1
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Hatse S, Lambrechts Y, Antoranz Martinez A, De Schepper M, Geukens T, Vos H, Berben L, Messiaen J, Marcelis L, Van Herck Y, Neven P, Smeets A, Desmedt C, De Smet F, Bosisio FM, Wildiers H, Floris G. Dissecting the immune infiltrate of primary luminal B-like breast carcinomas in relation to age. J Pathol 2024; 264:344-356. [PMID: 39344093 DOI: 10.1002/path.6354] [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: 01/17/2024] [Revised: 06/26/2024] [Accepted: 08/24/2024] [Indexed: 10/01/2024]
Abstract
The impact of aging on the immune landscape of luminal breast cancer (Lum-BC) is poorly characterized. Understanding the age-related dynamics of immune editing in Lum-BC is anticipated to improve the therapeutic benefit of immunotherapy in older patients. To this end, here we applied the 'multiple iterative labeling by antibody neo-deposition' (MILAN) technique, a spatially resolved single-cell multiplex immunohistochemistry method. We created tissue microarrays by sampling both the tumor center and invasive front of luminal breast tumors collected from a cohort of treatment-naïve patients enrolled in the prospective monocentric IMAGE (IMmune system and AGEing) study. Patients were subdivided into three nonoverlapping age categories (35-45 = 'young', n = 12; 55-65 = 'middle', n = 15; ≥70 = 'old', n = 26). Additionally, depending on localization and amount of cytotoxic T lymphocytes, the tumor immune types 'desert' (n = 22), 'excluded' (n = 19), and 'inflamed' (n = 12) were identified. For the MILAN technique we used 58 markers comprising phenotypic and functional markers allowing in-depth characterization of T and B lymphocytes (T&B-lym). These were compared between age groups and tumor immune types using Wilcoxon's test and Pearson's correlation. Cytometric analysis revealed a decline of the immune cell compartment with aging. T&B-lym were numerically less abundant in tumors from middle-aged and old compared to young patients, regardless of the geographical tumor zone. Likewise, desert-type tumors showed the smallest immune-cell compartment and were not represented in the group of young patients. Analysis of immune checkpoint molecules revealed a heterogeneous geographical pattern of expression, indicating higher numbers of PD-L1 and OX40-positive T&B-lym in young compared to old patients. Despite the numerical decline of immune infiltration, old patients retained higher expression levels of OX40 in T helper cells located near cancer cells, compared to middle-aged and young patients. Aging is associated with important numerical and functional changes of the immune landscape in Lum-BC. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sigrid Hatse
- Laboratory of Experimental Oncology (LEO), Department of Oncology, KU Leuven, Leuven, Belgium
| | - Yentl Lambrechts
- Laboratory of Experimental Oncology (LEO), Department of Oncology, KU Leuven, Leuven, Belgium
| | - Asier Antoranz Martinez
- Laboratory for Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Maxim De Schepper
- Laboratory for Translational Breast Cancer Research (LTBCR), Department of Oncology, KU Leuven, Leuven, Belgium
| | - Tatjana Geukens
- Laboratory for Translational Breast Cancer Research (LTBCR), Department of Oncology, KU Leuven, Leuven, Belgium
| | - Hanne Vos
- Department of Surgical Oncology, University Hospitals Leuven/KU Leuven, Leuven, Belgium
| | - Lieze Berben
- Laboratory of Experimental Oncology (LEO), Department of Oncology, KU Leuven, Leuven, Belgium
| | - Julie Messiaen
- Laboratory for Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Lukas Marcelis
- Laboratory for Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Yannick Van Herck
- Laboratory of Experimental Oncology (LEO), Department of Oncology, KU Leuven, Leuven, Belgium
| | - Patrick Neven
- Multidisciplinary Breast Center, University Hospitals Leuven, Leuven, Belgium
| | - Ann Smeets
- Department of Surgical Oncology, University Hospitals Leuven/KU Leuven, Leuven, Belgium
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research (LTBCR), Department of Oncology, KU Leuven, Leuven, Belgium
| | - Frederik De Smet
- Laboratory for Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Francesca Maria Bosisio
- Laboratory for Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Hans Wildiers
- Laboratory of Experimental Oncology (LEO), Department of Oncology, KU Leuven, Leuven, Belgium
- Multidisciplinary Breast Center, University Hospitals Leuven, Leuven, Belgium
| | - Giuseppe Floris
- Laboratory for Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
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2
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Driessen A, Unger S, Nguyen AP, Ries RE, Meshinchi S, Kreutmair S, Alberti C, Sumazin P, Aplenc R, Redell MS, Becher B, Rodríguez Martínez M. Identification of single-cell blasts in pediatric acute myeloid leukemia using an autoencoder. Life Sci Alliance 2024; 7:e202402674. [PMID: 39191488 PMCID: PMC11358707 DOI: 10.26508/lsa.202402674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 08/09/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024] Open
Abstract
Pediatric acute myeloid leukemia (AML) is an aggressive blood cancer with a poor prognosis and high relapse rate. Current challenges in the identification of immunotherapy targets arise from patient-specific blast immunophenotypes and their change during disease progression. To overcome this, we present a new computational research tool to rapidly identify malignant cells. We generated single-cell flow cytometry profiles of 21 pediatric AML patients with matched samples at diagnosis, remission, and relapse. We coupled a classifier to an autoencoder for anomaly detection and classified malignant blasts with 90% accuracy. Moreover, our method assigns a developmental stage to blasts at the single-cell level, improving current classification approaches based on differentiation of the dominant phenotype. We observed major immunophenotype and developmental stage alterations between diagnosis and relapse. Patients with KMT2A rearrangement had more profound changes in their blast immunophenotypes at relapse compared to patients with other molecular features. Our method provides new insights into the immunophenotypic composition of AML blasts in an unbiased fashion and can help to define immunotherapy targets that might improve personalized AML treatment.
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Affiliation(s)
- Alice Driessen
- https://ror.org/02js37d36 Data and AI Research, IBM Research Europe, Zürich, Switzerland
- ETH Zürich, Zürich, Switzerland
| | - Susanne Unger
- https://ror.org/02crff812 Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - An-Phi Nguyen
- https://ror.org/02js37d36 Data and AI Research, IBM Research Europe, Zürich, Switzerland
| | - Rhonda E Ries
- https://ror.org/007ps6h72 Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Soheil Meshinchi
- https://ror.org/007ps6h72 Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stefanie Kreutmair
- https://ror.org/02crff812 Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
- https://ror.org/01462r250 Department of Medical Oncology and Hematology, University Hospital Zürich, Zürich, Switzerland
| | - Chiara Alberti
- https://ror.org/02crff812 Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Pavel Sumazin
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Richard Aplenc
- https://ror.org/01z7r7q48 Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michele S Redell
- Texas Children's Cancer and Hematology Center, Baylor College of Medicine, Houston, TX, USA
| | - Burkhard Becher
- https://ror.org/02crff812 Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
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3
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Kabakibo TS, Arnold E, Padhan K, Lemieux A, Ortega-Delgado GG, Routy JP, Shoukry N, Dubé M, Kaufmann DE. Artificial antigen-presenting cell system reveals CD28's role in modulating T cell functions during human immunodeficiency virus infection. iScience 2024; 27:110947. [PMID: 39381752 PMCID: PMC11460474 DOI: 10.1016/j.isci.2024.110947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/16/2024] [Accepted: 09/10/2024] [Indexed: 10/10/2024] Open
Abstract
T cell immune dysfunction is a prominent feature of chronic HIV infection. To evaluate non-specific dysfunction, a method involving both generic activation and T cell receptor (TCR) stimulation is necessary. We created a tunable artificial antigen-presenting cell (aAPC) system. This system consists of lipid bilayers on cytometry-compatible silica microbeads (5 μm). When only anti-CD3 is incorporated, T cell activation is limited. Introducing anti-CD28 agonists significantly elevates the cytokine expression and upregulation of activation-induced markers. CD28 co-stimulation modulates the response profile, preferentially promoting IL-2 expression relative to other cytokines. aAPCs-stimulated CD4+ and CD8+ T cells from untreated HIV-infected individuals exhibit altered effector functions and diminished CD28 dependence. These functions are skewed toward TNFα, IFNγ and CD107a, with reduced IL-2. Antiretroviral therapy partially normalizes this distorted profile in CD4+ T cells, but not in CD8+ T cells. Our findings show T cell intrinsic biases that may contribute to persistent systemic T cell dysfunction associated with HIV pathogenesis.
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Affiliation(s)
- Tayma Shaaban Kabakibo
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Université de Montréal, Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H2X 0A9, Canada
| | - Edwige Arnold
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Université de Montréal, Montréal, QC, Canada
| | - Kartika Padhan
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Audrée Lemieux
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Université de Montréal, Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H2X 0A9, Canada
| | | | - Jean-Pierre Routy
- Chronic Viral Illnesses Service and Division of Hematology, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, QC, Canada
| | - Naglaa Shoukry
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Université de Montréal, Montréal, QC, Canada
- Département de Médecine, Université de Montréal, Montréal, QC H2X 0A9, Canada
| | - Mathieu Dubé
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Daniel E. Kaufmann
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Université de Montréal, Montréal, QC, Canada
- Département de Médecine, Université de Montréal, Montréal, QC H2X 0A9, Canada
- Division of Infectious Diseases, Department of Medicine, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
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4
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Romero R, Chu T, González Robles TJ, Smith P, Xie Y, Kaur H, Yoder S, Zhao H, Mao C, Kang W, Pulina MV, Lawrence KE, Gopalan A, Zaidi S, Yoo K, Choi J, Fan N, Gerstner O, Karthaus WR, DeStanchina E, Ruggles KV, Westcott PMK, Chaligné R, Pe'er D, Sawyers CL. The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1. NATURE CANCER 2024:10.1038/s43018-024-00838-6. [PMID: 39394434 DOI: 10.1038/s43018-024-00838-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 09/06/2024] [Indexed: 10/13/2024]
Abstract
Lineage plasticity is a hallmark of cancer progression that impacts therapy outcomes, yet the mechanisms mediating this process remain unclear. Here, we introduce a versatile in vivo platform to interrogate neuroendocrine lineage transformation throughout prostate cancer progression. Transplanted mouse prostate organoids with human-relevant driver mutations (Rb1-/-; Trp53-/-; cMyc+ or Pten-/-; Trp53-/-; cMyc+) develop adenocarcinomas, but only those with Rb1 deletion advance to aggressive, ASCL1+ neuroendocrine prostate cancer (NEPC) resistant to androgen receptor signaling inhibitors. Notably, this transition requires an in vivo microenvironment not replicated by conventional organoid culture. Using multiplexed immunofluorescence and spatial transcriptomics, we reveal that ASCL1+ cells arise from KRT8+ luminal cells, progressing into transcriptionally heterogeneous ASCL1+;KRT8- NEPC. Ascl1 loss in established NEPC causes transient regression followed by recurrence, but its deletion before transplantation abrogates lineage plasticity, resulting in castration-sensitive adenocarcinomas. This dynamic model highlights the importance of therapy timing and offers a platform to identify additional lineage plasticity drivers.
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Affiliation(s)
- Rodrigo Romero
- Human Oncology and Pathogenesis Program, 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
| | - Tania J González Robles
- Institute of Systems Genetics, Department of Precision Medicine, NYU Grossman School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Perianne Smith
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yubin Xie
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Harmanpreet Kaur
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sara Yoder
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Huiyong Zhao
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chenyi Mao
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wenfei Kang
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria V Pulina
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kayla E Lawrence
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anuradha Gopalan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samir Zaidi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Genitourinary Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kwangmin Yoo
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Ning Fan
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olivia Gerstner
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wouter R Karthaus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa DeStanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kelly V Ruggles
- Institute of Systems Genetics, Department of Precision Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Ronan Chaligné
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 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, Chevy Chase, MD, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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5
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Park C, Mani S, Beltran-Velez N, Maurer K, Huang T, Li S, Gohil S, Livak KJ, Knowles DA, Wu CJ, Azizi E. A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data. Genome Res 2024; 34:1384-1396. [PMID: 39237300 DOI: 10.1101/gr.279126.124] [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: 02/15/2024] [Accepted: 09/03/2024] [Indexed: 09/07/2024]
Abstract
Characterizing cell-cell communication and tracking its variability over time are crucial for understanding the coordination of biological processes mediating normal development, disease progression, and responses to perturbations such as therapies. Existing tools fail to capture time-dependent intercellular interactions and primarily rely on databases compiled from limited contexts. We introduce DIISCO, a Bayesian framework designed to characterize the temporal dynamics of cellular interactions using single-cell RNA-sequencing data from multiple time points. Our method utilizes structured Gaussian process regression to unveil time-resolved interactions among diverse cell types according to their coevolution and incorporates prior knowledge of receptor-ligand complexes. We show the interpretability of DIISCO in simulated data and new data collected from T cells cocultured with lymphoma cells, demonstrating its potential to uncover dynamic cell-cell cross talk.
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Affiliation(s)
- Cameron Park
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, USA;
- Irving Institute for Cancer Dynamics, Columbia University, New York, New York 10027, USA
| | - Shouvik Mani
- Irving Institute for Cancer Dynamics, Columbia University, New York, New York 10027, USA
- Department of Computer Science, Columbia University, New York, New York 10027, USA
| | | | - Katie Maurer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Teddy Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Satyen Gohil
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - David A Knowles
- Department of Computer Science, Columbia University, New York, New York 10027, USA
- Data Science Institute, Columbia University, New York, New York 10027, USA
- New York Genome Center, New York, New York 10013, USA
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Elham Azizi
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, USA;
- Irving Institute for Cancer Dynamics, Columbia University, New York, New York 10027, USA
- Department of Computer Science, Columbia University, New York, New York 10027, USA
- Data Science Institute, Columbia University, New York, New York 10027, USA
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6
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Chen Y, Zhang J, Hu W, Li X, Sun K, Shen Y, Zhang M, Wu J, Gao S, Yu J, Que R, Zhang Y, Yang F, Xia W, Zhang A, Tang X, Bai X, Liang T. Envafolimab plus lenvatinib and transcatheter arterial chemoembolization for unresectable hepatocellular carcinoma: a prospective, single-arm, phase II study. Signal Transduct Target Ther 2024; 9:280. [PMID: 39384742 PMCID: PMC11464841 DOI: 10.1038/s41392-024-01991-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 09/17/2024] [Accepted: 09/25/2024] [Indexed: 10/11/2024] Open
Abstract
Evidences regarding the feasibility of transcatheter arterial chemoembolization (TACE)-based therapy for unresectable hepatocellular carcinoma (uHCC) remains limited. This study aimed to investigate the efficacy and safety of TACE combined with envafolimab and lenvatinib for uHCC. Eligible patients with uHCC received envafolimab and lenvatinib after TACE until disease progression, conversion to surgery, intolerable toxicities, or death. The primary endpoint was the objective response rate (ORR) assessed according to Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 criteria. Between March 2022 and July 2022, 38 patients were included for safety analysis, and 36 patients were included for efficacy analysis. As of the data cutoff (13 December 2023), the median follow-up was 16.9 months. The ORR was 50%, and disease control rate (DCR) was 83.3% per RECIST 1.1 (ORR and DCR of both 83.3% per modified RECIST (mRECIST)). The median progression-free survival (PFS) was 7.58 months. Of 36 patients, 17 patients were converted to resectable HCC with a surgical conversion rate of 47.2%, and 16 patients underwent surgery with R0 resection rate of 100%, pathologic complete response (pCR) rate of 31.3%. Overall incidences of treatment-related adverse events (TRAEs) of any grade was 97.4%. Grade ≥ 3 TRAEs were observed in 52.6% patients. No treatment-related deaths occurred. Image mass cytometry (IMC) analysis revealed that combined treatment improved the immune status of the tumor microenvironment, and resident macrophages had the potential to predict efficacy of this treatment. Envafolimab plus lenvatinib and TACE yielded promising survival outcomes and conversion efficiency with a tolerable safety profile. Trial registration Clinical trials: NCT05213221.
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Affiliation(s)
- Yiwen Chen
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, Zhejiang, China
- Zhejiang Provincial Clinical Research Center for the Study of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Junlei Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, Zhejiang, China
- Zhejiang Provincial Clinical Research Center for the Study of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wendi Hu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiang Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, Zhejiang, China
- Zhejiang Provincial Clinical Research Center for the Study of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ke Sun
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yan Shen
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Min Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jian Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shunliang Gao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jun Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Risheng Que
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Fuchun Yang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Weiliang Xia
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Aibin Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaofeng Tang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, Zhejiang, China.
- Zhejiang Provincial Clinical Research Center for the Study of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, Zhejiang, China.
- Zhejiang Provincial Clinical Research Center for the Study of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
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7
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Boudigou M, Frutoso M, Hémon P, Le Dantec C, Chatzis L, Devauchelle V, Jamin C, Cornec D, Pers JO, Le Pottier L, Hillion S. Phenotypic, transcriptomic, and spatial characterization of CD45RB + naïve mature B cells: Implications in Sjögren's disease. Clin Immunol 2024:110378. [PMID: 39393568 DOI: 10.1016/j.clim.2024.110378] [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: 06/11/2024] [Revised: 09/23/2024] [Accepted: 10/05/2024] [Indexed: 10/13/2024]
Abstract
The conventional classification of mature B cells overlooks the diversity within IgD+ CD27- naïve B cells. Here, to identify distinct mature naïve B cells, we categorized CD45RBMEM55- B cells (NA RB-) and CD45RBMEM55+ B cells (NA RB+) and explore their function and localization in circulation and tissues under physiological and pathological conditions. NA RB+ B cells, found in secondary lymphoid organs, differentiate into plasmablasts and secrete IgM. In Sjögren's disease, their numbers decrease, and they show over-activation and abnormal migration, suggesting an adaptive disease response. NA RB+ B cells also appear in inflamed salivary glands, indicating involvement in local immune responses. These findings highlight the distinct roles of NA RB+ B cells in health and Sjögren's disease.
