201
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Garrity R, Arora N, Haque MA, Weis D, Trinh RT, Neerukonda SV, Kumari S, Cortez I, Ubogu EE, Mahalingam R, Tavares-Ferreira D, Price TJ, Kavelaars A, Heijnen CJ, Shepherd AJ. Fibroblast-derived PI16 sustains inflammatory pain via regulation of CD206 + myeloid cells. Brain Behav Immun 2023; 112:220-234. [PMID: 37315702 PMCID: PMC10527931 DOI: 10.1016/j.bbi.2023.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/26/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023] Open
Abstract
Originally identified in fibroblasts, Protease Inhibitor (PI)16 was recently shown to be crucial for the development of neuropathic pain via effects on blood-nerve barrier permeability and leukocyte infiltration, though its impact on inflammatory pain has not been established. Using the complete Freund's Adjuvant inflammatory pain model, we show that Pi16-/- mice are protected against sustained inflammatory pain. Accordingly, intrathecal delivery of a PI16 neutralizing antibody in wild-type mice prevented sustained CFA pain. In contrast to neuropathic pain models, we did not observe any changes in blood-nerve barrier permeability due to PI16 deletion. Instead, Pi16-/- mice display reduced macrophage density in the CFA-injected hindpaw. Furthermore, there was a significant bias toward CD206hi (anti-inflammatory) macrophages in the hindpaw and associated dorsal root ganglia. Following CFA, intrathecal depletion of CD206+ macrophages using mannosylated clodronate liposomes promoted sustained pain in Pi16-/- mice. Similarly, an IL-10 neutralizing antibody also promoted sustained CFA pain in the Pi16-/ when administered intrathecally. Collectively, our results point to fibroblast-derived PI16 mediating substantial differences in macrophage phenotype in the pain neuroaxis under conditions of inflammation. The co-expression of PI16 alongside fibroblast markers in human DRG raise the likelihood that a similar mechanism operates in human inflammatory pain states. Collectively, our findings may have implications for targeting fibroblast-immune cell crosstalk for the treatment of chronic pain.
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Affiliation(s)
- Rachelle Garrity
- Laboratories of Neuroimmunology, Department of Symptom Research, Division of Internal Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Neha Arora
- Laboratories of Neuroimmunology, Department of Symptom Research, Division of Internal Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Md Areeful Haque
- Laboratories of Neuroimmunology, Department of Symptom Research, Division of Internal Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Drew Weis
- Laboratories of Neuroimmunology, Department of Symptom Research, Division of Internal Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ronnie T Trinh
- Laboratories of Neuroimmunology, Department of Symptom Research, Division of Internal Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sanjay V Neerukonda
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX, United States
| | - Susmita Kumari
- Laboratories of Neuroimmunology, Department of Symptom Research, Division of Internal Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ibdanelo Cortez
- Laboratories of Neuroimmunology, Department of Symptom Research, Division of Internal Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Eroboghene E Ubogu
- Neuromuscular Immunopathology Research Laboratory, Division of Neuromuscular Disease, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Rajasekaran Mahalingam
- Laboratories of Neuroimmunology, Department of Symptom Research, Division of Internal Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Diana Tavares-Ferreira
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX, United States
| | - Theodore J Price
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX, United States
| | - Annemieke Kavelaars
- Laboratories of Neuroimmunology, Department of Symptom Research, Division of Internal Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Cobi J Heijnen
- Laboratories of Neuroimmunology, Department of Symptom Research, Division of Internal Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States; Department of Psychological Sciences, Rice University, Houston, TX, United States
| | - Andrew J Shepherd
- Laboratories of Neuroimmunology, Department of Symptom Research, Division of Internal Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States.
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202
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Abstract
Tumour cells migrate very early from primary sites to distant sites, and yet metastases often take years to manifest themselves clinically or never even surface within a patient's lifetime. This pause in cancer progression emphasizes the existence of barriers that constrain the growth of disseminated tumour cells (DTCs) at distant sites. Although the nature of these barriers to metastasis might include DTC-intrinsic traits, recent studies have established that the local microenvironment also controls the formation of metastases. In this Perspective, I discuss how site-specific differences of the immune system might be a major selective growth restraint on DTCs, and argue that harnessing tissue immunity will be essential for the next stage in immunotherapy development that reliably prevents the establishment of metastases.
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203
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Di X, Gao X, Peng L, Ai J, Jin X, Qi S, Li H, Wang K, Luo D. Cellular mechanotransduction in health and diseases: from molecular mechanism to therapeutic targets. Signal Transduct Target Ther 2023; 8:282. [PMID: 37518181 PMCID: PMC10387486 DOI: 10.1038/s41392-023-01501-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 08/01/2023] Open
Abstract
Cellular mechanotransduction, a critical regulator of numerous biological processes, is the conversion from mechanical signals to biochemical signals regarding cell activities and metabolism. Typical mechanical cues in organisms include hydrostatic pressure, fluid shear stress, tensile force, extracellular matrix stiffness or tissue elasticity, and extracellular fluid viscosity. Mechanotransduction has been expected to trigger multiple biological processes, such as embryonic development, tissue repair and regeneration. However, prolonged excessive mechanical stimulation can result in pathological processes, such as multi-organ fibrosis, tumorigenesis, and cancer immunotherapy resistance. Although the associations between mechanical cues and normal tissue homeostasis or diseases have been identified, the regulatory mechanisms among different mechanical cues are not yet comprehensively illustrated, and no effective therapies are currently available targeting mechanical cue-related signaling. This review systematically summarizes the characteristics and regulatory mechanisms of typical mechanical cues in normal conditions and diseases with the updated evidence. The key effectors responding to mechanical stimulations are listed, such as Piezo channels, integrins, Yes-associated protein (YAP) /transcriptional coactivator with PDZ-binding motif (TAZ), and transient receptor potential vanilloid 4 (TRPV4). We also reviewed the key signaling pathways, therapeutic targets and cutting-edge clinical applications of diseases related to mechanical cues.
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Affiliation(s)
- Xingpeng Di
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Xiaoshuai Gao
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Liao Peng
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Jianzhong Ai
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Xi Jin
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Shiqian Qi
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Hong Li
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Kunjie Wang
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China.
| | - Deyi Luo
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China.
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204
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Cords L, Tietscher S, Anzeneder T, Langwieder C, Rees M, de Souza N, Bodenmiller B. Cancer-associated fibroblast classification in single-cell and spatial proteomics data. Nat Commun 2023; 14:4294. [PMID: 37463917 DOI: 10.1038/s41467-023-39762-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/26/2023] [Indexed: 07/20/2023] Open
Abstract
Cancer-associated fibroblasts (CAFs) are a diverse cell population within the tumour microenvironment, where they have critical effects on tumour evolution and patient prognosis. To define CAF phenotypes, we analyse a single-cell RNA sequencing (scRNA-seq) dataset of over 16,000 stromal cells from tumours of 14 breast cancer patients, based on which we define and functionally annotate nine CAF phenotypes and one class of pericytes. We validate this classification system in four additional cancer types and use highly multiplexed imaging mass cytometry on matched breast cancer samples to confirm our defined CAF phenotypes at the protein level and to analyse their spatial distribution within tumours. This general CAF classification scheme will allow comparison of CAF phenotypes across studies, facilitate analysis of their functional roles, and potentially guide development of new treatment strategies in the future.
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Affiliation(s)
- Lena Cords
- Department of Quantitative Biomedicine, University of Zurich, CH-8057, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, CH-8093, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH Zurich and University of Zurich, CH-8057, Zurich, Switzerland
| | - Sandra Tietscher
- Department of Quantitative Biomedicine, University of Zurich, CH-8057, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, CH-8093, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH Zurich and University of Zurich, CH-8057, Zurich, Switzerland
| | | | | | - Martin Rees
- Pathology at Josefshaus, D-44137, Dortmund, Germany
| | - Natalie de Souza
- Department of Quantitative Biomedicine, University of Zurich, CH-8057, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, CH-8093, Zurich, Switzerland
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, CH-8057, Zurich, Switzerland.
- Institute of Molecular Health Sciences, ETH Zurich, CH-8093, Zurich, Switzerland.
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205
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Wu X, Zhang D, Boström KI, Yao Y. COVID-19 Infection May Drive EC-like Myofibroblasts towards Myofibroblasts to Contribute to Pulmonary Fibrosis. Int J Mol Sci 2023; 24:11500. [PMID: 37511258 PMCID: PMC10380846 DOI: 10.3390/ijms241411500] [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: 06/05/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
COVID-19 has an extensive impact on Homo sapiens globally. Patients with COVID-19 are at an increased risk of developing pulmonary fibrosis. A previous study identified that myofibroblasts could be derived from pulmonary endothelial lineage cells as an important cell source that contributes to pulmonary fibrosis. Here, we analyzed publicly available data and showed that COVID-19 infection drove endothelial lineage cells towards myofibroblasts in pulmonary fibrosis of patients with COVID-19. We also discovered a similar differentiation trajectory in mouse lungs after viral infection. The results suggest that COVID-19 infection leads to the development of pulmonary fibrosis partly through the activation of endothelial cell (EC)-like myofibroblasts.
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Affiliation(s)
- Xiuju Wu
- Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Daoqin Zhang
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Kristina I. Boström
- Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- The Molecular Biology Institute at UCLA, Los Angeles, CA 90095, USA
| | - Yucheng Yao
- Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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206
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Inoue C, Miki Y, Suzuki T. New Perspectives on Sex Steroid Hormones Signaling in Cancer-Associated Fibroblasts of Non-Small Cell Lung Cancer. Cancers (Basel) 2023; 15:3620. [PMID: 37509283 PMCID: PMC10377312 DOI: 10.3390/cancers15143620] [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: 04/30/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
The importance of sex hormones, especially estrogen, in the pathogenesis of non-small-cell lung cancer (NSCLC) has attracted attention due to its high incidence among young adults and nonsmokers, especially those who are female. Cancer-associated fibroblasts (CAFs) reside in the cancer stroma and influence cancer growth, invasion, metastasis, and acquisition of drug resistance through interactions with cancer cells and other microenvironmental components. Hormone-mediated cell-cell interactions are classic cell-cell interactions and well-known phenomena in breast cancer and prostate cancer CAFs. In cancers of other organs, including NSCLC, the effects of CAFs on hormone-receptor expression and hormone production in cancer tissues have been reported; however, there are few such studies. Many more studies have been performed on breast and prostate cancers. Recent advances in technology, particularly single-cell analysis techniques, have led to significant advances in the classification and function of CAFs. However, the importance of sex hormones in cell-cell interactions of CAFs in NSCLC remains unclear. This review summarizes reports on CAFs in NSCLC and sex hormones in cancer and immune cells surrounding CAFs. Furthermore, we discuss the prospects of sex-hormone research involving CAFs in NSCLC.
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Affiliation(s)
- Chihiro Inoue
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Yasuhiro Miki
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Takashi Suzuki
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
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207
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Li T, Wang X, Niu M, Wang M, Zhou J, Wu K, Yi M. Bispecific antibody targeting TGF-β and PD-L1 for synergistic cancer immunotherapy. Front Immunol 2023; 14:1196970. [PMID: 37520520 PMCID: PMC10373067 DOI: 10.3389/fimmu.2023.1196970] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
The PD-1/PD-L1 signaling pathway plays a crucial role in cancer immune evasion, and the use of anti-PD-1/PD-L1 antibodies represents a significant milestone in cancer immunotherapy. However, the low response rate observed in unselected patients and the development of therapeutic resistance remain major obstacles to their clinical application. Accumulating studies showed that overexpressed TGF-β is another immunosuppressive factor apart from traditional immune checkpoints. Actually, the effects of PD-1 and TGF-β pathways are independent and interactive, which work together contributing to the immune evasion of cancer cell. It has been verified that blocking TGF-β and PD-L1 simultaneously could enhance the efficacy of PD-L1 monoclonal antibody and overcome its treatment resistance. Based on the bispecific antibody or fusion protein technology, multiple bispecific and bifunctional antibodies have been developed. In the preclinical and clinical studies, these updated antibodies exhibited potent anti-tumor activity, superior to anti-PD-1/PD-L1 monotherapies. In the review, we summarized the advances of bispecific antibodies targeting TGF-β and PD-L1 in cancer immunotherapy. We believe these next-generation immune checkpoint inhibitors would substantially alter the cancer treatment paradigm, especially in anti-PD-1/PD-L1-resistant patients.
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Affiliation(s)
- Tianye Li
- Department of Gynecology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Xinrun Wang
- Department of Gynecology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Mengke Niu
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Mingli Wang
- Department of Gynecology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Jianwei Zhou
- Department of Gynecology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Kongming Wu
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ming Yi
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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208
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Nabhan AN, Webster JD, Adams JJ, Blazer L, Everrett C, Eidenschenk C, Arlantico A, Fleming I, Brightbill HD, Wolters PJ, Modrusan Z, Seshagiri S, Angers S, Sidhu SS, Newton K, Arron JR, Dixit VM. Targeted alveolar regeneration with Frizzled-specific agonists. Cell 2023; 186:2995-3012.e15. [PMID: 37321220 DOI: 10.1016/j.cell.2023.05.022] [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: 07/28/2022] [Revised: 03/24/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023]
Abstract
Wnt ligands oligomerize Frizzled (Fzd) and Lrp5/6 receptors to control the specification and activity of stem cells in many species. How Wnt signaling is selectively activated in different stem cell populations, often within the same organ, is not understood. In lung alveoli, we show that distinct Wnt receptors are expressed by epithelial (Fzd5/6), endothelial (Fzd4), and stromal (Fzd1) cells. Fzd5 is uniquely required for alveolar epithelial stem cell activity, whereas fibroblasts utilize distinct Fzd receptors. Using an expanded repertoire of Fzd-Lrp agonists, we could activate canonical Wnt signaling in alveolar epithelial stem cells via either Fzd5 or, unexpectedly, non-canonical Fzd6. A Fzd5 agonist (Fzd5ag) or Fzd6ag stimulated alveolar epithelial stem cell activity and promoted survival in mice after lung injury, but only Fzd6ag promoted an alveolar fate in airway-derived progenitors. Therefore, we identify a potential strategy for promoting regeneration without exacerbating fibrosis during lung injury.
