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1
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Jana S, Glabman RA, Koehne AL. Bridging the gap between histopathology and genomics: Spotlighting spatial omics. Vet Pathol 2025:3009858251322729. [PMID: 40138497 DOI: 10.1177/03009858251322729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2025]
Abstract
Spatial biology has emerged as a transformative field, offering insights into cellular interactions and organization within tissues. The field has evolved rapidly since the coining of the term "spatial omics." Now, the ability to spatially resolve proteins, RNA, chromatin, and lipids is becoming widespread, and the technologies are continually refined. Reagents to support the analysis of veterinary species are available and more are emerging. These new tools will allow pathologists and scientists to unravel the intricate interplay between tissue architecture and diverse cellular phenotypes. By integrating histological observations with spatially resolved genomic data, spatial biology holds immense potential for advancing diagnostic and therapeutic strategies in veterinary medicine. These tools will undoubtedly equip veterinary pathologists to better decipher complex disease processes and identify novel therapeutic targets.
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Liu Y, Sinjab A, Min J, Han G, Paradiso F, Zhang Y, Wang R, Pei G, Dai Y, Liu Y, Cho KS, Dai E, Basi A, Burks JK, Rajapakshe KI, Chu Y, Jiang J, Zhang D, Yan X, Guerrero PA, Serrano A, Li M, Hwang TH, Futreal A, Ajani JA, Solis Soto LM, Jazaeri AA, Kadara H, Maitra A, Wang L. Conserved spatial subtypes and cellular neighborhoods of cancer-associated fibroblasts revealed by single-cell spatial multi-omics. Cancer Cell 2025:S1535-6108(25)00083-2. [PMID: 40154487 DOI: 10.1016/j.ccell.2025.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 08/09/2024] [Accepted: 03/03/2025] [Indexed: 04/01/2025]
Abstract
Cancer-associated fibroblasts (CAFs) are a multifaceted cell population essential for shaping the tumor microenvironment (TME) and influencing therapy responses. Characterizing the spatial organization and interactions of CAFs within complex tissue environments provides critical insights into tumor biology and immunobiology. In this study, through integrative analyses of over 14 million cells from 10 cancer types across 7 spatial transcriptomics and proteomics platforms, we discover, validate, and characterize four distinct spatial CAF subtypes. These subtypes are conserved across cancer types and independent of spatial omics platforms. Notably, they exhibit distinct spatial organizational patterns, neighboring cell compositions, interaction networks, and transcriptomic profiles. Their abundance and composition vary across tissues, shaping TME characteristics, such as levels, distribution, and state composition of tumor-infiltrating immune cells, tumor immune phenotypes, and patient survival. This study enriches our understanding of CAF spatial heterogeneity in cancer and paves the way for novel approaches to target and modulate CAFs.
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Affiliation(s)
- Yunhe Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ansam Sinjab
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jimin Min
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Francesca Paradiso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yuanyuan Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guangsheng Pei
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yibo Dai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences (GSBS), Houston, TX 77030, USA
| | - Yang Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kyung Serk Cho
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Enyu Dai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Akshay Basi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jared K Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kimal I Rajapakshe
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yanshuo Chu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiahui Jiang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daiwei Zhang
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xinmiao Yan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Paola A Guerrero
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alejandra Serrano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tae Hyun Hwang
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luisa M Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Amir A Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences (GSBS), Houston, TX 77030, USA.
| | - Anirban Maitra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences (GSBS), Houston, TX 77030, USA; The James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Institute for Data Science in Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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3
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Young JS, Cho NW, Lucas CHG, Najem H, Mirchia K, Chen WC, Seo K, Zakimi N, Daggubati V, Casey-Clyde T, Nguyen MP, Chen A, Phillips JJ, Ozawa T, Aghi MK, Taylor JW, DeRisi JL, Bhaduri A, Berger MS, Heimberger AB, Butowski N, Spitzer MH, Raleigh DR. IL-6 underlies microenvironment immunosuppression and resistance to therapy in glioblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.12.642800. [PMID: 40161763 PMCID: PMC11952432 DOI: 10.1101/2025.03.12.642800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
The glioblastoma tumor immune microenvironment (TIME) is an immunosuppressive barrier to therapy that encumbers glioblastoma responses to immune checkpoint inhibition (ICI). Immunosuppressive cytokines, pro-tumor myeloid cells, and exhausted T-cells are hallmarks of the glioblastoma TIME. Here we integrate spatial and single-cell analyses of patient-matched human glioblastoma samples before and after ICI with genetic, immunologic, single-cell, and pharmacologic studies in preclinical models to reveal that interleukin-6 (IL-6) inhibition reprograms the glioblastoma TIME to sensitize mouse glioblastoma to ICI and radiotherapy. Rare human glioblastoma patients who achieve clinical responses to ICI have lower pre-treatment IL-6 levels compared to glioblastomas who do not respond to ICI. Immune stimulatory gene therapy suppresses IL-6 tumor levels in preclinical murine models of glioblastoma. Furthermore, survival was longer in Il-6 knockout mice with orthotopic SB28 glioblastoma relative to wild-type mice. IL-6 blockade with a neutralizing antibody transiently sensitizes mouse glioblastoma to anti-PD-1 by increasing MHCII+ monocytes, CD103+ migratory dendritic cells (DCs), CD11b+ conventional DCs, and effector CD8+ T cells, and decreasing immunosuppressive Tregs. To translate these findings to a combination treatment strategy for recurrent glioblastoma patients, we show that IL-6 blockade plus ICI durably sensitizes mouse glioblastoma to high-dose radiotherapy.
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Affiliation(s)
- Jacob S. Young
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nam Woo Cho
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Department of Otolaryngology, University of California San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Calixto-Hope G. Lucas
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University, Baltimore, MD, USA
| | - Hinda Najem
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Kanish Mirchia
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - William C. Chen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Kyounghee Seo
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Naomi Zakimi
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Vikas Daggubati
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Tim Casey-Clyde
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Minh P. Nguyen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Arya Chen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Joanna J. Phillips
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Tomoko Ozawa
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Manish K. Aghi
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jennie W. Taylor
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Mitchel S. Berger
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Amy B. Heimberger
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Nicholas Butowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Matthew H. Spitzer
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Department of Otolaryngology, University of California San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - David R. Raleigh
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
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4
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Guan A, Quek C. Single-Cell Multi-Omics: Insights into Therapeutic Innovations to Advance Treatment in Cancer. Int J Mol Sci 2025; 26:2447. [PMID: 40141092 PMCID: PMC11942442 DOI: 10.3390/ijms26062447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2025] [Revised: 03/04/2025] [Accepted: 03/07/2025] [Indexed: 03/28/2025] Open
Abstract
Advances in single-cell multi-omics technologies have deepened our understanding of cancer biology by integrating genomic, transcriptomic, epigenomic, and proteomic data at single-cell resolution. These single-cell multi-omics technologies provide unprecedented insights into tumour heterogeneity, tumour microenvironment, and mechanisms of therapeutic resistance, enabling the development of precision medicine strategies. The emerging field of single-cell multi-omics in genomic medicine has improved patient outcomes. However, most clinical applications still depend on bulk genomic approaches, which fail to directly capture the genomic variations driving cellular heterogeneity. In this review, we explore the common single-cell multi-omics platforms and discuss key analytical steps for data integration. Furthermore, we highlight emerging knowledge in therapeutic resistance and immune evasion, and the potential of new therapeutic innovations informed by single-cell multi-omics. Finally, we discuss the future directions of the application of single-cell multi-omics technologies. By bridging the gap between technological advancements and clinical implementation, this review provides a roadmap for leveraging single-cell multi-omics to improve cancer treatment and patient outcomes.