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Affiliation(s)
| | | | | | | | - Loukas Chatzis
- UMR1227, LBAI, Univ Brest, Inserm, Brest, France; Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | | | | | - Divi Cornec
- UMR1227, LBAI, Univ Brest, Inserm, and CHU Brest, Brest, France
| | | | | | - Sophie Hillion
- UMR1227, LBAI, Univ Brest, Inserm, and CHU Brest, Brest, France.
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8
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Saggau C, Bacher P, Esser D, Rasa M, Meise S, Mohr N, Kohlstedt N, Hutloff A, Schacht SS, Dargvainiene J, Martini GR, Stürner KH, Schröder I, Markewitz R, Hartl J, Hastermann M, Duchow A, Schindler P, Becker M, Bautista C, Gottfreund J, Walter J, Polansky JK, Yang M, Naghavian R, Wendorff M, Schuster EM, Dahl A, Petzold A, Reinhardt S, Franke A, Wieczorek M, Henschel L, Berger D, Heine G, Holtsche M, Häußler V, Peters C, Schmidt E, Fillatreau S, Busch DH, Wandinger KP, Schober K, Martin R, Paul F, Leypoldt F, Scheffold A. Autoantigen-specific CD4 + T cells acquire an exhausted phenotype and persist in human antigen-specific autoimmune diseases. Immunity 2024; 57:2416-2432.e8. [PMID: 39226901 DOI: 10.1016/j.immuni.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/14/2024] [Accepted: 08/07/2024] [Indexed: 09/05/2024]
Abstract
Pro-inflammatory autoantigen-specific CD4+ T helper (auto-Th) cells are central orchestrators of autoimmune diseases (AIDs). We aimed to characterize these cells in human AIDs with defined autoantigens by combining human leukocyte antigen (HLA)-tetramer-based and activation-based multidimensional ex vivo analyses. In aquaporin4-antibody-positive neuromyelitis optica spectrum disorder (AQP4-NMOSD) patients, auto-Th cells expressed CD154, but proliferative capacity and pro-inflammatory cytokines were strongly reduced. Instead, exhaustion-associated co-inhibitory receptors were expressed together with FOXP3, the canonical regulatory T cell (Treg) transcription factor. Auto-Th cells responded in vitro to checkpoint inhibition and provided potent B cell help. Cells with the same exhaustion-like (ThEx) phenotype were identified in soluble liver antigen (SLA)-antibody-autoimmune hepatitis and BP180-antibody-positive bullous pemphigoid, AIDs of the liver and skin, respectively. While originally described in cancer and chronic infection, our data point to T cell exhaustion as a common mechanism of adaptation to chronic (self-)stimulation across AID types and link exhausted CD4+ T cells to humoral autoimmune responses, with implications for therapeutic targeting.
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Affiliation(s)
- Carina Saggau
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein (UKSH), Kiel, Germany
| | - Petra Bacher
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein (UKSH), Kiel, Germany; Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Daniela Esser
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Mahdi Rasa
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein (UKSH), Kiel, Germany; Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Silja Meise
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein (UKSH), Kiel, Germany
| | - Nicola Mohr
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein (UKSH), Kiel, Germany
| | - Nora Kohlstedt
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein (UKSH), Kiel, Germany
| | - Andreas Hutloff
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein (UKSH), Kiel, Germany; Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Sarah-Sophie Schacht
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein (UKSH), Kiel, Germany
| | - Justina Dargvainiene
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Gabriela Rios Martini
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein (UKSH), Kiel, Germany; Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Klarissa H Stürner
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Lübeck, Germany; Department of Neurology, University Hospital Schleswig-Holstein Kiel, Kiel, Germany
| | - Ina Schröder
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Robert Markewitz
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Johannes Hartl
- Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Maria Hastermann
- Experimental and Clinical Research Center, Max Delbrueck Center for Molecular Medicine and Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Ankelien Duchow
- Experimental and Clinical Research Center, Max Delbrueck Center for Molecular Medicine and Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Patrick Schindler
- Experimental and Clinical Research Center, Max Delbrueck Center for Molecular Medicine and Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Mareike Becker
- Institute of Experimental Dermatology, Lübeck, Germany; Department of Pediatric Dermatology, Catholic Children's Hospital Wilhelmstift, Hamburg, Germany
| | - Carolin Bautista
- Department of Dermatology, Allergy and Venerology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Judith Gottfreund
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Julia K Polansky
- Berlin Institute of Health (BIH) at Charité Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Augustenburger Platz 1, 13353 Berlin, Germany; German Rheumatism Research Centre, a Leibniz Institute (DRFZ), Charité Platz 1, 10117 Berlin, Germany
| | - Mingxing Yang
- Berlin Institute of Health (BIH) at Charité Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Reza Naghavian
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland; Cellerys AG, Wagistrasse 21, 8952 Schlieren, Switzerland
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany; Leibniz Institute for Science and Mathematics Education, Kiel, Germany
| | - Ev-Marie Schuster
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Wasserturmstr. 3/5, 91054 Erlangen, Germany
| | - Andreas Dahl
- DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), Technical University of Dresden, Dresden, Germany
| | - Andreas Petzold
- DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), Technical University of Dresden, Dresden, Germany
| | - Susanne Reinhardt
- DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), Technical University of Dresden, Dresden, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Marek Wieczorek
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429 Bergisch Gladbach, Germany
| | - Lea Henschel
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429 Bergisch Gladbach, Germany
| | - Daniel Berger
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429 Bergisch Gladbach, Germany
| | - Guido Heine
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Maike Holtsche
- Institute of Experimental Dermatology, University of Lübeck, Department of Dermatology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Vivien Häußler
- Clinic and Polyclinic for Neurology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Christian Peters
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein (UKSH), Kiel, Germany
| | - Enno Schmidt
- Institute of Experimental Dermatology, University of Lübeck, Department of Dermatology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Simon Fillatreau
- Université Paris Cité, CNRS, INSERM, Institut Necker Enfants Malades-INEM, 75015 Paris, France; Université Paris Cité, Faculté de Médecine, Paris, France; AP-HP, Hôpital Necker-Enfants Malades, Paris, France
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Klaus-Peter Wandinger
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Kilian Schober
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Wasserturmstr. 3/5, 91054 Erlangen, Germany; Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054 Erlangen, Germany
| | - Roland Martin
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland; Cellerys AG, Wagistrasse 21, 8952 Schlieren, Switzerland; Institute of Experimental Immunology, University of Zurich, Wintherturerstrasse 191, 8057 Zurich, Switzerland; Department of Clinical Neuroscience, Karolinska Institute, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Friedemann Paul
- Experimental and Clinical Research Center, Max Delbrueck Center for Molecular Medicine and Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Frank Leypoldt
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Lübeck, Germany; Department of Neurology, University Hospital Schleswig-Holstein Kiel, Kiel, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein (UKSH), Kiel, Germany.
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9
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Deep D, Gudjonson H, Brown CC, Rose SA, Sharma R, Paucar Iza YA, Hong S, Hemmers S, Schizas M, Wang ZM, Chen Y, Wesemann DR, Pascual V, Pe'er D, Rudensky AY. Precursor central memory versus effector cell fate and naïve CD4+ T cell heterogeneity. J Exp Med 2024; 221:e20231193. [PMID: 39321257 PMCID: PMC11448869 DOI: 10.1084/jem.20231193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 03/08/2024] [Accepted: 08/12/2024] [Indexed: 09/27/2024] Open
Abstract
Upon antigenic stimulation, naïve CD4+ T cells can give rise to phenotypically distinct effector T helper cells and long-lived memory T cells. We computationally reconstructed the in vivo trajectory of CD4+ T cell differentiation during a type I inflammatory immune response and identified two distinct differentiation paths for effector and precursor central memory T cells arising directly from naïve CD4+ T cells. Unexpectedly, our studies revealed heterogeneity among naïve CD4+ T cells, which are typically considered homogeneous save for their diverse T cell receptor usage. Specifically, a previously unappreciated population of naïve CD4+ T cells sensing environmental type I IFN exhibited distinct activation thresholds, suggesting that naïve CD4+ T cell differentiation potential may be influenced by environmental cues. This population was expanded in human viral infection and type I IFN response-lined autoimmunity. Understanding the relevance of naïve T cell heterogeneity to beneficial and maladaptive T cell responses may have therapeutic implications for adoptive T cell therapies in cancer immunotherapy and vaccination.
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Affiliation(s)
- Deeksha Deep
- Immunology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, The Rockefeller University and Memorial Sloan Kettering Cancer Center , New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences , New York, NY, USA
| | - Herman Gudjonson
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
| | - Chrysothemis C Brown
- Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel A Rose
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
| | - Roshan Sharma
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
| | - Yoselin A Paucar Iza
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences , New York, NY, USA
| | - Seunghee Hong
- Drukier Institute for Children's Health at Weill Cornell Medicine , New York, NY, USA
| | - Saskia Hemmers
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
| | - Michail Schizas
- Immunology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
| | - Zhong-Min Wang
- Immunology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
- Gerstner Sloan Kettering Graduate School in Biomedical Sciences, Memorial Sloan Kettering Cancer Center , New York, NY, USA
- Immunology Discovery, Genentech Inc. , South San Francisco, CA, USA
| | - Yuezhou Chen
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Duane R Wesemann
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Virginia Pascual
- Drukier Institute for Children's Health at Weill Cornell Medicine , New York, NY, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
- Howard Hughes Medical Institute , Chevy Chase, MD, USA
| | - Alexander Y Rudensky
- Immunology Program, Memorial Sloan Kettering Cancer Center , New York, NY, USA
- Howard Hughes Medical Institute , Chevy Chase, MD, USA
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10
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Hou X, Liang F, Li J, Yang Y, Wang C, Qi T, Sheng W. Mapping cell diversity in human sporadic cerebral cavernous malformations. Gene 2024; 924:148605. [PMID: 38788816 DOI: 10.1016/j.gene.2024.148605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Cerebral cavernous malformation (CCM) is a low-flow, bleeding-prone vascular disease that can cause cerebral hemorrhage, seizure and neurological deficits. Its inheritance mode includes sporadic or autosomal dominant inheritance with incomplete penetrance, namely sporadic CCM (SCCM) and familial CCM. SCCM is featured by single lesion and single affection in a family. Among CCM patients especially SCCM, the pathogenesis of the corresponding phenotypes and pathological features or candidate genes have not been fully elucidated yet. METHODS Here, we performed in-depth single-cell RNA sequencing (scRNA-Seq) and bulk assay for transposase-accessible chromatin sequencing (ATAC-Seq) in SCCM and control patients. Further validation was conducted for the gene of interest using qPCR and RNA in situ hybridization (RNA FISH) techniques to provide further atlas and evidence for SCCM generative process. RESULTS We identified six cell types in the SCCM and control vessels and found that the expression of NEK1, RNPC3, FBRSL1, IQGAP2, MCUB, AP3B1, ESCO1, MYO9B and PVT1 were up-regulated in SCCM tissues. Among the six cell types, we found that compared with control conditions, PVT1 showed a rising peak which followed the pseudo-time axis in endothelial cell clusters of SCCM samples, while showed an increasing trend in smooth muscle cell clusters of SCCM samples. Further experiments indicated that, compared with the control vessels, PVT1 exhibited significantly elevated expression in SCCM samples. CONCLUSION In SCCM conditions, We found that in the process of development from control to lesion conditions, PVT1 showed a rising peak in endothelial cells and showed an increasing trend in smooth muscle cells at the same time. Overall, there was a significantly elevated expression of NEK1, RNPC3, FBRSL1, IQGAP2, MCUB, AP3B1, ESCO1, MYO9B and PVT1 in SCCM specimens compared to control samples.
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Affiliation(s)
- Xiaocan Hou
- Department of Rehabilitation Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Road 2, Guangzhou, 510080, China
| | - Feng Liang
- Department of Neurosurgery, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Road 2, Guangzhou, 510080, China
| | - Jiaoxing Li
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, No.58 Zhongshan Road 2, Guangzhou, 510080, China
| | - Yibing Yang
- Department of Neurosurgery, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Road 2, Guangzhou, 510080, China
| | - Chuhuai Wang
- Department of Rehabilitation Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Road 2, Guangzhou, 510080, China.
| | - Tiewei Qi
- Department of Neurosurgery, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Road 2, Guangzhou, 510080, China.
| | - Wenli Sheng
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, No.58 Zhongshan Road 2, Guangzhou, 510080, China.
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11
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Wang Z, Santa-Maria CA, Popel AS, Sulam J. Bi-level Graph Learning Unveils Prognosis-Relevant Tumor Microenvironment Patterns in Breast Multiplexed Digital Pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590118. [PMID: 38712207 PMCID: PMC11071347 DOI: 10.1101/2024.04.22.590118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The tumor microenvironment is widely recognized for its central role in driving cancer progression and influencing prognostic outcomes. There have been increasing efforts dedicated to characterizing this complex and heterogeneous environment, including developing potential prognostic tools by leveraging modern deep learning methods. However, the identification of generalizable data-driven biomarkers has been limited, in part due to the inability to interpret the complex, black-box predictions made by these models. In this study, we introduce a data-driven yet interpretable approach for identifying patterns of cell organizations in the tumor microenvironment that are associated with patient prognoses. Our methodology relies on the construction of a bi-level graph model: (i) a cellular graph, which models the intricate tumor microenvironment, and (ii) a population graph that captures inter-patient similarities, given their respective cellular graphs, by means of a soft Weisfeiler-Lehman subtree kernel. This systematic integration of information across different scales enables us to identify patient subgroups exhibiting unique prognoses while unveiling tumor microenvironment patterns that characterize them. We demonstrate our approach in a cohort of breast cancer patients and show that the identified tumor microenvironment patterns result in a risk stratification system that provides new complementary information with respect to standard stratification systems. Our results, which are validated in two independent cohorts, allow for new insights into the prognostic implications of the breast tumor microenvironment. This methodology could be applied to other cancer types more generally, providing insights into the cellular patterns of organization associated with different outcomes.
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12
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Zhang W, Sen A, Pena JK, Reitsma A, Alexander OC, Tajima T, Martinez OM, Krams SM. Application of Mass Cytometry Platforms to Solid Organ Transplantation. Transplantation 2024; 108:2034-2044. [PMID: 38467594 PMCID: PMC11390974 DOI: 10.1097/tp.0000000000004925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Transplantation serves as the cornerstone of treatment for patients with end-stage organ disease. The prevalence of complications, such as allograft rejection, infection, and malignancies, underscores the need to dissect the complex interactions of the immune system at the single-cell level. In this review, we discuss studies using mass cytometry or cytometry by time-of-flight, a cutting-edge technology enabling the characterization of immune populations and cell-to-cell interactions in granular detail. We review the application of mass cytometry in human and experimental animal studies in the context of transplantation, uncovering invaluable contributions of the tool to understanding rejection and other transplant-related complications. We discuss recent innovations that have the potential to streamline and standardize mass cytometry workflows for application to multisite clinical trials. Additionally, we introduce imaging mass cytometry, a technique that couples the power of mass cytometry with spatial context, thereby mapping cellular interactions within tissue microenvironments. The synergistic integration of mass cytometry and imaging mass cytometry data with other omics data sets and high-dimensional data platforms to further define immune dynamics is discussed. In conclusion, mass cytometry technologies, when integrated with other tools and data, shed light on the intricate landscape of the immune response in transplantation. This approach holds significant potential for enhancing patient outcomes by advancing our understanding and facilitating the development of new diagnostics and therapeutics.
