understood. Using droplet-based single-cell RNA sequencing we profile 50,236 transcriptomes from paired tumor and healthy adjacent kidney tissues. Our analysis reveals significant heterogeneity and inter-patient variability of the tumor microenvironment. Notably, we discover a previously uncharacterized vasculature subpopulation associated with epithelial-mesenchymal transition. The cell-cell communication analysis reveals multiple modes of immunosuppressive interactions within the tumor microenvironment, including clinically relevant interactions between tumor vasculature and stromal cells with immune cells. The upregulation of the genes involved in these interactions is associated with worse survival in the TCGA KIRC cohort. Our findings demonstrate the role of tumor vasculature and stromal cell populations in shaping the ccRCC microenvironment and uncover a subpopulation of cells within the tumor vasculature that is associated with an angiogenic phenotype.
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Affiliation(s)
- Justina Zvirblyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
| | - Juozas Nainys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
- Droplet Genomics, Vilnius, 10257, Lithuania
| | - Simonas Juzenas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
| | - Karolis Goda
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
| | - Raimonda Kubiliute
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
| | - Darius Dasevicius
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Klinikos, Vilnius, 08406, Lithuania
| | | | - Albertas Ulys
- National Cancer Institute, Vilnius, 08660, Lithuania
| | - Sonata Jarmalaite
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania.
- National Cancer Institute, Vilnius, 08660, Lithuania.
| | - Linas Mazutis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania.
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42
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Almeida PP, Moraes JA, Barja-Fidalgo TC, Renovato-Martins M. Extracellular vesicles as modulators of monocyte and macrophage function in tumors. AN ACAD BRAS CIENC 2024; 96:e20231212. [PMID: 38922279 DOI: 10.1590/0001-3765202420231212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/17/2024] [Indexed: 06/27/2024] Open
Abstract
The tumor microenvironment (TME) harbors several cell types, such as tumor cells, immune cells, and non-immune cells. These cells communicate through several mechanisms, such as cell-cell contact, cytokines, chemokines, and extracellular vesicles (EVs). Tumor-derived vesicles are known to have the ability to modulate the immune response. Monocytes are a subset of circulating innate immune cells and play a crucial role in immune surveillance, being recruited to tissues where they differentiate into macrophages. In the context of tumors, it has been observed that tumor cells can attract monocytes to the TME and induce their differentiation into tumor-associated macrophages with a pro-tumor phenotype. Tumor-derived EVs have emerged as essential structures mediating this process. Through the transfer of specific molecules and signaling factors, tumor-derived EVs can shape the phenotype and function of monocytes, inducing the expression of cytokines and molecules by these cells, thus modulating the TME towards an immunosuppressive environment.
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Affiliation(s)
- Palloma P Almeida
- Universidade Federal Fluminense, Departamento de Biologia Celular e Molecular, Instituto de Biologia, Laboratório de Inflamação e Metabolismo, Rua Professor Marcos Waldemar de Freitas Reis, s/n, 24020-140 Niterói, RJ, Brazil
- Universidade Federal do Rio de Janeiro, Instituto de Ciências Biomédicas, Laboratório de Biologia Redox, Av. Carlos Chagas Filho, 373, Prédio do ICB - Anexo B1F3, Ilha do Fundão, 21941-902 Rio de Janeiro, RJ, Brazil
- Universidade do Estado do Rio de Janeiro, Departamento de Biologia Celular, Instituto de Biologia Roberto Alcantara Gomes - IBRAG, Laboratório de Farmacologia Celular e Molecular, Av. 28 de setembro, 87, 20551-030 Rio de Janeiro, RJ, Brazil
| | - João Alfredo Moraes
- Universidade Federal do Rio de Janeiro, Instituto de Ciências Biomédicas, Laboratório de Biologia Redox, Av. Carlos Chagas Filho, 373, Prédio do ICB - Anexo B1F3, Ilha do Fundão, 21941-902 Rio de Janeiro, RJ, Brazil
| | - Thereza Christina Barja-Fidalgo
- Universidade do Estado do Rio de Janeiro, Departamento de Biologia Celular, Instituto de Biologia Roberto Alcantara Gomes - IBRAG, Laboratório de Farmacologia Celular e Molecular, Av. 28 de setembro, 87, 20551-030 Rio de Janeiro, RJ, Brazil
| | - Mariana Renovato-Martins
- Universidade Federal Fluminense, Departamento de Biologia Celular e Molecular, Instituto de Biologia, Laboratório de Inflamação e Metabolismo, Rua Professor Marcos Waldemar de Freitas Reis, s/n, 24020-140 Niterói, RJ, Brazil
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43
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Jing ZQ, Luo ZQ, Chen SR, Sun ZJ. Heterogeneity of myeloid cells in common cancers: Single cell insights and targeting strategies. Int Immunopharmacol 2024; 134:112253. [PMID: 38735257 DOI: 10.1016/j.intimp.2024.112253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/02/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