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Affiliation(s)
- Angel Guan
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia;
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Camelia Quek
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia;
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
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5
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Cottrell TR, Lotze MT, Ali A, Bifulco CB, Capitini CM, Chow LQM, Cillo AR, Collyar D, Cope L, Deutsch JS, Dubrovsky G, Gnjatic S, Goh D, Halabi S, Kohanbash G, Maecker HT, Maleki Vareki S, Mullin S, Seliger B, Taube J, Vos W, Yeong J, Anderson KG, Bruno TC, Chiuzan C, Diaz-Padilla I, Garrett-Mayer E, Glitza Oliva IC, Grandi P, Hill EG, Hobbs BP, Najjar YG, Pettit Nassi P, Simons VH, Subudhi SK, Sullivan RJ, Takimoto CH. Society for Immunotherapy of Cancer (SITC) consensus statement on essential biomarkers for immunotherapy clinical protocols. J Immunother Cancer 2025; 13:e010928. [PMID: 40054999 DOI: 10.1136/jitc-2024-010928] [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] [Accepted: 02/05/2025] [Indexed: 03/12/2025] Open
Abstract
Immunotherapy of cancer is now an essential pillar of treatment for patients with many individual tumor types. Novel immune targets and technical advances are driving a rapid exploration of new treatment strategies incorporating immune agents in cancer clinical practice. Immunotherapies perturb a complex system of interactions among genomically unstable tumor cells, diverse cells within the tumor microenvironment including the systemic adaptive and innate immune cells. The drive to develop increasingly effective immunotherapy regimens is tempered by the risk of immune-related adverse events. Evidence-based biomarkers that measure the potential for therapeutic response and/or toxicity are critical to guide optimal patient care and contextualize the results of immunotherapy clinical trials. Responding to the lack of guidance on biomarker testing in early-phase immunotherapy clinical trials, we propose a definition and listing of essential biomarkers recommended for inclusion in all such protocols. These recommendations are based on consensus provided by the Society for Immunotherapy of Cancer (SITC) Clinical Immuno-Oncology Network (SCION) faculty with input from the SITC Pathology and Biomarker Committees and the Journal for ImmunoTherapy of Cancer readership. A consensus-based selection of essential biomarkers was conducted using a Delphi survey of SCION faculty. Regular updates to these recommendations are planned. The inaugural list of essential biomarkers includes complete blood count with differential to generate a neutrophil-to-lymphocyte ratio or systemic immune-inflammation index, serum lactate dehydrogenase and albumin, programmed death-ligand 1 immunohistochemistry, microsatellite stability assessment, and tumor mutational burden. Inclusion of these biomarkers across early-phase immunotherapy clinical trials will capture variation among trials, provide deeper insight into the novel and established therapies, and support improved patient selection and stratification for later-phase clinical trials.
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Affiliation(s)
- Tricia R Cottrell
- Queen's University Sinclair Cancer Research Institute, Kingston, Ontario, Canada
| | | | - Alaa Ali
- Stem Cell Transplant and Cellular Immunotherapy Program, Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, Washington, DC, USA
| | - Carlo B Bifulco
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Christian M Capitini
- University of Wisconsin School of Medicine and Public Health and Carbone Cancer Center, Madison, Wisconsin, USA
| | | | - Anthony R Cillo
- UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Deborah Collyar
- Patient Advocates In Research (PAIR), Danville, California, USA
| | - Leslie Cope
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | | | | | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Denise Goh
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore
| | - Susan Halabi
- Duke School of Medicine and Duke Cancer Institute, Durham, North Carolina, USA
| | - Gary Kohanbash
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Holden T Maecker
- Stanford University School of Medicine, Stanford, California, USA
| | - Saman Maleki Vareki
- Department of Oncology and Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Sarah Mullin
- Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Barbara Seliger
- Campus Brandenburg an der Havel, Brandenburg Medical School, Halle, Germany
| | - Janis Taube
- Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Wim Vos
- Radiomics.bio, Liège, Belgium
| | - Joe Yeong
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Kristin G Anderson
- Department of Microbiology, Immunology and Cancer Biology, Department of Obstetrics and Gynecology, Beirne B. Carter Center for Immunology Research and the University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia, USA
| | - Tullia C Bruno
- UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Codruta Chiuzan
- Institute of Health System Science, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, New York, USA
| | | | | | | | | | - Elizabeth G Hill
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Brian P Hobbs
- Dell Medical School, The University of Texas, Austin, Texas, USA
| | - Yana G Najjar
- UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | | | | | - Sumit K Subudhi
- The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ryan J Sullivan
- Massachusetts General Hospital, Harvard Medical School, Needham, Massachusetts, USA
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6
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Yip RKH, Hawkins ED, Bowden R, Rogers KL. Towards deciphering the bone marrow microenvironment with spatial multi-omics. Semin Cell Dev Biol 2025; 167:10-21. [PMID: 39889539 DOI: 10.1016/j.semcdb.2025.01.001] [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: 10/09/2024] [Revised: 12/23/2024] [Accepted: 01/18/2025] [Indexed: 02/03/2025]
Abstract
The tissue microenvironment refers to a localised tissue area where a complex combination of cells, structural components, and signalling molecules work together to support specific biological activities. A prime example is the bone marrow microenvironment, particularly the hematopoietic stem cell (HSC) niche, which is of immense interest due to its critical role in supporting lifelong blood cell production and the growth of malignant cells. In this review, we summarise the current understanding of HSC niche biology, highlighting insights gained from advanced imaging and genomic techniques. We also discuss the potential of emerging technologies such as spatial multi-omics to unravel bone marrow architecture in unprecedented detail.
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Affiliation(s)
- Raymond K H Yip
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia; Colonial Foundation Diagnostics Centre, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.
| | - Edwin D Hawkins
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia; Colonial Foundation Diagnostics Centre, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Rory Bowden
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kelly L Rogers
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
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7
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Krestensen KK, Hendriks TFE, Grgic A, Derweduwe M, De Smet F, Heeren RMA, Cuypers E. Molecular Profiling of Glioblastoma Patient-Derived Single Cells Using Combined MALDI-MSI and MALDI-IHC. Anal Chem 2025; 97:3846-3854. [PMID: 39932302 DOI: 10.1021/acs.analchem.4c03821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2025]
Abstract
In recent years, mass spectrometry-based imaging techniques have improved at unprecedented speeds, particularly in spatial resolution, and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) experiments can now routinely image molecular profiles of single cells in an untargeted fashion. With the introduction of MALDI-immunohistochemistry (IHC), multiplexed visualization of targeted proteins in their native tissue location has become accessible and joins the suite of multimodal imaging techniques that help unravel molecular complexities. However, MALDI-IHC has not been validated for use with cell cultures at single-cell level. Here, we introduce a workflow for combining MALDI-MSI and MALDI-IHC on single, isolated cells. Patient-derived cells from glioblastoma tumor samples were imaged, first with high-resolution MSI to obtain a lipid profile, followed by MALDI-IHC highlighting cell-specific protein markers. The multimodal imaging revealed cell type specific lipid profiles when comparing glioblastoma cells and neuronal cells. Furthermore, the initial MSI measurement and its sample preparation showed no significant differences in the subsequent MALDI-IHC ion intensities. Finally, an automated recognition model was created based on the MALDI-MSI data and was able to accurately classify cells into their respective cell type in agreement with the MALDI-IHC markers, with triglycerides, phosphatidylcholines, and sphingomyelins being the most important classifiers. These results show how MALDI-IHC can provide additional valuable molecular information on single-cell measurements, even after an initial MSI measurement without reduced efficacy. Investigation of heterogeneous single-cell samples has the potential of giving a unique insight into the dynamics of how cell-to-cell interaction drives intratumor heterogeneity, thus highlighting the perspective of this work.
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Affiliation(s)
- Kasper K Krestensen
- The Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Tim F E Hendriks
- The Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Andrej Grgic
- The Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Marleen Derweduwe
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Unit, KU Leuven, 3001 Leuven, Belgium
| | - Frederik De Smet
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Unit, KU Leuven, 3001 Leuven, Belgium
| | - Ron M A Heeren
- The Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Eva Cuypers
- The Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
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8
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Najem H, Pacheco S, Turunen J, Tripathi S, Steffens A, McCortney K, Walshon J, Chandler J, Stupp R, Lesniak MS, Horbinski CM, Winkowski D, Kowal J, Burks JK, Heimberger AB. High Dimensional Proteomic Multiplex Imaging of the Central Nervous System Using the COMET™ System. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.14.638299. [PMID: 40027731 PMCID: PMC11870576 DOI: 10.1101/2025.02.14.638299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Sequential multiplex methodologies such as Akoya CODEX, Miltenyi MACSima, Rarecyte Orion, and others require modification of the antibodies by conjugation to an oligo or a specific fluorophore which means the use of off-the-shelf reagents is not possible. Modifications of these antibodies are typically performed via reduction chemistry and thus require verification and validation post-modification. Fixed panels are therefore developed due to various limitations including spectral overlap that creates spectral unmixing issues, steric hindrance, harsh antibody removal, and tissue degradation throughout the labeling. As such, a complex interrogation evaluating multiple study hypotheses and/or endpoints requires the development of sequential panels, reconstruction, and realignment of the tissue that necessitate a z-stack strategy. Standardized antibody panels are typically fixed and require substantial validation efforts to modify a single target and thus do not evolve with the pace of research interests. To increase the throughput of profiling cells within the human central nervous system (CNS), we developed and validated a CNS-specific library with an associated analysis platform using the newly developed Lunaphore COMET TM platform. The COMET TM is an automated staining/imaging instrument integrating a reagent deck for staining buffers and off-the-shelf label-free primary antibodies and fluorophore-labeled secondary antibodies, which feed into a circular plate holding up to 4 slides that are automatically imaged in microscope-operated control software. For this study, standard formalin fixed paraffin embedded histology slides are used. However, the COMET is capable of imaging fresh-frozen samples using specialized settings. Our methodologies address an unmet need in the neuroscience field while leveraging prior developmental efforts in the domain of immunology spatial profiling. Cataloging and validating a large series of antibodies on the COMET™ along with developing CNS autofluorescence management strategies while optimizing standard operating procedures have allowed for the visualization at the subcellular level. Forty analytes can be used to analyze one specimen which has clinical utility in cases in which the CNS can only be sampled by biopsy. CNS biopsies, depending on the anatomical location, can have limited available volume to a degree that requires prioritization and restriction to select analysis. In-depth bioinformatic imaging analysis can be done using standard bioinformatic tools and software such as Visiopharm®. These results establish a general framework for imaging and quantifying cell populations and networks within the CNS while providing the scientific community with standard operating procedures.