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Affiliation(s)
- Wenming Zhang
- Department of Surgery, Stanford University, Stanford, CA, United States
| | - Ayantika Sen
- Department of Surgery, Stanford University, Stanford, CA, United States
| | - Josselyn K. Pena
- Department of Surgery, Stanford University, Stanford, CA, United States
| | - Andrea Reitsma
- Department of Surgery, Stanford University, Stanford, CA, United States
| | - Oliver C. Alexander
- Department of Surgery, Stanford University, Stanford, CA, United States
- Meharry Medical College, School of Medicine, Nashville, TN, United States
| | - Tetsuya Tajima
- Department of Surgery, Stanford University, Stanford, CA, United States
| | | | - Sheri M. Krams
- Department of Surgery, Stanford University, Stanford, CA, United States
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13
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Beber SA, Moshkelgosha S, White M, Zehong G, Cheung M, Hedley D, Levy L, Samuels J, Renaud-Picard B, Hwang D, Martinu T, Juvet S. The CD8 + T cell content of transbronchial biopsies from patients with a first episode of clinically stable grade A1 cellular rejection is associated with future chronic lung allograft dysfunction. J Heart Lung Transplant 2024; 43:1654-1664. [PMID: 38852935 DOI: 10.1016/j.healun.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/05/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND T cells drive acute cellular rejection (ACR) and its progression to chronic lung allograft dysfunction (CLAD) following lung transplantation. International Society for Heart and Lung Transplantation grade A1 ACR without associated allograft dysfunction is often untreated, yet some patients develop progressive graft dysfunction. T-cell composition of A1 ACR lesions may have prognostic value; therefore, protein-level and epigenetic techniques were applied to transbronchial biopsy tissue to determine whether differential T-cell infiltration in recipients experiencing a first episode of stable grade A1 ACR (StA1R) is associated with early CLAD. METHODS Sixty-two patients experiencing a first episode of StA1R were divided into those experiencing CLAD within 2 years (n = 13) and those remaining CLAD-free for 5 or more years (n = 49). Imaging mass cytometry (IMC) was used to profile the spectrum and distribution of intragraft T cell phenotypes on a subcohort (n = 16; 8 early-CLAD and 8 no early-CLAD). Immunofluorescence was used to quantify CD4+, CD8+, and FOXP3+ cells. Separately, CD3+ cells were fluorescently labeled, micro-dissected, and the degree of Treg-specific demethylated region methylation was determined. RESULTS PhenoGraph unsupervised clustering on IMC revealed 50 unique immune cell subpopulations. Methylation and immunofluorescence analyses demonstrated no significant differences in Tregs between early-CLAD and no early-CLAD groups. Immunofluorescence revealed that patients who developed CLAD within 2 years of lung transplantation showed greater CD8+ T cell infiltration compared to those who remained CLAD-free for 5 or more years. CONCLUSIONS In asymptomatic patients with a first episode of A1 rejection, greater CD8+ T cell content may be indicative of worse long-term outlook.
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Affiliation(s)
- Samuel A Beber
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Medicine, New York Medical College, Valhalla, New York
| | - Sajad Moshkelgosha
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Matthew White
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Guan Zehong
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - May Cheung
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - David Hedley
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Liran Levy
- Department of Medicine, Sheba Medical Center, Tel-Aviv University, Tel Aviv, Israel
| | - Joel Samuels
- Department of Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | | | - David Hwang
- Department of Pathology, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Tereza Martinu
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada; Ajmera Transplant Center, Toronto Lung Transplant Program, Toronto, Ontario, Canada; Division of Respirology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Stephen Juvet
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada; Ajmera Transplant Center, Toronto Lung Transplant Program, Toronto, Ontario, Canada; Division of Respirology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.
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14
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Bjørnstad OV, Carrasco M, Finne K, Ardawatia V, Winge I, Askeland C, Arnes JB, Knutsvik G, Kleftogiannis D, Paulo JA, Akslen LA, Vethe H. Global and single-cell proteomics view of the co-evolution between neural progenitors and breast cancer cells in a co-culture model. EBioMedicine 2024; 108:105325. [PMID: 39232464 PMCID: PMC11404160 DOI: 10.1016/j.ebiom.2024.105325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 08/15/2024] [Accepted: 08/22/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND Presence of nerves in tumours, by axonogenesis and neurogenesis, is gaining increased attention for its impact on cancer initiation and development, and the new field of cancer neuroscience is emerging. A recent study in prostate cancer suggested that the tumour microenvironment may influence cancer progression by recruitment of Doublecortin (DCX)-expressing neural progenitor cells (NPCs). However, the presence of such cells in human breast tumours has not been comprehensively explored. METHODS Here, we investigate the presence of DCX-expressing cells in breast cancer stromal tissue from patients using Imaging Mass Cytometry. Single-cell analysis of 372,468 cells across histopathological images of 107 breast cancers enabled spatial resolution of neural elements in the stromal compartment in correlation with clinicopathological features of these tumours. In parallel, we established a 3D in vitro model mimicking breast cancer neural progenitor-innervation and examined the two cell types as they co-evolved in co-culture by using mass spectrometry-based global proteomics. FINDINGS Stromal presence of DCX + cells is associated with tumours of higher histological grade, a basal-like phenotype, and shorter patient survival in tumour tissue from patients with breast cancer. Global proteomics analysis revealed significant changes in the proteomic landscape of both breast cancer cells and neural progenitors in co-culture. INTERPRETATION These results support that neural involvement plays an active role in breast cancer and warrants further studies on the relevance of nerve elements for tumour progression. FUNDING This work was supported by the Research Council of Norway through its Centre of Excellence funding scheme, project number 223250 (to L.A.A), the Norwegian Cancer Society (to L.A.A. and H.V.), the Regional Health Trust Western Norway (Helse Vest) (to L.A.A.), the Meltzer Research Fund (to H.V.) and the National Institutes of Health (NIH)/NIGMS grant R01 GM132129 (to J.A.P.).
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Affiliation(s)
- Ole Vidhammer Bjørnstad
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen N-5021, Norway
| | - Manuel Carrasco
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen N-5021, Norway
| | - Kenneth Finne
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen N-5021, Norway
| | - Vandana Ardawatia
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen N-5021, Norway
| | - Ingeborg Winge
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen N-5021, Norway
| | - Cecilie Askeland
- Department of Pathology, Haukeland University Hospital, Bergen N-5021, Norway
| | - Jarle B Arnes
- Department of Pathology, Haukeland University Hospital, Bergen N-5021, Norway
| | - Gøril Knutsvik
- Department of Pathology, Haukeland University Hospital, Bergen N-5021, Norway
| | - Dimitrios Kleftogiannis
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen N-5021, Norway; Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen N-5021, Norway
| | - Joao A Paulo
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen N-5021, Norway; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Lars A Akslen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen N-5021, Norway; Department of Pathology, Haukeland University Hospital, Bergen N-5021, Norway
| | - Heidrun Vethe
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen N-5021, Norway.
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15
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Dufour A, Heydari Olya A, Foulon S, Réda C, Mokhtari A, Faivre V, Hua J, Bokobza C, Griffiths AD, Nghe P, Gressens P, Delahaye-Duriez A, Van Steenwinckel J. Neonatal inflammation impairs developmentally-associated microglia and promotes a highly reactive microglial subset. Brain Behav Immun 2024; 123:466-482. [PMID: 39322088 DOI: 10.1016/j.bbi.2024.09.019] [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] [Received: 05/13/2024] [Revised: 09/10/2024] [Accepted: 09/13/2024] [Indexed: 09/27/2024] Open
Abstract
Microglia and border-associated macrophages play critical roles in both immunity and neurodevelopment. The disruption of microglial development trajectories by neonatal inflammation is an important issue in research on neurodevelopmental disorders (NDDs), as models have suggested a strong association between inflammation and cognitive deficits. Here, we explored by single-cell RNA sequencing and flow cytometry the impact of neonatal inflammation in a mouse NDD model on brain myeloid cell subsets. A specific subset of microglia expressing the complement receptor C5ar1 has been identified, in which inflammatory pathways are most strongly activated. Based on transcriptional similarity, this subset appears to originate from the most mature and "homeostatic" microglia at this stage of development and demonstrated hypersensitivity to inflammation. Besides that, Spp1-microglia supporting oligodendrocyte differentiation, primitive and proliferative microglia were reduced by inflammation. These findings suggest major changes in microglial subsets developmental trajectories and reactivity contributing to NDDs induced by neonatal inflammation.
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Affiliation(s)
- Adrien Dufour
- NeuroDiderot, INSERM, Université Paris Cité, Paris, France; Université Paris Saclay, INRAE, AgroParisTech, GABI, Domaine de Vilvert, 78350 Jouy en Josas, France
| | | | - Sophie Foulon
- Laboratoire de Biochimie, UMR CBI 8231, ESPCI Paris,10 rue Vauquelin 75005 Paris, France
| | - Clémence Réda
- NeuroDiderot, INSERM, Université Paris Cité, Paris, France
| | | | - Valérie Faivre
- NeuroDiderot, INSERM, Université Paris Cité, Paris, France
| | - Jennifer Hua
- NeuroDiderot, INSERM, Université Paris Cité, Paris, France
| | - Cindy Bokobza
- NeuroDiderot, INSERM, Université Paris Cité, Paris, France
| | - Andrew D Griffiths
- Laboratoire de Biochimie, UMR CBI 8231, ESPCI Paris,10 rue Vauquelin 75005 Paris, France
| | - Philippe Nghe
- Laboratoire de Biochimie, UMR CBI 8231, ESPCI Paris,10 rue Vauquelin 75005 Paris, France; Laboratoire Biophysique et Evolution, UMR CBI 8231, ESPCI Paris,10 rue Vauquelin 75005 Paris, France
| | | | - Andrée Delahaye-Duriez
- NeuroDiderot, INSERM, Université Paris Cité, Paris, France; Unité fonctionnelle de médecine génomique et génétique clinique, Hôpital Jean Verdier, AP-HP, 93140 Bondy, France; Université Sorbonne Paris Nord, UFR de santé, médecine et biologie humaine, 93000 Bobigny, France.
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16
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Donovan ML, Jhaveri N, Ma N, Cheikh BB, DeRosa J, Mihani R, Berrell N, Suen JY, Monkman J, Fraser JF, Kulasinghe A. Protocol for high-plex, whole-slide imaging of human formalin-fixed paraffin-embedded tissue using PhenoCycler-Fusion. STAR Protoc 2024; 5:103226. [PMID: 39031553 PMCID: PMC11314888 DOI: 10.1016/j.xpro.2024.103226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/03/2024] [Accepted: 07/05/2024] [Indexed: 07/22/2024] Open
Abstract
Single-cell spatial analysis of proteins is rapidly becoming increasingly important in revealing biological insights. Here, we present a protocol for automated high-plex multi-slide immunofluorescence staining and imaging of human head and neck cancer formalin-fixed paraffin-embedded (FFPE) sections using PhenoCycler-Fusion 2.0 technology. We describe steps for preparing human head and neck cancer FFPE tissues, staining with a panel of immunophenotyping markers, and Flow Cell assembly. We then detail procedures for setting up for a PhenoCycler-Fusion run, post-run Flow Cell removal, and downstream analyses. For complete details on the use and execution of this protocol, please refer to Jhaveri et al.1.
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Affiliation(s)
- Meg L Donovan
- Queensland Spatial Biology Centre, Wesley Research Institute, Level 8 East Wing, The Wesley Hospital, Auchenflower, QLD 4066, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Niyati Jhaveri
- Akoya Biosciences, The Spatial Biology Company, Marlborough, MA, USA
| | - Ning Ma
- Akoya Biosciences, The Spatial Biology Company, Marlborough, MA, USA
| | - Bassem Ben Cheikh
- Akoya Biosciences, The Spatial Biology Company, Marlborough, MA, USA
| | - James DeRosa
- Akoya Biosciences, The Spatial Biology Company, Marlborough, MA, USA
| | - Ritu Mihani
- Akoya Biosciences, The Spatial Biology Company, Marlborough, MA, USA
| | - Naomi Berrell
- Queensland Spatial Biology Centre, Wesley Research Institute, Level 8 East Wing, The Wesley Hospital, Auchenflower, QLD 4066, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Jacky Y Suen
- Critical Care Research Group, The Prince Charles Hospital, Brisbane, QLD 4032, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - James Monkman
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - John F Fraser
- Queensland Spatial Biology Centre, Wesley Research Institute, Level 8 East Wing, The Wesley Hospital, Auchenflower, QLD 4066, Australia; Critical Care Research Group, The Prince Charles Hospital, Brisbane, QLD 4032, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Arutha Kulasinghe
- Queensland Spatial Biology Centre, Wesley Research Institute, Level 8 East Wing, The Wesley Hospital, Auchenflower, QLD 4066, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia.
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17
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Thomas RA, Sirois J, Li S, Gestin A, Deyab G, Piscopo VE, Lépine P, Mathur M, Chen CXQ, Soubannier V, Goldsmith TM, Fawaz L, Durcan TM, Fon EA. CelltypeR: A flow cytometry pipeline to characterize single cells from brain organoids. iScience 2024; 27:110613. [PMID: 39224516 PMCID: PMC11367488 DOI: 10.1016/j.isci.2024.110613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 02/06/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
Motivated by the cellular heterogeneity in complex tissues, particularly in brain and induced pluripotent stem cell (iPSC)-derived brain models, we developed a complete workflow to reproducibly characterize cell types in complex tissues. Our approach combines a flow cytometry (FC) antibody panel with our computational pipeline CelltypeR, enabling dataset aligning, unsupervised clustering optimization, cell type annotating, and statistical comparisons. Applied to human iPSC derived midbrain organoids, it successfully identified the major brain cell types. We performed fluorescence-activated cell sorting of CelltypeR-defined astrocytes, radial glia, and neurons, exploring transcriptional states by single-cell RNA sequencing. Among the sorted neurons, we identified subgroups of dopamine neurons: one reminiscent of substantia nigra cells most vulnerable in Parkinson's disease. Finally, we used our workflow to track cell types across a time course of organoid differentiation. Overall, our adaptable analysis framework provides a generalizable method for reproducibly identifying cell types across FC datasets in complex tissues.
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Affiliation(s)
- Rhalena A. Thomas
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC H3A 2B4, Canada
| | - Julien Sirois
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC H3A 2B4, Canada
| | - Shuming Li
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC H3A 2B4, Canada
| | - Alexandre Gestin
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Ghislaine Deyab
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Valerio E.C. Piscopo
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC H3A 2B4, Canada
| | - Paula Lépine
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC H3A 2B4, Canada
| | - Meghna Mathur
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC H3A 2B4, Canada
| | - Carol X.-Q. Chen
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC H3A 2B4, Canada
| | - Vincent Soubannier
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC H3A 2B4, Canada
| | - Taylor M. Goldsmith
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC H3A 2B4, Canada
| | - Lama Fawaz
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Thomas M. Durcan
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC H3A 2B4, Canada
| | - Edward A. Fon
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC H3A 2B4, Canada
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18
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Xiao Y, Li Y, Zhao H. Spatiotemporal metabolomic approaches to the cancer-immunity panorama: a methodological perspective. Mol Cancer 2024; 23:202. [PMID: 39294747 PMCID: PMC11409752 DOI: 10.1186/s12943-024-02113-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 09/05/2024] [Indexed: 09/21/2024] Open
Abstract
Metabolic reprogramming drives the development of an immunosuppressive tumor microenvironment (TME) through various pathways, contributing to cancer progression and reducing the effectiveness of anticancer immunotherapy. However, our understanding of the metabolic landscape within the tumor-immune context has been limited by conventional metabolic measurements, which have not provided comprehensive insights into the spatiotemporal heterogeneity of metabolism within TME. The emergence of single-cell, spatial, and in vivo metabolomic technologies has now enabled detailed and unbiased analysis, revealing unprecedented spatiotemporal heterogeneity that is particularly valuable in the field of cancer immunology. This review summarizes the methodologies of metabolomics and metabolic regulomics that can be applied to the study of cancer-immunity across single-cell, spatial, and in vivo dimensions, and systematically assesses their benefits and limitations.
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Affiliation(s)
- Yang Xiao
- Chongqing University Cancer Hospital, School of Medicine, Chongqing University, Chongqing, 400044, China
| | - Yongsheng Li
- Chongqing University Cancer Hospital, School of Medicine, Chongqing University, Chongqing, 400044, China.
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China.
| | - Huakan Zhao
- Chongqing University Cancer Hospital, School of Medicine, Chongqing University, Chongqing, 400044, China.
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China.
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19
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Sun H, Yu S, Casals AM, Bäckström A, Lu Y, Lindskog C, Lundberg E, Murphy RF. Flexible and robust cell type annotation for highly multiplexed tissue images. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.12.612510. [PMID: 39345395 PMCID: PMC11429614 DOI: 10.1101/2024.09.12.612510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Identifying cell types in highly multiplexed images is essential for understanding tissue spatial organization. Current cell type annotation methods often rely on extensive reference images and manual adjustments. In this work, we present a tool, Robust Image-Based Cell Annotator (RIBCA), that enables accurate, automated, unbiased, and fine-grained cell type annotation for images with a wide range of antibody panels, without requiring additional model training or human intervention. Our tool has successfully annotated over 1 million cells, revealing the spatial organization of various cell types across more than 40 different human tissues. It is open-source and features a modular design, allowing for easy extension to additional cell types.
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Affiliation(s)
- Huangqingbo Sun
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Shiqiu Yu
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | | | - Anna Bäckström
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Yuxin Lu
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Emma Lundberg
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
- Department of Pathology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA
| | - Robert F Murphy
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
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20
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Goggin SM, Zunder ER. ESCHR: a hyperparameter-randomized ensemble approach for robust clustering across diverse datasets. Genome Biol 2024; 25:242. [PMID: 39285487 PMCID: PMC11406744 DOI: 10.1186/s13059-024-03386-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 08/30/2024] [Indexed: 09/19/2024] Open
Abstract
Clustering is widely used for single-cell analysis, but current methods are limited in accuracy, robustness, ease of use, and interpretability. To address these limitations, we developed an ensemble clustering method that outperforms other methods at hard clustering without the need for hyperparameter tuning. It also performs soft clustering to characterize continuum-like regions and quantify clustering uncertainty, demonstrated here by mapping the connectivity and intermediate transitions between MNIST handwritten digits and between hypothalamic tanycyte subpopulations. This hyperparameter-randomized ensemble approach improves the accuracy, robustness, ease of use, and interpretability of single-cell clustering, and may prove useful in other fields as well.
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Affiliation(s)
- Sarah M Goggin
- Neuroscience Graduate Program, School of Medicine, University of Virginia, Charlottesville, VA, 22902, USA
| | - Eli R Zunder
- Neuroscience Graduate Program, School of Medicine, University of Virginia, Charlottesville, VA, 22902, USA.