Tumor microenvironment (TME), is characterized by a complex and heterogenous composition involving a substantial population of immune cells. Myeloid cells comprising over half of the solid tumor mass, are undoubtedly one of the most prominent cell populations associated with tumors. Studies have unambiguously established that myeloid cells play a key role in tumor development, including immune suppression, pro-inflammation, promote tumor metastasis and angiogenesis, for example, tumor-associated macrophages promote tumor progression in a variety of common tumors, including lung cancer, through direct or indirect interactions with the TME. However, due to previous technological constraints, research on myeloid cells often tended to be conducted as studies with low throughput and limited resolution. For example, the conventional categorization of macrophages into M1-like and M2-like subsets based solely on their anti-tumor and pro-tumor roles has disregarded their continuum of states, resulting in an inadequate analysis of the high heterogeneity characterizing myeloid cells. The widespread adoption of single-cell RNA sequencing (scRNA-seq) in tumor immunology has propelled researchers into a new realm of understanding, leading to the establishment of novel subsets and targets. In this review, the origin of myeloid cells in high-incidence cancers, the functions of myeloid cell subsets examined through traditional and single-cell perspectives, as well as specific targeting strategies, are comprehensively outlined. As a result of this endeavor, we will gain a better understanding of myeloid cell heterogeneity, as well as contribute to the development of new therapeutic approaches.
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Affiliation(s)
- Zhi-Qian Jing
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Science, Wuhan University, Wuhan 430079, China
| | - Zhi-Qi Luo
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Science, Wuhan University, Wuhan 430079, China
| | - Si-Rui Chen
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Science, Wuhan University, Wuhan 430079, China
| | - Zhi-Jun Sun
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Science, Wuhan University, Wuhan 430079, China.
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44
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Mazzoccoli L, Liu B. Dendritic Cells in Shaping Anti-Tumor T Cell Response. Cancers (Basel) 2024; 16:2211. [PMID: 38927916 PMCID: PMC11201542 DOI: 10.3390/cancers16122211] [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: 05/07/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Among professional antigen-presenting cells, dendritic cells (DCs) orchestrate innate and adaptive immunity and play a pivotal role in anti-tumor immunity. DCs are a heterogeneous population with varying functions in the tumor microenvironment (TME). Tumor-associated DCs differentiate developmentally and functionally into three main subsets: conventional DCs (cDCs), plasmacytoid DCs (pDCs), and monocyte-derived DCs (MoDCs). There are two major subsets of cDCs in TME, cDC1 and cDC2. cDC1 is critical for cross-presenting tumor antigens to activate cytotoxic CD8+ T cells and is also required for priming earlier CD4+ T cells in certain solid tumors. cDC2 is vital for priming anti-tumor CD4+ T cells in multiple tumor models. pDC is a unique subset of DCs and produces type I IFN through TLR7 and TLR9. Studies have shown that pDCs are related to immunosuppression in the TME through the secretion of immunosuppressive cytokines and by promoting regulatory T cells. MoDCs differentiate separately from monocytes in response to inflammatory cues and infection. Also, MoDCs can cross-prime CD8+ T cells. In this review, we summarize the subsets and functions of DCs. We also discuss the role of different DC subsets in shaping T cell immunity in TME and targeting DCs for potential immunotherapeutic benefits against cancer.
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Affiliation(s)
- Luciano Mazzoccoli
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA;
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Bei Liu
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA;
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
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45
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Zhu J, Zhang K, Chen Y, Ge X, Wu J, Xu P, Yao J. Progress of single-cell RNA sequencing combined with spatial transcriptomics in tumour microenvironment and treatment of pancreatic cancer. J Transl Med 2024; 22:563. [PMID: 38867230 PMCID: PMC11167806 DOI: 10.1186/s12967-024-05307-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/16/2024] [Indexed: 06/14/2024] Open
Abstract
In recent years, single-cell analyses have revealed the heterogeneity of the tumour microenvironment (TME) at the genomic, transcriptomic, and proteomic levels, further improving our understanding of the mechanisms of tumour development. Single-cell RNA sequencing (scRNA-seq) technology allow analysis of the transcriptome at the single-cell level and have unprecedented potential for exploration of the characteristics involved in tumour development and progression. These techniques allow analysis of transcript sequences at higher resolution, thereby increasing our understanding of the diversity of cells found in the tumour microenvironment and how these cells interact in complex tumour tissue. Although scRNA-seq has emerged as an important tool for studying the tumour microenvironment in recent years, it cannot be used to analyse spatial information for cells. In this regard, spatial transcriptomics (ST) approaches allow researchers to understand the functions of individual cells in complex multicellular organisms by understanding their physical location in tissue sections. In particular, in related research on tumour heterogeneity, ST is an excellent complementary approach to scRNA-seq, constituting a new method for further exploration of tumour heterogeneity, and this approach can also provide unprecedented insight into the development of treatments for pancreatic cancer (PC). In this review, based on the methods of scRNA-seq and ST analyses, research progress on the tumour microenvironment and treatment of pancreatic cancer is further explained.