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Affiliation(s)
- Hinda Najem
- Department of Neurological Surgery, Northwestern University, Chicago, IL
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | - Sebastian Pacheco
- Department of Neurological Surgery, Northwestern University, Chicago, IL
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | - Jillyn Turunen
- Department of Neurological Surgery, Northwestern University, Chicago, IL
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | - Shashwat Tripathi
- Department of Neurological Surgery, Northwestern University, Chicago, IL
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | - Alicia Steffens
- Department of Neurological Surgery, Northwestern University, Chicago, IL
- Department of Pathology Feinberg School of Medicine, Northwestern University, Chicago, IL
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | - Kathleen McCortney
- Department of Neurological Surgery, Northwestern University, Chicago, IL
- Department of Pathology Feinberg School of Medicine, Northwestern University, Chicago, IL
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | - Jordain Walshon
- Department of Neurological Surgery, Northwestern University, Chicago, IL
- Department of Pathology Feinberg School of Medicine, Northwestern University, Chicago, IL
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | - James Chandler
- Department of Neurological Surgery, Northwestern University, Chicago, IL
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | - Roger Stupp
- Department of Neurological Surgery, Northwestern University, Chicago, IL
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | - Maciej S. Lesniak
- Department of Neurological Surgery, Northwestern University, Chicago, IL
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | - Craig M. Horbinski
- Department of Neurological Surgery, Northwestern University, Chicago, IL
- Department of Pathology Feinberg School of Medicine, Northwestern University, Chicago, IL
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | | | - Joanna Kowal
- Lunaphore, Tolochenaz Switzerland, The University of Texas MD Anderson Cancer Center, Houston, Tx, 77030
| | - Jared K. Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Tx, 77030
| | - Amy B. Heimberger
- Department of Neurological Surgery, Northwestern University, Chicago, IL
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
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9
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Lutz R, Poos AM, Solé-Boldo L, John L, Wagner J, Prokoph N, Baertsch MA, Vonficht D, Palit S, Brobeil A, Mechtersheimer G, Hildenbrand N, Hemmer S, Steiger S, Horn S, Pepke W, Spranz DM, Rehnitz C, Sant P, Mallm JP, Friedrich MJ, Reichert P, Huhn S, Trumpp A, Rippe K, Haghverdi L, Fröhling S, Müller-Tidow C, Hübschmann D, Goldschmidt H, Willimsky G, Sauer S, Raab MS, Haas S, Weinhold N. Bone marrow breakout lesions act as key sites for tumor-immune cell diversification in multiple myeloma. Sci Immunol 2025; 10:eadp6667. [PMID: 39919199 DOI: 10.1126/sciimmunol.adp6667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 01/03/2025] [Indexed: 02/09/2025]
Abstract
The bone marrow microenvironment plays a crucial role in the development of multiple myeloma. As the disease progresses, malignant myeloma cells can evolve to survive outside the bone marrow. However, the processes underlying bone marrow independence and their consequences for immune control remain poorly understood. Here, we conducted single-cell and spatial multiomics analyses of bone marrow-confined intramedullary disease and paired breakout lesions that disrupt the cortical bone. These analyses revealed a distinct cellular microenvironment and architectural features of breakout lesions, characterized by extensive areas of malignant plasma cells interspersed with lesion-specific solitary natural killer and macrophage populations, as well as focal accumulations of immune cell agglomerates. Within these agglomerates, spatially confined T cell clones expanded alongside various immune cells, coinciding with the local genomic evolution of tumor cells. These analyses identify breakout lesions as a hotspot for tumor-immune cell interactions and diversification, representing a key event in myeloma pathogenesis.
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Affiliation(s)
- Raphael Lutz
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexandra M Poos
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Llorenç Solé-Boldo
- Berlin Institute of Health (BIH) at Charité Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Lukas John
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johanna Wagner
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Nina Prokoph
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc A Baertsch
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominik Vonficht
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Subarna Palit
- Berlin Institute of Health (BIH) at Charité Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
| | - Alexander Brobeil
- Department of Pathology, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Tissue Bank of the National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Gunhild Mechtersheimer
- Department of Pathology, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Nina Hildenbrand
- Department of Orthopaedics, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Stefan Hemmer
- Department of Orthopaedics, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Simon Steiger
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Sabrina Horn
- Berlin Institute of Health (BIH) at Charité Universitätsmedizin Berlin, Berlin, Germany
- Institute of Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Wojciech Pepke
- Department of Orthopaedics, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - David M Spranz
- Department of Orthopaedics, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Christoph Rehnitz
- Department of Radiology, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Pooja Sant
- Single Cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan-Philipp Mallm
- Single Cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mirco J Friedrich
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Philipp Reichert
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Stefanie Huhn
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Laleh Haghverdi
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Carsten Müller-Tidow
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Daniel Hübschmann
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hartmut Goldschmidt
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- GMMG-Study Group at Heidelberg University Hospital, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Gerald Willimsky
- Berlin Institute of Health (BIH) at Charité Universitätsmedizin Berlin, Berlin, Germany
- Institute of Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandra Sauer
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Marc S Raab
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simon Haas
- Berlin Institute of Health (BIH) at Charité Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany
| | - Niels Weinhold
- Heidelberg Myeloma Center, Department of Internal Medicine V, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
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10
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Kulasinghe A, Berrell N, Donovan ML, Nilges BS. Spatial-Omics Methods and Applications. Methods Mol Biol 2025; 2880:101-146. [PMID: 39900756 DOI: 10.1007/978-1-0716-4276-4_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] [Indexed: 02/05/2025]
Abstract
Traditional tissue profiling approaches have evolved from bulk studies to single-cell analysis over the last decade; however, the spatial context in tissues and microenvironments has always been lost. Over the last 5 years, spatial technologies have emerged that enabled researchers to investigate tissues in situ for proteins and transcripts without losing anatomy and histology. The field of spatial-omics enables highly multiplexed analysis of biomolecules like RNAs and proteins in their native spatial context-and has matured from initial proof-of-concept studies to a thriving field with widespread applications from basic research to translational and clinical studies. While there has been wide adoption of spatial technologies, there remain challenges with the standardization of methodologies, sample compatibility, throughput, resolution, and ease of use. In this chapter, we discuss the current state of the field and highlight technological advances and limitations.
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Affiliation(s)
- Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Queensland Spatial Biology Centre, Wesley Research Institute, The Wesley Hospital, Auchenflower, QLD, Australia
| | - Naomi Berrell
- Queensland Spatial Biology Centre, Wesley Research Institute, The Wesley Hospital, Auchenflower, QLD, Australia
| | - Meg L Donovan
- Queensland Spatial Biology Centre, Wesley Research Institute, The Wesley Hospital, Auchenflower, QLD, Australia
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11
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Milshteyn L, Villamejor A, Merchant A, Lownik J. A novel murine syngeneic CD8 peripheral T-cell lymphoma model with preclinical applications. Leuk Lymphoma 2025; 66:102-108. [PMID: 39291652 DOI: 10.1080/10428194.2024.2404253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/26/2024] [Accepted: 09/08/2024] [Indexed: 09/19/2024]
Abstract
Peripheral T-cell Lymphoma (PTCL) represents a heterogenous group of aggressive non-Hodgkin Lymphomas with poor prognostic outcomes and limited treatment options. The development and refinement of therapeutic strategies for PTCL are impeded by a paucity of reliable preclinical models that accurately mimic the disease's pathophysiology. There is a dire need for more physiologically relevant models for PTCL. Here we describe a spontaneousCD8+ peripheral T-cell lymphoma cell line (LM-23) derived from a 12-week-old female Balb/cJ mouse. Both intravenous and subcutaneous administration of this cell line to syngeneic Balb/cJ mice resulted in rapid establishment of tumor growth. CHOP and anti-PD1 treatment both displayed no benefit to mice in regulating tumor growth. Such results along with its phenotypic characteristics, rapid growth, and metastatic behavior in syngeneic mice highlight its value in studying the elusive disease and discovery of novel therapeutics.