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Affiliation(s)
- Ahmad N Nabhan
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Joshua D Webster
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jarret J Adams
- AntlerA Therapeutics, 348 Hatch Drive, Foster City, CA 94404, USA
| | - Levi Blazer
- AntlerA Therapeutics, 348 Hatch Drive, Foster City, CA 94404, USA
| | - Christine Everrett
- Department of Molecular Discovery and Cancer Cell Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Celine Eidenschenk
- Department of Molecular Discovery and Cancer Cell Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Alexander Arlantico
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Isabel Fleming
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hans D Brightbill
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Paul J Wolters
- Department of Medicine, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | | | - Stephane Angers
- AntlerA Therapeutics, 348 Hatch Drive, Foster City, CA 94404, USA; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 1A2, Canada; Department of Biochemistry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sachdev S Sidhu
- AntlerA Therapeutics, 348 Hatch Drive, Foster City, CA 94404, USA; School of Pharmacy, University of Waterloo, Kitchener, ON N2G 1C5, Canada
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Joseph R Arron
- Department of Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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209
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Inamo J, Keegan J, Griffith A, Ghosh T, Horisberger A, Howard K, Pulford J, Murzin E, Hancock B, Jonsson AH, Seifert J, Feser ML, Norris JM, Cao Y, Apruzzese W, Louis Bridges S, Bykerk V, Goodman S, Donlin L, Firestein GS, Perlman H, Bathon JM, Hughes LB, Tabechian D, Filer A, Pitzalis C, Anolik JH, Moreland L, Guthridge JM, James JA, Brenner MB, Raychaudhuri S, Sparks JA, Michael Holers V, Deane KD, Lederer JA, Rao DA, Zhang F. Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547507. [PMID: 37461737 PMCID: PMC10349983 DOI: 10.1101/2023.07.03.547507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease with currently no universally highly effective prevention strategies. Identifying pathogenic immune phenotypes in 'At-Risk' populations prior to clinical disease onset is crucial to establishing effective prevention strategies. Here, we applied mass cytometry to deeply characterize the immunophenotypes in blood from At-Risk individuals identified through the presence of serum antibodies to citrullinated protein antigens (ACPA) and/or first-degree relative (FDR) status (n=52), as compared to established RA (n=67), and healthy controls (n=48). We identified significant cell expansions in At-Risk individuals compared with controls, including CCR2+CD4+ T cells, T peripheral helper (Tph) cells, type 1 T helper cells, and CXCR5+CD8+ T cells. We also found that CD15+ classical monocytes were specifically expanded in ACPA-negative FDRs, and an activated PAX5 low naïve B cell population was expanded in ACPA-positive FDRs. Further, we developed an "RA immunophenotype score" classification method based on the degree of enrichment of cell states relevant to established RA patients. This score significantly distinguished At-Risk individuals from controls. In all, we systematically identified activated lymphocyte phenotypes in At-Risk individuals, along with immunophenotypic differences among both ACPA+ and ACPA-FDR At-Risk subpopulations. Our classification model provides a promising approach for understanding RA pathogenesis with the goal to further improve prevention strategies and identify novel therapeutic targets.
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210
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Yang D, Liu J, Qian H, Zhuang Q. Cancer-associated fibroblasts: from basic science to anticancer therapy. Exp Mol Med 2023:10.1038/s12276-023-01013-0. [PMID: 37394578 PMCID: PMC10394065 DOI: 10.1038/s12276-023-01013-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/09/2023] [Accepted: 03/15/2023] [Indexed: 07/04/2023] Open
Abstract
Cancer-associated fibroblasts (CAFs), as a central component of the tumor microenvironment in primary and metastatic tumors, profoundly influence the behavior of cancer cells and are involved in cancer progression through extensive interactions with cancer cells and other stromal cells. Furthermore, the innate versatility and plasticity of CAFs allow their education by cancer cells, resulting in dynamic alterations in stromal fibroblast populations in a context-dependent manner, which highlights the importance of precise assessment of CAF phenotypical and functional heterogeneity. In this review, we summarize the proposed origins and heterogeneity of CAFs as well as the molecular mechanisms regulating the diversity of CAF subpopulations. We also discuss current strategies to selectively target tumor-promoting CAFs, providing insights and perspectives for future research and clinical studies involving stromal targeting.
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Affiliation(s)
- Dakai Yang
- Department of General Practice, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China.
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, People's Republic of China.
| | - Jing Liu
- Microbiology and Immunity Department, Shanghai, People's Republic of China
- Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine & Health Sciences, Shanghai, People's Republic of China
| | - Hui Qian
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, People's Republic of China.
| | - Qin Zhuang
- Department of General Practice, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China.
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211
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Lütge M, De Martin A, Gil-Cruz C, Perez-Shibayama C, Stanossek Y, Onder L, Cheng HW, Kurz L, Cadosch N, Soneson C, Robinson MD, Stoeckli SJ, Ludewig B, Pikor NB. Conserved stromal-immune cell circuits secure B cell homeostasis and function. Nat Immunol 2023; 24:1149-1160. [PMID: 37202489 PMCID: PMC10307622 DOI: 10.1038/s41590-023-01503-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 04/03/2023] [Indexed: 05/20/2023]
Abstract
B cell zone reticular cells (BRCs) form stable microenvironments that direct efficient humoral immunity with B cell priming and memory maintenance being orchestrated across lymphoid organs. However, a comprehensive understanding of systemic humoral immunity is hampered by the lack of knowledge of global BRC sustenance, function and major pathways controlling BRC-immune cell interactions. Here we dissected the BRC landscape and immune cell interactome in human and murine lymphoid organs. In addition to the major BRC subsets underpinning the follicle, including follicular dendritic cells, PI16+ RCs were present across organs and species. As well as BRC-produced niche factors, immune cell-driven BRC differentiation and activation programs governed the convergence of shared BRC subsets, overwriting tissue-specific gene signatures. Our data reveal that a canonical set of immune cell-provided cues enforce bidirectional signaling programs that sustain functional BRC niches across lymphoid organs and species, thereby securing efficient humoral immunity.
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Affiliation(s)
- Mechthild Lütge
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | - Angelina De Martin
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | - Cristina Gil-Cruz
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | | | - Yves Stanossek
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland
- Department of Otorhinolaryngology Head and Neck Surgery, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | - Lucas Onder
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | - Hung-Wei Cheng
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | - Lisa Kurz
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | - Nadine Cadosch
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | - Charlotte Soneson
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Sandro J Stoeckli
- Department of Otorhinolaryngology Head and Neck Surgery, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | - Burkhard Ludewig
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland.
| | - Natalia B Pikor
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland.
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Smith MH, Gao VR, Periyakoil PK, Kochen A, DiCarlo EF, Goodman SM, Norman TM, Donlin LT, Leslie CS, Rudensky AY. Drivers of heterogeneity in synovial fibroblasts in rheumatoid arthritis. Nat Immunol 2023; 24:1200-1210. [PMID: 37277655 PMCID: PMC10307631 DOI: 10.1038/s41590-023-01527-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/04/2023] [Indexed: 06/07/2023]
Abstract
Inflammation of non-barrier immunologically quiescent tissues is associated with a massive influx of blood-borne innate and adaptive immune cells. Cues from the latter are likely to alter and expand activated states of the resident cells. However, local communications between immigrant and resident cell types in human inflammatory disease remain poorly understood. Here, we explored drivers of fibroblast-like synoviocyte (FLS) heterogeneity in inflamed joints of patients with rheumatoid arthritis using paired single-cell RNA and ATAC sequencing, multiplexed imaging and spatial transcriptomics along with in vitro modeling of cell-extrinsic factor signaling. These analyses suggest that local exposures to myeloid and T cell-derived cytokines, TNF, IFN-γ, IL-1β or lack thereof, drive four distinct FLS states some of which closely resemble fibroblast states in other disease-affected tissues including skin and colon. Our results highlight a role for concurrent, spatially distributed cytokine signaling within the inflamed synovium.
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Affiliation(s)
- Melanie H Smith
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, USA.
- Howard Hughes Medical Institute and Immunology Program at Sloan Kettering Institute, Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Vianne R Gao
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College and Graduate School, New York, NY, USA
| | - Preethi K Periyakoil
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alejandro Kochen
- Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Edward F DiCarlo
- Department of Pathology and Laboratory Medicine, Hospital for Special Surgery, New York, NY, USA
| | - Susan M Goodman
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medical College and Graduate School, New York, NY, USA
| | - Thomas M Norman
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura T Donlin
- Weill Cornell Medical College and Graduate School, New York, NY, USA
- Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program at Sloan Kettering Institute, Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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213
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Baker DJ, Arany Z, Baur JA, Epstein JA, June CH. CAR T therapy beyond cancer: the evolution of a living drug. Nature 2023; 619:707-715. [PMID: 37495877 DOI: 10.1038/s41586-023-06243-w] [Citation(s) in RCA: 89] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/22/2023] [Indexed: 07/28/2023]
Abstract
Engineering a patient's own T cells to selectively target and eliminate tumour cells has cured patients with untreatable haematologic cancers. These results have energized the field to apply chimaeric antigen receptor (CAR) T therapy throughout oncology. However, evidence from clinical and preclinical studies underscores the potential of CAR T therapy beyond oncology in treating autoimmunity, chronic infections, cardiac fibrosis, senescence-associated disease and other conditions. Concurrently, the deployment of new technologies and platforms provides further opportunity for the application of CAR T therapy to noncancerous pathologies. Here we review the rationale behind CAR T therapy, current challenges faced in oncology, a synopsis of preliminary reports in noncancerous diseases, and a discussion of relevant emerging technologies. We examine potential applications for this therapy in a wide range of contexts. Last, we highlight concerns regarding specificity and safety and outline the path forward for CAR T therapy beyond cancer.
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Affiliation(s)
- Daniel J Baker
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA.
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Zoltan Arany
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph A Baur
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan A Epstein
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Carl H June
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA.
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214
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Serrano-Lopez R, Morandini AC. Fibroblasts at the curtain call: from ensemble to principal dancers in immunometabolism and inflammaging. J Appl Oral Sci 2023; 31:e20230050. [PMID: 37377310 PMCID: PMC10392869 DOI: 10.1590/1678-7757-2023-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/08/2023] [Indexed: 06/29/2023] Open
Abstract
Inflammation is a necessary step in response to injuries, being vital in restoring homeostasis and facilitating tissue healing. Among the cells that play a crucial role in inflammatory responses, stromal cells, including fibroblasts, have an undeniable significance in fine-tuning the magnitude of mediators that directly affect hyper-inflammatory responses and tissue destruction. Fibroblasts, the dominant cells in the gingival connective tissue, are a very heterogeneous population of cells, and more recently they have been receiving well deserved attention as central players and often the 'principal dancers' of many pathological processes ranging from inflammation and fibrosis to altered immunity and cancer. The goal of the current investigation is to dive into the exact role of the stromal fibroblast and the responsible mechanistic factors involved in both regulation and dysregulation of the inflammatory responses. This article reviews the most recent literature on how fibroblasts, in their different activation states or subtypes, play a crucial role in contributing to inflammatory outcomes. We will focus on recent findings on inflammatory diseases. We will also provide connections regarding the stromal-immune relationship, which supports the idea of fibroblast coming out from the 'ensemble' of cell types to the protagonist role in immunometabolism and inflammaging. Additionally, we discuss the current advances in variation of fibroblast nomenclature and division into clusters with their own suggested function and particularities in gene expression. Here, we provide a perspective for the periodontal implications, discussing the fibroblast role in the infection-driven and inflammatory mediated diseases such as periodontitis.