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Affiliation(s)
- Jie Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China
| | - Ke Zhang
- Dalian Medical University, Dalian, China
| | - Yuan Chen
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China
| | - Xinyu Ge
- Dalian Medical University, Dalian, China
| | - Junqing Wu
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China
| | - Peng Xu
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China.
| | - Jie Yao
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China.
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Sun X, Nagahama Y, Singh SK, Kozakai Y, Nabeshima H, Fukushima K, Tanaka H, Motooka D, Fukui E, Vivier E, Diez D, Akira S. Deletion of the mRNA endonuclease Regnase-1 promotes NK cell anti-tumor activity via OCT2-dependent transcription of Ifng. Immunity 2024; 57:1360-1377.e13. [PMID: 38821052 DOI: 10.1016/j.immuni.2024.05.006] [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: 07/13/2023] [Revised: 12/31/2023] [Accepted: 05/07/2024] [Indexed: 06/02/2024]
Abstract
Limited infiltration and activity of natural killer (NK) and T cells within the tumor microenvironment (TME) correlate with poor immunotherapy responses. Here, we examined the role of the endonuclease Regnase-1 on NK cell anti-tumor activity. NK cell-specific deletion of Regnase-1 (Reg1ΔNK) augmented cytolytic activity and interferon-gamma (IFN-γ) production in vitro and increased intra-tumoral accumulation of Reg1ΔNK-NK cells in vivo, reducing tumor growth dependent on IFN-γ. Transcriptional changes in Reg1ΔNK-NK cells included elevated IFN-γ expression, cytolytic effectors, and the chemokine receptor CXCR6. IFN-γ induced expression of the CXCR6 ligand CXCL16 on myeloid cells, promoting further recruitment of Reg1ΔNK-NK cells. Mechanistically, Regnase-1 deletion increased its targets, the transcriptional regulators OCT2 and IκBζ, following interleukin (IL)-12 and IL-18 stimulation, and the resulting OCT2-IκBζ-NF-κB complex induced Ifng transcription. Silencing Regnase-1 in human NK cells increased the expression of IFNG and POU2F2. Our findings highlight NK cell dysfunction in the TME and propose that targeting Regnase-1 could augment active NK cell persistence for cancer immunotherapy.
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Affiliation(s)
- Xin Sun
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Quantitative Immunology Unit, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Joint Research Chair of Innate Immunity for Drug Discovery, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yasuharu Nagahama
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Host Defense Laboratory, Immunology Unit, Department of Medical Innovations, Osaka Research Center for Drug Discovery, Otsuka Pharmaceutical Co. Ltd., 5-1-35 Saito-aokita, Minoh, Osaka 562-0029, Japan; Joint Research Chair of Innate Immunity for Drug Discovery, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Shailendra Kumar Singh
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Joint Research Chair of Innate Immunity for Drug Discovery, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yuuki Kozakai
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Nabeshima
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Host Defense Laboratory, Immunology Unit, Department of Medical Innovations, Osaka Research Center for Drug Discovery, Otsuka Pharmaceutical Co. Ltd., 5-1-35 Saito-aokita, Minoh, Osaka 562-0029, Japan; Joint Research Chair of Innate Immunity for Drug Discovery, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Kiyoharu Fukushima
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Joint Research Chair of Innate Immunity for Drug Discovery, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Hiroki Tanaka
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Daisuke Motooka
- NGS Core Facility of the Genome Information Research Center, RIMD, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Eriko Fukui
- Department of General Thoracic Surgery, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Eric Vivier
- Aix-Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d'Immunologie de Marseille-Luminy, Marseille, France; Innate Pharma Research Laboratories, Marseille, France; APHM, Hôpital de la Timone, Marseille-Immunopole, Marseille, France
| | - Diego Diez
- Quantitative Immunology Unit, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Shizuo Akira
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Joint Research Chair of Innate Immunity for Drug Discovery, WPI-IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Center for Advanced Modalities and Drug Delivery System (CAMaD), Osaka University, 2-8 Yamada-oka, Suita, Osaka 565-0871, Japan.