- Department of Biomedical Engineering, School of Engineering, University of Virginia, Charlottesville, VA, 22902, USA.
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21
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Snacel-Fazy E, Soubéran A, Grange M, Joseph K, Colin C, Morando P, Luche H, Pagano A, Brustlein S, Debarbieux F, Toutain S, Siret C, van de Pavert SA, Rougon G, Figarella-Branger D, Ravi VM, Tabouret E, Tchoghandjian A. SMAC mimetic drives microglia phenotype and glioblastoma immune microenvironment. Cell Death Dis 2024; 15:676. [PMID: 39278921 PMCID: PMC11402972 DOI: 10.1038/s41419-024-07056-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 09/02/2024] [Accepted: 09/04/2024] [Indexed: 09/18/2024]
Abstract
Tumor-associated macrophages/microglia (TAMs) are highly plastic and heterogeneous immune cells that can be immune-supportive or tumor-supportive depending of the microenvironment. TAMs are the most abundant immune cells in glioblastoma (GB), and play a key role in immunosuppression. Therefore, TAMs reprogramming toward immune-supportive cells is a promising strategy to overcome immunosuppression. By leveraging scRNAseq human GB databases, we identified that Inhibitor of Apoptosis Proteins (IAP) were expressed by TAMs. To investigate their role in TAMs-related immunosuppression, we antagonized IAP using the central nervous system permeant SMAC mimetic GDC-0152 (SMg). On explants and cultured immune cells isolated from human GB samples, SMg modified TAMs activity. We showed that SMg treatment promoted microglia pro-apoptotic and anti-tumoral function via caspase-3 pro-inflammatory cleavage and the inhibition of tumoroids growth. Then we designed a relevant immunogenic mouse GB model to decipher the spatio-temporal densities, distribution, phenotypes and function of TAMs with or without SMg treatment. We used 3D imaging techniques, a transgenic mouse with fluorescent TAM subsets and mass cytometry. We confirmed that SMg promoted microglia activation, antigen-presenting function and tumor infiltration. In addition, we observed a remodeling of blood vessels, a decrease in anti-inflammatory macrophages and an increased level of monocytes and their mo-DC progeny. This remodeling of the TAM landscape is associated with an increase in CD8 T cell density and activation. Altogether, these results demonstrated that SMg drives the immunosuppressive basal microglia toward an active phenotype with pro-apoptotic and anti-tumoral function and modifies the GB immune landscape. This identifies IAP as targets of choice for a potential mechanism-based therapeutic strategy and SMg as a promising molecule for this application.
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Affiliation(s)
- Emmanuel Snacel-Fazy
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France
- Aix-Marseille Univ, Réseau Préclinique et Translationnel de Recherche en Neuro-Oncologie, Plateforme PETRA"TECH", Marseille, France
| | - Aurélie Soubéran
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France
- Aix-Marseille Univ, Réseau Préclinique et Translationnel de Recherche en Neuro-Oncologie, Plateforme PETRA"TECH", Marseille, France
- APHM, CHU Timone, Service de Neurooncologie, Marseille, France
| | - Magali Grange
- Centre d'Immunophénomique (CIPHE), Aix Marseille Université, Inserm, CNRS, Marseille, France
| | - Kevin Joseph
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany
- 3D-Brain Models for Neurodegenerative Diseases, Medical Center, University of Freiburg, Freiburg, Germany
- Center of Advanced Surgical Tissue Analysis (CAST), University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carole Colin
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France
- Aix-Marseille Univ, Réseau Préclinique et Translationnel de Recherche en Neuro-Oncologie, Plateforme PETRA"TECH", Marseille, France
| | - Philippe Morando
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France
- Aix-Marseille Univ, Réseau Préclinique et Translationnel de Recherche en Neuro-Oncologie, Plateforme PETRA"TECH", Marseille, France
| | - Hervé Luche
- Centre d'Immunophénomique (CIPHE), Aix Marseille Université, Inserm, CNRS, Marseille, France
| | - Alessandra Pagano
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France
| | - Sophie Brustlein
- Aix-Marseille Univ, INSERM, INMED, Turing Center for Living System, Marseille, France
| | - Franck Debarbieux
- Aix-Marseille Univ, CNRS, INT, Institut de Neurosciences de la Timone, Marseille, France
| | - Soline Toutain
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France
- Aix-Marseille Univ, Réseau Préclinique et Translationnel de Recherche en Neuro-Oncologie, Plateforme PETRA"TECH", Marseille, France
| | - Carole Siret
- Aix-Marseille Univ, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Serge A van de Pavert
- Aix-Marseille Univ, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Geneviève Rougon
- Aix-Marseille Univ, CNRS, INT, Institut de Neurosciences de la Timone, Marseille, France
| | | | - Vidhya Madapusi Ravi
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany
- 3D-Brain Models for Neurodegenerative Diseases, Medical Center, University of Freiburg, Freiburg, Germany
- Center of Advanced Surgical Tissue Analysis (CAST), University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Emeline Tabouret
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France
- APHM, CHU Timone, Service de Neurooncologie, Marseille, France
- Aix-Marseille Univ, Réseau Préclinique et Translationnel de Recherche en Neuro-Oncologie, Plateforme PE"TRANSLA", Marseille, France
| | - Aurélie Tchoghandjian
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, GlioME Team, Marseille, France.
- Aix-Marseille Univ, Réseau Préclinique et Translationnel de Recherche en Neuro-Oncologie, Plateforme PETRA"TECH", Marseille, France.
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22
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Kitanovski S, Cao Y, Ttoouli D, Farahpour F, Wang J, Hoffmann D. scBubbletree: computational approach for visualization of single cell RNA-seq data. BMC Bioinformatics 2024; 25:302. [PMID: 39271980 PMCID: PMC11401305 DOI: 10.1186/s12859-024-05927-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 09/09/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Visualization approaches transform high-dimensional data from single cell RNA sequencing (scRNA-seq) experiments into two-dimensional plots that are used for analysis of cell relationships, and as a means of reporting biological insights. Yet, many standard approaches generate visuals that suffer from overplotting, lack of quantitative information, and distort global and local properties of biological patterns relative to the original high-dimensional space. RESULTS We present scBubbletree, a new, scalable method for visualization of scRNA-seq data. The method identifies clusters of cells of similar transcriptomes and visualizes such clusters as "bubbles" at the tips of dendrograms (bubble trees), corresponding to quantitative summaries of cluster properties and relationships. scBubbletree stacks bubble trees with further cluster-associated information in a visually easily accessible way, thus facilitating quantitative assessment and biological interpretation of scRNA-seq data. We demonstrate this with large scRNA-seq data sets, including one with over 1.2 million cells. CONCLUSIONS To facilitate coherent quantification and visualization of scRNA-seq data we developed the R-package scBubbletree, which is freely available as part of the Bioconductor repository at: https://bioconductor.org/packages/scBubbletree/.
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Affiliation(s)
- Simo Kitanovski
- Bioinformatics and Computational Biophysics, Faculty of Biology and Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45141, Essen, Germany.
| | - Yingying Cao
- Bioinformatics and Computational Biophysics, Faculty of Biology and Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45141, Essen, Germany
| | - Dimitris Ttoouli
- Bioinformatics and Computational Biophysics, Faculty of Biology and Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45141, Essen, Germany
| | - Farnoush Farahpour
- Bioinformatics and Computational Biophysics, Faculty of Biology and Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45141, Essen, Germany
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Jun Wang
- Bioinformatics and Computational Biophysics, Faculty of Biology and Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45141, Essen, Germany
- National Clinical Research Centre for Infectious Diseases, The Third People's Hospital of Shenzhen and The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, 518112, Guangdong Province, China
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Faculty of Biology and Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45141, Essen, Germany.
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23
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Booth JS, Rapaka RR, McArthur MA, Fresnay S, Darton TC, Blohmke CJ, Jones C, Waddington CS, Levine MM, Pollard AJ, Sztein MB. Role of circulating T follicular helper subsets following Ty21a immunization and oral challenge with wild type S. Typhi in humans. Front Immunol 2024; 15:1384642. [PMID: 39328410 PMCID: PMC11424897 DOI: 10.3389/fimmu.2024.1384642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 08/16/2024] [Indexed: 09/28/2024] Open
Abstract
Despite decades of intense research, our understanding of the correlates of protection against Salmonella Typhi (S. Typhi) infection and disease remains incomplete. T follicular helper cells (TFH), an important link between cellular and humoral immunity, play an important role in the development and production of high affinity antibodies. While traditional TFH cells reside in germinal centers, circulating TFH (cTFH) (a memory subset of TFH) are present in blood. We used specimens from a typhoid controlled human infection model whereby participants were immunized with Ty21a live attenuated S. Typhi vaccine and then challenged with virulent S. Typhi. Some participants developed typhoid disease (TD) and some did not (NoTD), which allowed us to assess the association of cTFH subsets in the development and prevention of typhoid disease. Of note, the frequencies of cTFH were higher in NoTD than in TD participants, particularly 7 days after challenge. Furthermore, the frequencies of cTFH2 and cTFH17, but not cTFH1 subsets were higher in NoTD than TD participants. However, we observed that ex-vivo expression of activation and homing markers were higher in TD than in NoTD participants, particularly after challenge. Moreover, cTFH subsets produced higher levels of S. Typhi-specific responses (cytokines/chemokines) in both the immunization and challenge phases. Interestingly, unsupervised analysis revealed unique clusters with distinct signatures for each cTFH subset that may play a role in either the development or prevention of typhoid disease. Importantly, we observed associations between frequencies of defined cTFH subsets and anti-S. Typhi antibodies. Taken together, our results suggest that circulating TFH2 and TFH17 subsets might play an important role in the development or prevention of typhoid disease. The contribution of these clusters was found to be distinct in the immunization and/or challenge phases. These results have important implications for vaccines aimed at inducing long-lived protective T cell and antibody responses.
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Affiliation(s)
- Jayaum S Booth
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Rekha R Rapaka
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Monica A McArthur
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
- Global Clinical Development, Sanofi, Swiftwater, PA, United States
| | - Stephanie Fresnay
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
- Rockville Center for Vaccine Research, GlaxsoSmithKline (GSK), Rockville, MD, United States
| | - Thomas C Darton
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, and the National Institute for Health and Care Research (NIHR), Oxford Biomedical Research Centre, Oxford, United Kingdom
- Clinical Infection Research Group, Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, and the National Institute for Health and Care Research (NIHR), Sheffield Biomedical Research Centre, Sheffield, United Kingdom
| | - Christoph J Blohmke
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, and the National Institute for Health and Care Research (NIHR), Oxford Biomedical Research Centre, Oxford, United Kingdom
- GlaxsoSmithKline (GSK) Vaccines, London, United Kingdom
| | - Claire Jones
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, and the National Institute for Health and Care Research (NIHR), Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Claire S Waddington
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, and the National Institute for Health and Care Research (NIHR), Oxford Biomedical Research Centre, Oxford, United Kingdom
- Department of Infection, Imperial College Healthcare, National Health Service (NHS) Trust, London, United Kingdom
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Myron M Levine
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, and the National Institute for Health and Care Research (NIHR), Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Marcelo B Sztein
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Tumor Immunology and Immunotherapy Program, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, United States
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24
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Gan S, Macalinao DG, Shahoei SH, Tian L, Jin X, Basnet H, Bibby C, Muller JT, Atri P, Seffar E, Chatila W, Karacay A, Chanda P, Hadjantonakis AK, Schultz N, Brogi E, Bale TA, Moss NS, Murali R, Pe'er D, Massagué J. Distinct tumor architectures and microenvironments for the initiation of breast cancer metastasis in the brain. Cancer Cell 2024:S1535-6108(24)00314-3. [PMID: 39270646 DOI: 10.1016/j.ccell.2024.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 12/15/2023] [Accepted: 08/20/2024] [Indexed: 09/15/2024]
Abstract
Brain metastasis, a serious complication of cancer, hinges on the initial survival, microenvironment adaptation, and outgrowth of disseminated cancer cells. To understand the early stages of brain colonization, we investigated two prevalent sources of cerebral relapse, triple-negative (TNBC) and HER2+ (HER2BC) breast cancers. Using mouse models and human tissue samples, we found that these tumor types colonize the brain, with a preference for distinctive tumor architectures, stromal interfaces, and autocrine programs. TNBC models tend to form perivascular sheaths with diffusive contact with astrocytes and microglia. In contrast, HER2BC models tend to form compact spheroids driven by autonomous tenascin C production, segregating stromal cells to the periphery. Single-cell transcriptomics of the tumor microenvironment revealed that these architectures evoke differential Alzheimer's disease-associated microglia (DAM) responses and engagement of the GAS6 receptor AXL. The spatial features of the two modes of brain colonization have relevance for leveraging the stroma to treat brain metastasis.
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Affiliation(s)
- Siting Gan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Danilo G Macalinao
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sayyed Hamed Shahoei
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lin Tian
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xin Jin
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province 310024, China; Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Harihar Basnet
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Catherine Bibby
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - James T Muller
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Pranita Atri
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Evan Seffar
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Walid Chatila
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ali Karacay
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Pharto Chanda
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nikolaus Schultz
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Edi Brogi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tejus A Bale
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nelson S Moss
- Department of Neurological Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rajmohan Murali
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA
| | - Joan Massagué
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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25
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Da Silva Filho J, Herder V, Gibbins MP, Dos Reis MF, Melo GC, Haley MJ, Judice CC, Val FFA, Borba M, Tavella TA, de Sousa Sampaio V, Attipa C, McMonagle F, Wright D, de Lacerda MVG, Costa FTM, Couper KN, Marcelo Monteiro W, de Lima Ferreira LC, Moxon CA, Palmarini M, Marti M. A spatially resolved single-cell lung atlas integrated with clinical and blood signatures distinguishes COVID-19 disease trajectories. Sci Transl Med 2024; 16:eadk9149. [PMID: 39259811 DOI: 10.1126/scitranslmed.adk9149] [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: 09/26/2023] [Revised: 02/15/2024] [Accepted: 08/05/2024] [Indexed: 09/13/2024]
Abstract
COVID-19 is characterized by a broad range of symptoms and disease trajectories. Understanding the correlation between clinical biomarkers and lung pathology during acute COVID-19 is necessary to understand its diverse pathogenesis and inform more effective treatments. Here, we present an integrated analysis of longitudinal clinical parameters, peripheral blood markers, and lung pathology in 142 Brazilian patients hospitalized with COVID-19. We identified core clinical and peripheral blood signatures differentiating disease progression between patients who recovered from severe disease compared with those who succumbed to the disease. Signatures were heterogeneous among fatal cases yet clustered into two patient groups: "early death" (<15 days until death) and "late death" (>15 days). Progression to early death was characterized systemically and in lung histopathological samples by rapid endothelial and myeloid activation and the presence of thrombi associated with SARS-CoV-2+ macrophages. In contrast, progression to late death was associated with fibrosis, apoptosis, and SARS-CoV-2+ epithelial cells in postmortem lung tissue. In late death cases, cytotoxicity, interferon, and T helper 17 (TH17) signatures were only detectable in the peripheral blood after 2 weeks of hospitalization. Progression to recovery was associated with higher lymphocyte counts, TH2 responses, and anti-inflammatory-mediated responses. By integrating antemortem longitudinal blood signatures and spatial single-cell lung signatures from postmortem lung samples, we defined clinical parameters that could be used to help predict COVID-19 outcomes.
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Affiliation(s)
- João Da Silva Filho
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Institute of Parasitology Zurich (IPZ), VetSuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Vanessa Herder
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Matthew P Gibbins
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Institute of Parasitology Zurich (IPZ), VetSuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Monique Freire Dos Reis
- Department of Education and Research, Oncology Control Centre of Amazonas State (FCECON), Manaus, Brazil
- Postgraduate Program in Tropical Medicine, University of Amazonas State, Manaus, Brazil
- Federal University of Amazonas, Manaus, Brazil
- Amazonas Oncology Control Center Foundation, Manaus, Brazil
| | | | - Michael J Haley
- Department of Immunology, Immunity to Infection and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Carla Cristina Judice
- Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, Campinas, Brazil
| | - Fernando Fonseca Almeida Val
- Postgraduate Program in Tropical Medicine, University of Amazonas State, Manaus, Brazil
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Mayla Borba
- Postgraduate Program in Tropical Medicine, University of Amazonas State, Manaus, Brazil
- Delphina Rinaldi Abdel Aziz Emergency Hospital (HPSDRA), Manaus, Brazil
| | - Tatyana Almeida Tavella
- Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, Campinas, Brazil
- INSERM U1016, CNRS UMR8104, University of Paris Cité, Institut Cochin, Paris, France
| | | | - Charalampos Attipa
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Fiona McMonagle
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Glasgow Imaging Facility/School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Derek Wright
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Marcus Vinicius Guimaraes de Lacerda
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil
- Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
- University of Texas Medical Branch, Galveston, TX, USA
| | | | - Kevin N Couper
- Department of Immunology, Immunity to Infection and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Wuelton Marcelo Monteiro
- Postgraduate Program in Tropical Medicine, University of Amazonas State, Manaus, Brazil
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Luiz Carlos de Lima Ferreira
- Postgraduate Program in Tropical Medicine, University of Amazonas State, Manaus, Brazil
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Christopher Alan Moxon
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | | | - Matthias Marti
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Institute of Parasitology Zurich (IPZ), VetSuisse Faculty, University of Zurich, Zurich, Switzerland
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26
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Raeber ME, Caspar DP, Zurbuchen Y, Guo N, Schmid J, Michler J, Martin AC, Steiner UC, Moor AE, Koning F, Boyman O. Interleukin-2 immunotherapy reveals human regulatory T cell subsets with distinct functional and tissue-homing characteristics. Immunity 2024; 57:2232-2250.e10. [PMID: 39137779 DOI: 10.1016/j.immuni.2024.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 05/24/2024] [Accepted: 07/18/2024] [Indexed: 08/15/2024]
Abstract
Due to its stimulatory potential for immunomodulatory CD4+ regulatory T (Treg) cells, low-dose interleukin-2 (IL-2) immunotherapy has gained considerable attention for the treatment of autoimmune diseases. In this investigator-initiated single-arm non-placebo-controlled phase-2 clinical trial of low-dose IL-2 immunotherapy in systemic lupus erythematosus (SLE) patients, we generated a comprehensive atlas of in vivo human immune responses to low-dose IL-2. We performed an in-depth study of circulating and cutaneous immune cells by imaging mass cytometry, high-parameter flow cytometry, transcriptomics, and targeted serum proteomics. Low-dose IL-2 stimulated various circulating immune cells, including Treg cells with a skin-homing phenotype that appeared in the skin of SLE patients in close interaction with endothelial cells. Analysis of surface proteins and transcriptomes revealed different IL-2-driven Treg cell activation programs, including gut-homing CD38+, skin-homing HLA-DR+, and highly proliferative inflammation-homing CD38+ HLA-DR+ Treg cells. Collectively, these data define the distinct human Treg cell subsets that are responsive to IL-2 immunotherapy.