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Affiliation(s)
- Rogelio Serrano-Lopez
- Augusta University, Dental College of Georgia, Department of Oral Biology and Diagnostic Sciences, Augusta, GA, USA
- Augusta University, Honors Program, College of Science and Mathematics, Augusta, GA, USA
| | - Ana Carolina Morandini
- Augusta University, Dental College of Georgia, Department of Oral Biology and Diagnostic Sciences, Augusta, GA, USA
- Augusta University, Dental College of Georgia, Department of Periodontics, Augusta, GA, USA
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215
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Wang Y, Chen Y, Xiao Y, Ruan J, Tian Q, Cheng Q, Chang K, Yi X. Distinct subtypes of endometriosis identified based on stromal-immune microenvironment and gene expression: implications for hormone therapy. Front Immunol 2023; 14:1133672. [PMID: 37426659 PMCID: PMC10324653 DOI: 10.3389/fimmu.2023.1133672] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/31/2023] [Indexed: 07/11/2023] Open
Abstract
Background Endometriosis (EMs) is a chronic inflammatory condition that is highly heterogeneous. Current clinical staging fails to accurately predict drug responses and prognosis. In this study, we aimed to reveal the heterogeneity of ectopic lesions and investigate the possible underlying mechanisms using transcriptomic data and clinical information. Methods The EMs microarray dataset GSE141549 was obtained from the Gene Expression Omnibus database. Unsupervised hierarchical clustering was performed to identify EMs subtypes, which was followed by the functional enrichment analysis and estimation of immune infiltrates. Subtype-associated gene signatures were identified and further validated in other independent datasets, including GSE25628, E-MTAB-694, and GSE23339. Additionally, tissue microarrays (TMAs) were generated from premenopausal patients with EMs to investigate the potential clinical implications of the two identified subtypes. Results The unsupervised clustering analysis revealed that ectopic EMs lesions can be classified into two distinct subtypes: stroma-enriched (S1) and immune-enriched (S2). The functional analysis revealed that S1 correlated with fibroblast activation and extracellular matrix remodeling in the ectopic milieu, whereas S2 was characterized by the upregulation of immune pathways and a higher positive correlation with the immunotherapy response. Moreover, we identified a subtype signature composed of FHL1 and SORBS1, and constructed a subtype diagnostic model. Based on the cohort data from the TMAs, we found that S2 was strongly associated with the failure of/intolerance to hormone therapy. Conclusions This study identified two distinct subtypes that are varyingly associated with hormone resistance, stroma-immunity, and molecular features, thereby highlighting the importance of this stromal-immune heterogeneity in identifying EMs subtypes and providing novel insights into future personalized hormone-free therapy in EMs.
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Affiliation(s)
- Yuning Wang
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Yun Chen
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Yinping Xiao
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Jingyao Ruan
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Qi Tian
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Qi Cheng
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Kaikai Chang
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Xiaofang Yi
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
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216
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Zhang H, Zhu Q, Ji Y, Wang M, Zhang Q, Liu W, Li R, Zhang J, Xu P, Song X, Lv C. hucMSCs treatment prevents pulmonary fibrosis by reducing circANKRD42-YAP1-mediated mechanical stiffness. Aging (Albany NY) 2023; 15:5514-5534. [PMID: 37335082 PMCID: PMC10333056 DOI: 10.18632/aging.204805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/23/2023] [Indexed: 06/21/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fibrosing interstitial pneumonia of unknown cause. The most typical characteristic of IPF is gradual weakening of pulmonary elasticity and increase in hardness/rigidity with aging. This study aims to identify a novel treatment approach for IPF and explore mechanism of mechanical stiffness underlying human umbilical cord mesenchymal stem cells (hucMSCs) therapy. Target ability of hucMSCs was examined by labeling with cell membrane dye Dil. Anti-pulmonary fibrosis effect of hucMSCs therapy by reducing mechanical stiffness was evaluated by lung function analysis and MicroCT imaging system and atomic force microscope in vivo and in vitro. Results showed that stiff environment of fibrogenesis caused cells to establish a mechanical connection between cytoplasm and nucleus, initiating expression of related mechanical genes such as Myo1c and F-actin. HucMSCs treatment blocked force transmission and reduced mechanical force. For further exploration of mechanism, ATGGAG was mutated to CTTGCG (the binding site of miR-136-5p) in the full-length sequence of circANKRD42. Wildtype and mutant plasmids of circANKRD42 were packaged into adenovirus vectors and sprayed into lungs of mice. Mechanistic dissection revealed that hucMSCs treatment repressed circANKRD42 reverse splicing biogenesis by inhibiting hnRNP L, which in turn promoted miR-136-5p binds to 3'-Untranslated Region (3'-UTR) of YAP1 mRNA directly, thus inhibiting translation of YAP1 and reducing YAP1 protein entering nucleus. The condition repressed expression of related mechanical genes to block force transmission and reduce mechanical forces. The mechanosensing mechanism mediated directly by circANKRD42-YAP1 axis in hucMSCs treatment, which has potential general applicability in IPF treatment.
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Affiliation(s)
- Haitong Zhang
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou 256603, China
| | - Qi Zhu
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Yunxia Ji
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou 256603, China
| | - Meirong Wang
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Qian Zhang
- Department of Pathology, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou 256603, China
| | - Weili Liu
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou 256603, China
| | - Ruiqiong Li
- Department of Clinical Nursing, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou 256603, China
| | - Jinjin Zhang
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Pan Xu
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou 256603, China
| | - Xiaodong Song
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Changjun Lv
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou 256603, China
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217
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Fletcher AL, Good-Jacobson KL. New fibroblast network connections support lymphocytic cellular service. Nat Immunol 2023:10.1038/s41590-023-01537-7. [PMID: 37322180 DOI: 10.1038/s41590-023-01537-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Anne L Fletcher
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.
- Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Kim L Good-Jacobson
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.
- Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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218
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Muraoka A, Suzuki M, Hamaguchi T, Watanabe S, Iijima K, Murofushi Y, Shinjo K, Osuka S, Hariyama Y, Ito M, Ohno K, Kiyono T, Kyo S, Iwase A, Kikkawa F, Kajiyama H, Kondo Y. Fusobacterium infection facilitates the development of endometriosis through the phenotypic transition of endometrial fibroblasts. Sci Transl Med 2023; 15:eadd1531. [PMID: 37315109 DOI: 10.1126/scitranslmed.add1531] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 05/24/2023] [Indexed: 06/16/2023]
Abstract
Retrograde menstruation is a widely accepted cause of endometriosis. However, not all women who experience retrograde menstruation develop endometriosis, and the mechanisms underlying these observations are not yet understood. Here, we demonstrated a pathogenic role of Fusobacterium in the formation of ovarian endometriosis. In a cohort of women, 64% of patients with endometriosis but <10% of controls were found to have Fusobacterium infiltration in the endometrium. Immunohistochemical and biochemical analyses revealed that activated transforming growth factor-β (TGF-β) signaling resulting from Fusobacterium infection of endometrial cells led to the transition from quiescent fibroblasts to transgelin (TAGLN)-positive myofibroblasts, which gained the ability to proliferate, adhere, and migrate in vitro. Fusobacterium inoculation in a syngeneic mouse model of endometriosis resulted in a marked increase in TAGLN-positive myofibroblasts and increased number and weight of endometriotic lesions. Furthermore, antibiotic treatment largely prevented establishment of endometriosis and reduced the number and weight of established endometriotic lesions in the mouse model. Our data support a mechanism for the pathogenesis of endometriosis via Fusobacterium infection and suggest that eradication of this bacterium could be an approach to treat endometriosis.
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Affiliation(s)
- Ayako Muraoka
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Miho Suzuki
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Tomonari Hamaguchi
- Division of Neurogenetics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Shinya Watanabe
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Kenta Iijima
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Yoshiteru Murofushi
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Keiko Shinjo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Satoko Osuka
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Yumi Hariyama
- Department of Obstetrics and Gynecology, Toyota Kosei Hospital, 500-1, Ihohara, Zyosui-cho, Toyota 470-0396, Japan
| | - Mikako Ito
- Division of Neurogenetics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Tohru Kiyono
- Project for Prevention of HPV-related Cancer, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwanoha 6-5-1, Kashiwa 277-8577, Japan
| | - Satoru Kyo
- Department of Obstetrics and Gynecology, Shimane University Faculty of Medicine, 89-1 Enya-Cho, Izumo 693-8501, Japan
| | - Akira Iwase
- Department of Obstetrics and Gynecology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi 371-8511, Japan
| | - Fumitaka Kikkawa
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Hiroaki Kajiyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Yutaka Kondo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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219
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Strasser MK, Gibbs DL, Gascard P, Bons J, Hickey JW, Schürch CM, Tan Y, Black S, Chu P, Ozkan A, Basisty N, Sangwan V, Rose J, Shah S, Camilleri-Broet S, Fiset PO, Bertos N, Berube J, Djambazian H, Li R, Oikonomopoulos S, Fels-Elliott DR, Vernovsky S, Shimshoni E, Collyar D, Russell A, Ragoussis I, Stachler M, Goldenring JR, McDonald S, Ingber DE, Schilling B, Nolan GP, Tlsty TD, Huang S, Ferri LE. Concerted epithelial and stromal changes during progression of Barrett's Esophagus to invasive adenocarcinoma exposed by multi-scale, multi-omics analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544265. [PMID: 37333362 PMCID: PMC10274886 DOI: 10.1101/2023.06.08.544265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Esophageal adenocarcinoma arises from Barrett's esophagus, a precancerous metaplastic replacement of squamous by columnar epithelium in response to chronic inflammation. Multi-omics profiling, integrating single-cell transcriptomics, extracellular matrix proteomics, tissue-mechanics and spatial proteomics of 64 samples from 12 patients' paths of progression from squamous epithelium through metaplasia, dysplasia to adenocarcinoma, revealed shared and patient-specific progression characteristics. The classic metaplastic replacement of epithelial cells was paralleled by metaplastic changes in stromal cells, ECM and tissue stiffness. Strikingly, this change in tissue state at metaplasia was already accompanied by appearance of fibroblasts with characteristics of carcinoma-associated fibroblasts and of an NK cell-associated immunosuppressive microenvironment. Thus, Barrett's esophagus progresses as a coordinated multi-component system, supporting treatment paradigms that go beyond targeting cancerous cells to incorporating stromal reprogramming.
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220
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Yan R, Moresco P, Gegenhuber B, Fearon DT. T cell-Mediated Development of Stromal Fibroblasts with an Immune-Enhancing Chemokine Profile. Cancer Immunol Res 2023; 11:OF1-OF11. [PMID: 37285176 PMCID: PMC10700667 DOI: 10.1158/2326-6066.cir-22-0593] [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: 07/22/2022] [Revised: 01/31/2023] [Accepted: 05/18/2023] [Indexed: 05/24/2023]
Abstract
Stromal fibroblasts reside in inflammatory tissues that are characterized by either immune suppression or activation. Whether and how fibroblasts adapt to these contrasting microenvironments remains unknown. Cancer-associated fibroblasts (CAF) mediate immune quiescence by producing the chemokine CXCL12, which coats cancer cells to suppress T-cell infiltration. We examined whether CAFs can also adopt an immune-promoting chemokine profile. Single-cell RNA sequencing of CAFs from mouse pancreatic adenocarcinomas identified a subpopulation of CAFs with decreased expression of Cxcl12 and increased expression of the T cell-attracting chemokine Cxcl9 in association with T-cell infiltration. TNFα and IFNγ containing conditioned media from activated CD8+ T cells converted stromal fibroblasts from a CXCL12+/CXCL9- immune-suppressive phenotype into a CXCL12-/CXCL9+ immune-activating phenotype. Recombinant IFNγ and TNFα acted together to augment CXCL9 expression, whereas TNFα alone suppressed CXCL12 expression. This coordinated chemokine switch led to increased T-cell infiltration in an in vitro chemotaxis assay. Our study demonstrates that CAFs have a phenotypic plasticity that allows their adaptation to contrasting immune tissue microenvironments.
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Affiliation(s)
- Ran Yan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Philip Moresco
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794
- Medical Scientist Training Program, Stony Brook University Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794
| | - Bruno Gegenhuber
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115
| | - Douglas T. Fearon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065
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221
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Rodriguez LR, Tang SY, Barboza WR, Murthy A, Tomer Y, Cai TQ, Iyer S, Chavez K, Das US, Ghosh S, Dimopoulos T, Babu A, Connelly C, FitzGerald GA, Beers MF. Disruption of Prostaglandin F 2α Receptor Signaling Attenuates Fibrotic Remodeling and Alters Fibroblast Population Dynamics in A Preclinical Murine Model of Idiopathic Pulmonary Fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.543956. [PMID: 37333249 PMCID: PMC10274762 DOI: 10.1101/2023.06.07.543956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Idiopathic Pulmonary Fibrosis (IPF) is a chronic parenchymal lung disease characterized by repetitive alveolar cell injury, myofibroblast proliferation, and excessive extracellular matrix deposition for which unmet need persists for effective therapeutics. The bioactive eicosanoid, prostaglandin F2α, and its cognate receptor FPr (Ptfgr) are implicated as a TGFβ1 independent signaling hub for IPF. To assess this, we leveraged our published murine PF model (IER - SftpcI73T) expressing a disease-associated missense mutation in the surfactant protein C (Sftpc) gene. Tamoxifen treated IER-SftpcI73T mice develop an early multiphasic alveolitis and transition to spontaneous fibrotic remodeling by 28 days. IER-SftpcI73T mice crossed to a Ptgfr null (FPr-/-) line showed attenuated weight loss and gene dosage dependent rescue of mortality compared to FPr+/+ cohorts. IER-SftpcI73T/FPr-/- mice also showed reductions in multiple fibrotic endpoints for which administration of nintedanib was not additive. Single cell RNA sequencing, pseudotime analysis, and in vitro assays demonstrated Ptgfr expression predominantly within adventitial fibroblasts which were reprogrammed to an "inflammatory/transitional" cell state in a PGF2α/FPr dependent manner. Collectively, the findings provide evidence for a role for PGF2α signaling in IPF, mechanistically identify a susceptible fibroblast subpopulation, and establish a benchmark effect size for disruption of this pathway in mitigating fibrotic lung remodeling.