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Zhao C, Yang Z, Li Y, Wen Z. Macrophages in tissue repair and regeneration: insights from zebrafish. CELL REGENERATION (LONDON, ENGLAND) 2024; 13:12. [PMID: 38861103 PMCID: PMC11166613 DOI: 10.1186/s13619-024-00195-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/31/2024] [Indexed: 06/12/2024]
Abstract
Macrophages play crucial and versatile roles in regulating tissue repair and regeneration upon injury. However, due to their complex compositional heterogeneity and functional plasticity, deciphering the nature of different macrophage subpopulations and unraveling their dynamics and precise roles during the repair process have been challenging. With its distinct advantages, zebrafish (Danio rerio) has emerged as an invaluable model for studying macrophage development and functions, especially in tissue repair and regeneration, providing valuable insights into our understanding of macrophage biology in health and diseases. In this review, we present the current knowledge and challenges associated with the role of macrophages in tissue repair and regeneration, highlighting the significant contributions made by zebrafish studies. We discuss the unique advantages of the zebrafish model, including its genetic tools, imaging techniques, and regenerative capacities, which have greatly facilitated the investigation of macrophages in these processes. Additionally, we outline the potential of zebrafish research in addressing the remaining challenges and advancing our understanding of the intricate interplay between macrophages and tissue repair and regeneration.
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Affiliation(s)
- Changlong Zhao
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhiyong Yang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Division of Life Science, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yunbo Li
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Division of Life Science, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Zilong Wen
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
- Shenzhen Bay Laboratory, Shenzhen, 518055, China.
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48
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Lee CY, Clatworthy MR, Withers DR. Decoding changes in tumor-infiltrating leukocytes through dynamic experimental models and single-cell technologies. Immunol Cell Biol 2024. [PMID: 38853634 DOI: 10.1111/imcb.12787] [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: 03/25/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024]
Abstract
The ability to characterize immune cells and explore the molecular interactions that govern their functions has never been greater, fueled in recent years by the revolutionary advance of single-cell analysis platforms. However, precisely how immune cells respond to different stimuli and where differentiation processes and effector functions operate remain incompletely understood. Inferring cellular fate within single-cell transcriptomic analyses is now omnipresent, despite the assumptions typically required in such analyses. Recently developed experimental models support dynamic analyses of the immune response, providing insights into the temporal changes that occur within cells and the tissues in which such transitions occur. Here we will review these approaches and discuss how these can be combined with single-cell technologies to develop a deeper understanding of the immune responses that should support the development of better therapeutic options for patients.
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Affiliation(s)
- Colin Yc Lee
- Cambridge Institute of Therapeutic Immunology and Infection Disease, University of Cambridge, Cambridge, UK
| | - Menna R Clatworthy
- Cambridge Institute of Therapeutic Immunology and Infection Disease, University of Cambridge, Cambridge, UK
| | - David R Withers
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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Sazinsky S, Zafari M, Klebanov B, Ritter J, Nguyen PA, Phennicie RT, Wahle J, Kauffman KJ, Razlog M, Manfra D, Feldman I, Novobrantseva T. Antibodies Targeting Human or Mouse VSIG4 Repolarize Tumor-Associated Macrophages Providing the Potential of Potent and Specific Clinical Anti-Tumor Response Induced across Multiple Cancer Types. Int J Mol Sci 2024; 25:6160. [PMID: 38892347 PMCID: PMC11172757 DOI: 10.3390/ijms25116160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
V-set immunoglobulin domain-containing 4 (VSIG4) is a B7 family protein with known roles as a C3 fragment complement receptor involved in pathogen clearance and a negative regulator of T cell activation by an undetermined mechanism. VSIG4 expression is specific for tumor-associated and select tissue-resident macrophages. Increased expression of VSIG4 has been associated with worse survival in multiple cancer indications. Based upon computational analysis of transcript data across thousands of tumor and normal tissue samples, we hypothesized that VSIG4 has an important role in promoting M2-like immune suppressive macrophages and that targeting VSIG4 could relieve VSIG4-mediated macrophage suppression by repolarizing tumor-associated macrophages (TAMs) to an inflammatory phenotype. We have also observed a cancer-specific pattern of VSIG4 isoform distribution, implying a change in the functional regulation in cancer. Through a series of in vitro, in vivo, and ex vivo assays we demonstrate that anti-VSIG4 antibodies repolarize M2 macrophages and induce an immune response culminating in T cell activation. Anti-VSIG4 antibodies induce pro-inflammatory cytokines in M-CSF plus IL-10-driven human monocyte-derived M2c macrophages. Across patient-derived tumor samples from multiple tumor types, anti-VSIG4 treatment resulted in the upregulation of cytokines associated with TAM repolarization and T cell activation and chemokines involved in immune cell recruitment. VSIG4 blockade is also efficacious in a syngeneic mouse model as monotherapy as it enhances efficacy in combination with anti-PD-1, and the effect is dependent on the systemic availability of CD8+ T cells. Thus, VSIG4 represents a promising new target capable of triggering an anti-cancer response via multiple key immune mechanisms.