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Affiliation(s)
- Miro E Raeber
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland; Faculty of Medicine, University of Zurich, 8032 Zurich, Switzerland; Center of Human Immunology, University of Zurich, 8006 Zurich, Switzerland
| | - Dominic P Caspar
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Yves Zurbuchen
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Nannan Guo
- Department of Immunology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Jonas Schmid
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Jan Michler
- Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Alina C Martin
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Urs C Steiner
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland; Faculty of Medicine, University of Zurich, 8032 Zurich, Switzerland; Center of Human Immunology, University of Zurich, 8006 Zurich, Switzerland; Faculty of Science, University of Zurich, 8057 Zurich, Switzerland.
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27
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Argerich J, Garma LD, López-Cano M, Álvarez-Montoya P, Gómez-Acero L, Fernández-Dueñas V, Muñoz-Manchado AB, Aso E, Boxer A, Andres-Benito P, Svenningsson P, Ciruela F. GPR37 processing in neurodegeneration: a potential marker for Parkinson's Disease progression rate. NPJ Parkinsons Dis 2024; 10:172. [PMID: 39256360 PMCID: PMC11387472 DOI: 10.1038/s41531-024-00788-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 08/27/2024] [Indexed: 09/12/2024] Open
Abstract
The orphan G protein-coupled receptor 37 (GPR37), widely associated with Parkinson's disease (PD), undergoes proteolytic processing under physiological conditions. The N-terminus domain is proteolyzed by a disintegrin and metalloproteinase 10 (ADAM-10), which generates various membrane receptor forms and ectodomain shedding (ecto-GPR37) in the extracellular environment. We investigated the processing and density of GPR37 in several neurodegenerative conditions, including Lewy body disease (LBD), multiple system atrophy (MSA), corticobasal degeneration (CBD), progressive supranuclear palsy (PSP), and Alzheimer's disease (AD). The presence of ecto-GPR37 peptides in the cerebrospinal fluid (CSF) of PD, MSA, CBD and PSP patients was assessed through an in-house nanoluciferase-based immunoassay. This study identified increased receptor processing in early-stage LBD within the PFC and striatum, key brain areas in neurodegeneration. In MSA only the 52 kDa form of GPR37 appeared in the striatum. This form was also significantly elevated in the striatum of AD necropsies. On the contrary, GPR37 processing remained unchanged in the brains of CBD and PSP patients. Furthermore, while CSF ecto-GPR37 increased in PD patients, its levels remained unchanged in MSA, CBD, and PSP subjects. Importantly, patients with PD with rapid progression of the disease did not have elevated ecto-GPR37 in the CSF, while those with slow progression showed a significant increase, suggesting a possible prognostic use of ecto-GPR37 in PD. This research underscores the distinctive processing and density patterns of GPR37 in neurodegenerative diseases, providing crucial insights into its potential role as an indicator of PD progression rates.
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Affiliation(s)
- Josep Argerich
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907, L'Hospitalet de Llobregat, Spain
- Neuropharmacology & Pain Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, 08907, L'Hospitalet de Llobregat, Spain
| | - Leonardo D Garma
- Breast Cancer Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas - CNIO, 28029, Madrid, Spain
| | - Marc López-Cano
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907, L'Hospitalet de Llobregat, Spain
- Neuropharmacology & Pain Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, 08907, L'Hospitalet de Llobregat, Spain
| | - Paula Álvarez-Montoya
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907, L'Hospitalet de Llobregat, Spain
- Neuropharmacology & Pain Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, 08907, L'Hospitalet de Llobregat, Spain
| | - Laura Gómez-Acero
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907, L'Hospitalet de Llobregat, Spain
- Neuropharmacology & Pain Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, 08907, L'Hospitalet de Llobregat, Spain
| | - Víctor Fernández-Dueñas
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907, L'Hospitalet de Llobregat, Spain
- Neuropharmacology & Pain Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, 08907, L'Hospitalet de Llobregat, Spain
| | - Ana B Muñoz-Manchado
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17177, Sweden
- Department of Pathological Anatomy, Cellular Biology, Histology, History of Science, Legal and Forensic Medicine and Toxicology. Biomedical Research and Innovation Institute of Cadiz (INiBICA). University of Cádiz, 11002, Cádiz, Spain
| | - Ester Aso
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907, L'Hospitalet de Llobregat, Spain
- Neuropharmacology & Pain Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, 08907, L'Hospitalet de Llobregat, Spain
| | - Adam Boxer
- Memory and Aging Center, University of California, San Francisco, CA, 94158, USA
| | - Pol Andres-Benito
- Neurological disorders and neurogenetics Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, 08907, L'Hospitalet de Llobregat, Spain
| | - Per Svenningsson
- Laboratory of Translational Neuropharmacology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, SE-17177, Sweden.
- Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
| | - Francisco Ciruela
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907, L'Hospitalet de Llobregat, Spain.
- Neuropharmacology & Pain Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, 08907, L'Hospitalet de Llobregat, Spain.
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28
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Arya D, Jaggi U, Wang S, Tormanen K, Che M, Mahov S, Jin L, Ghiasi H. A novel GFP-based strategy to quantitate cellular spatial associations in HSV-1 viral pathogenesis. mBio 2024:e0145424. [PMID: 39248563 DOI: 10.1128/mbio.01454-24] [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: 05/10/2024] [Accepted: 08/13/2024] [Indexed: 09/10/2024] Open
Abstract
Periodic reactivation of herpes simplex virus type 1 (HSV-1) triggers immune responses that result in corneal scarring (CS), known as herpes stromal keratitis (HSK). Despite considerable research, fully understanding HSK and eliminating it remains challenging due to a lack of comprehensive analysis of HSV-1-infected immune cells in both corneas and trigeminal ganglia (TG). We engineered a recombinant HSV-1 expressing green fluorescent protein (GFP) in the virulent McKrae virus strain that does not require corneal scarification for efficient virus replication (GFP-McKrae). Next-generation sequencing (NGS) analysis, along with in vitro and in vivo assays, showed that GFP-McKrae virus was similar to WT-McKrae virus. Furthermore, corneal cells infected with GFP-McKrae were quantitatively analyzed using image mass cytometry (IMC). The single-cell reconstruction data generated cellular maps of corneas based on the expression of 25 immune cell markers in GFP-McKrae-infected mice. Corneas from mock control mice showed the presence of T cells and macrophages, whereas corneas from GFP-McKrae-infected mice on days 3 and 5 post-infection (PI) exhibited increased immune cells. Notably, on day 3 PI, increased GFP expression was observed in closely situated clusters of DCs, macrophages, and epithelial cells. By day 5 PI, macrophages and T cells became prominent. Finally, immunostaining methods detected HSV-1 or GFP and gD proteins in latently infected TG. This study presents a valuable strategy for identifying cellular spatial associations in viral pathogenesis and holds promise for future therapeutic applications.IMPORTANCEThe goal of this study was to establish quantitative approaches to analyze immune cell markers in HSV-1-infected intact corneas and trigeminal ganglia from primary and latently infected mice. This allowed us to define spatial and temporal interactions between specific immune cells and their potential roles in virus replication and latency. To accomplish this important goal, we took advantage of the utility of GFP-McKrae virus as a valuable research tool while also highlighting its potential to uncover previously unrecognized cell types that play pivotal roles in HSV-1 replication and latency. Such insights will pave the way for developing targeted therapeutic approaches to tackle HSV-1 infections more effectively.
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Affiliation(s)
- Deepak Arya
- Center for Neurobiology and Vaccine Development, Ophthalmology Research, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ujjaldeep Jaggi
- Center for Neurobiology and Vaccine Development, Ophthalmology Research, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shaohui Wang
- Center for Neurobiology and Vaccine Development, Ophthalmology Research, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kati Tormanen
- Center for Neurobiology and Vaccine Development, Ophthalmology Research, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Mingtian Che
- Applied Genomics, Computation, and Translational Core, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Simeon Mahov
- Applied Genomics, Computation, and Translational Core, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ling Jin
- Department of Biomedical Sciences, Oregon State University, College of Veterinary Medicine, Corvallis, Oregon, USA
| | - Homayon Ghiasi
- Center for Neurobiology and Vaccine Development, Ophthalmology Research, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
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29
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Sun J, Choy D, Sompairac N, Jamshidi S, Mishto M, Kordasti S. ImmCellTyper facilitates systematic mass cytometry data analysis for deep immune profiling. eLife 2024; 13:RP95494. [PMID: 39240985 PMCID: PMC11379455 DOI: 10.7554/elife.95494] [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] [Indexed: 09/08/2024] Open
Abstract
Mass cytometry is a cutting-edge high-dimensional technology for profiling marker expression at the single-cell level, advancing clinical research in immune monitoring. Nevertheless, the vast data generated by cytometry by time-of-flight (CyTOF) poses a significant analytical challenge. To address this, we describe ImmCellTyper (https://github.com/JingAnyaSun/ImmCellTyper), a novel toolkit for CyTOF data analysis. This framework incorporates BinaryClust, an in-house developed semi-supervised clustering tool that automatically identifies main cell types. BinaryClust outperforms existing clustering tools in accuracy and speed, as shown in benchmarks with two datasets of approximately 4 million cells, matching the precision of manual gating by human experts. Furthermore, ImmCellTyper offers various visualisation and analytical tools, spanning from quality control to differential analysis, tailored to users' specific needs for a comprehensive CyTOF data analysis solution. The workflow includes five key steps: (1) batch effect evaluation and correction, (2) data quality control and pre-processing, (3) main cell lineage characterisation and quantification, (4) in-depth investigation of specific cell types; and (5) differential analysis of cell abundance and functional marker expression across study groups. Overall, ImmCellTyper combines expert biological knowledge in a semi-supervised approach to accurately deconvolute well-defined main cell lineages, while maintaining the potential of unsupervised methods to discover novel cell subsets, thus facilitating high-dimensional immune profiling.
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Affiliation(s)
- Jing Sun
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Desmond Choy
- School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Nicolas Sompairac
- School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Shirin Jamshidi
- School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
- Research Group of Molecular Immunology, Francis Crick Institute, London, United Kingdom
| | - Shahram Kordasti
- School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
- Haematology Department, Guy's Hospital, London, United Kingdom
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
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30
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Clark PA, Gogoi M, Rodriguez-Rodriguez N, Ferreira ACF, Murphy JE, Walker JA, Crisp A, Jolin HE, Shields JD, McKenzie ANJ. Recipient tissue microenvironment determines developmental path of intestinal innate lymphoid progenitors. Nat Commun 2024; 15:7809. [PMID: 39242588 PMCID: PMC11379955 DOI: 10.1038/s41467-024-52155-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/27/2024] [Indexed: 09/09/2024] Open
Abstract
Innate lymphoid cells (ILCs) are critical in maintaining tissue homeostasis, and during infection and inflammation. Here we identify, by using combinatorial reporter mice, a rare ILC progenitor (ILCP) population, resident to the small intestinal lamina propria (siLP) in adult mice. Transfer of siLP-ILCP into recipients generates group 1 ILCs (including ILC1 and NK cells), ILC2s and ILC3s within the intestinal microenvironment, but almost exclusively group 1 ILCs in the liver, lung and spleen. Single cell gene expression analysis and high dimensional spectral cytometry analysis of the siLP-ILCPs and ILC progeny indicate that the phenotype of the group 1 ILC progeny is also influenced by the tissue microenvironment. Thus, a local pool of siLP-ILCP can contribute to pan-ILC generation in the intestinal microenvironment but has more restricted potential in other tissues, with a greater propensity than bone marrow-derived ILCPs to favour ILC1 and ILC3 production. Therefore, ILCP potential is influenced by both tissue of origin and the microenvironment during development. This may provide additional flexibility during the tuning of immune reactions.
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Affiliation(s)
- Paula A Clark
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.
| | - Mayuri Gogoi
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | | | - Jane E Murphy
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Alastair Crisp
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Helen E Jolin
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Jacqueline D Shields
- Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, United Kingdom
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31
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Wang X, Lin J, Liu H, Zhao C, Tu Z, Xu D, Zhang E, Zhou Z, Qi X, Wang X, Lin Z. Single-cell and spatial sequencing identifies senescent and germinal tumor cells in adamantinomatous craniopharyngiomas. Cell Biosci 2024; 14:112. [PMID: 39223689 PMCID: PMC11370139 DOI: 10.1186/s13578-024-01299-1] [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: 06/17/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024] Open
Abstract
Adamantinomatous craniopharyngioma (ACP) is a clinically aggressive tumor without effective treatment method. Previous studies proposed a paracrine tumorigenesis model, in which oncogenic β-catenin induces senescence in pituitary stem cells and the senescent cells lead the formation of paracrine tumors through secretion of pro-tumorigenic factors. However, there lacks characterization on senescent cells in ACPs. Here, we profiled 12 ACPs with single-cell RNA and TCR-sequencing to elucidate the cellular atlas in ACPs and 3 of them were also subject to spatial sequencing to localize different subpopulations of the tumor cells. In total, we obtained the transcriptome profiles of 70,682 cells. Tumor cells, which were unambiguously identified through the cellular mutation status of the driver CTNNB1 mutations, were clustered into 6 subsets. The whorl-like cluster (WC) cells show distinct molecular features from the other tumor cells and the palisading epithelium (PE) cells consists of a proliferating subset. Other than typical PE and WC, we identified two novel subpopulations of the tumor cells. In one subpopulation, the cells express a high level of cytokines, e.g., FDCSP and S100A8/A9, and are enriched with the senescence-associated secretory phenotype (SASP) factors. Hematoxylin and eosin staining reveals that these SASP cells lack an ordered structures and their nuclei are elongated. In the other subpopulation, the cell sizes are small and they are tightly packed together with an unusual high density expressing a high level of mitochondrial genes (median 10.9%). These cells are the origin of the tumor developmental trajectories revealed by RNA velocity and pseudo-time analysis. Single-cell RNA and TCR analysis reveals that some ACPs are infiltrated with clonally expanded cytotoxic T cells. We propose a hypothesis that WC and PE are formed via different negative regulation mechanisms of the overactivated WNT/β-catenin signaling which provides a new understanding on the tumorigenesis of ACPs. The study lays a foundation for future studies on targeting senescent cells in ACPs with senolytic compounds or other therapeutic agents.
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Affiliation(s)
- Xianlong Wang
- Department of Bioinformatics, School of Medical Technology and Engineering, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.
| | - Jincheng Lin
- Department of Bioinformatics, School of Medical Technology and Engineering, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Hongxing Liu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Chuan Zhao
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
- Department of Neuro-Oncology, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Zhiwei Tu
- Department of Bioinformatics, School of Medical Technology and Engineering, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Dapeng Xu
- Department of Bioinformatics, School of Medical Technology and Engineering, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - En Zhang
- Department of Bioinformatics, School of Medical Technology and Engineering, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Zhongqing Zhou
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Xueling Qi
- Department of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Xingfu Wang
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Zhixiong Lin
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China.