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Affiliation(s)
- Luis R Rodriguez
- Pulmonary, Allergy, and Critical Care Division Department of Medicine; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
- PENN-CHOP Lung Biology Institute; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
| | - Soon Yew Tang
- Institute for Translational Medicine and Therapeutics; Department of Systems Pharmacology and Translational Therapeutics; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
| | - Willy Roque Barboza
- Pulmonary, Allergy, and Critical Care Division Department of Medicine; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
- PENN-CHOP Lung Biology Institute; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
| | - Aditi Murthy
- Pulmonary, Allergy, and Critical Care Division Department of Medicine; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
- PENN-CHOP Lung Biology Institute; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
| | - Yaniv Tomer
- Pulmonary, Allergy, and Critical Care Division Department of Medicine; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
- PENN-CHOP Lung Biology Institute; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
| | - Tian-Quan Cai
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | - Swati Iyer
- Pulmonary, Allergy, and Critical Care Division Department of Medicine; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
- PENN-CHOP Lung Biology Institute; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
| | - Katrina Chavez
- Pulmonary, Allergy, and Critical Care Division Department of Medicine; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
- PENN-CHOP Lung Biology Institute; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
| | - Ujjalkumar Subhash Das
- Institute for Translational Medicine and Therapeutics; Department of Systems Pharmacology and Translational Therapeutics; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
| | - Soumita Ghosh
- Institute for Translational Medicine and Therapeutics; Department of Systems Pharmacology and Translational Therapeutics; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
| | - Thalia Dimopoulos
- Pulmonary, Allergy, and Critical Care Division Department of Medicine; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
- PENN-CHOP Lung Biology Institute; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
| | - Apoorva Babu
- PENN-CHOP Lung Biology Institute; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
| | | | - Garret A FitzGerald
- Institute for Translational Medicine and Therapeutics; Department of Systems Pharmacology and Translational Therapeutics; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
| | - Michael F Beers
- Pulmonary, Allergy, and Critical Care Division Department of Medicine; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
- PENN-CHOP Lung Biology Institute; Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA 19104
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222
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Werner G, Sanyal A, Mirizio E, Hutchins T, Tabib T, Lafyatis R, Jacobe H, Torok KS. Single-Cell Transcriptome Analysis Identifies Subclusters with Inflammatory Fibroblast Responses in Localized Scleroderma. Int J Mol Sci 2023; 24:9796. [PMID: 37372943 DOI: 10.3390/ijms24129796] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/19/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
Localized scleroderma (LS) is an autoimmune disease with both inflammatory and fibrotic components causing an abnormal deposition of collagen in the skin and underlying tissue, often leading to disfigurement and disability. Much of its pathophysiology is extrapolated from systemic sclerosis (SSc) since the histopathology findings in the skin are nearly identical. However, LS is critically understudied. Single-cell RNA sequencing (scRNA seq) technology provides a novel way to obtain detailed information at the individual cellular level, overcoming this barrier. Here, we analyzed the affected skin of 14 patients with LS (pediatric and adult) and 14 healthy controls. Fibroblast populations were the focus, since they are the main drivers of fibrosis in SSc. We identified 12 fibroblast subclusters in LS, which overall had an inflammatory gene expression (IFN and HLA-associated genes). A myofibroblast-like cluster (SFRP4/PRSS23) was more prevalent in LS subjects and shared many upregulated genes expressed in SSc-associated myofibroblasts, though it also had strong expression of CXCL9/10/11, known CXCR3 ligands. A CXCL2/IRF1 cluster identified was unique to LS, with a robust inflammatory gene signature, including IL-6, and according to cell communication analysis are influenced by macrophages. In summary, potential disease-propagating fibroblasts and associated gene signatures were identified in LS skin via scRNA seq.
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Affiliation(s)
- Giffin Werner
- Department of Pediatrics (Rheumatology), University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Anwesha Sanyal
- Department of Pediatrics (Rheumatology), University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Emily Mirizio
- Department of Pediatrics (Rheumatology), University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Theresa Hutchins
- Department of Pediatrics (Rheumatology), University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Heidi Jacobe
- Department of Dermatology, University of Texas Southwestern, Dallas, TX 75390, USA
| | - Kathryn S Torok
- Department of Pediatrics (Rheumatology), University of Pittsburgh, Pittsburgh, PA 15224, USA
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223
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Kenney HM, Peng Y, de Mesy Bentley KL, Xing L, Ritchlin CT, Schwarz EM. The Enigmas of Lymphatic Muscle Cells: Where Do They Come From, How Are They Maintained, and Can They Regenerate? Curr Rheumatol Rev 2023; 19:246-259. [PMID: 36705238 PMCID: PMC10257750 DOI: 10.2174/1573397119666230127144711] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/29/2022] [Accepted: 12/02/2022] [Indexed: 01/28/2023]
Abstract
Lymphatic muscle cell (LMC) contractility and coverage of collecting lymphatic vessels (CLVs) are integral to effective lymphatic drainage and tissue homeostasis. In fact, defects in lymphatic contractility have been identified in various conditions, including rheumatoid arthritis, inflammatory bowel disease, and obesity. However, the fundamental role of LMCs in these pathologic processes is limited, primarily due to the difficulty in directly investigating the enigmatic nature of this poorly characterized cell type. LMCs are a unique cell type that exhibit dual tonic and phasic contractility with hybrid structural features of both vascular smooth muscle cells (VSMCs) and cardiac myocytes. While advances have been made in recent years to better understand the biochemistry and function of LMCs, central questions regarding their origins, investiture into CLVs, and homeostasis remain unanswered. To summarize these discoveries, unexplained experimental results, and critical future directions, here we provide a focused review of current knowledge and open questions related to LMC progenitor cells, recruitment, maintenance, and regeneration. We also highlight the high-priority research goal of identifying LMC-specific genes towards genetic conditional- inducible in vivo gain and loss of function studies. While our interest in LMCs has been focused on understanding lymphatic dysfunction in an arthritic flare, these concepts are integral to the broader field of lymphatic biology, and have important potential for clinical translation through targeted therapeutics to control lymphatic contractility and drainage.
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Grants
- R01AG059775,R01AG059775,R01AG059775 NIA NIH HHS
- R01AR056702,R01AR069000,T32AR076950,P30AR069655,R01AR056702,R01AR069000,P30AR069655,T32AR076950,R01AR056702,R01AR069000,T32AR076950,P30AR069655 NIAMS NIH HHS
- P30 AR069655 NIAMS NIH HHS
- R01 AR069000 NIAMS NIH HHS
- T32 GM007356 NIGMS NIH HHS
- R01 AG059775 NIA NIH HHS
- T32GM007356,T32GM007356,T32GM007356,T32GM007356 NIGMS NIH HHS
- T32 AR076950 NIAMS NIH HHS
- R01 AR056702 NIAMS NIH HHS
- F30 AG076326 NIA NIH HHS
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Affiliation(s)
- H. Mark Kenney
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Ave, Box 665, Rochester, NY, 14642, USA
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Yue Peng
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Ave, Box 665, Rochester, NY, 14642, USA
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Karen L. de Mesy Bentley
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Ave, Box 665, Rochester, NY, 14642, USA
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
- Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY, USA
| | - Lianping Xing
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Ave, Box 665, Rochester, NY, 14642, USA
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Christopher T. Ritchlin
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Ave, Box 665, Rochester, NY, 14642, USA
- Department of Medicine, Division of Allergy, Immunology, Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Edward M. Schwarz
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Ave, Box 665, Rochester, NY, 14642, USA
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
- Department of Medicine, Division of Allergy, Immunology, Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
- Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY, USA
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224
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Timperi E, Romano E. Stromal circuits involving tumor-associated macrophages and cancer-associated fibroblasts. Front Immunol 2023; 14:1194642. [PMID: 37342322 PMCID: PMC10277481 DOI: 10.3389/fimmu.2023.1194642] [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: 03/27/2023] [Accepted: 05/19/2023] [Indexed: 06/22/2023] Open
Abstract
The tumor associated macrophages (TAM) represent one of most abundant subpopulations across several solid cancers and their number/frequency is associated with a poor clinical outcome. It has been clearly demonstrated that stromal cells, such as the cancer associated fibroblasts (CAFs), may orchestrate TAM recruitment, survival and reprogramming. Today, single cell-RNA sequencing (sc-RNA seq) technologies allowed a more granular knowledge about TAMs and CAFs phenotypical and functional programs. In this mini-review we discuss the recent discoveries in the sc-RNA seq field focusing on TAM and CAF identity and their crosstalk in the tumor microenvironment (TME) of solid cancers.
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Affiliation(s)
- Eleonora Timperi
- Department of Immunology, INSERM U932, Université Paris Sciences et Lettres (PSL) Research University, Institut Curie, Paris, France
| | - Emanuela Romano
- Department of Immunology, INSERM U932, Université Paris Sciences et Lettres (PSL) Research University, Institut Curie, Paris, France
- Department of Medical Oncology, Center for Cancer Immunotherapy, Institut Curie, Paris, France
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225
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Combes AJ, Samad B, Krummel MF. Defining and using immune archetypes to classify and treat cancer. Nat Rev Cancer 2023:10.1038/s41568-023-00578-2. [PMID: 37277485 DOI: 10.1038/s41568-023-00578-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2023] [Indexed: 06/07/2023]
Abstract
Tumours are surrounded by a host immune system that can suppress or promote tumour growth. The tumour microenvironment (TME) has often been framed as a singular entity, suggesting a single type of immune state that is defective and in need of therapeutic intervention. By contrast, the past few years have highlighted a plurality of immune states that can surround tumours. In this Perspective, we suggest that different TMEs have 'archetypal' qualities across all cancers - characteristic and repeating collections of cells and gene-expression profiles at the level of the bulk tumour. We discuss many studies that together support a view that tumours typically draw from a finite number (around 12) of 'dominant' immune archetypes. In considering the likely evolutionary origin and roles of these archetypes, their associated TMEs can be predicted to have specific vulnerabilities that can be leveraged as targets for cancer treatment with expected and addressable adverse effects for patients.
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Affiliation(s)
- Alexis J Combes
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA.
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, USA.
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA.
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Bushra Samad
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Matthew F Krummel
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA.
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, USA.
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226
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Rivera-Gonzalez GC, Butka EG, Gonzalez CE, Kong W, Jindal K, Morris SA. Single-cell lineage tracing reveals hierarchy and mechanism of adipocyte precursor maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543318. [PMID: 37398135 PMCID: PMC10312565 DOI: 10.1101/2023.06.01.543318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
White adipose tissue is crucial in various physiological processes. In response to high caloric intake, adipose tissue may expand by generating new adipocytes. Adipocyte precursor cells (progenitors and preadipocytes) are essential for generating mature adipocytes, and single-cell RNA sequencing provides new means to identify these populations. Here, we characterized adipocyte precursor populations in the skin, an adipose depot with rapid and robust generation of mature adipocytes. We identified a new population of immature preadipocytes, revealed a biased differentiation potential of progenitor cells, and identified Sox9 as a critical factor in driving progenitors toward adipose commitment, the first known mechanism of progenitor differentiation. These findings shed light on the specific dynamics and molecular mechanisms underlying rapid adipogenesis in the skin.
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Affiliation(s)
- Guillermo C. Rivera-Gonzalez
- Department of Developmental Biology, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Emily G. Butka
- Department of Developmental Biology, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Carolynn E. Gonzalez
- Department of Developmental Biology, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Kunal Jindal
- Department of Developmental Biology, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Samantha A. Morris
- Department of Developmental Biology, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine; 660 S. Euclid Avenue, St. Louis, MO 63110, USA
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227
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Diwanji R, O'Brien NA, Choi JE, Nguyen B, Laszewski T, Grauel AL, Yan Z, Xu X, Wu J, Ruddy DA, Piquet M, Pelletier MR, Savchenko A, Charette L, Rodrik-Outmezguine V, Baum J, Millholland JM, Wong CC, Martin AM, Dranoff G, Pruteanu-Malinici I, Cremasco V, Sabatos-Peyton C, Jayaraman P. Targeting the IL1β Pathway for Cancer Immunotherapy Remodels the Tumor Microenvironment and Enhances Antitumor Immune Responses. Cancer Immunol Res 2023; 11:777-791. [PMID: 37040466 DOI: 10.1158/2326-6066.cir-22-0290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 12/14/2022] [Accepted: 04/07/2023] [Indexed: 04/13/2023]
Abstract
High levels of IL1β can result in chronic inflammation, which in turn can promote tumor growth and metastasis. Inhibition of IL1β could therefore be a promising therapeutic option in the treatment of cancer. Here, the effects of IL1β blockade induced by the mAbs canakinumab and gevokizumab were evaluated alone or in combination with docetaxel, anti-programmed cell death protein 1 (anti-PD-1), anti-VEGFα, and anti-TGFβ treatment in syngeneic and humanized mouse models of cancers of different origin. Canakinumab and gevokizumab did not show notable efficacy as single-agent therapies; however, IL1β blockade enhanced the effectiveness of docetaxel and anti-PD-1. Accompanying these effects, blockade of IL1β alone or in combination induced significant remodeling of the tumor microenvironment (TME), with decreased numbers of immune suppressive cells and increased tumor infiltration by dendritic cells (DC) and effector T cells. Further investigation revealed that cancer-associated fibroblasts (CAF) were the cell type most affected by treatment with canakinumab or gevokizumab in terms of change in gene expression. IL1β inhibition drove phenotypic changes in CAF populations, particularly those with the ability to influence immune cell recruitment. These results suggest that the observed remodeling of the TME following IL1β blockade may stem from changes in CAF populations. Overall, the results presented here support the potential use of IL1β inhibition in cancer treatment. Further exploration in ongoing clinical studies will help identify the best combination partners for different cancer types, cancer stages, and lines of treatment.