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Affiliation(s)
| | | | | | - Joseph Lownik
- Department of Pathology & Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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12
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Lubo I, Hernandez S, Wistuba II, Solis Soto LM. Novel Spatial Approaches to Dissect the Lung Cancer Immune Microenvironment. Cancers (Basel) 2024; 16:4145. [PMID: 39766047 PMCID: PMC11674389 DOI: 10.3390/cancers16244145] [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: 11/12/2024] [Revised: 12/07/2024] [Accepted: 12/10/2024] [Indexed: 01/11/2025] Open
Abstract
Lung cancer is a deadly disease with the highest rates of mortality. Over recent decades, a better understanding of the biological mechanisms implicated in its pathogenesis has led to the development of targeted therapies and immunotherapy, resulting in improvements in patient outcomes. To better understand lung cancer tumor biology and advance towards precision oncology, a comprehensive tumor profile is necessary. In recent years, novel in situ spatial multiomics approaches have emerged offering a more detailed view of the spatial location of tumor and tumor microenvironment cells, identifying their unique composition and functional status. In this sense, novel multiomics platforms have been developed to evaluate tumor heterogeneity, gene expression, metabolic reprogramming, signaling pathway activation, cell-cell interactions, and immune cell programs. In lung cancer research, several studies have used these spatial technologies to locate cells and associated them with histological features that are relevant to the pathogenesis of lung adenocarcinoma. These advancements may unveil further molecular and immune mechanisms in tumor biology that will lead to the discovery of biomarkers for treatment prediction and prognosis. In this review, we provide an overview of more widely used and emerging pathology-based approaches for spatial immune profiling in lung cancer and how they enhance our understanding of tumor biology and immune response.
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Affiliation(s)
| | | | | | - Luisa Maren Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (I.L.); (S.H.); (I.I.W.)
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13
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Carranza FG, Diaz FC, Ninova M, Velazquez-Villarreal E. Current state and future prospects of spatial biology in colorectal cancer. Front Oncol 2024; 14:1513821. [PMID: 39711954 PMCID: PMC11660798 DOI: 10.3389/fonc.2024.1513821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Accepted: 11/15/2024] [Indexed: 12/24/2024] Open
Abstract
Over the past century, colorectal cancer (CRC) has become one of the most devastating cancers impacting the human population. To gain a deeper understanding of the molecular mechanisms driving this solid tumor, researchers have increasingly turned their attention to the tumor microenvironment (TME). Spatial transcriptomics and proteomics have emerged as a particularly powerful technology for deciphering the complexity of CRC tumors, given that the TME and its spatial organization are critical determinants of disease progression and treatment response. Spatial transcriptomics enables high-resolution mapping of the whole transcriptome. While spatial proteomics maps protein expression and function across tissue sections. Together, they provide a detailed view of the molecular landscape and cellular interactions within the TME. In this review, we delve into recent advances in spatial biology technologies applied to CRC research, highlighting both the methodologies and the challenges associated with their use, such as the substantial tissue heterogeneity characteristic of CRC. We also discuss the limitations of current approaches and the need for novel computational tools to manage and interpret these complex datasets. To conclude, we emphasize the importance of further developing and integrating spatial transcriptomics into CRC precision medicine strategies to enhance therapeutic targeting and improve patient outcomes.
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Affiliation(s)
- Francisco G. Carranza
- Department of Integrative Translational Sciences, City of Hope, Beckman Research Institute, Duarte, CA, United States
| | - Fernando C. Diaz
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
| | - Maria Ninova
- Department of Biochemistry, University of California, Riverside, Riverside, CA, United States
| | - Enrique Velazquez-Villarreal
- Department of Integrative Translational Sciences, City of Hope, Beckman Research Institute, Duarte, CA, United States
- City of Hope Comprehensive Cancer Center, Duarte, CA, United States
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14
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Semba T, Ishimoto T. Spatial analysis by current multiplexed imaging technologies for the molecular characterisation of cancer tissues. Br J Cancer 2024; 131:1737-1747. [PMID: 39438630 PMCID: PMC11589153 DOI: 10.1038/s41416-024-02882-6] [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: 06/29/2024] [Revised: 10/09/2024] [Accepted: 10/11/2024] [Indexed: 10/25/2024] Open
Abstract
Tumours are composed of tumour cells and the surrounding tumour microenvironment (TME), and the molecular characterisation of the various elements of the TME and their interactions is essential for elucidating the mechanisms of tumour progression and developing better therapeutic strategies. Multiplex imaging is a technique that can quantify the expression of multiple protein markers on the same tissue section while maintaining spatial positioning, and this method has been rapidly developed in cancer research in recent years. Many multiplex imaging technologies and spatial analysis methods are emerging, and the elucidation of their principles and features is essential. In this review, we provide an overview of the latest multiplex imaging techniques by type of imaging and staining method and an introduction to image analysis methods, primarily focusing on spatial cellular properties, providing deeper insight into tumour organisation and spatial molecular biology in the TME.
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Affiliation(s)
- Takashi Semba
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takatsugu Ishimoto
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.
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15
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Chap BS, Rayroux N, Grimm AJ, Ghisoni E, Dangaj Laniti D. Crosstalk of T cells within the ovarian cancer microenvironment. Trends Cancer 2024; 10:1116-1130. [PMID: 39341696 DOI: 10.1016/j.trecan.2024.09.001] [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: 06/28/2024] [Revised: 09/02/2024] [Accepted: 09/03/2024] [Indexed: 10/01/2024]
Abstract
Ovarian cancer (OC) represents ecosystems of highly diverse tumor microenvironments (TMEs). The presence of tumor-infiltrating lymphocytes (TILs) is linked to enhanced immune responses and long-term survival. In this review we present emerging evidence suggesting that cellular crosstalk tightly regulates the distribution of TILs within the TME, underscoring the need to better understand key cellular networks that promote or impede T cell infiltration in OC. We also capture the emergent methodologies and computational techniques that enable the dissection of cell-cell crosstalk. Finally, we present innovative ex vivo TME models that can be leveraged to map and perturb cellular communications to enhance T cell infiltration and immune reactivity.
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Affiliation(s)
- Bovannak S Chap
- Department of Oncology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland; Agora Cancer Research Center, Lausanne, Switzerland
| | - Nicolas Rayroux
- Department of Oncology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland; Agora Cancer Research Center, Lausanne, Switzerland
| | - Alizée J Grimm
- Department of Oncology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland; Agora Cancer Research Center, Lausanne, Switzerland
| | - Eleonora Ghisoni
- Department of Oncology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland; Agora Cancer Research Center, Lausanne, Switzerland
| | - Denarda Dangaj Laniti
- Department of Oncology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland; Agora Cancer Research Center, Lausanne, Switzerland.
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16
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Wu J, Koelzer VH. Towards generative digital twins in biomedical research. Comput Struct Biotechnol J 2024; 23:3481-3488. [PMID: 39435342 PMCID: PMC11491725 DOI: 10.1016/j.csbj.2024.09.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 09/30/2024] [Accepted: 09/30/2024] [Indexed: 10/23/2024] Open
Abstract
Digital twins in biomedical research, i.e. virtual replicas of biological entities such as cells, organs, or entire organisms, hold great potential to advance personalized healthcare. As all biological processes happen in space, there is a growing interest in modeling biological entities within their native context. Leveraging generative artificial intelligence (AI) and high-volume biomedical data profiled with spatial technologies, researchers can recreate spatially-resolved digital representations of a physical entity with high fidelity. In application to biomedical fields such as computational pathology, oncology, and cardiology, these generative digital twins (GDT) thus enable compelling in silico modeling for simulated interventions, facilitating the exploration of 'what if' causal scenarios for clinical diagnostics and treatments tailored to individual patients. Here, we outline recent advancements in this novel field and discuss the challenges and future research directions.