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32
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Reyes JGA, Ni D, Santner-Nanan B, Pinget GV, Kraftova L, Ashhurst TM, Marsh-Wakefield F, Wishart CL, Tan J, Hsu P, King NJC, Macia L, Nanan R. A unique human cord blood CD8 +CD45RA +CD27 +CD161 + T-cell subset identified by flow cytometric data analysis using Seurat. Immunology 2024; 173:106-124. [PMID: 38798051 DOI: 10.1111/imm.13803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
Advances in single-cell level analytical techniques, especially cytometric approaches, have led to profound innovation in biomedical research, particularly in the field of clinical immunology. This has resulted in an expansion of high-dimensional data, posing great challenges for comprehensive and unbiased analysis. Conventional manual analysis is thus becoming untenable to handle these challenges. Furthermore, most newly developed computational methods lack flexibility and interoperability, hampering their accessibility and usability. Here, we adapted Seurat, an R package originally developed for single-cell RNA sequencing (scRNA-seq) analysis, for high-dimensional flow cytometric data analysis. Based on a 20-marker antibody panel and analyses of T-cell profiles in both adult blood and cord blood (CB), we showcased the robust capacity of Seurat in flow cytometric data analysis, which was further validated by Spectre, another high-dimensional cytometric data analysis package, and conventional manual analysis. Importantly, we identified a unique CD8+ T-cell population defined as CD8+CD45RA+CD27+CD161+ T cell that was predominantly present in CB. We characterised its IFN-γ-producing and potential cytotoxic properties using flow cytometry experiments and scRNA-seq analysis from a published dataset. Collectively, we identified a unique human CB CD8+CD45RA+CD27+CD161+ T-cell subset and demonstrated that Seurat, a widely used package for scRNA-seq analysis, possesses great potential to be repurposed for cytometric data analysis. This facilitates an unbiased and thorough interpretation of complicated high-dimensional data using a single analytical pipeline and opens a novel avenue for data-driven investigation in clinical immunology.
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Affiliation(s)
- Julen Gabirel Araneta Reyes
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Duan Ni
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Brigitte Santner-Nanan
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Gabriela Veronica Pinget
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Lucie Kraftova
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Thomas Myles Ashhurst
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
| | - Felix Marsh-Wakefield
- Liver Injury and Cancer Program, Centenary Institute, Sydney, New South Wales, Australia
- Human Cancer and Viral Immunology Laboratory, The University of Sydney, Sydney, New South Wales, Australia
| | - Claire Leana Wishart
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Viral immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Ramaciotti Facility for Human System Biology, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
| | - Jian Tan
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter Hsu
- Kids Research, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Nicholas Jonathan Cole King
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
- Viral immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Ramaciotti Facility for Human System Biology, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
- The University of Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Nano, The University of Sydney, Sydney, New South Wales, Australia
| | - Laurence Macia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Ralph Nanan
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
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33
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Su P, Liu Y, Chen T, Xue Y, Zeng Y, Zhu G, Chen S, Teng M, Ci X, Guo M, He MY, Hao J, Chu V, Xu W, Wang S, Mehdipour P, Xu X, Marhon SA, Soares F, Pham NA, Wu BX, Her PH, Feng S, Alshamlan N, Khalil M, Krishnan R, Yu F, Chen C, Burrows F, Hakem R, Lupien M, Harding S, Lok BH, O'Brien C, Berlin A, De Carvalho DD, Brooks DG, Schramek D, Tsao MS, He HH. In vivo CRISPR screens identify a dual function of MEN1 in regulating tumor-microenvironment interactions. Nat Genet 2024; 56:1890-1902. [PMID: 39227744 PMCID: PMC11387198 DOI: 10.1038/s41588-024-01874-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 07/18/2024] [Indexed: 09/05/2024]
Abstract
Functional genomic screens in two-dimensional cell culture models are limited in identifying therapeutic targets that influence the tumor microenvironment. By comparing targeted CRISPR-Cas9 screens in a two-dimensional culture with xenografts derived from the same cell line, we identified MEN1 as the top hit that confers differential dropout effects in vitro and in vivo. MEN1 knockout in multiple solid cancer types does not impact cell proliferation in vitro but significantly promotes or inhibits tumor growth in immunodeficient or immunocompetent mice, respectively. Mechanistically, MEN1 knockout redistributes MLL1 chromatin occupancy, increasing H3K4me3 at repetitive genomic regions, activating double-stranded RNA expression and increasing neutrophil and CD8+ T cell infiltration in immunodeficient and immunocompetent mice, respectively. Pharmacological inhibition of the menin-MLL interaction reduces tumor growth in a CD8+ T cell-dependent manner. These findings reveal tumor microenvironment-dependent oncogenic and tumor-suppressive functions of MEN1 and provide a rationale for targeting MEN1 in solid cancers.
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Affiliation(s)
- Peiran Su
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yin Liu
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tianyi Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yibo Xue
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yong Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Guanghui Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- West China School of Public Health and West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Sujun Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- West China School of Public Health and West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Mona Teng
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Xinpei Ci
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mengdi Guo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Michael Y He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jun Hao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Vivian Chu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wenxi Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shiyan Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Parinaz Mehdipour
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Xin Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sajid A Marhon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Fraser Soares
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Bell Xi Wu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Peter Hyunwuk Her
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shengrui Feng
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Najd Alshamlan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Maryam Khalil
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Rehna Krishnan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Fangyou Yu
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | | | - Razqallah Hakem
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mathieu Lupien
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shane Harding
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Benjamin H Lok
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Catherine O'Brien
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alejandro Berlin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Daniel D De Carvalho
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - David G Brooks
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Schramek
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Housheng Hansen He
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
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34
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Liu JB, Yuan HL, Zhang G, Ke JB. Comprehensive Characterization of a Subfamily of Ca 2+-Binding Proteins in Mouse and Human Retinal Neurons at Single-Cell Resolution. eNeuro 2024; 11:ENEURO.0145-24.2024. [PMID: 39260891 PMCID: PMC11419601 DOI: 10.1523/eneuro.0145-24.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 08/20/2024] [Accepted: 09/03/2024] [Indexed: 09/13/2024] Open
Abstract
Ca2+-binding proteins (CaBPs; CaBP1-5) are a subfamily of neuronal Ca2+ sensors with high homology to calmodulin. Notably, CaBP4, which is exclusively expressed in rod and cone photoreceptors, is crucial for maintaining normal retinal functions. However, the functional roles of CaBP1, CaBP2, and CaBP5 in the retina remain elusive, primarily due to limited understanding of their expression patterns within inner retinal neurons. In this study, we conducted a comprehensive transcript analysis using single-cell RNA sequencing datasets to investigate the gene expression profiles of CaBPs in mouse and human retinal neurons. Our findings revealed notable similarities in the overall expression patterns of CaBPs across both species. Specifically, nearly all amacrine cell, ganglion cell, and horizontal cell types exclusively expressed CaBP1. In contrast, the majority of bipolar cell types, including rod bipolar (RB) cells, expressed distinct combinations of CaBP1, CaBP2, and CaBP5, rather than a single CaBP as previously hypothesized. Remarkably, mouse rods and human cones exclusively expressed CaBP4, whereas mouse cones and human rods coexpressed both CaBP4 and CaBP5. Our single-cell reverse transcription polymerase chain reaction analysis confirmed the coexpression CaBP1 and CaBP5 in individual RBs from mice of either sex. Additionally, all three splice variants of CaBP1, primarily L-CaBP1, were detected in mouse RBs. Taken together, our study offers a comprehensive overview of the distribution of CaBPs in mouse and human retinal neurons, providing valuable insights into their roles in visual functions.
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Affiliation(s)
- Jun-Bin Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - He-Lan Yuan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Gong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jiang-Bin Ke
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou 325000, China
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
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35
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Lötstedt B, Stražar M, Xavier R, Regev A, Vickovic S. Spatial host-microbiome sequencing reveals niches in the mouse gut. Nat Biotechnol 2024; 42:1394-1403. [PMID: 37985876 PMCID: PMC11392810 DOI: 10.1038/s41587-023-01988-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/12/2023] [Indexed: 11/22/2023]
Abstract
Mucosal and barrier tissues, such as the gut, lung or skin, are composed of a complex network of cells and microbes forming a tight niche that prevents pathogen colonization and supports host-microbiome symbiosis. Characterizing these networks at high molecular and cellular resolution is crucial for understanding homeostasis and disease. Here we present spatial host-microbiome sequencing (SHM-seq), an all-sequencing-based approach that captures tissue histology, polyadenylated RNAs and bacterial 16S sequences directly from a tissue by modifying spatially barcoded glass surfaces to enable simultaneous capture of host transcripts and hypervariable regions of the 16S bacterial ribosomal RNA. We applied our approach to the mouse gut as a model system, used a deep learning approach for data mapping and detected spatial niches defined by cellular composition and microbial geography. We show that subpopulations of gut cells express specific gene programs in different microenvironments characteristic of regional commensal bacteria and impact host-bacteria interactions. SHM-seq should enhance the study of native host-microbe interactions in health and disease.
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Affiliation(s)
- Britta Lötstedt
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- New York Genome Center, New York, NY, USA
| | | | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts, General Hospital, Harvard Medical School, Boston, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Genentech, South San Francisco, CA, USA.
| | - Sanja Vickovic
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- New York Genome Center, New York, NY, USA.
- Department of Biomedical Engineering and Herbert Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA.
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Beijer Laboratory for Gene and Neuro Research, Uppsala University, Uppsala, Sweden.
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36
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Altay A, Vingron M. scATAcat: cell-type annotation for scATAC-seq data. NAR Genom Bioinform 2024; 6:lqae135. [PMID: 39380946 PMCID: PMC11459382 DOI: 10.1093/nargab/lqae135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 09/11/2024] [Accepted: 09/23/2024] [Indexed: 10/10/2024] Open
Abstract
Cells whose accessibility landscape has been profiled with scATAC-seq cannot readily be annotated to a particular cell type. In fact, annotating cell-types in scATAC-seq data is a challenging task since, unlike in scRNA-seq data, we lack knowledge of 'marker regions' which could be used for cell-type annotation. Current annotation methods typically translate accessibility to expression space and rely on gene expression patterns. We propose a novel approach, scATAcat, that leverages characterized bulk ATAC-seq data as prototypes to annotate scATAC-seq data. To mitigate the inherent sparsity of single-cell data, we aggregate cells that belong to the same cluster and create pseudobulk. To demonstrate the feasibility of our approach we collected a number of datasets with respective annotations to quantify the results and evaluate performance for scATAcat. scATAcat is available as a python package at https://github.com/aybugealtay/scATAcat.
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Affiliation(s)
- Aybuge Altay
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
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Mueller KAL, Langnau C, Harm T, Sigle M, Mott K, Droppa M, Borst O, Rohlfing AK, Gekeler S, Günter M, Goebel N, Franke UF, Radwan M, Schlensak C, Janning H, Scheuermann S, Seitz CM, Rath D, Kreisselmeier KP, Castor T, Mueller II, Schulze H, Autenrieth SE, Gawaz MP. Macrophage Migration Inhibitory Factor Promotes Thromboinflammation and Predicts Fast Progression of Aortic Stenosis. Arterioscler Thromb Vasc Biol 2024; 44:2118-2135. [PMID: 38989580 PMCID: PMC11335082 DOI: 10.1161/atvbaha.124.321000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/18/2024] [Indexed: 07/12/2024]
Abstract
BACKGROUND Aortic stenosis (AS) is driven by progressive inflammatory and fibrocalcific processes regulated by circulating inflammatory and valve resident endothelial and interstitial cells. The impact of platelets, platelet-derived mediators, and platelet-monocyte interactions on the acceleration of local valvular inflammation and mineralization is presently unknown. METHODS We prospectively enrolled 475 consecutive patients with severe symptomatic AS undergoing aortic valve replacement. Clinical workup included repetitive echocardiography, analysis of platelets, monocytes, chemokine profiling, aortic valve tissue samples for immunohistochemistry, and gene expression analysis. RESULTS The patients were classified as fast-progressive AS by the median ∆Vmax of 0.45 m/s per year determined by echocardiography. Immunohistological aortic valve analysis revealed enhanced cellularity in fast-progressive AS (slow- versus fast-progressive AS; median [interquartile range], 247 [142.3-504] versus 717.5 [360.5-1234]; P<0.001) with less calcification (calcification area, mm2: 33.74 [27.82-41.86] versus 20.54 [13.52-33.41]; P<0.001). MIF (macrophage migration inhibitory factor)-associated gene expression was significantly enhanced in fast-progressive AS accompanied by significantly elevated MIF plasma levels (mean±SEM; 6877±379.1 versus 9959±749.1; P<0.001), increased platelet activation, and decreased intracellular MIF expression indicating enhanced MIF release upon platelet activation (CD62P, %: median [interquartile range], 16.8 [11.58-23.8] versus 20.55 [12.48-32.28], P=0.005; MIF, %: 4.85 [1.48-9.75] versus 2.3 [0.78-5.9], P<0.001). Regression analysis confirmed that MIF-associated biomarkers are strongly associated with an accelerated course of AS. CONCLUSIONS Our findings suggest a key role for platelet-derived MIF and its interplay with circulating and valve resident monocytes/macrophages in local and systemic thromboinflammation during accelerated AS. MIF-based biomarkers predict an accelerated course of AS and represent a novel pharmacological target to attenuate progression of AS.
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Affiliation(s)
- Karin Anne Lydia Mueller
- Department of Cardiology and Angiology (K.A.L.M., C.L., T.H., M.S., M.D., O.B., A.-K.R., S.G., H.J., D.R., K.-P.K., T.C., I.I.M., M.P.G.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
| | - Carolin Langnau
- Department of Cardiology and Angiology (K.A.L.M., C.L., T.H., M.S., M.D., O.B., A.-K.R., S.G., H.J., D.R., K.-P.K., T.C., I.I.M., M.P.G.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
| | - Tobias Harm
- Department of Cardiology and Angiology (K.A.L.M., C.L., T.H., M.S., M.D., O.B., A.-K.R., S.G., H.J., D.R., K.-P.K., T.C., I.I.M., M.P.G.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
| | - Manuel Sigle
- Department of Cardiology and Angiology (K.A.L.M., C.L., T.H., M.S., M.D., O.B., A.-K.R., S.G., H.J., D.R., K.-P.K., T.C., I.I.M., M.P.G.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
| | - Kristina Mott
- Institute for Experimental Biomedicine, Chair I University Hospital Würzburg, Germany (K.M., H.S.)
| | - Michal Droppa
- Department of Cardiology and Angiology (K.A.L.M., C.L., T.H., M.S., M.D., O.B., A.-K.R., S.G., H.J., D.R., K.-P.K., T.C., I.I.M., M.P.G.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
| | - Oliver Borst
- Department of Cardiology and Angiology (K.A.L.M., C.L., T.H., M.S., M.D., O.B., A.-K.R., S.G., H.J., D.R., K.-P.K., T.C., I.I.M., M.P.G.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
- DFG Heisenberg Group Thrombocardiology (O.B.), University of Tübingen, Germany
| | - Anne-Katrin Rohlfing
- Department of Cardiology and Angiology (K.A.L.M., C.L., T.H., M.S., M.D., O.B., A.-K.R., S.G., H.J., D.R., K.-P.K., T.C., I.I.M., M.P.G.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
| | - Sarah Gekeler
- Department of Cardiology and Angiology (K.A.L.M., C.L., T.H., M.S., M.D., O.B., A.-K.R., S.G., H.J., D.R., K.-P.K., T.C., I.I.M., M.P.G.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
| | - Manina Günter
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology (M.G., S.E.A.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
- Dendritic Cells in Infection and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany (M.G., S.E.A.)
| | - Nora Goebel
- Robert-Bosch Hospital, Department of Cardiovascular Surgery, Stuttgart, Germany (N.G., U.F.W.F.)
| | - Ulrich F.W. Franke
- Robert-Bosch Hospital, Department of Cardiovascular Surgery, Stuttgart, Germany (N.G., U.F.W.F.)
| | - Medhat Radwan
- Department of Thoracic and Cardiovascular Surgery (M.R., C.S.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
| | - Christian Schlensak
- Department of Thoracic and Cardiovascular Surgery (M.R., C.S.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
| | - Henrik Janning
- Department of Cardiology and Angiology (K.A.L.M., C.L., T.H., M.S., M.D., O.B., A.-K.R., S.G., H.J., D.R., K.-P.K., T.C., I.I.M., M.P.G.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
| | - Sophia Scheuermann
- Cluster of Excellence iFIT (EXC 2180) Image-Guided and Functionally Instructed Tumor Therapies (S.S., C.M.S.), University of Tübingen, Germany
- Department of Pediatric Hematology and Oncology, University Children’s Hospital Tuebingen, Germany (S.S., C.M.S.)
| | - Christian M. Seitz
- Cluster of Excellence iFIT (EXC 2180) Image-Guided and Functionally Instructed Tumor Therapies (S.S., C.M.S.), University of Tübingen, Germany
- Department of Pediatric Hematology and Oncology, University Children’s Hospital Tuebingen, Germany (S.S., C.M.S.)
| | - Dominik Rath
- Department of Cardiology and Angiology (K.A.L.M., C.L., T.H., M.S., M.D., O.B., A.-K.R., S.G., H.J., D.R., K.-P.K., T.C., I.I.M., M.P.G.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
| | - Klaus-Peter Kreisselmeier
- Department of Cardiology and Angiology (K.A.L.M., C.L., T.H., M.S., M.D., O.B., A.-K.R., S.G., H.J., D.R., K.-P.K., T.C., I.I.M., M.P.G.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
| | - Tatsiana Castor
- Department of Cardiology and Angiology (K.A.L.M., C.L., T.H., M.S., M.D., O.B., A.-K.R., S.G., H.J., D.R., K.-P.K., T.C., I.I.M., M.P.G.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
| | - Iris Irmgard Mueller
- Department of Cardiology and Angiology (K.A.L.M., C.L., T.H., M.S., M.D., O.B., A.-K.R., S.G., H.J., D.R., K.-P.K., T.C., I.I.M., M.P.G.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
| | - Harald Schulze
- Institute for Experimental Biomedicine, Chair I University Hospital Würzburg, Germany (K.M., H.S.)