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Affiliation(s)
- Rohan Diwanji
- Immuno Oncology, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Neil A O'Brien
- Division of Hematology/Oncology, Department of Medicine, Geffen School of Medicine at University of California, Los Angeles (UCLA), Los Angeles, California
| | - Jiyoung E Choi
- Immuno Oncology, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Beverly Nguyen
- Immuno Oncology, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Tyler Laszewski
- Immuno Oncology, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Angelo L Grauel
- Immuno Oncology, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Zheng Yan
- Oncology Translational Research, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Xin Xu
- Oncology Data Sciences, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Jincheng Wu
- Oncology Data Sciences, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - David A Ruddy
- Oncology, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Michelle Piquet
- Oncology, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Marc R Pelletier
- Oncology Translational Research, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | | | | | - Jason Baum
- Precision Medicine, Novartis Pharmaceuticals, Cambridge, Massachusetts
| | | | - Connie C Wong
- Precision Medicine, Novartis Pharmaceuticals, Cambridge, Massachusetts
| | - Anne-Marie Martin
- Precision Medicine, Novartis Pharmaceuticals, Cambridge, Massachusetts
| | - Glenn Dranoff
- Immuno Oncology, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - Viviana Cremasco
- Immuno Oncology, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - Pushpa Jayaraman
- Immuno Oncology, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
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228
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Carpenter ES, Elhossiny AM, Kadiyala P, Li J, McGue J, Griffith BD, Zhang Y, Edwards J, Nelson S, Lima F, Donahue KL, Du W, Bischoff AC, Alomari D, Watkoske HR, Mattea M, The S, Espinoza CE, Barrett M, Sonnenday CJ, Olden N, Chen CT, Peterson N, Gunchick V, Sahai V, Rao A, Bednar F, Shi J, Frankel TL, Pasca di Magliano M. Analysis of Donor Pancreata Defines the Transcriptomic Signature and Microenvironment of Early Neoplastic Lesions. Cancer Discov 2023; 13:1324-1345. [PMID: 37021392 PMCID: PMC10236159 DOI: 10.1158/2159-8290.cd-23-0013] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/03/2023] [Accepted: 03/15/2023] [Indexed: 04/07/2023]
Abstract
The adult healthy human pancreas has been poorly studied given the lack of indication to obtain tissue from the pancreas in the absence of disease and rapid postmortem degradation. We obtained pancreata from brain dead donors, thus avoiding any warm ischemia time. The 30 donors were diverse in age and race and had no known pancreas disease. Histopathologic analysis of the samples revealed pancreatic intraepithelial neoplasia (PanIN) lesions in most individuals irrespective of age. Using a combination of multiplex IHC, single-cell RNA sequencing, and spatial transcriptomics, we provide the first-ever characterization of the unique microenvironment of the adult human pancreas and of sporadic PanIN lesions. We compared healthy pancreata to pancreatic cancer and peritumoral tissue and observed distinct transcriptomic signatures in fibroblasts and, to a lesser extent, macrophages. PanIN epithelial cells from healthy pancreata were remarkably transcriptionally similar to cancer cells, suggesting that neoplastic pathways are initiated early in tumorigenesis. SIGNIFICANCE Precursor lesions to pancreatic cancer are poorly characterized. We analyzed donor pancreata and discovered that precursor lesions are detected at a much higher rate than the incidence of pancreatic cancer, setting the stage for efforts to elucidate the microenvironmental and cell-intrinsic factors that restrain or, conversely, promote malignant progression. See related commentary by Hoffman and Dougan, p. 1288. This article is highlighted in the In This Issue feature, p. 1275.
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Affiliation(s)
- Eileen S. Carpenter
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Ahmed M. Elhossiny
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Padma Kadiyala
- Immunology Graduate Program, University of Michigan, Ann Arbor, Michigan
| | - Jay Li
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan
| | - Jake McGue
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | | | - Yaqing Zhang
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | - Jacob Edwards
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | - Sarah Nelson
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | - Fatima Lima
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | | | - Wenting Du
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | | | - Danyah Alomari
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan
| | | | - Michael Mattea
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Stephanie The
- Cancer Data Science Resource, University of Michigan, Ann Arbor, Michigan
| | | | - Meredith Barrett
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | | | | | - Chin-Tung Chen
- Colorectal Cancer Research Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicole Peterson
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Valerie Gunchick
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Vaibhav Sahai
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Arvind Rao
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
- Cancer Data Science Resource, University of Michigan, Ann Arbor, Michigan
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - Filip Bednar
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | - Jiaqi Shi
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Timothy L. Frankel
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
- Immunology Graduate Program, University of Michigan, Ann Arbor, Michigan
| | - Marina Pasca di Magliano
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
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229
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Peeney D, Fan Y, Gurung S, Lazaroff C, Ratnayake S, Warner A, Karim B, Meerzaman D, Stetler-Stevenson WG. Whole organism profiling of the Timp gene family. Matrix Biol Plus 2023; 18:100132. [PMID: 37095886 PMCID: PMC10121480 DOI: 10.1016/j.mbplus.2023.100132] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/04/2023] Open
Abstract
Tissue inhibitor of metalloproteinases (TIMPs/Timps) are an endogenous family of widely expressed matrisome-associated proteins that were initially identified as inhibitors of matrix metalloproteinase activity (Metzincin family proteases). Consequently, TIMPs are often considered simply as protease inhibitors by many investigators. However, an evolving list of new metalloproteinase-independent functions for TIMP family members suggests that this concept is outdated. These novel TIMP functions include direct agonism/antagonism of multiple transmembrane receptors, as well as functional interactions with matrisome targets. While the family was fully identified over two decades ago, there has yet to be an in-depth study describing the expression of TIMPs in normal tissues of adult mammals. An understanding of the tissues and cell-types that express TIMPs 1 through 4, in both normal and disease states are important to contextualize the growing functional capabilities of TIMP proteins, which are often dismissed as non-canonical. Using publicly available single cell RNA sequencing data from the Tabula Muris Consortium, we analyzed approximately 100,000 murine cells across eighteen tissues from non-diseased organs, representing seventy-three annotated cell types, to define the diversity in Timp gene expression across healthy tissues. We describe the unique expression profiles across tissues and organ-specific cell types that all four Timp genes display. Within annotated cell-types, we identify clear and discrete cluster-specific patterns of Timp expression, particularly in cells of stromal and endothelial origins. RNA in-situ hybridization across four organs expands on the scRNA sequencing analysis, revealing novel compartments associated with individual Timp expression. These analyses emphasize a need for specific studies investigating the functional significance of Timp expression in the identified tissues and cell sub-types. This understanding of the tissues, specific cell types and microenvironment conditions in which Timp genes are expressed adds important physiological context to the growing array of novel functions for TIMP proteins.
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Affiliation(s)
- David Peeney
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Yu Fan
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institute of Health, Rockville, MD, USA
| | - Sadeechya Gurung
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Carolyn Lazaroff
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Shashikala Ratnayake
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institute of Health, Rockville, MD, USA
| | - Andrew Warner
- Molecular Histopathology Laboratory, Frederick National Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Baktiar Karim
- Molecular Histopathology Laboratory, Frederick National Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Daoud Meerzaman
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institute of Health, Rockville, MD, USA
| | - William G. Stetler-Stevenson
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
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230
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Ginebaugh SP, Hagner M, Ray A, Erzurum SC, Comhair SAA, Denlinger LC, Jarjour NN, Castro M, Woodruff PG, Christenson SA, Bleecker ER, Meyers DA, Hastie AT, Moore WC, Mauger DT, Israel E, Levy BD, Wenzel SE, Camiolo MJ. Bronchial epithelial cell transcriptional responses to inhaled corticosteroids dictate severe asthmatic outcomes. J Allergy Clin Immunol 2023; 151:1513-1524. [PMID: 36796454 PMCID: PMC10257752 DOI: 10.1016/j.jaci.2023.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 01/08/2023] [Accepted: 01/12/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Inhaled corticosteroids (CSs) are the backbone of asthma treatment, improving quality of life, exacerbation rates, and mortality. Although effective for most, a subset of patients with asthma experience CS-resistant disease despite receiving high-dose medication. OBJECTIVE We sought to investigate the transcriptomic response of bronchial epithelial cells (BECs) to inhaled CSs. METHODS Independent component analysis was performed on datasets, detailing the transcriptional response of BECs to CS treatment. The expression of these CS-response components was examined in 2 patient cohorts and investigated in relation to clinical parameters. Supervised learning was used to predict BEC CS responses using peripheral blood gene expression. RESULTS We identified a signature of CS response that was closely correlated with CS use in patients with asthma. Participants could be separated on the basis of CS-response genes into groups with high and low signature expression. Patients with low expression of CS-response genes, particularly those with a severe asthma diagnosis, showed worse lung function and quality of life. These individuals demonstrated enrichment for T-lymphocyte infiltration in endobronchial brushings. Supervised machine learning identified a 7-gene signature from peripheral blood that reliably identified patients with poor CS-response expression in BECs. CONCLUSIONS Loss of CS transcriptional responses within bronchial epithelium was related to impaired lung function and poor quality of life, particularly in patients with severe asthma. These individuals were identified using minimally invasive blood sampling, suggesting these findings may enable earlier triage to alternative treatments.
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Affiliation(s)
- Scott P Ginebaugh
- Integrative Systems Biology, University of Pittsburgh, Pittsburgh, Pa
| | | | - Anuradha Ray
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pa; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | | | | | - Loren C Denlinger
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Nizar N Jarjour
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Mario Castro
- University of Kansas School of Medicine, Kansas City, Mo
| | - Prescott G Woodruff
- University of California, San Francisco School of Medicine, San Francisco, Calif
| | | | - Eugene R Bleecker
- Division for Genetics, Genomics and Personalized Medicine, University of Arizona College of Medicine, Tucson, Ariz
| | - Deborah A Meyers
- Division for Genetics, Genomics and Personalized Medicine, University of Arizona College of Medicine, Tucson, Ariz
| | | | - Wendy C Moore
- Wake Forest University School of Medicine, Winston-Salem, NC
| | | | - Elliot Israel
- Department of Medicine, Divisions of Pulmonary & Critical Care Medicine & Allergy & Immunology, Brigham & Women's Hospital, Harvard Medical School, Boston, Mass
| | - Bruce D Levy
- Department of Medicine, Divisions of Pulmonary & Critical Care Medicine & Allergy & Immunology, Brigham & Women's Hospital, Harvard Medical School, Boston, Mass
| | - Sally E Wenzel
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pa; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pa; Department of Environmental Medicine and Occupational Health, Graduate School of Public Health, University of Pittsburgh School of Medicine, Pittsburgh, Pa
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231
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Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M, van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. An integrated cell atlas of the lung in health and disease. Nat Med 2023; 29:1563-1577. [PMID: 37291214 PMCID: PMC10287567 DOI: 10.1038/s41591-023-02327-2] [Citation(s) in RCA: 128] [Impact Index Per Article: 128.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 03/30/2023] [Indexed: 06/10/2023]
Abstract
Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1+ profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.
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Grants
- P50 AR080612 NIAMS NIH HHS
- R01 HL153375 NHLBI NIH HHS
- R01 HL127349 NHLBI NIH HHS
- U54 HL165443 NHLBI NIH HHS
- P01 HL107202 NHLBI NIH HHS
- U01 HL148856 NHLBI NIH HHS
- R21 HL156124 NHLBI NIH HHS
- U54 AG075931 NIA NIH HHS
- Wellcome Trust
- R01 HL146557 NHLBI NIH HHS
- R01 HL123766 NHLBI NIH HHS
- U01 HL148861 NHLBI NIH HHS
- R01 HL141852 NHLBI NIH HHS
- R01 ES034350 NIEHS NIH HHS
- UL1 TR001863 NCATS NIH HHS
- R01 HL126176 NHLBI NIH HHS
- R21 HL161760 NHLBI NIH HHS
- R01 HL145372 NHLBI NIH HHS
- P01 AG049665 NIA NIH HHS
- K12 HD105271 NICHD NIH HHS
- U19 AI135964 NIAID NIH HHS
- P30 CA008748 NCI NIH HHS
- R01 HL142568 NHLBI NIH HHS
- R01 HL153312 NHLBI NIH HHS
- U54 AG079754 NIA NIH HHS
- R56 HL157632 NHLBI NIH HHS
- R01 HL158139 NHLBI NIH HHS
- R01 HL135156 NHLBI NIH HHS
- R01 HL153045 NHLBI NIH HHS
- U54 HL145608 NHLBI NIH HHS
- P50 AR060780 NIAMS NIH HHS
- R01 HL128439 NHLBI NIH HHS
- R01 HL146519 NHLBI NIH HHS
- R01 HL117004 NHLBI NIH HHS
- R01 HL068702 NHLBI NIH HHS
- U01 HL145567 NHLBI NIH HHS
- P01 HL132821 NHLBI NIH HHS
- MR/R015635/1 Medical Research Council
- R01 MD010443 NIMHD NIH HHS
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” NIH 1U54HL145608-01 CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- ESPOD fellowship of EMBL-EBI and Sanger Institute
- 3IA Cote d’Azur PhD program
- The Ministry of Economic Affairs and Climate Policy by means of the PPP
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- Joachim Herz Stiftung (Joachim Herz Foundation)
- P50 AR060780-06A1
- University College London, Birkbeck MRC Doctoral Training Programme
- Jikei University School of Medicine (Jikei University)
- 5R01HL14254903, 4UH3CA25513503
- R01HL127349, R01HL141852, U01HL145567 and CZI
- MRC Clinician Scientist Fellowship (MR/W00111X/1)
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” 2R01HL068702
- R01 HL135156, R01 MD010443, R01 HL128439, P01 HL132821, P01 HL107202, R01 HL117004, and DOD Grant W81WH-16-2-0018
- HL142568 and HL14507 from the NHLBI
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0”, 2R01HL068702
- Wellcome (WT211276/Z/18/Z) Sanger core grant WT206194 CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- R21HL156124, R56HL157632, and R21HL161760
- CZI, 5U01HL148856
- CZI, 5U01HL148856, R01 HL153045
- U.S. Department of Defense (United States Department of Defense)
- The National Institute of Health R01HL145372
- Fondation pour la Recherche Médicale (Foundation for Medical Research in France)
- Conseil Départemental des Alpes Maritimes
- Inserm Cross-cutting Scientific Program HuDeCA 2018, ANR SAHARRA (ANR-19-CE14–0027), ANR-19-P3IA-0002–3IA, the National Infrastructure France Génomique (ANR-10-INBS-09-03), PPIA 4D-OMICS (21-ESRE-0052), and the Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0”.