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Affiliation(s)
- Stephen Sazinsky
- Verseau Therapeutics, 2000 Commonwealth Ave., Auburndale, MA 02466, USA
| | - Mohammad Zafari
- Verseau Therapeutics, 2000 Commonwealth Ave., Auburndale, MA 02466, USA
- Alloy Therapeutics, 275 Second Ave., Suite 200, Waltham, MA 02451, USA
| | - Boris Klebanov
- Verseau Therapeutics, 2000 Commonwealth Ave., Auburndale, MA 02466, USA
| | - Jessica Ritter
- Verseau Therapeutics, 2000 Commonwealth Ave., Auburndale, MA 02466, USA
| | - Phuong A. Nguyen
- Verseau Therapeutics, 2000 Commonwealth Ave., Auburndale, MA 02466, USA
| | - Ryan T. Phennicie
- Verseau Therapeutics, 2000 Commonwealth Ave., Auburndale, MA 02466, USA
- Sanofi, 55 Corporate Driver, Bridgewater, NJ 08807, USA
| | - Joe Wahle
- Verseau Therapeutics, 2000 Commonwealth Ave., Auburndale, MA 02466, USA
- HotSpot Therapeutics, One Design Center Pl. Suite 19-600, Boston, MA 02210, USA
| | - Kevin J. Kauffman
- Verseau Therapeutics, 2000 Commonwealth Ave., Auburndale, MA 02466, USA
| | - Maja Razlog
- Verseau Therapeutics, 2000 Commonwealth Ave., Auburndale, MA 02466, USA
| | - Denise Manfra
- Verseau Therapeutics, 2000 Commonwealth Ave., Auburndale, MA 02466, USA
| | - Igor Feldman
- Verseau Therapeutics, 2000 Commonwealth Ave., Auburndale, MA 02466, USA
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50
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Sinha S, Vegesna R, Mukherjee S, Kammula AV, Dhruba SR, Wu W, Kerr DL, Nair NU, Jones MG, Yosef N, Stroganov OV, Grishagin I, Aldape KD, Blakely CM, Jiang P, Thomas CJ, Benes CH, Bivona TG, Schäffer AA, Ruppin E. PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors. NATURE CANCER 2024; 5:938-952. [PMID: 38637658 DOI: 10.1038/s43018-024-00756-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 03/08/2024] [Indexed: 04/20/2024]
Abstract
Tailoring optimal treatment for individual cancer patients remains a significant challenge. To address this issue, we developed PERCEPTION (PERsonalized Single-Cell Expression-Based Planning for Treatments In ONcology), a precision oncology computational pipeline. Our approach uses publicly available matched bulk and single-cell (sc) expression profiles from large-scale cell-line drug screens. These profiles help build treatment response models based on patients' sc-tumor transcriptomics. PERCEPTION demonstrates success in predicting responses to targeted therapies in cultured and patient-tumor-derived primary cells, as well as in two clinical trials for multiple myeloma and breast cancer. It also captures the resistance development in patients with lung cancer treated with tyrosine kinase inhibitors. PERCEPTION outperforms published state-of-the-art sc-based and bulk-based predictors in all clinical cohorts. PERCEPTION is accessible at https://github.com/ruppinlab/PERCEPTION . Our work, showcasing patient stratification using sc-expression profiles of their tumors, will encourage the adoption of sc-omics profiling in clinical settings, enhancing precision oncology tools based on sc-omics.
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Affiliation(s)
- Sanju Sinha
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA.
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.
| | - Rahulsimham Vegesna
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
| | - Sumit Mukherjee
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
| | - Ashwin V Kammula
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
- University of Maryland, College Park, MD, USA
| | | | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - D Lucas Kerr
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nishanth Ulhas Nair
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
| | - Matthew G Jones
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute, Cambridge, MA, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA
| | | | - Ivan Grishagin
- Rancho BioSciences, San Diego, CA, USA
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Peng Jiang
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cyril H Benes
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub Investigator, San Francisco, CA, USA
| | | | - Eytan Ruppin
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA.
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