| | - Stella E. Autenrieth
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology (M.G., S.E.A.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
- Dendritic Cells in Infection and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany (M.G., S.E.A.)
| | - Meinrad Paul Gawaz
- Department of Cardiology and Angiology (K.A.L.M., C.L., T.H., M.S., M.D., O.B., A.-K.R., S.G., H.J., D.R., K.-P.K., T.C., I.I.M., M.P.G.), University Hospital Tuebingen, Eberhard Karls University Tuebingen, Germany
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Banu MA, Dovas A, Argenziano MG, Zhao W, Sperring CP, Cuervo Grajal H, Liu Z, Higgins DM, Amini M, Pereira B, Ye LF, Mahajan A, Humala N, Furnari JL, Upadhyayula PS, Zandkarimi F, Nguyen TT, Teasley D, Wu PB, Hai L, Karan C, Dowdy T, Razavilar A, Siegelin MD, Kitajewski J, Larion M, Bruce JN, Stockwell BR, Sims PA, Canoll P. A cell state-specific metabolic vulnerability to GPX4-dependent ferroptosis in glioblastoma. EMBO J 2024:10.1038/s44318-024-00176-4. [PMID: 39192032 DOI: 10.1038/s44318-024-00176-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/12/2024] [Accepted: 07/01/2024] [Indexed: 08/29/2024] Open
Abstract
Glioma cells hijack developmental programs to control cell state. Here, we uncover a glioma cell state-specific metabolic liability that can be therapeutically targeted. To model cell conditions at brain tumor inception, we generated genetically engineered murine gliomas, with deletion of p53 alone (p53) or with constitutively active Notch signaling (N1IC), a pathway critical in controlling astrocyte differentiation during brain development. N1IC tumors harbored quiescent astrocyte-like transformed cell populations while p53 tumors were predominantly comprised of proliferating progenitor-like cell states. Further, N1IC transformed cells exhibited increased mitochondrial lipid peroxidation, high ROS production and depletion of reduced glutathione. This altered mitochondrial phenotype rendered the astrocyte-like, quiescent populations more sensitive to pharmacologic or genetic inhibition of the lipid hydroperoxidase GPX4 and induction of ferroptosis. Treatment of patient-derived early-passage cell lines and glioma slice cultures generated from surgical samples with a GPX4 inhibitor induced selective depletion of quiescent astrocyte-like glioma cell populations with similar metabolic profiles. Collectively, these findings reveal a specific therapeutic vulnerability to ferroptosis linked to mitochondrial redox imbalance in a subpopulation of quiescent astrocyte-like glioma cells resistant to standard forms of treatment.
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Affiliation(s)
- Matei A Banu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Athanassios Dovas
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael G Argenziano
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Wenting Zhao
- Department of System Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Colin P Sperring
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Zhouzerui Liu
- Department of System Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Dominique Mo Higgins
- Department of Neurological Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Misha Amini
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Brianna Pereira
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ling F Ye
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Aayushi Mahajan
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Nelson Humala
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Julia L Furnari
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Pavan S Upadhyayula
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Fereshteh Zandkarimi
- Department of Biological Sciences, Department of Chemistry and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Trang Tt Nguyen
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Damian Teasley
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter B Wu
- Department of Neurological Surgery, UCLA Geffen School of Medicine, Los Angeles, CA, USA
| | - Li Hai
- Sulzberger Columbia Genome Center, Columbia University, New York, NY, USA
| | - Charles Karan
- Sulzberger Columbia Genome Center, Columbia University, New York, NY, USA
| | | | - Aida Razavilar
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Markus D Siegelin
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jan Kitajewski
- University of Illinois Cancer Center, Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, USA
| | | | - Jeffrey N Bruce
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Brent R Stockwell
- Department of Biological Sciences, Department of Chemistry and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Peter A Sims
- Department of System Biology, Columbia University Irving Medical Center, New York, NY, USA.
| | - Peter Canoll
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
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Brooks ER, Moorman AR, Bhattacharya B, Prudhomme I, Land M, Alcorn HL, Sharma R, Pe'er D, Zallen JA. A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.25.609458. [PMID: 39229123 PMCID: PMC11370589 DOI: 10.1101/2024.08.25.609458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
The formation of the mammalian brain requires regionalization and morphogenesis of the cranial neural plate, which transforms from an epithelial sheet into a closed tube that provides the structural foundation for neural patterning and circuit formation. Sonic hedgehog (SHH) signaling is important for cranial neural plate patterning and closure, but the transcriptional changes that give rise to the spatially regulated cell fates and behaviors that build the cranial neural tube have not been systematically analyzed. Here we used single-cell RNA sequencing to generate an atlas of gene expression at six consecutive stages of cranial neural tube closure in the mouse embryo. Ordering transcriptional profiles relative to the major axes of gene expression predicted spatially regulated expression of 870 genes along the anterior-posterior and mediolateral axes of the cranial neural plate and reproduced known expression patterns with over 85% accuracy. Single-cell RNA sequencing of embryos with activated SHH signaling revealed distinct SHH-regulated transcriptional programs in the developing forebrain, midbrain, and hindbrain, suggesting a complex interplay between anterior-posterior and mediolateral patterning systems. These results define a spatiotemporally resolved map of gene expression during cranial neural tube closure and provide a resource for investigating the transcriptional events that drive early mammalian brain development.
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Affiliation(s)
- Eric R Brooks
- HHMI and Developmental Biology Program, Sloan Kettering Institute
- North Carolina State University
| | - Andrew R Moorman
- HHMI and Computational and Systems Biology Program, Sloan Kettering Institute
| | | | - Ian Prudhomme
- HHMI and Developmental Biology Program, Sloan Kettering Institute
| | - Max Land
- HHMI and Computational and Systems Biology Program, Sloan Kettering Institute
| | - Heather L Alcorn
- HHMI and Developmental Biology Program, Sloan Kettering Institute
| | - Roshan Sharma
- HHMI and Computational and Systems Biology Program, Sloan Kettering Institute
| | - Dana Pe'er
- HHMI and Computational and Systems Biology Program, Sloan Kettering Institute
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40
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Souto EP, Gong P, Landua JD, Srinivasan RR, Ganesan A, Dobrolecki LE, Purdy SC, Pan X, Zeosky M, Chung A, Yi SS, Ford HL, Lewis MT. The interferon/STAT1 signaling axis is a common feature of tumor-initiating cells in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.15.557958. [PMID: 37745510 PMCID: PMC10515955 DOI: 10.1101/2023.09.15.557958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
A tumor cell subpopulation of tumor-initiating cells (TIC), or "cancer stem cells", are associated with therapeutic resistance, as well as both local and distant recurrence. Enriched populations of TIC are identified by markers including aldehyde dehydrogenase (ALDH1) activity, the cell surface marker combination CD44 + /CD24 - , or fluorescent reporters for signaling pathways that regulate TIC function. We showed previously that S ignal T ransducer and A ctivator of T ranscription (STAT)-mediated transcription allows enrichment for TIC in claudin-low models of human triple-negative breast cancer using a STAT-responsive reporter. However, the molecular phenotypes of STAT TIC are not well understood, and there is no existing method to lineage-trace TIC as they undergo cell state changes. Using a new STAT-responsive lineage-tracing (LT) system in conjunction with our original reporter, we enriched for cells with enhanced mammosphere-forming potential in some, but not all, basal-like triple-negative breast cancer (TNBC) xenograft models (TNBC) indicating TIC-related and TIC-independent functions for STAT signaling. Single-cell RNA sequencing (scRNAseq) of reporter-tagged xenografts and clinical samples identified a common interferon (IFN)/STAT1-associated transcriptional state, previously linked to inflammation and macrophage differentiation, in TIC. Surprisingly, most of the genes we identified are not present in previously published TIC signatures derived using bulk RNA sequencing. Finally, we demonstrated that bone marrow stromal cell antigen 2 (BST2), is a cell surface marker of this state, and that it functionally regulates TIC frequency. These results suggest TIC may exploit the IFN/STAT1 signaling axis to promote their activity, and that targeting this pathway may help eliminate TIC. Significance TIC differentially express interferon response genes, which were not previously reported in bulk RNA sequencing-derived TIC signatures, highlighting the importance of coupling single-cell transcriptomics with enrichment to derive TIC signatures.
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41
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Saraswathy VM, Zhou L, Mokalled MH. Single-cell analysis of innate spinal cord regeneration identifies intersecting modes of neuronal repair. Nat Commun 2024; 15:6808. [PMID: 39147780 PMCID: PMC11327264 DOI: 10.1038/s41467-024-50628-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 07/11/2024] [Indexed: 08/17/2024] Open
Abstract
Adult zebrafish have an innate ability to recover from severe spinal cord injury. Here, we report a comprehensive single nuclear RNA sequencing atlas that spans 6 weeks of regeneration. We identify cooperative roles for adult neurogenesis and neuronal plasticity during spinal cord repair. Neurogenesis of glutamatergic and GABAergic neurons restores the excitatory/inhibitory balance after injury. In addition, a transient population of injury-responsive neurons (iNeurons) show elevated plasticity 1 week post-injury. We found iNeurons are injury-surviving neurons that acquire a neuroblast-like gene expression signature after injury. CRISPR/Cas9 mutagenesis showed iNeurons are required for functional recovery and employ vesicular trafficking as an essential mechanism that underlies neuronal plasticity. This study provides a comprehensive resource of the cells and mechanisms that direct spinal cord regeneration and establishes zebrafish as a model of plasticity-driven neural repair.
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Affiliation(s)
- Vishnu Muraleedharan Saraswathy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Lili Zhou
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Mayssa H Mokalled
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.
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42
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Lehmann M, Weixler B, Elezkurtaj S, Loddenkemper C, Kühl AA, Siegmund B. Spatial Single Cell Profiling Using Imaging Mass Cytometry: Inflammatory Versus Penetrating Crohn's Disease. J Crohns Colitis 2024; 18:1305-1318. [PMID: 38465390 DOI: 10.1093/ecco-jcc/jjae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
BACKGROUND AND AIMS Fistula formation is a major complication in Crohn's disease [CD] and the role of the immune cell compartment remains to be elucidated. Thus, we compared the immune cell compartment of CD fistula to inflammatory CD colitis using imaging mass cytometry [IMC] and immunofluorescence. METHODS A 36-marker panel including structural, functional, and lineage markers for use in IMC was established. This panel was applied to analyse paraffin-embedded CD fistula tract [n = 11], CD colitis [n = 10], and colon samples from non-inflamed controls [n = 12]. Computational methods for cell segmentation, dimensionality reduction, and cell type clustering were used to define cell populations for cell frequency, marker distribution, and spatial neighbourhood analysis. Multiplex immunofluorescence was used for higher resolution spatial analysis. RESULTS Analysis of cell frequencies in CD fistulas compared to CD colitis and control colonic samples revealed a significant increase in neutrophils, effector cytotoxic T cells, and inflammatory macrophages in CD fistula samples, whereas regulatory T cells were decreased. Neutrophils in CD fistula expressed significantly more matrix metalloproteinase 9 [MMP9], correlating with extracellular matrix remodelling. Neighbourhood analysis revealed a strong association between MMP9+ neutrophils and effector cytotoxic T cells in both CD fistulas and colitis. CONCLUSIONS This study presents the first highly multiplexed single cell analysis of the immune cell compartment of CD fistulas and their spatial context. It links immune cell dynamics, particularly MMP9+ neutrophils, to extracellular matrix remodelling in CD fistulas, offering insights into the complex network of cellular interactions and potential therapeutic targets for CD complications.
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Affiliation(s)
- Malte Lehmann
- Department of Gastroenterology, Infectious Diseases and Rheumatology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200, Berlin, Germany
| | - Benjamin Weixler
- Department of General and Visceral Surgery, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sefer Elezkurtaj
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christopher Loddenkemper
- PathoTres, Gemeinschaftspraxis für Pathologie und Neuropathologie, Teltowkanalstr. 2, 12247, Berlin, Germany
| | - Anja A Kühl
- iPATH.Berlin, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Britta Siegmund
- Department of Gastroenterology, Infectious Diseases and Rheumatology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200, Berlin, Germany
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Delconte RB, Owyong M, Santosa EK, Srpan K, Sheppard S, McGuire TJ, Abbasi A, Diaz-Salazar C, Chun J, Rogatsky I, Hsu KC, Jordan S, Merad M, Sun JC. Fasting reshapes tissue-specific niches to improve NK cell-mediated anti-tumor immunity. Immunity 2024; 57:1923-1938.e7. [PMID: 38878769 DOI: 10.1016/j.immuni.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 04/19/2024] [Accepted: 05/22/2024] [Indexed: 08/16/2024]
Abstract
Fasting is associated with improved outcomes in cancer. Here, we investigated the impact of fasting on natural killer (NK) cell anti-tumor immunity. Cyclic fasting improved immunity against solid and metastatic tumors in an NK cell-dependent manner. During fasting, NK cells underwent redistribution from peripheral tissues to the bone marrow (BM). In humans, fasting also reduced circulating NK cell numbers. NK cells in the spleen of fasted mice were metabolically rewired by elevated concentrations of fatty acids and glucocorticoids, augmenting fatty acid metabolism via increased expression of the enzyme CPT1A, and Cpt1a deletion impaired NK cell survival and function in this setting. In parallel, redistribution of NK cells to the BM during fasting required the trafficking mediators S1PR5 and CXCR4. These cells were primed by an increased pool of interleukin (IL)-12-expressing BM myeloid cells, which improved IFN-γ production. Our findings identify a link between dietary restriction and optimized innate immune responses, with the potential to enhance immunotherapy strategies.
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Affiliation(s)
- Rebecca B Delconte
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Mark Owyong
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medical College, New York, NY 10065, USA
| | - Endi K Santosa
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medical College, New York, NY 10065, USA
| | - Katja Srpan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sam Sheppard
- Department of Life Sciences, Imperial College London, London, UK
| | - Tomi J McGuire
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medical College, New York, NY 10065, USA
| | - Aamna Abbasi
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Carlos Diaz-Salazar
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Inez Rogatsky
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medical College, New York, NY 10065, USA; Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY 10021, USA
| | - Katharine C Hsu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stefan Jordan
- Institute of Microbiology, Infectious Diseases and Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Miriam Merad
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph C Sun
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medical College, New York, NY 10065, USA.
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Chen Y, Shao Z, Hao Z, Xin Z, Chen X, Huang L, Chen D, Lin M, Liu Q, Xu X, Li J, Wu D, Yan J, Chai Y, Wu P. Epithelium/imcDC2 axis facilitates the resistance of neoadjuvant anti-PD-1 in human NSCLC. J Immunother Cancer 2024; 12:e007854. [PMID: 39134346 PMCID: PMC11332012 DOI: 10.1136/jitc-2023-007854] [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] [Accepted: 07/27/2024] [Indexed: 08/21/2024] Open
Abstract
BACKGROUND Therapeutic resistance is a main obstacle to achieve long-term benefits from immune checkpoint inhibitors. The underlying mechanism of neoadjuvant anti-PD-1 resistance remains unclear. METHODS Multi-omics analysis, including mass cytometry, single-cell RNA-seq, bulk RNA-seq, and polychromatic flow cytometry, was conducted using the resected tumor samples in a cohort of non-small cell lung cancer (NSCLC) patients received neoadjuvant anti-PD-1 therapy. Tumor and paired lung samples acquired from treatment-naïve patients were used as a control. In vitro experiments were conducted using primary cells isolated from fresh tissues and lung cancer cell lines. A Lewis-bearing mouse model was used in the in vivo experiment. RESULTS The quantity, differentiation status, and clonal expansion of tissue-resident memory CD8+ T cells (CD8+ TRMs) are positively correlated with therapeutic efficacy of neoadjuvant anti-PD-1 therapy in human NSCLC. In contrast, the quantity of immature CD1c+ classical type 2 dendritic cells (imcDC2) and galectin-9+ cancer cells is negatively correlated with therapeutic efficacy. An epithelium/imDC2 suppressive axis that restrains the antitumor response of CD8+ TRMs via galectin-9/TIM-3 was uncovered. The expression level of CD8+ TRMs and galectin-9+ cancer cell-related genes predict the clinical outcome of anti-PD-1 neoadjuvant therapy in human NSCLC patients. Finally, blockade of TIM-3 and PD-1 could improve the survival of tumor-bearing mouse by promoting the antigen presentation of imcDC2 and CD8+ TRMs-mediated tumor-killing. CONCLUSION Galectin-9 expressing tumor cells sustained the primary resistance of neoadjuvant anti-PD-1 therapy in NSCLC through galectin-9/TIM-3-mediated suppression of imcDC2 and CD8+ TRMs. Supplement of anti-TIM-3 could break the epithelium/imcDC2/CD8+ TRMs suppressive loop to overcome anti-PD-1 resistance. TRIAL REGISTRATION NUMBER NCT03732664.