- Wellcome Trust (Wellcome)
- Sanger core grant WT206194 Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- Doris Duke Charitable Foundation (DDCF)
- The National Institute of Health R01HL145372 Department of Defense W81XWH-19-1-0416
- The National Institute of Health R01HL146557 and R01HL153375 and funds from Chan Zuckerberg Initiative - Human Lung Cell Atlas-pilot award
- 1U54HL145608-01
- CZI Deep Visual Proteomics
- 1U54HL145608-01, U01HL148861-03
- 1) the Chan Zuckerberg Initiative, LLC Seed Network grant CZF2019-002438 “Lung Cell Atlas 1.0”; 2) R01 HL153312; 3) U19 AI135964; 4) P01 AG049665
- Netherlands Lung Foundation project nos. 5.1.14.020 and 4.1.18.226, LLC Seed Network grant CZF2019-002438 “Lung Cell Atlas 1.0”
- grant number 2019-002438 from the Chan Zuckerberg Foundation, by the Helmholtz Association’s Initiative and Networking Fund through Helmholtz AI [ZT-I-PF-5-01] and by the Bavarian Ministry of Science and the Arts in the framework of the Bavarian Research Association “ForInter” (Interaction of human brain cells)
- 1 U01 HL14555-01, R01 HL123766-04
- NIH U54 AG075931, 5R01 HL146519
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Affiliation(s)
- Lisa Sikkema
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Ciro Ramírez-Suástegui
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Daniel C Strobl
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Tessa E Gillett
- Experimental Pulmonary and Inflammatory Research, Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Luke Zappia
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | | | - Nikolay S Markov
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Laure-Emmanuelle Zaragosi
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Yuge Ji
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Meshal Ansari
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Marie-Jeanne Arguel
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Leonie Apperloo
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Martin Banchero
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Christophe Bécavin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Marijn Berg
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Antoine Collin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
- 3IA Côte d'Azur, Nice, France
| | - Aurore C A Gay
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Janine Gote-Schniering
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Baharak Hooshiar Kashani
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Kemal Inecik
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Manu Jain
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Theodore S Kapellos
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Tessa M Kole
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sylvie Leroy
- Pulmonology Department, Fédération Hospitalo-Universitaire OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Christoph H Mayr
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | | | | | - Lance Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J Taylor
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Chuan Xu
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Linh T Bui
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Carlo De Donno
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Leander Dony
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry and International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Alen Faiz
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- School of Life Sciences, Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Sydney, Australia
| | - Minzhe Guo
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, US
| | | | - Lukas Heumos
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Ni Huang
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Ignacio L Ibarra
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Nathan D Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Preetish Kadur Lakshminarasimha Murthy
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Pharmacology and Regenerative Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Mohammad Lotfollahi
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carlos Talavera-López
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, Klinikum der Lüdwig-Maximilians-Universität, Munich, Germany
| | - Kyle J Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kaylee B Worlock
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Masahiro Yoshida
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Tushar J Desai
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mark A Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marko Z Nikolic
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Joseph E Powell
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Mauricio Rojas
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cellular and Tissue Genomics, Genentech, South San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Department of Pediatrics, National Jewish Health, Denver, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Dean Sheppard
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Douglas P Shepherd
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Don D Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Whitsett
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yan Xu
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
- 3IA Côte d'Azur, Nice, France
| | - Thu Elizabeth Duong
- Department of Pediatrics, Division of Respiratory Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Christine S Falk
- Institute for Transplant Immunology, Hannover Medical School, Hannover, Germany
| | | | - Jonathan A Kropski
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Dana Pe'er
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Herbert B Schiller
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | | | - Joachim L Schultze
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen and University of Bonn, Bonn, Germany
| | - Sara A Teichmann
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Malte D Luecken
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany.
| | - Fabian J Theis
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
- Department of Mathematics, Technical University of Munich, Garching, Germany.
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232
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Glasner A, Rose SA, Sharma R, Gudjonson H, Chu T, Green JA, Rampersaud S, Valdez IK, Andretta ES, Dhillon BS, Schizas M, Dikiy S, Mendoza A, Hu W, Wang ZM, Chaudhary O, Xu T, Mazutis L, Rizzuto G, Quintanal-Villalonga A, Manoj P, de Stanchina E, Rudin CM, Pe'er D, Rudensky AY. Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs new combination cancer therapy strategies. Nat Immunol 2023; 24:1020-1035. [PMID: 37127830 PMCID: PMC10232368 DOI: 10.1038/s41590-023-01504-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
While regulatory T (Treg) cells are traditionally viewed as professional suppressors of antigen presenting cells and effector T cells in both autoimmunity and cancer, recent findings of distinct Treg cell functions in tissue maintenance suggest that their regulatory purview extends to a wider range of cells and is broader than previously assumed. To elucidate tumoral Treg cell 'connectivity' to diverse tumor-supporting accessory cell types, we explored immediate early changes in their single-cell transcriptomes upon punctual Treg cell depletion in experimental lung cancer and injury-induced inflammation. Before any notable T cell activation and inflammation, fibroblasts, endothelial and myeloid cells exhibited pronounced changes in their gene expression in both cancer and injury settings. Factor analysis revealed shared Treg cell-dependent gene programs, foremost, prominent upregulation of VEGF and CCR2 signaling-related genes upon Treg cell deprivation in either setting, as well as in Treg cell-poor versus Treg cell-rich human lung adenocarcinomas. Accordingly, punctual Treg cell depletion combined with short-term VEGF blockade showed markedly improved control of PD-1 blockade-resistant lung adenocarcinoma progression in mice compared to the corresponding monotherapies, highlighting a promising factor-based querying approach to elucidating new rational combination treatments of solid organ cancers.
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Affiliation(s)
- Ariella Glasner
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel A Rose
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roshan Sharma
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Herman Gudjonson
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tinyi Chu
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jesse A Green
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sham Rampersaud
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Izabella K Valdez
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emma S Andretta
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bahawar S Dhillon
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michail Schizas
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stanislav Dikiy
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alejandra Mendoza
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Hu
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhong-Min Wang
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ojasvi Chaudhary
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tianhao Xu
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Linas Mazutis
- Institute of Biotechnology, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Gabrielle Rizzuto
- Human Oncology & Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology & Laboratory Medicine, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Parvathy Manoj
- Department of Medicine, Thoracic Oncology Service, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Thoracic Oncology Service, New York, NY, USA
| | - Dana Pe'er
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Alexander Y Rudensky
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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233
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Masuda S, Matsuura K, Shimizu T. GATA6 regulates anti-angiogenic properties in human cardiac fibroblasts via modulating LYPD1 expression. Regen Ther 2023; 23:8-16. [DOI: 10.1016/j.reth.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/10/2023] [Accepted: 02/22/2023] [Indexed: 03/16/2023] Open
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234
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Hu KH, Kuhn NF, Courau T, Tsui J, Samad B, Ha P, Kratz JR, Combes AJ, Krummel MF. Transcriptional space-time mapping identifies concerted immune and stromal cell patterns and gene programs in wound healing and cancer. Cell Stem Cell 2023; 30:885-903.e10. [PMID: 37267918 PMCID: PMC10843988 DOI: 10.1016/j.stem.2023.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 03/13/2023] [Accepted: 05/02/2023] [Indexed: 06/04/2023]
Abstract
Tissue repair responses in metazoans are highly coordinated by different cell types over space and time. However, comprehensive single-cell-based characterization covering this coordination is lacking. Here, we captured transcriptional states of single cells over space and time during skin wound closure, revealing choreographed gene-expression profiles. We identified shared space-time patterns of cellular and gene program enrichment, which we call multicellular "movements" spanning multiple cell types. We validated some of the discovered space-time movements using large-volume imaging of cleared wounds and demonstrated the value of this analysis to predict "sender" and "receiver" gene programs in macrophages and fibroblasts. Finally, we tested the hypothesis that tumors are like "wounds that never heal" and found conserved wound healing movements in mouse melanoma and colorectal tumor models, as well as human tumor samples, revealing fundamental multicellular units of tissue biology for integrative studies.
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Affiliation(s)
- Kenneth H Hu
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Nicholas F Kuhn
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tristan Courau
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jessica Tsui
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Otolaryngology Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bushra Samad
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Patrick Ha
- Department of Otolaryngology Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Johannes R Kratz
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexis J Combes
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew F Krummel
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA.
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235
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Dolivo DM, Rodrigues AE, Mustoe TA, Galiano RD, Hong SJ. Comment on "Scar-Degrading Endothelial Cells as a Treatment for Advanced Liver Fibrosis". ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207396. [PMID: 36932884 DOI: 10.1002/advs.202207396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/19/2023] [Indexed: 06/15/2023]
Abstract
Cellular therapies show promise for treatment of fibrosis. A recent article presents a strategy and proof-of-concept for delivering stimulated cells to degrade hepatic collagen in vivo. A discussion is presented surrounding the strengths of this approach and the potential to generalize this strategy of optimizing cell sources and activation stimuli to treat other types of fibrosis.
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Affiliation(s)
- David M Dolivo
- Division of Plastic Surgery, Department of Surgery, Northwestern University-Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Adrian E Rodrigues
- Division of Plastic Surgery, Department of Surgery, Northwestern University-Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Thomas A Mustoe
- Division of Plastic Surgery, Department of Surgery, Northwestern University-Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Robert D Galiano
- Division of Plastic Surgery, Department of Surgery, Northwestern University-Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Seok Jong Hong
- Division of Plastic Surgery, Department of Surgery, Northwestern University-Feinberg School of Medicine, Chicago, IL, 60611, USA
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236
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Ortiz-Muñoz G, Brown M, Carbone CB, Pechuan-Jorge X, Rouilly V, Lindberg H, Ritter AT, Raghupathi G, Sun Q, Nicotra T, Mantri SR, Yang A, Doerr J, Nagarkar D, Darmanis S, Haley B, Mariathasan S, Wang Y, Gomez-Roca C, de Andrea CE, Spigel D, Wu T, Delamarre L, Schöneberg J, Modrusan Z, Price R, Turley SJ, Mellman I, Moussion C. In situ tumour arrays reveal early environmental control of cancer immunity. Nature 2023:10.1038/s41586-023-06132-2. [PMID: 37258670 DOI: 10.1038/s41586-023-06132-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
The immune phenotype of a tumour is a key predictor of its response to immunotherapy1-4. Patients who respond to checkpoint blockade generally present with immune-inflamed5-7 tumours that are highly infiltrated by T cells. However, not all inflamed tumours respond to therapy, and even lower response rates occur among tumours that lack T cells (immune desert) or that spatially exclude T cells to the periphery of the tumour lesion (immune excluded)8. Despite the importance of these tumour immune phenotypes in patients, little is known about their development, heterogeneity or dynamics owing to the technical difficulty of tracking these features in situ. Here we introduce skin tumour array by microporation (STAMP)-a preclinical approach that combines high-throughput time-lapse imaging with next-generation sequencing of tumour arrays. Using STAMP, we followed the development of thousands of arrayed tumours in vivo to show that tumour immune phenotypes and outcomes vary between adjacent tumours and are controlled by local factors within the tumour microenvironment. Particularly, the recruitment of T cells by fibroblasts and monocytes into the tumour core was supportive of T cell cytotoxic activity and tumour rejection. Tumour immune phenotypes were dynamic over time and an early conversion to an immune-inflamed phenotype was predictive of spontaneous or therapy-induced tumour rejection. Thus, STAMP captures the dynamic relationships of the spatial, cellular and molecular components of tumour rejection and has the potential to translate therapeutic concepts into successful clinical strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Carlos Gomez-Roca
- IUCT, Institut Universitaire du Cancer de Toulouse, Toulouse, France
| | | | - David Spigel
- Sarah Cannon Research Institute, Nashville, TN, USA
| | - Thomas Wu
- Genentech, South San Francisco, CA, USA
| | | | - Johannes Schöneberg
- Department of Pharmacology, UCSD, San Diego, CA, USA
- Department of Chemistry & Biochemistry, UCSD, San Diego, CA, USA
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237
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Adler M, Moriel N, Goeva A, Avraham-Davidi I, Mages S, Adams TS, Kaminski N, Macosko EZ, Regev A, Medzhitov R, Nitzan M. Emergence of division of labor in tissues through cell interactions and spatial cues. Cell Rep 2023; 42:112412. [PMID: 37086403 PMCID: PMC10242439 DOI: 10.1016/j.celrep.2023.112412] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/26/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023] Open
Abstract
Most cell types in multicellular organisms can perform multiple functions. However, not all functions can be optimally performed simultaneously by the same cells. Functions incompatible at the level of individual cells can be performed at the cell population level, where cells divide labor and specialize in different functions. Division of labor can arise due to instruction by tissue environment or through self-organization. Here, we develop a computational framework to investigate the contribution of these mechanisms to division of labor within a cell-type population. By optimizing collective cellular task performance under trade-offs, we find that distinguishable expression patterns can emerge from cell-cell interactions versus instructive signals. We propose a method to construct ligand-receptor networks between specialist cells and use it to infer division-of-labor mechanisms from single-cell RNA sequencing (RNA-seq) and spatial transcriptomics data of stromal, epithelial, and immune cells. Our framework can be used to characterize the complexity of cell interactions within tissues.