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Affiliation(s)
- Jiqing Wu
- Department of Biomedical Engineering, University of Basel, Basel, Switzerland
| | - Viktor H. Koelzer
- Department of Biomedical Engineering, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
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17
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Ghajar-Rahimi G, Barwinska D, Whipple GE, Kamocka MM, Khan S, Winfree S, Lafontaine J, Soliman RH, Melkonian AL, Zmijewska AA, Cheung MD, Traylor AM, Jiang Y, Yang Z, Bolisetty S, Zarjou A, Lee T, George JF, El-Achkar TM, Agarwal A. Acute kidney injury results in long-term alterations of kidney lymphatics in mice. Am J Physiol Renal Physiol 2024; 327:F869-F884. [PMID: 39323387 PMCID: PMC11563594 DOI: 10.1152/ajprenal.00120.2024] [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: 04/17/2024] [Revised: 08/14/2024] [Accepted: 09/11/2024] [Indexed: 09/27/2024] Open
Abstract
The long-term effects of a single episode of acute kidney injury (AKI) induced by bilateral ischemia-reperfusion injury (BIRI) on kidney lymphatic dynamics are not known. The purpose of this study was to determine if alterations in kidney lymphatics are sustained in the long term and how they relate to inflammation and injury. Mice underwent BIRI as a model of AKI and were followed up to 9 mo. Although kidney function markers normalized following initial injury, histological analysis revealed sustained tissue damage and inflammation for up to 9 mo. Transcriptional analysis showed both acute and late-stage lymphangiogenesis, supported by increased expression of lymphatic markers, with unique signatures at each phase. Expression of Ccl21a was distinctly upregulated during late-stage lymphangiogenesis. Three-dimensional tissue cytometry confirmed increased lymphatic vessel abundance, particularly in the renal cortex, at early and late timepoints postinjury. In addition, the study identified the formation of tertiary lymphoid structures composed of CCR7+ lymphocytes and observed changes in immune cell composition over time, suggesting a complex and dynamic response to AKI involving tissue remodeling and immune cell involvement. This study provides new insights into the role of lymphatics in the progression of AKI to chronic kidney disease.NEW & NOTEWORTHY Here, we perform the first, comprehensive study of long-term lymphatic dynamics following a single acute kidney injury (AKI) event. Using improved three-dimensional image analysis and an expanded panel of transcriptional markers, we identify multiple stages of lymphatic responses with distinct transcriptional signatures, associations with the immune microenvironment, and collagen deposition. This research advances kidney lymphatic biology, emphasizing the significance of longitudinal studies in understanding AKI and the transition to chronic kidney disease.
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Affiliation(s)
- Gelare Ghajar-Rahimi
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Daria Barwinska
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Grace E Whipple
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Malgorzata M Kamocka
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Shehnaz Khan
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Seth Winfree
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States
| | - Jennifer Lafontaine
- Birmingham Veterans Administration Medical Center, Birmingham, Alabama, United States
| | - Reham H Soliman
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Arin L Melkonian
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Anna A Zmijewska
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Matthew D Cheung
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Amie M Traylor
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Yanlin Jiang
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Zhengqin Yang
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Subhashini Bolisetty
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Abolfazl Zarjou
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Timmy Lee
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
- Birmingham Veterans Administration Medical Center, Birmingham, Alabama, United States
| | - James F George
- Division of Cardiothoracic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Tarek M El-Achkar
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Indianapolis Veterans Affairs Medical Center, Indianapolis, Indiana, United States
| | - Anupam Agarwal
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
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18
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Bollhagen A, Bodenmiller B. Highly Multiplexed Tissue Imaging in Precision Oncology and Translational Cancer Research. Cancer Discov 2024; 14:2071-2088. [PMID: 39485249 PMCID: PMC11528208 DOI: 10.1158/2159-8290.cd-23-1165] [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: 10/05/2023] [Revised: 05/24/2024] [Accepted: 08/13/2024] [Indexed: 11/03/2024]
Abstract
Precision oncology tailors treatment strategies to a patient's molecular and health data. Despite the essential clinical value of current diagnostic methods, hematoxylin and eosin morphology, immunohistochemistry, and gene panel sequencing offer an incomplete characterization. In contrast, highly multiplexed tissue imaging allows spatial analysis of dozens of markers at single-cell resolution enabling analysis of complex tumor ecosystems; thereby it has the potential to advance our understanding of cancer biology and supports drug development, biomarker discovery, and patient stratification. We describe available highly multiplexed imaging modalities, discuss their advantages and disadvantages for clinical use, and potential paths to implement these into clinical practice. Significance: This review provides guidance on how high-resolution, multiplexed tissue imaging of patient samples can be integrated into clinical workflows. It systematically compares existing and emerging technologies and outlines potential applications in the field of precision oncology, thereby bridging the ever-evolving landscape of cancer research with practical implementation possibilities of highly multiplexed tissue imaging into routine clinical practice.
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Affiliation(s)
- Alina Bollhagen
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
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19
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Pakula H, Pederzoli F, Fanelli GN, Nuzzo PV, Rodrigues S, Loda M. Deciphering the Tumor Microenvironment in Prostate Cancer: A Focus on the Stromal Component. Cancers (Basel) 2024; 16:3685. [PMID: 39518123 PMCID: PMC11544791 DOI: 10.3390/cancers16213685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 10/25/2024] [Accepted: 10/29/2024] [Indexed: 11/16/2024] Open
Abstract
Prostate cancer progression is significantly affected by its tumor microenvironment, in which mesenchymal cells play a crucial role. Stromal cells are modified by cancer mutations, response to androgens, and lineage plasticity, and in turn, engage with epithelial tumor cells via a complex array of signaling pathways and ligand-receptor interactions, ultimately affecting tumor growth, immune interaction, and response to therapy. The metabolic rewiring and interplay in the microenvironment play an additional role in affecting the growth and progression of prostate cancer. Finally, therapeutic strategies and novel clinical trials with agents that target the stromal microenvironment or disrupt the interaction between cellular compartments are described. This review underscores cancer-associated fibroblasts as essential contributors to prostate cancer biology, emphasizing their potential as prognostic indicators and therapeutic targets.
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Affiliation(s)
- Hubert Pakula
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; (H.P.); (F.P.); (G.N.F.); (P.V.N.); (S.R.)
| | - Filippo Pederzoli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; (H.P.); (F.P.); (G.N.F.); (P.V.N.); (S.R.)
| | - Giuseppe Nicolò Fanelli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; (H.P.); (F.P.); (G.N.F.); (P.V.N.); (S.R.)
| | - Pier Vitale Nuzzo
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; (H.P.); (F.P.); (G.N.F.); (P.V.N.); (S.R.)
| | - Silvia Rodrigues
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; (H.P.); (F.P.); (G.N.F.); (P.V.N.); (S.R.)
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; (H.P.); (F.P.); (G.N.F.); (P.V.N.); (S.R.)
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Belfer Research Building, 413 East 69th Street, New York, NY 10021, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave, Boston, MA 02215, USA
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX1 2JD, UK
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20
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Eremina OE, Vazquez C, Larson KN, Mouchawar A, Fernando A, Zavaleta C. The evolution of immune profiling: will there be a role for nanoparticles? NANOSCALE HORIZONS 2024; 9:1896-1924. [PMID: 39254004 PMCID: PMC11887860 DOI: 10.1039/d4nh00279b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Immune profiling provides insights into the functioning of the immune system, including the distribution, abundance, and activity of immune cells. This understanding is essential for deciphering how the immune system responds to pathogens, vaccines, tumors, and other stimuli. Analyzing diverse immune cell types facilitates the development of personalized medicine approaches by characterizing individual variations in immune responses. With detailed immune profiles, clinicians can tailor treatment strategies to the specific immune status and needs of each patient, maximizing therapeutic efficacy while minimizing adverse effects. In this review, we discuss the evolution of immune profiling, from interrogating bulk cell samples in solution to evaluating the spatially-rich molecular profiles across intact preserved tissue sections. We also review various multiplexed imaging platforms recently developed, based on immunofluorescence and imaging mass spectrometry, and their impact on the field of immune profiling. Identifying and localizing various immune cell types across a patient's sample has already provided important insights into understanding disease progression, the development of novel targeted therapies, and predicting treatment response. We also offer a new perspective by highlighting the unprecedented potential of nanoparticles (NPs) that can open new horizons in immune profiling. NPs are known to provide enhanced detection sensitivity, targeting specificity, biocompatibility, stability, multimodal imaging features, and multiplexing capabilities. Therefore, we summarize the recent developments and advantages of NPs, which can contribute to advancing our understanding of immune function to facilitate precision medicine. Overall, NPs have the potential to offer a versatile and robust approach to profile the immune system with improved efficiency and multiplexed imaging power.
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Affiliation(s)
- Olga E Eremina
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA.
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Celine Vazquez
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA.
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Kimberly N Larson
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA.
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Anthony Mouchawar
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA.
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Augusta Fernando
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA.
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Cristina Zavaleta
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA.