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Affiliation(s)
- Yongyuan Chen
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zheyu Shao
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhixing Hao
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhongwei Xin
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated of Shandong First Medical University, Jinan, Shandong, China
| | - Xiaoke Chen
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lijian Huang
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Di Chen
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mingjie Lin
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qinyuan Liu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xia Xu
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jinfan Li
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dang Wu
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jun Yan
- Division of Immunotherapy, The Hiram C. Polk, Jr., Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
| | - Ying Chai
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Pin Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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45
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Torija A, Matignon M, Vincenti F, Casanova-Ferrer F, Pilon C, Tambur AR, Donadeu L, Crespo E, Kervella D, Meneghini M, Torres IB, Hafkamp F, Martinez-Lacalle A, Carrera C, Zúñiga J, Brar A, Cruzado J, Gaber AO, Lee H, Montgomery RA, Stegall M, Carmagnat M, Usureau C, Moreso F, Grimbert P, Bestard O. Anti-HLA serologic response to CD38-targeting desensitization therapy is challenged by peripheral memory B cells in highly sensitized kidney transplant candidates. Am J Transplant 2024:S1600-6135(24)00490-8. [PMID: 39134120 DOI: 10.1016/j.ajt.2024.08.004] [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: 06/07/2024] [Revised: 07/17/2024] [Accepted: 08/06/2024] [Indexed: 09/09/2024]
Abstract
High human leukocyte antigen (HLA) sensitization limits access to compatible transplantation. New CD38-targeting agents have been shown to reduce anti-HLA antibodies, although with important interpatient variability. Thus, pretreatment identification of responder and nonresponder (NR) patients is needed for treatment decision-making. We analyzed 26 highly sensitized (HS) patients from 2 desensitization trials using anti-CD38 monoclonal antibodies. Hierarchical clustering identified 3 serologic responder groups: high responders, low responders, and NR. Spectral flow cytometry and functional HLA-specific memory B cell (mBC) assessment were first conducted on peripheral blood mononuclear cells and bone marrow samples from 16 patients treated with isatuximab (NCT04294459). Isatuximab effectively depleted bone marrow plasma cells, peripheral CD38-expressing plasmablasts, plasma cells, transitional B cells, and class-switch mBCs, ultimately reducing frequencies of HLA-specific immunoglobulin G (IgG)-producing mBCs. Multidimensional spectral flow cytometry with partial least squares discriminant analysis revealed that pretreatment abundance of specific circulating mBC phenotypes, especially CD38neg class-switch mBCs, accurately distinguished between high serologic responders and low responders or NR (AUC 0.958, 0.860-1.000, P = .009), who also displayed significantly lower frequencies of HLA-specific IgG-producing mBCs (P < .0001). This phenotypical mBC signature predicting response to therapy was validated in an external HS patient cohort (n = 10) receiving daratumumab (NCT04204980). This study identifies critical circulating mBC subset phenotypes that distinguish HS patients with successful serologic responses to CD38-targeting desensitization therapies, potentially guiding treatment decision-making.
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Affiliation(s)
- Alba Torija
- Nephrology and Kidney Transplantation Laboratory, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Marie Matignon
- AP-HP, Service de Néphrologie et de Transplantation Rénale, Fédération Hospitalo-Universitaire, Innovative Therapy for Immune Disorders, CHU Henri Mondor, Créteil, France; University of Paris-Est-Créteil, Institut National de la Santé et de la Recherche Médicale (INSERM) U955, Team 21, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Flavio Vincenti
- Departments of Medicine and Surgery, University of California San Francisco, San Francisco, California, USA
| | - Franc Casanova-Ferrer
- Nephrology and Kidney Transplantation Laboratory, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Caroline Pilon
- University of Paris-Est-Créteil, Institut National de la Santé et de la Recherche Médicale (INSERM) U955, Team 21, Institut Mondor de Recherche Biomédicale, Créteil, France; AP-HP, Centre d'Investigation Clinique Biothérapie, Fédération Hospitalo-Universitaire, Innovative Therapy for Immune Disorders, CHU Henri Mondor, Créteil, France
| | - Anat R Tambur
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Laura Donadeu
- Nephrology and Kidney Transplantation Laboratory, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Elena Crespo
- Nephrology and Kidney Transplantation Laboratory, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Delphine Kervella
- Nephrology and Kidney Transplantation Laboratory, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain; Department of Nephrology and Kidney Transplantation, University Hospital Vall d'Hebron, Barcelona, Spain
| | - Maria Meneghini
- Nephrology and Kidney Transplantation Laboratory, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain; Department of Nephrology and Kidney Transplantation, University Hospital Vall d'Hebron, Barcelona, Spain
| | - Irina B Torres
- Nephrology and Kidney Transplantation Laboratory, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain; Department of Nephrology and Kidney Transplantation, University Hospital Vall d'Hebron, Barcelona, Spain
| | - Florianne Hafkamp
- Nephrology and Kidney Transplantation Laboratory, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Anna Martinez-Lacalle
- Nephrology and Kidney Transplantation Laboratory, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Claudia Carrera
- Nephrology and Kidney Transplantation Laboratory, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain; Department of Nephrology and Kidney Transplantation, University Hospital Vall d'Hebron, Barcelona, Spain
| | - José Zúñiga
- Nephrology and Kidney Transplantation Laboratory, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain; Department of Nephrology and Kidney Transplantation, University Hospital Vall d'Hebron, Barcelona, Spain
| | - Amarpali Brar
- Departments of Medicine and Surgery, University of California San Francisco, San Francisco, California, USA
| | - Josep Cruzado
- Department of Nephrology, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - A Osama Gaber
- Department of Surgery, Houston Methodist Hospital, Houston, Texas, USA
| | - Helen Lee
- Sanofi, Cambridge, Massachusetts, USA
| | - Robert A Montgomery
- Department of Surgery, Transplant Institute, New York University Langone Health, New York, New York, USA
| | - Mark Stegall
- Department of Surgery, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Maryvonnick Carmagnat
- AP-HP, Centre d'Investigation Clinique Biothérapie, Fédération Hospitalo-Universitaire, Innovative Therapy for Immune Disorders, CHU Henri Mondor, Créteil, France
| | - Cédric Usureau
- AP-HP, Centre d'Investigation Clinique Biothérapie, Fédération Hospitalo-Universitaire, Innovative Therapy for Immune Disorders, CHU Henri Mondor, Créteil, France
| | - Francesc Moreso
- Nephrology and Kidney Transplantation Laboratory, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain; Department of Nephrology and Kidney Transplantation, University Hospital Vall d'Hebron, Barcelona, Spain
| | - Philippe Grimbert
- AP-HP, Service de Néphrologie et de Transplantation Rénale, Fédération Hospitalo-Universitaire, Innovative Therapy for Immune Disorders, CHU Henri Mondor, Créteil, France; University of Paris-Est-Créteil, Institut National de la Santé et de la Recherche Médicale (INSERM) U955, Team 21, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Oriol Bestard
- Nephrology and Kidney Transplantation Laboratory, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain; Department of Nephrology and Kidney Transplantation, University Hospital Vall d'Hebron, Barcelona, Spain.
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Zuo Z, Cheng X, Ferdous S, Shao J, Li J, Bao Y, Li J, Lu J, Jacobo Lopez A, Wohlschlegel J, Prieve A, Thomas MG, Reh TA, Li Y, Moshiri A, Chen R. Single cell dual-omic atlas of the human developing retina. Nat Commun 2024; 15:6792. [PMID: 39117640 PMCID: PMC11310509 DOI: 10.1038/s41467-024-50853-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
The development of the retina is under tight temporal and spatial control. To gain insights into the molecular basis of this process, we generate a single-nuclei dual-omic atlas of the human developing retina with approximately 220,000 nuclei from 14 human embryos and fetuses aged between 8 and 23-weeks post-conception with matched macular and peripheral tissues. This atlas captures all major cell classes in the retina, along with a large proportion of progenitors and cell-type-specific precursors. Cell trajectory analysis reveals a transition from continuous progression in early progenitors to a hierarchical development during the later stages of cell type specification. Both known and unrecorded candidate transcription factors, along with gene regulatory networks that drive the transitions of various cell fates, are identified. Comparisons between the macular and peripheral retinae indicate a largely consistent yet distinct developmental pattern. This atlas offers unparalleled resolution into the transcriptional and chromatin accessibility landscapes during development, providing an invaluable resource for deeper insights into retinal development and associated diseases.
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Affiliation(s)
- Zhen Zuo
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Xuesen Cheng
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Salma Ferdous
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Jianming Shao
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Jin Li
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Yourong Bao
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Jean Li
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Jiaxiong Lu
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Antonio Jacobo Lopez
- Department of Ophthalmology & Vision Science, UC Davis School of Medicine, 4860 Y St, Sacramento, CA, USA
| | - Juliette Wohlschlegel
- Department of Biological Structure, University of Washington, 1410 NE Campus Pkwy, Seattle, WA, USA
| | - Aric Prieve
- Department of Biological Structure, University of Washington, 1410 NE Campus Pkwy, Seattle, WA, USA
| | - Mervyn G Thomas
- Ulverscroft Eye Unit, School of Psychology and Vision Sciences, The University of Leicester, Leicester, UK
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, 1410 NE Campus Pkwy, Seattle, WA, USA
| | - Yumei Li
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Ala Moshiri
- Department of Ophthalmology & Vision Science, UC Davis School of Medicine, 4860 Y St, Sacramento, CA, USA
| | - Rui Chen
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA.
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA.
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA.
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California Irvine School of Medicine, Irvine, USA.
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47
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Jeong Y, Ronen J, Kopp W, Lutsik P, Akalin A. scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data. BMC Bioinformatics 2024; 25:257. [PMID: 39107690 PMCID: PMC11304929 DOI: 10.1186/s12859-024-05880-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
The recent advances in high-throughput single-cell sequencing have created an urgent demand for computational models which can address the high complexity of single-cell multiomics data. Meticulous single-cell multiomics integration models are required to avoid biases towards a specific modality and overcome sparsity. Batch effects obfuscating biological signals must also be taken into account. Here, we introduce a new single-cell multiomics integration model, Single-cell Multiomics Autoencoder Integration (scMaui) based on variational product-of-experts autoencoders and adversarial learning. scMaui calculates a joint representation of multiple marginal distributions based on a product-of-experts approach which is especially effective for missing values in the modalities. Furthermore, it overcomes limitations seen in previous VAE-based integration methods with regard to batch effect correction and restricted applicable assays. It handles multiple batch effects independently accepting both discrete and continuous values, as well as provides varied reconstruction loss functions to cover all possible assays and preprocessing pipelines. We demonstrate that scMaui achieves superior performance in many tasks compared to other methods. Further downstream analyses also demonstrate its potential in identifying relations between assays and discovering hidden subpopulations.
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Affiliation(s)
- Yunhee Jeong
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
- Faculty of Mathematics and Informatics, Heidelberg University, Im Neuenheimer Feld 205, Heidelberg, Germany
| | - Jonathan Ronen
- Bioinformatics and Omics Data Science Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Inceptive Nucleics, Inc., Palo Alto, CA, USA
| | - Wolfgang Kopp
- Bioinformatics and Omics Data Science Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Roche Diagnostics GmbH, Penzberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany.
- Department of Oncology, Catholic University (KU) Leuven, Leuven, Belgium.
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany.
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Lambroia L, Conca Dioguardi CM, Puccio S, Pansa A, Alvisi G, Basso G, Cibella J, Colombo FS, Marano S, Basato S, Alfieri R, Giudici S, Castoro C, Peano C. Definition of a Multi-Omics Signature for Esophageal Adenocarcinoma Prognosis Prediction. Cancers (Basel) 2024; 16:2748. [PMID: 39123475 PMCID: PMC11311406 DOI: 10.3390/cancers16152748] [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: 06/29/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Esophageal cancer is a highly lethal malignancy, representing 5% of all cancer-related deaths. The two main subtypes are esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). While most research has focused on ESCC, few studies have analyzed EAC for transcriptional signatures linked to diagnosis or prognosis. In this study, we utilized single-cell RNA sequencing and bulk RNA sequencing to identify specific immune cell types that contribute to anti-tumor responses, as well as differentially expressed genes (DEGs). We have characterized transcriptional signatures, validated against a wide cohort of TCGA patients, that are capable of predicting clinical outcomes and the prognosis of EAC post-surgery with efficacy comparable to the currently accepted prognostic factors. In conclusion, our findings provide insights into the immune landscape and therapeutic targets of EAC, proposing novel immunological biomarkers for predicting prognosis, aiding in patient stratification for post-surgical outcomes, follow-up, and personalized adjuvant therapy decisions.
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Affiliation(s)
- Luca Lambroia
- Humanitas Research Hospital-IRCCS, 20072 Rozzano, Italy;
| | | | - Simone Puccio
- Institute of Genetic and Biomedical Research, National Research Council, UoS of Milan, 20072 Milan, Italy;
- Laboratory of Translational Immunology and Humanitas Flow Cytometry Core, Humanitas Research Hospital, 20072 Milan, Italy (F.S.C.)
| | - Andrea Pansa
- Upper Gastrointestinal Surgery Unit, IRCCS Humanitas Research Hospital, 20089 Milan, Italy; (A.P.)
| | - Giorgia Alvisi
- Laboratory of Translational Immunology and Humanitas Flow Cytometry Core, Humanitas Research Hospital, 20072 Milan, Italy (F.S.C.)
| | - Gianluca Basso
- Genomic Unit, Humanitas Research Hospital, 20072 Milan, Italy
| | - Javier Cibella
- Human Technopole, 20157 Milan, Italy; (C.M.C.D.); (J.C.)
| | - Federico Simone Colombo
- Laboratory of Translational Immunology and Humanitas Flow Cytometry Core, Humanitas Research Hospital, 20072 Milan, Italy (F.S.C.)
| | - Salvatore Marano
- Upper Gastrointestinal Surgery Unit, IRCCS Humanitas Research Hospital, 20089 Milan, Italy; (A.P.)
| | - Silvia Basato
- Upper Gastrointestinal Surgery Unit, IRCCS Humanitas Research Hospital, 20089 Milan, Italy; (A.P.)
| | - Rita Alfieri
- Upper Gastrointestinal Surgery Unit, IRCCS Humanitas Research Hospital, 20089 Milan, Italy; (A.P.)
| | - Simone Giudici
- Upper Gastrointestinal Surgery Unit, IRCCS Humanitas Research Hospital, 20089 Milan, Italy; (A.P.)
| | - Carlo Castoro
- Upper Gastrointestinal Surgery Unit, IRCCS Humanitas Research Hospital, 20089 Milan, Italy; (A.P.)
- Department of Biomedical Sciences, Humanitas University, 20072 Milan, Italy
| | - Clelia Peano
- Human Technopole, 20157 Milan, Italy; (C.M.C.D.); (J.C.)
- Institute of Genetic and Biomedical Research, National Research Council, UoS of Milan, 20072 Milan, Italy;
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49
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Li J, Shyr Y, Liu Q. aKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph. Genome Biol 2024; 25:203. [PMID: 39090647 PMCID: PMC11293182 DOI: 10.1186/s13059-024-03339-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/16/2024] [Indexed: 08/04/2024] Open
Abstract
Typical clustering methods for single-cell and spatial transcriptomics struggle to identify rare cell types, while approaches tailored to detect rare cell types gain this ability at the cost of poorer performance for grouping abundant ones. Here, we develop aKNNO to simultaneously identify abundant and rare cell types based on an adaptive k-nearest neighbor graph with optimization. Benchmarking on 38 simulated and 20 single-cell and spatial transcriptomics datasets demonstrates that aKNNO identifies both abundant and rare cell types more accurately than general and specialized methods. Using only gene expression aKNNO maps abundant and rare cells more precisely compared to integrative approaches.
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Affiliation(s)
- Jia Li
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Yu Shyr
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.
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50
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Harnik Y, Yakubovsky O, Hoefflin R, Novoselsky R, Bahar Halpern K, Barkai T, Korem Kohanim Y, Egozi A, Golani O, Addadi Y, Kedmi M, Keidar Haran T, Levin Y, Savidor A, Keren-Shaul H, Mayer C, Pencovich N, Pery R, Shouval DS, Tirosh I, Nachmany I, Itzkovitz S. A spatial expression atlas of the adult human proximal small intestine. Nature 2024; 632:1101-1109. [PMID: 39112711 DOI: 10.1038/s41586-024-07793-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 07/05/2024] [Indexed: 08/17/2024]
Abstract
The mouse small intestine shows profound variability in gene expression along the crypt-villus axis1,2. Whether similar spatial heterogeneity exists in the adult human gut remains unclear. Here we use spatial transcriptomics, spatial proteomics and single-molecule fluorescence in situ hybridization to reconstruct a comprehensive spatial expression atlas of the adult human proximal small intestine. We describe zonated expression and cell type representation for epithelial, mesenchymal and immune cell types. We find that migrating enterocytes switch from lipid droplet assembly and iron uptake at the villus bottom to chylomicron biosynthesis and iron release at the tip. Villus tip cells are pro-immunogenic, recruiting γδ T cells and macrophages to the tip, in contrast to their immunosuppressive roles in mouse. We also show that the human small intestine contains abundant serrated and branched villi that are enriched at the tops of circular folds. Our study presents a detailed resource for understanding the biology of the adult human small intestine.
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Affiliation(s)
- Yotam Harnik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Oran Yakubovsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rouven Hoefflin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Roy Novoselsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Barkai
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Sheba Medical Center, Ramat Gan, Israel
| | - Yael Korem Kohanim
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Adi Egozi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yoseph Addadi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Kedmi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Keidar Haran
- Department of Pathology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Yishai Levin
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Keren-Shaul
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Chen Mayer
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Niv Pencovich
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ron Pery
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dror S Shouval
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Nachmany
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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