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Affiliation(s)
- Miri Adler
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Tananbaum Center for Theoretical and Analytical Human Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Noa Moriel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Aleksandrina Goeva
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Inbal Avraham-Davidi
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Simon Mages
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Evan Z Macosko
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Massachusetts General Hospital, Department of Psychiatry, Boston, MA, USA
| | - Aviv Regev
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Ruslan Medzhitov
- Tananbaum Center for Theoretical and Analytical Human Biology, Yale University School of Medicine, New Haven, CT, USA; Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
| | - Mor Nitzan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, Israel; Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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238
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Sitnik KM, Krstanović F, Gödecke N, Rand U, Kubsch T, Maaß H, Kim Y, Brizić I, Čičin-Šain L. Fibroblasts are a site of murine cytomegalovirus lytic replication and Stat1-dependent latent persistence in vivo. Nat Commun 2023; 14:3087. [PMID: 37248241 DOI: 10.1038/s41467-023-38449-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 04/29/2023] [Indexed: 05/31/2023] Open
Abstract
To date, no herpesvirus has been shown to latently persist in fibroblastic cells. Here, we show that murine cytomegalovirus, a β-herpesvirus, persists for the long term and across organs in PDGFRα-positive fibroblastic cells, with similar or higher genome loads than in the previously known sites of murine cytomegalovirus latency. Whereas murine cytomegalovirus gene transcription in PDGFRα-positive fibroblastic cells is almost completely silenced at 5 months post-infection, these cells give rise to reactivated virus ex vivo, arguing that they support latent murine cytomegalovirus infection. Notably, PDGFRα-positive fibroblastic cells also support productive virus replication during primary murine cytomegalovirus infection. Mechanistically, Stat1-deficiency promotes lytic infection but abolishes latent persistence of murine cytomegalovirus in PDGFRα-positive fibroblastic cells in vivo. In sum, fibroblastic cells have a dual role as a site of lytic murine cytomegalovirus replication and a reservoir of latent murine cytomegalovirus in vivo and STAT1 is required for murine cytomegalovirus latent persistence in vivo.
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Affiliation(s)
- Katarzyna M Sitnik
- Department of Viral Immunology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany.
- Department of Biomedical Sciences, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
| | - Fran Krstanović
- Center for Proteomics, Faculty of Medicine, University of Rijeka, 51000, Rijeka, Croatia
| | - Natascha Gödecke
- Department of Viral Immunology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Ulfert Rand
- Department of Viral Immunology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Tobias Kubsch
- Department of Viral Immunology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Henrike Maaß
- Department of Viral Immunology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Yeonsu Kim
- Department of Viral Immunology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Ilija Brizić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, 51000, Rijeka, Croatia
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany.
- Centre for Individualized Infection Medicine, a joint venture of HZI and MHH, 30625, Hannover, Germany.
- German Centre for Infection Research (DZIF), Hannover-Braunschweig site, 38124, Braunschweig, Germany.
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239
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Delcroix V, Mauduit O, Lee HS, Ivanova A, Umazume T, Knox SM, de Paiva CS, Dartt DA, Makarenkova HP. The First Transcriptomic Atlas of the Adult Lacrimal Gland Reveals Epithelial Complexity and Identifies Novel Progenitor Cells in Mice. Cells 2023; 12:1435. [PMID: 37408269 PMCID: PMC10216974 DOI: 10.3390/cells12101435] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 07/07/2023] Open
Abstract
The lacrimal gland (LG) secretes aqueous tears. Previous studies have provided insights into the cell lineage relationships during tissue morphogenesis. However, little is known about the cell types composing the adult LG and their progenitors. Using scRNAseq, we established the first comprehensive cell atlas of the adult mouse LG to investigate the cell hierarchy, its secretory repertoire, and the sex differences. Our analysis uncovered the complexity of the stromal landscape. Epithelium subclustering revealed myoepithelial cells, acinar subsets, and two novel acinar subpopulations: Tfrchi and Car6hi cells. The ductal compartment contained Wfdc2+ multilayered ducts and an Ltf+ cluster formed by luminal and intercalated duct cells. Kit+ progenitors were identified as: Krt14+ basal ductal cells, Aldh1a1+ cells of Ltf+ ducts, and Sox10+ cells of the Car6hi acinar and Ltf+ epithelial clusters. Lineage tracing experiments revealed that the Sox10+ adult populations contribute to the myoepithelial, acinar, and ductal lineages. Using scRNAseq data, we found that the postnatally developing LG epithelium harbored key features of putative adult progenitors. Finally, we showed that acinar cells produce most of the sex-biased lipocalins and secretoglobins detected in mouse tears. Our study provides a wealth of new data on LG maintenance and identifies the cellular origin of sex-biased tear components.
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Affiliation(s)
- Vanessa Delcroix
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA; (V.D.); (H.S.L.); (A.I.); (T.U.)
| | - Olivier Mauduit
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA; (V.D.); (H.S.L.); (A.I.); (T.U.)
| | - Hyun Soo Lee
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA; (V.D.); (H.S.L.); (A.I.); (T.U.)
- Department of Ophthalmology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Anastasiia Ivanova
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA; (V.D.); (H.S.L.); (A.I.); (T.U.)
| | - Takeshi Umazume
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA; (V.D.); (H.S.L.); (A.I.); (T.U.)
| | - Sarah M. Knox
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA 94143, USA;
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Cintia S. de Paiva
- The Ocular Surface Center, Department of Ophthalmology, Cullen Eye Institute, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Darlene A. Dartt
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA;
| | - Helen P. Makarenkova
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA; (V.D.); (H.S.L.); (A.I.); (T.U.)
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240
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Faust HJ, Cheng TY, Korsunsky I, Watts GFM, Gal-Oz ST, Trim W, Kongthong K, Jonsson AH, Simmons DP, Zhang F, Padera R, Chubinskaya S, Wei K, Raychaudhuri S, Lynch L, Moody DB, Brenner MB. Adipocytes regulate fibroblast function, and their loss contributes to fibroblast dysfunction in inflammatory diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.540975. [PMID: 37292637 PMCID: PMC10245775 DOI: 10.1101/2023.05.16.540975] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fibroblasts play critical roles in tissue homeostasis, but in pathologic states can drive fibrosis, inflammation, and tissue destruction. In the joint synovium, fibroblasts provide homeostatic maintenance and lubrication. Little is known about what regulates the homeostatic functions of fibroblasts in healthy conditions. We performed RNA sequencing of healthy human synovial tissue and identified a fibroblast gene expression program characterized by enhanced fatty acid metabolism and lipid transport. We found that fat-conditioned media reproduces key aspects of the lipid-related gene signature in cultured fibroblasts. Fractionation and mass spectrometry identified cortisol in driving the healthy fibroblast phenotype, confirmed using glucocorticoid receptor gene ( NR3C1 ) deleted cells. Depletion of synovial adipocytes in mice resulted in loss of the healthy fibroblast phenotype and revealed adipocytes as a major contributor to active cortisol generation via Hsd11 β 1 expression. Cortisol signaling in fibroblasts mitigated matrix remodeling induced by TNFα- and TGFβ, while stimulation with these cytokines repressed cortisol signaling and adipogenesis. Together, these findings demonstrate the importance of adipocytes and cortisol signaling in driving the healthy synovial fibroblast state that is lost in disease.
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241
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De Martin A, Stanossek Y, Lütge M, Cadosch N, Onder L, Cheng HW, Brandstadter JD, Maillard I, Stoeckli SJ, Pikor NB, Ludewig B. PI16 + reticular cells in human palatine tonsils govern T cell activity in distinct subepithelial niches. Nat Immunol 2023:10.1038/s41590-023-01502-4. [PMID: 37202490 DOI: 10.1038/s41590-023-01502-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 04/03/2023] [Indexed: 05/20/2023]
Abstract
Fibroblastic reticular cells (FRCs) direct the interaction and activation of immune cells in discrete microenvironments of lymphoid organs. Despite their important role in steering innate and adaptive immunity, the age- and inflammation-associated changes in the molecular identity and functional properties of human FRCs have remained largely unknown. Here, we show that human tonsillar FRCs undergo dynamic reprogramming during life and respond vigorously to inflammatory perturbation in comparison to other stromal cell types. The peptidase inhibitor 16 (PI16)-expressing reticular cell (PI16+ RC) subset of adult tonsils exhibited the strongest inflammation-associated structural remodeling. Interactome analysis combined with ex vivo and in vitro validation revealed that T cell activity within subepithelial niches is controlled by distinct molecular pathways during PI16+ RC-lymphocyte interaction. In sum, the topological and molecular definition of the human tonsillar stromal cell landscape reveals PI16+ RCs as a specialized FRC niche at the core of mucosal immune responses in the oropharynx.
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Affiliation(s)
- Angelina De Martin
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Yves Stanossek
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Department of Otorhinolaryngology, Head and Neck Surgery, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Mechthild Lütge
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Nadine Cadosch
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Lucas Onder
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Hung-Wei Cheng
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Joshua D Brandstadter
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ivan Maillard
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sandro J Stoeckli
- Department of Otorhinolaryngology, Head and Neck Surgery, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Natalia B Pikor
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Burkhard Ludewig
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.
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242
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Martinez-Zubiaurre I, Hellevik T. Cancer-associated fibroblasts in radiotherapy: Bystanders or protagonists? Cell Commun Signal 2023; 21:108. [PMID: 37170098 PMCID: PMC10173661 DOI: 10.1186/s12964-023-01093-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/26/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND The primary goal of radiotherapy (RT) is to induce cellular damage on malignant cells; however, it is becoming increasingly recognized the important role played by the tumor microenvironment (TME) in therapy outcomes. Therapeutic irradiation of tumor lesions provokes profound cellular and biological reconfigurations within the TME that ultimately may influence the fate of the therapy. MAIN CONTENT Cancer-associated fibroblasts (CAFs) are known to participate in all stages of cancer progression and are increasingly acknowledged to contribute to therapy resistance. Accumulated evidence suggests that, upon radiation, fibroblasts/CAFs avoid cell death but instead enter a permanent senescent state, which in turn may influence the behavior of tumor cells and other components of the TME. Despite the proposed participation of senescent fibroblasts on tumor radioprotection, it is still incompletely understood the impact that RT has on CAFs and the ultimate role that irradiated CAFs have on therapy outcomes. Some of the current controversies may emerge from generalizing observations obtained using normal fibroblasts and CAFs, which are different cell entities that may respond differently to radiation exposure. CONCLUSION In this review we present current knowledge on the field of CAFs role in radiotherapy; we discuss the potential tumorigenic functions of radiation-induced senescent fibroblasts and CAFs and we make an effort to integrate the knowledge emerging from preclinical experimentation with observations from the clinics. Video Abstract.
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Affiliation(s)
- Inigo Martinez-Zubiaurre
- Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Postbox 6050, 9037, Langnes, Tromsö, Norway.
| | - Turid Hellevik
- Department of Radiation Oncology, University Hospital of North Norway, Postbox 100, 9038, Tromsö, Norway
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Cadinu P, Sivanathan KN, Misra A, Xu RJ, Mangani D, Yang E, Rone JM, Tooley K, Kye YC, Bod L, Geistlinger L, Lee T, Ono N, Wang G, Sanmarco L, Quintana FJ, Anderson AC, Kuchroo VK, Moffitt JR, Nowarski R. Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539701. [PMID: 37214800 PMCID: PMC10197602 DOI: 10.1101/2023.05.08.539701] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Gut inflammation involves contributions from immune and non-immune cells, whose interactions are shaped by the spatial organization of the healthy gut and its remodeling during inflammation. The crosstalk between fibroblasts and immune cells is an important axis in this process, but our understanding has been challenged by incomplete cell-type definition and biogeography. To address this challenge, we used MERFISH to profile the expression of 940 genes in 1.35 million cells imaged across the onset and recovery from a mouse colitis model. We identified diverse cell populations; charted their spatial organization; and revealed their polarization or recruitment in inflammation. We found a staged progression of inflammation-associated tissue neighborhoods defined, in part, by multiple inflammation-associated fibroblasts, with unique expression profiles, spatial localization, cell-cell interactions, and healthy fibroblast origins. Similar signatures in ulcerative colitis suggest conserved human processes. Broadly, we provide a framework for understanding inflammation-induced remodeling in the gut and other tissues.