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
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21
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Gong D, Arbesfeld-Qiu JM, Perrault E, Bae JW, Hwang WL. Spatial oncology: Translating contextual biology to the clinic. Cancer Cell 2024; 42:1653-1675. [PMID: 39366372 DOI: 10.1016/j.ccell.2024.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 08/01/2024] [Accepted: 09/06/2024] [Indexed: 10/06/2024]
Abstract
Microscopic examination of cells in their tissue context has been the driving force behind diagnostic histopathology over the past two centuries. Recently, the rise of advanced molecular biomarkers identified through single cell profiling has increased our understanding of cellular heterogeneity in cancer but have yet to significantly impact clinical care. Spatial technologies integrating molecular profiling with microenvironmental features are poised to bridge this translational gap by providing critical in situ context for understanding cellular interactions and organization. Here, we review how spatial tools have been used to study tumor ecosystems and their clinical applications. We detail findings in cell-cell interactions, microenvironment composition, and tissue remodeling for immune evasion and therapeutic resistance. Additionally, we highlight the emerging role of multi-omic spatial profiling for characterizing clinically relevant features including perineural invasion, tertiary lymphoid structures, and the tumor-stroma interface. Finally, we explore strategies for clinical integration and their augmentation of therapeutic and diagnostic approaches.
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Affiliation(s)
- Dennis Gong
- Center for Systems Biology, Department of Radiation Oncology, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeanna M Arbesfeld-Qiu
- Center for Systems Biology, Department of Radiation Oncology, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard University, Graduate School of Arts and Sciences, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Ella Perrault
- Center for Systems Biology, Department of Radiation Oncology, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard University, Graduate School of Arts and Sciences, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Jung Woo Bae
- Center for Systems Biology, Department of Radiation Oncology, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William L Hwang
- Center for Systems Biology, Department of Radiation Oncology, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard University, Graduate School of Arts and Sciences, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA.
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22
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Wu M, Tao H, Xu T, Zheng X, Wen C, Wang G, Peng Y, Dai Y. Spatial proteomics: unveiling the multidimensional landscape of protein localization in human diseases. Proteome Sci 2024; 22:7. [PMID: 39304896 DOI: 10.1186/s12953-024-00231-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 09/01/2024] [Indexed: 09/22/2024] Open
Abstract
Spatial proteomics is a multidimensional technique that studies the spatial distribution and function of proteins within cells or tissues across both spatial and temporal dimensions. This field multidimensionally reveals the complex structure of the human proteome, including the characteristics of protein spatial distribution, dynamic protein translocation, and protein interaction networks. Recently, as a crucial method for studying protein spatial localization, spatial proteomics has been applied in the clinical investigation of various diseases. This review summarizes the fundamental concepts and characteristics of tissue-level spatial proteomics, its research progress in common human diseases such as cancer, neurological disorders, cardiovascular diseases, autoimmune diseases, and anticipates its future development trends. The aim is to highlight the significant impact of spatial proteomics on understanding disease pathogenesis, advancing diagnostic methods, and developing potential therapeutic targets in clinical research.
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Affiliation(s)
- Mengyao Wu
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Huihui Tao
- School of Medicine, Anhui University of Science & Technology, Huainan, China.
- Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institutes, Huainan, China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Huainan, China.
| | - Tiantian Xu
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Xuejia Zheng
- The First Hospital of Anhui University of Science and Technology, Huainan, China
| | - Chunmei Wen
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Guoying Wang
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Yali Peng
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Yong Dai
- School of Medicine, Anhui University of Science & Technology, Huainan, China
- The First Hospital of Anhui University of Science and Technology, Huainan, China
- Joint Research Center for Occupational Medicine and Health of IHM, Anhui University of Science and Technology, Huainan, China
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23
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Bialy N, Alber F, Andrews B, Angelo M, Beliveau B, Bintu L, Boettiger A, Boehm U, Brown CM, Maina MB, Chambers JJ, Cimini BA, Eliceiri K, Errington R, Faklaris O, Gaudreault N, Germain RN, Goscinski W, Grunwald D, Halter M, Hanein D, Hickey JW, Lacoste J, Laude A, Lundberg E, Ma J, Malacrida L, Moore J, Nelson G, Neumann EK, Nitschke R, Onami S, Pimentel JA, Plant AL, Radtke AJ, Sabata B, Schapiro D, Schöneberg J, Spraggins JM, Sudar D, Vierdag WMAM, Volkmann N, Wählby C, Wang SS, Yaniv Z, Strambio-De-Castillia C. Harmonizing the Generation and Pre-publication Stewardship of FAIR bioimage data. ARXIV 2024:arXiv:2401.13022v5. [PMID: 38351940 PMCID: PMC10862930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance the scientific understanding of complex cellular systems and to advance predictive and personalized therapeutic products for human health. For this potential to be realized, quality-assured bioimage data must be shared among labs at a global scale to be compared, pooled, and reanalyzed, thus unleashing untold potential beyond the original purpose for which the data was generated. There are two broad sets of requirements to enable bioimage data sharing in the life sciences. One set of requirements is articulated in the companion White Paper entitled "Enabling Global Image Data Sharing in the Life Sciences," which is published in parallel and addresses the need to build the cyberinfrastructure for sharing bioimage data (arXiv:2401.13023 [q-bio.OT], https://doi.org/10.48550/arXiv.2401.13023). Here, we detail a broad set of requirements, which involves collecting, managing, presenting, and propagating contextual information essential to assess the quality, understand the content, interpret the scientific implications, and reuse bioimage data in the context of the experimental details. We start by providing an overview of the main lessons learned to date through international community activities, which have recently made generating community standard practices for imaging Quality Control (QC) and metadata (Faklaris et al., 2022; Hammer et al., 2021; Huisman et al., 2021; Microscopy Australia, 2016; Montero Llopis et al., 2021; Rigano et al., 2021; Sarkans et al., 2021). We then provide a clear set of recommendations for amplifying this work. The driving goal is to address remaining challenges and democratize access to common practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location.
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Affiliation(s)
- Nikki Bialy
- Morgridge Institute for Research, Madison, USA
| | | | | | | | | | | | | | | | | | | | | | - Beth A Cimini
- Broad Institute of MIT and Harvard, Imaging Platform, Cambridge, USA
| | - Kevin Eliceiri
- Morgridge Institute for Research, Madison, USA
- University of Wisconsin-Madison, Madison, USA
| | | | | | | | - Ronald N Germain
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | | | - Michael Halter
- National Institute of Standards and Technology, Gaithersburg, USA
| | | | | | | | - Alex Laude
- Newcastle University, Newcastle upon Tyne, UK
| | - Emma Lundberg
- Stanford University, Palo Alto, USA
- SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jian Ma
- Carnegie Mellon University, Pittsburgh, USA
| | - Leonel Malacrida
- Institut Pasteur de Montevideo, & Universidad de la República, Montevideo, Uruguay
| | - Josh Moore
- German BioImaging-Gesellschaft für Mikroskopie und Bildanalyse e.V., Constance, Germany
| | - Glyn Nelson
- Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Shuichi Onami
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | | | - Anne L Plant
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Andrea J Radtke
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | | | | | | | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, USA
| | | | | | | | | | - Ziv Yaniv
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
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24
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Wang S, Castro BA, Katz JL, Arrieta V, Najem H, Vazquez-Cervantes GI, Wan H, Olson IE, Hou D, Dapash M, Billingham LK, Chia TY, Wei C, Rashidi A, Platanias LC, McCortney K, Horbinski CM, Stupp R, Zhang P, Ahmed AU, Sonabend AM, Heimberger AB, Lesniak MS, Riviere-Cazaux C, Burns T, Miska J, Fischietti M, Lee-Chang C. B cell-based therapy produces antibodies that inhibit glioblastoma growth. J Clin Invest 2024; 134:e177384. [PMID: 39207859 PMCID: PMC11473152 DOI: 10.1172/jci177384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Glioblastoma (GBM) is a highly aggressive and malignant brain tumor with limited therapeutic options and a poor prognosis. Despite current treatments, the invasive nature of GBM often leads to recurrence. A promising alternative strategy is to harness the potential of the immune system against tumor cells. Our previous data showed that the BVax (B cell-based vaccine) can induce therapeutic responses in preclinical models of GBM. In this study, we aimed to characterize the antigenic reactivity of BVax-derived Abs and evaluate their therapeutic potential. We performed immunoproteomics and functional assays in murine models and samples from patients with GBM. Our investigations revealed that BVax distributed throughout the GBM tumor microenvironment and then differentiated into Ab-producing plasmablasts. Proteomics analyses indicated that the Abs produced by BVax had unique reactivity, predominantly targeting factors associated with cell motility and the extracellular matrix. Crucially, these Abs inhibited critical processes such as GBM cell migration and invasion. These findings provide valuable insights into the therapeutic potential of BVax-derived Abs for patients with GBM, pointing toward a novel direction for GBM immunotherapy.