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Affiliation(s)
- Paolo Cadinu
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
- These authors contributed equally
| | - Kisha N. Sivanathan
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
- These authors contributed equally
| | - Aditya Misra
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Rosalind J. Xu
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138 USA
| | - Davide Mangani
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Evan Yang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Joseph M. Rone
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Katherine Tooley
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yoon-Chul Kye
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Lloyd Bod
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ludwig Geistlinger
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA 02115, USA
| | - Tyrone Lee
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA 02115, USA
| | - Noriaki Ono
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX 77030 USA
| | - Gang Wang
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Liliana Sanmarco
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Francisco J. Quintana
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| | - Ana C. Anderson
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| | - Vijay K. Kuchroo
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| | - Jeffrey R. Moffitt
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| | - Roni Nowarski
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
- Lead contact
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244
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Brichkina A, Polo P, Sharma SD, Visestamkul N, Lauth M. A Quick Guide to CAF Subtypes in Pancreatic Cancer. Cancers (Basel) 2023; 15:cancers15092614. [PMID: 37174079 PMCID: PMC10177377 DOI: 10.3390/cancers15092614] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/21/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Pancreatic cancer represents one of the most desmoplastic malignancies and is characterized by an extensive deposition of extracellular matrix. The latter is provided by activated cancer-associated fibroblasts (CAFs), which are abundant cells in the pancreatic tumor microenvironment. Many recent studies have made it clear that CAFs are not a singular cellular entity but represent a multitude of potentially dynamic subgroups that affect tumor biology at several levels. As mentioned before, CAFs significantly contribute to the fibrotic reaction and the biomechanical properties of the tumor, but they can also modulate the local immune environment and the response to targeted, chemo or radiotherapy. As the number of known and emerging CAF subgroups is steadily increasing, it is becoming increasingly difficult to keep up with these developments and to clearly discriminate the cellular subsets identified so far. This review aims to provide a helpful overview that enables readers to quickly familiarize themselves with field of CAF heterogeneity and to grasp the phenotypic, functional and therapeutic distinctions of the various stromal subpopulations.
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Affiliation(s)
- Anna Brichkina
- Center for Tumor and Immune Biology, Clinics for Gastroenterology, Endocrinology and Metabolism, Philipps University Marburg, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Pierfrancesco Polo
- Center for Tumor and Immune Biology, Clinics for Gastroenterology, Endocrinology and Metabolism, Philipps University Marburg, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Shrey Dharamvir Sharma
- Center for Tumor and Immune Biology, Clinics for Gastroenterology, Endocrinology and Metabolism, Philipps University Marburg, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Nico Visestamkul
- Center for Tumor and Immune Biology, Clinics for Gastroenterology, Endocrinology and Metabolism, Philipps University Marburg, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Matthias Lauth
- Center for Tumor and Immune Biology, Clinics for Gastroenterology, Endocrinology and Metabolism, Philipps University Marburg, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
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245
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Miranda AMA, Janbandhu V, Maatz H, Kanemaru K, Cranley J, Teichmann SA, Hübner N, Schneider MD, Harvey RP, Noseda M. Single-cell transcriptomics for the assessment of cardiac disease. Nat Rev Cardiol 2023; 20:289-308. [PMID: 36539452 DOI: 10.1038/s41569-022-00805-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/03/2022] [Indexed: 12/24/2022]
Abstract
Cardiovascular disease is the leading cause of death globally. An advanced understanding of cardiovascular disease mechanisms is required to improve therapeutic strategies and patient risk stratification. State-of-the-art, large-scale, single-cell and single-nucleus transcriptomics facilitate the exploration of the cardiac cellular landscape at an unprecedented level, beyond its descriptive features, and can further our understanding of the mechanisms of disease and guide functional studies. In this Review, we provide an overview of the technical challenges in the experimental design of single-cell and single-nucleus transcriptomics studies, as well as a discussion of the type of inferences that can be made from the data derived from these studies. Furthermore, we describe novel findings derived from transcriptomics studies for each major cardiac cell type in both health and disease, and from development to adulthood. This Review also provides a guide to interpreting the exhaustive list of newly identified cardiac cell types and states, and highlights the consensus and discordances in annotation, indicating an urgent need for standardization. We describe advanced applications such as integration of single-cell data with spatial transcriptomics to map genes and cells on tissue and define cellular microenvironments that regulate homeostasis and disease progression. Finally, we discuss current and future translational and clinical implications of novel transcriptomics approaches, and provide an outlook of how these technologies will change the way we diagnose and treat heart disease.
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Affiliation(s)
| | - Vaibhao Janbandhu
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Henrike Maatz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Kazumasa Kanemaru
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - James Cranley
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sarah A Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Deptartment of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Charite-Universitätsmedizin Berlin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | | | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, UK.
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246
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Sbierski-Kind J, Cautivo KM, Wagner JC, Dahlgren MW, Nilsson J, Krasilnikov M, Mroz NM, Lizama CO, Gan AL, Matatia PR, Taruselli MT, Chang AA, Caryotakis S, O'Leary CE, Kotas M, Mattis AN, Peng T, Locksley RM, Molofsky AB. Group 2 innate lymphoid cells constrain type 3/17 lymphocytes in shared stromal niches to restrict liver fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.537913. [PMID: 37163060 PMCID: PMC10168323 DOI: 10.1101/2023.04.26.537913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Group 2 innate lymphoid cells (ILC2s) cooperate with adaptive Th2 cells as key organizers of tissue type 2 immune responses, while a spectrum of innate and adaptive lymphocytes coordinate early type 3/17 immunity. Both type 2 and type 3/17 lymphocyte associated cytokines are linked to tissue fibrosis, but how their dynamic and spatial topographies may direct beneficial or pathologic organ remodelling is unclear. Here we used volumetric imaging in models of liver fibrosis, finding accumulation of periportal and fibrotic tract IL-5 + lymphocytes, predominantly ILC2s, in close proximity to expanded type 3/17 lymphocytes and IL-33 high niche fibroblasts. Ablation of IL-5 + lymphocytes worsened carbon tetrachloride-and bile duct ligation-induced liver fibrosis with increased niche IL-17A + type 3/17 lymphocytes, predominantly γδ T cells. In contrast, concurrent ablation of IL-5 + and IL-17A + lymphocytes reduced this progressive liver fibrosis, suggesting a cross-regulation of type 2 and type 3 lymphocytes at specialized fibroblast niches that tunes hepatic fibrosis.
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247
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Pærregaard SI, Wulff L, Schussek S, Niss K, Mörbe U, Jendholm J, Wendland K, Andrusaite AT, Brulois KF, Nibbs RJB, Sitnik K, Mowat AM, Butcher EC, Brunak S, Agace WW. The small and large intestine contain related mesenchymal subsets that derive from embryonic Gli1 + precursors. Nat Commun 2023; 14:2307. [PMID: 37085516 PMCID: PMC10121680 DOI: 10.1038/s41467-023-37952-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 04/06/2023] [Indexed: 04/23/2023] Open
Abstract
The intestinal lamina propria contains a diverse network of fibroblasts that provide key support functions to cells within their local environment. Despite this, our understanding of the diversity, location and ontogeny of fibroblasts within and along the length of the intestine remains incomplete. Here we show that the small and large intestinal lamina propria contain similar fibroblast subsets that locate in specific anatomical niches. Nevertheless, we find that the transcriptional profile of similar fibroblast subsets differs markedly between the small intestine and colon suggesting region specific functions. We perform in vivo transplantation and lineage-tracing experiments to demonstrate that adult intestinal fibroblast subsets, smooth muscle cells and pericytes derive from Gli1-expressing precursors present in embryonic day 12.5 intestine. Trajectory analysis of single cell RNA-seq datasets of E12.5 and adult mesenchymal cells suggest that adult smooth muscle cells and fibroblasts derive from distinct embryonic intermediates and that adult fibroblast subsets develop in a linear trajectory from CD81+ fibroblasts. Finally, we provide evidence that colonic subepithelial PDGFRαhi fibroblasts comprise several functionally distinct populations that originate from an Fgfr2-expressing fibroblast intermediate. Our results provide insights into intestinal stromal cell diversity, location, function, and ontogeny, with implications for intestinal development and homeostasis.
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Affiliation(s)
- Simone Isling Pærregaard
- Department of Health Technology, Technical University of Denmark, Kemitorvet, 2800 Kgs, Lyngby, Denmark
| | - Line Wulff
- Department of Health Technology, Technical University of Denmark, Kemitorvet, 2800 Kgs, Lyngby, Denmark
| | - Sophie Schussek
- Department of Health Technology, Technical University of Denmark, Kemitorvet, 2800 Kgs, Lyngby, Denmark
| | - Kristoffer Niss
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Urs Mörbe
- Department of Health Technology, Technical University of Denmark, Kemitorvet, 2800 Kgs, Lyngby, Denmark
| | - Johan Jendholm
- Department of Health Technology, Technical University of Denmark, Kemitorvet, 2800 Kgs, Lyngby, Denmark
| | | | - Anna T Andrusaite
- Institute of Infection, immunity and Inflammation, University of Glasgow, Glasgow, Scotland, UK
| | - Kevin F Brulois
- Laboratory of Immunology and Vascular Biology, Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Robert J B Nibbs
- Institute of Infection, immunity and Inflammation, University of Glasgow, Glasgow, Scotland, UK
| | - Katarzyna Sitnik
- Department of Health Technology, Technical University of Denmark, Kemitorvet, 2800 Kgs, Lyngby, Denmark
| | - Allan McI Mowat
- Institute of Infection, immunity and Inflammation, University of Glasgow, Glasgow, Scotland, UK
| | - Eugene C Butcher
- Laboratory of Immunology and Vascular Biology, Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
- The Center for Molecular Biology and Medicine, Veterans Affairs Palo Alto Health Care System and the Palo Alto Veterans Institute for Research (PAVIR), Palo Alto, CA, USA
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - William W Agace
- Department of Health Technology, Technical University of Denmark, Kemitorvet, 2800 Kgs, Lyngby, Denmark.
- Immunology Section, Lund University, Lund, 221 84, Sweden.
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248
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Chhabra Y, Weeraratna AT. Fibroblasts in cancer: Unity in heterogeneity. Cell 2023; 186:1580-1609. [PMID: 37059066 DOI: 10.1016/j.cell.2023.03.016] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 04/16/2023]
Abstract
Tumor cells do not exist in isolation in vivo, and carcinogenesis depends on the surrounding tumor microenvironment (TME), composed of a myriad of cell types and biophysical and biochemical components. Fibroblasts are integral in maintaining tissue homeostasis. However, even before a tumor develops, pro-tumorigenic fibroblasts in close proximity can provide the fertile 'soil' to the cancer 'seed' and are known as cancer-associated fibroblasts (CAFs). In response to intrinsic and extrinsic stressors, CAFs reorganize the TME enabling metastasis, therapeutic resistance, dormancy and reactivation by secreting cellular and acellular factors. In this review, we summarize the recent discoveries on CAF-mediated cancer progression with a particular focus on fibroblast heterogeneity and plasticity.
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Affiliation(s)
- Yash Chhabra
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Department of Oncology, Sidney Kimmel Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
| | - Ashani T Weeraratna
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Department of Oncology, Sidney Kimmel Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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249
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Wang D, Liu B, Zhang Z. Accelerating the understanding of cancer biology through the lens of genomics. Cell 2023; 186:1755-1771. [PMID: 37059071 DOI: 10.1016/j.cell.2023.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 01/11/2023] [Accepted: 02/08/2023] [Indexed: 04/16/2023]
Abstract
A core mission of cancer genomics is to comprehensively chart molecular underpinnings of cancer-driving events and to provide personalized therapeutic strategies. Primarily focused on cancer cells, cancer genomics studies have successfully uncovered many drivers for major cancer types. Since the emergence of cancer immune evasion as a critical cancer hallmark, the paradigm has been elevated to the holistic tumor ecosystem, with distinct cellular components and their functional states elucidated. We highlight the milestones of cancer genomics, depict the evolving path of the field, and discuss future directions in completing the understanding of the tumor ecosystem and in advancing therapeutic strategies.
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Affiliation(s)
- Dongfang Wang
- Biomedical Pioneering Innovative Center and School of Life Sciences, Peking University, Beijing 100871, China
| | - Baolin Liu
- Biomedical Pioneering Innovative Center and School of Life Sciences, Peking University, Beijing 100871, China
| | - Zemin Zhang
- Biomedical Pioneering Innovative Center and School of Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Changping Laboratory, Beijing, China.
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250
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Kabat AM, Pearce EL, Pearce EJ. Metabolism in type 2 immune responses. Immunity 2023; 56:723-741. [PMID: 37044062 PMCID: PMC10938369 DOI: 10.1016/j.immuni.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023]
Abstract
The immune response is tailored to the environment in which it takes place. Immune cells sense and adapt to changes in their surroundings, and it is now appreciated that in addition to cytokines made by stromal and epithelial cells, metabolic cues provide key adaptation signals. Changes in immune cell activation states are linked to changes in cellular metabolism that support function. Furthermore, metabolites themselves can signal between as well as within cells. Here, we discuss recent progress in our understanding of how metabolic regulation relates to type 2 immunity firstly by considering specifics of metabolism within type 2 immune cells and secondly by stressing how type 2 immune cells are integrated more broadly into the metabolism of the organism as a whole.
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Affiliation(s)
- Agnieszka M Kabat
- Bloomberg Kimmel Institute, and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Erika L Pearce
- Bloomberg Kimmel Institute, and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21287, USA
| | - Edward J Pearce
- Bloomberg Kimmel Institute, and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21287, USA.
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