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Affiliation(s)
- Si Wang
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Brandyn A. Castro
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Neurological Surgery, University of Chicago Medicine, Chicago, Illinois, USA
| | - Joshua L. Katz
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Victor Arrieta
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Hinda Najem
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Gustavo I. Vazquez-Cervantes
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Hanxiao Wan
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Ian E. Olson
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - David Hou
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Mark Dapash
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Leah K. Billingham
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Tzu-yi Chia
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Chao Wei
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Aida Rashidi
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Leonidas C. Platanias
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois, USA
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
| | - Kathleen McCortney
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Craig M. Horbinski
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Roger Stupp
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Peng Zhang
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Atique U. Ahmed
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Adam M. Sonabend
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Amy B. Heimberger
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Maciej S. Lesniak
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | | | - Terry Burns
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesotta, USA
| | - Jason Miska
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
| | - Mariafausta Fischietti
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois, USA
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Catalina Lee-Chang
- Department of Neurological Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Lou and Jean Malnati Brain Tumor Institute, Chicago, Illinois, USA
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25
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Deen AJ, Thorsson J, O’Roberts EM, Panshikar P, Ullman T, Krantz D, Oses C, Stadler C. Making Multiplexed Imaging Flexible: Combining Essential Markers With Established Antibody Panels. J Histochem Cytochem 2024; 72:517-544. [PMID: 39215640 PMCID: PMC11421402 DOI: 10.1369/00221554241274856] [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: 03/19/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
Multiplexed immunofluorescence (IF) can be achieved using different commercially available platforms, often making use of conjugated antibodies detected in iterative cycles. A growing portfolio of pre-conjugated antibodies is offered by the providers, as well as the possibility for in-house conjugation. For many conjugation methods and kits, there are limitations in which antibodies can be used, and conjugation results are sometimes irreproducible. The conjugation process can limit or slow down the progress of studies requiring conjugation of essential markers needed for a given project. Here, we demonstrate a protocol combining manual indirect immunofluorescence (IF) of primary antibodies, followed by antibody elution and staining with multiplexed panels of commercially pre-conjugated antibodies on the PhenoCycler platform. We present detailed protocols for applying the workflow on fresh frozen and formalin fixed paraffin embedded tissue sections. We also provide a ready to use workflow for coregistration of the images and demonstrate this for two examples.
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Affiliation(s)
- Ashik Jawahar Deen
- Department of Protein Science, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Johan Thorsson
- Department of Protein Science, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Eleanor M. O’Roberts
- Department of Protein Science, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Pranauti Panshikar
- Department of Protein Science, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Tony Ullman
- Department of Protein Science, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - David Krantz
- Department of Oncology-Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Carolina Oses
- Department of Protein Science, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Charlotte Stadler
- Department of Protein Science, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
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26
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Meza-Perez S, Liu M, Silva-Sanchez A, Morrow CD, Eipers PG, Lefkowitz EJ, Ptacek T, Scharer CD, Rosenberg AF, Hill DD, Arend RC, Gray MJ, Randall TD. Proteobacteria impair anti-tumor immunity in the omentum by consuming arginine. Cell Host Microbe 2024; 32:1177-1191.e7. [PMID: 38942027 PMCID: PMC11245731 DOI: 10.1016/j.chom.2024.06.003] [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: 11/16/2023] [Revised: 04/19/2024] [Accepted: 06/04/2024] [Indexed: 06/30/2024]
Abstract
Gut microbiota influence anti-tumor immunity, often by producing immune-modulating metabolites. However, microbes consume a variety of metabolites that may also impact host immune responses. We show that tumors grow unchecked in the omenta of microbe-replete mice due to immunosuppressive Tregs. By contrast, omental tumors in germ-free, neomycin-treated mice or mice colonized with altered Schaedler's flora (ASF) are spontaneously eliminated by CD8+ T cells. These mice lack Proteobacteria capable of arginine catabolism, causing increases in serum arginine that activate the mammalian target of the rapamycin (mTOR) pathway in Tregs to reduce their suppressive capacity. Transfer of the Proteobacteria, Escherichia coli (E. coli), but not a mutant unable to catabolize arginine, to ASF mice reduces arginine levels, restores Treg suppression, and prevents tumor clearance. Supplementary arginine similarly decreases Treg suppressive capacity, increases CD8+ T cell effectiveness, and reduces tumor burden. Thus, microbial consumption of arginine alters anti-tumor immunity, offering potential therapeutic strategies for tumors in visceral adipose tissue.
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Affiliation(s)
- Selene Meza-Perez
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Mingyong Liu
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aaron Silva-Sanchez
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Peter G Eipers
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Travis Ptacek
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alexander F Rosenberg
- Department of Biomedical Informatics and Data Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Dave D Hill
- Department of Biomedical Informatics and Data Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rebecca C Arend
- Department of Obstetrics and Gynecology, Division of Gynecological Oncology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael J Gray
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Troy D Randall
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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27
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Najem H, Pacheco S, Kowal J, Winkowski D, Burks JK, Heimberger AB. Protocol to quantify immune cell distribution from the vasculature to the glioma microenvironment on sequential immunofluorescence multiplex images. STAR Protoc 2024; 5:103079. [PMID: 38795354 PMCID: PMC11144811 DOI: 10.1016/j.xpro.2024.103079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/02/2024] [Accepted: 04/30/2024] [Indexed: 05/27/2024] Open
Abstract
Although myeloid-derived immune cells can be dispersed throughout the tumor microenvironment (TME), anti-tumor effector cells are confined to the perivascular space. Here, we present a protocol to quantify immune cell distribution from tumor vasculature to its glioma microenvironment on sequential immunofluorescence multiplex images. We describe steps for sequential immunofluorescence multiplex staining, image generation, and storage. We then detail the procedures for tissue, vessel, and nuclei segmentation; cell phenotyping; data extraction; and training using RStudio and Spyder.
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Affiliation(s)
- Hinda Najem
- Department of Neurological Surgery, Northwestern University, Chicago, IL 60611, USA; Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sebastian Pacheco
- Department of Neurological Surgery, Northwestern University, Chicago, IL 60611, USA; Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Joanna Kowal
- Lunaphore Technologies SA, 1131 Tolochenaz, Switzerland
| | | | | | - Amy B Heimberger
- Department of Neurological Surgery, Northwestern University, Chicago, IL 60611, USA; Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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28
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Zhang Y, Lee RY, Tan CW, Guo X, Yim WWY, Lim JC, Wee FY, Yang WU, Kharbanda M, Lee JYJ, Ngo NT, Leow WQ, Loo LH, Lim TK, Sobota RM, Lau MC, Davis MJ, Yeong J. Spatial omics techniques and data analysis for cancer immunotherapy applications. Curr Opin Biotechnol 2024; 87:103111. [PMID: 38520821 DOI: 10.1016/j.copbio.2024.103111] [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: 07/27/2023] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/25/2024]
Abstract
In-depth profiling of cancer cells/tissues is expanding our understanding of the genomic, epigenomic, transcriptomic, and proteomic landscape of cancer. However, the complexity of the cancer microenvironment, particularly its immune regulation, has made it difficult to exploit the potential of cancer immunotherapy. High-throughput spatial omics technologies and analysis pipelines have emerged as powerful tools for tackling this challenge. As a result, a potential revolution in cancer diagnosis, prognosis, and treatment is on the horizon. In this review, we discuss the technological advances in spatial profiling of cancer around and beyond the central dogma to harness the full benefits of immunotherapy. We also discuss the promise and challenges of spatial data analysis and interpretation and provide an outlook for the future.
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Affiliation(s)
- Yue Zhang
- Duke-NUS Medical School, Singapore 169856, Singapore
| | - Ren Yuan Lee
- Yong Loo Lin School of Medicine, National University of Singapore, 169856 Singapore; Singapore Thong Chai Medical Institution, Singapore 169874, Singapore
| | - Chin Wee Tan
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland 4102, Australia
| | - Xue Guo
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Willa W-Y Yim
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Jeffrey Ct Lim
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Felicia Yt Wee
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - W U Yang
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Malvika Kharbanda
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia; immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jia-Ying J Lee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore
| | - Nye Thane Ngo
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
| | - Wei Qiang Leow
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
| | - Lit-Hsin Loo
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore
| | - Tony Kh Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Mai Chan Lau
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A⁎STAR), Singapore 138648, Singapore
| | - Melissa J Davis
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland 4102, Australia; immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joe Yeong
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore; Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore.
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29
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Dowling P, Trollet C, Muraine L, Negroni E, Swandulla D, Ohlendieck K. The potential of proteomics for in-depth bioanalytical investigations of satellite cell function in applied myology. Expert Rev Proteomics 2024; 21:229-235. [PMID: 38753566 DOI: 10.1080/14789450.2024.2356578] [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: 02/19/2024] [Accepted: 05/11/2024] [Indexed: 05/18/2024]
Abstract
INTRODUCTION Regenerative myogenesis plays a crucial role in mature myofibers to counteract muscular injury or dysfunction due to neuromuscular disorders. The activation of specialized myogenic stem cells, called satellite cells, is intrinsically involved in proliferation and differentiation, followed by myoblast fusion and the formation of multinucleated myofibers. AREAS COVERED This report provides an overview of the role of satellite cells in the neuromuscular system and the potential future impact of proteomic analyses for biomarker discovery, as well as the identification of novel therapeutic targets in muscle disease. The article reviews the ways in which the systematic analysis of satellite cells, myoblasts, and myocytes by single-cell proteomics can help to better understand the process of myofiber regeneration. EXPERT OPINION In order to better comprehend satellite cell dysfunction in neuromuscular disorders, mass spectrometry-based proteomics is an excellent large-scale analytical tool for the systematic profiling of pathophysiological processes. The optimized isolation of muscle-derived cells can be routinely performed by mechanical/enzymatic dissociation protocols, followed by fluorescence-activated cell sorting in specialized flow cytometers. Ultrasensitive single-cell proteomics using label-free quantitation methods or approaches that utilize tandem mass tags are ideal bioanalytical approaches to study the pathophysiological role of stem cells in neuromuscular disease.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, KE, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, KE, Ireland
| | - Capucine Trollet
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, Paris, France
| | - Laura Muraine
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, Paris, France
| | - Elisa Negroni
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, Paris, France
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, KE, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, KE, Ireland
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30
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de Souza N, Zhao S, Bodenmiller B. Multiplex protein imaging in tumour biology. Nat Rev Cancer 2024; 24:171-191. [PMID: 38316945 DOI: 10.1038/s41568-023-00657-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/08/2023] [Indexed: 02/07/2024]
Abstract
Tissue imaging has become much more colourful in the past decade. Advances in both experimental and analytical methods now make it possible to image protein markers in tissue samples in high multiplex. The ability to routinely image 40-50 markers simultaneously, at single-cell or subcellular resolution, has opened up new vistas in the study of tumour biology. Cellular phenotypes, interaction, communication and spatial organization have become amenable to molecular-level analysis, and application to patient cohorts has identified clinically relevant cellular and tissue features in several cancer types. Here, we review the use of multiplex protein imaging methods to study tumour biology, discuss ongoing attempts to combine these approaches with other forms of spatial omics, and highlight challenges in the field.
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Affiliation(s)
- Natalie de Souza
- University of Zurich, Department of Quantitative Biomedicine, Zurich, Switzerland
- ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland
- ETH Zurich, Institute of Molecular Health Sciences, Zurich, Switzerland
| | - Shan Zhao
- University of Zurich, Department of Quantitative Biomedicine, Zurich, Switzerland
- ETH Zurich, Institute of Molecular Health Sciences, Zurich, Switzerland
| | - Bernd Bodenmiller
- University of Zurich, Department of Quantitative Biomedicine, Zurich, Switzerland.
- ETH Zurich, Institute of Molecular Health Sciences, Zurich, Switzerland.
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31
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Aung TN, Bates KM, Rimm DL. High-Plex Assessment of Biomarkers in Tumors. Mod Pathol 2024; 37:100425. [PMID: 38219953 DOI: 10.1016/j.modpat.2024.100425] [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: 08/30/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
The assessment of biomarkers plays a critical role in the diagnosis and treatment of many cancers. Biomarkers not only provide diagnostic, prognostic, or predictive information but also can act as effective targets for new pharmaceutical therapies. As the utility of biomarkers increases, it becomes more important to utilize accurate and efficient methods for biomarker discovery and, ultimately, clinical assessment. High-plex imaging studies, defined here as assessment of 8 or more biomarkers on a single slide, have become the method of choice for biomarker discovery and assessment of biomarker spatial context. In this review, we discuss methods of measuring biomarkers in slide-mounted tissue samples, detail the various high-plex methods that allow for the simultaneous assessment of multiple biomarkers in situ, and describe the impact of high-plex biomarker assessment on the future of anatomic pathology.
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Affiliation(s)
- Thazin N Aung
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Katherine M Bates
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut; Department of Internal Medicine (Medical Oncology), Yale University School of Medicine, New Haven, Connecticut.
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32
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Navikas V, Kowal J, Rodriguez D, Rivest F, Brajkovic S, Cassano M, Dupouy D. Semi-automated approaches for interrogating spatial heterogeneity of tissue samples. Sci Rep 2024; 14:5025. [PMID: 38424144 PMCID: PMC10904364 DOI: 10.1038/s41598-024-55387-w] [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: 10/13/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
Tissues are spatially orchestrated ecosystems composed of heterogeneous cell populations and non-cellular elements. Tissue components' interactions shape the biological processes that govern homeostasis and disease, thus comprehensive insights into tissues' composition are crucial for understanding their biology. Recently, advancements in the spatial biology field enabled the in-depth analyses of tissue architecture at single-cell resolution, while preserving the structural context. The increasing number of biomarkers analyzed, together with whole tissue imaging, generate datasets approaching several hundreds of gigabytes in size, which are rich sources of valuable knowledge but require investments in infrastructure and resources for extracting quantitative information. The analysis of multiplex whole-tissue images requires extensive training and experience in data analysis. Here, we showcase how a set of open-source tools can allow semi-automated image data extraction to study the spatial composition of tissues with a focus on tumor microenvironment (TME). With the use of Lunaphore COMET platform, we interrogated lung cancer specimens where we examined the expression of 20 biomarkers. Subsequently, the tissue composition was interrogated using an in-house optimized nuclei detection algorithm followed by a newly developed image artifact exclusion approach. Thereafter, the data was processed using several publicly available tools, highlighting the compatibility of COMET-derived data with currently available image analysis frameworks. In summary, we showcased an innovative semi-automated workflow that highlights the ease of adoption of multiplex imaging to explore TME composition at single-cell resolution using a simple slide in, data out approach. Our workflow is easily transferrable to various cohorts of specimens to provide a toolset for spatial cellular dissection of the tissue composition.
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Affiliation(s)
| | - Joanna Kowal
- Lunaphore Technologies SA, Tolochenaz, Switzerland
| | | | | | | | | | - Diego Dupouy
- Lunaphore Technologies SA, Tolochenaz, Switzerland.
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33
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Ferri-Borgogno S, Burks JK, Seeley EH, McKee TD, Stolley DL, Basi AV, Gomez JA, Gamal BT, Ayyadhury S, Lawson BC, Yates MS, Birrer MJ, Lu KH, Mok SC. Molecular, Metabolic, and Subcellular Mapping of the Tumor Immune Microenvironment via 3D Targeted and Non-Targeted Multiplex Multi-Omics Analyses. Cancers (Basel) 2024; 16:846. [PMID: 38473208 PMCID: PMC10930466 DOI: 10.3390/cancers16050846] [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: 02/07/2024] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
Most platforms used for the molecular reconstruction of the tumor-immune microenvironment (TIME) of a solid tumor fail to explore the spatial context of the three-dimensional (3D) space of the tumor at a single-cell resolution, and thus lack information about cell-cell or cell-extracellular matrix (ECM) interactions. To address this issue, a pipeline which integrated multiplex spatially resolved multi-omics platforms was developed to identify crosstalk signaling networks among various cell types and the ECM in the 3D TIME of two FFPE (formalin-fixed paraffin embedded) gynecologic tumor samples. These platforms include non-targeted mass spectrometry imaging (glycans, metabolites, and peptides) and Stereo-seq (spatial transcriptomics) and targeted seqIF (IHC proteomics). The spatially resolved imaging data in a two- and three-dimensional space demonstrated various cellular neighborhoods in both samples. The collection of spatially resolved analytes in a voxel (3D pixel) across serial sections of the tissue was also demonstrated. Data collected from this analytical pipeline were used to construct spatial 3D maps with single-cell resolution, which revealed cell identity, activation, and energized status. These maps will provide not only insights into the molecular basis of spatial cell heterogeneity in the TIME, but also novel predictive biomarkers and therapeutic targets, which can improve patient survival rates.
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Affiliation(s)
- Sammy Ferri-Borgogno
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA (K.H.L.)
| | - Jared K. Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.L.S.); (A.V.B.); (J.A.G.)
| | - Erin H. Seeley
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA;
| | - Trevor D. McKee
- Pathomics, Inc., Toronto, ON M4C 3K2, Canada; (T.D.M.); (S.A.)
| | - Danielle L. Stolley
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.L.S.); (A.V.B.); (J.A.G.)
| | - Akshay V. Basi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.L.S.); (A.V.B.); (J.A.G.)
| | - Javier A. Gomez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.L.S.); (A.V.B.); (J.A.G.)
| | - Basant T. Gamal
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA (K.H.L.)
| | | | - Barrett C. Lawson
- Department of Anatomical Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Melinda S. Yates
- Department of Pathology and Laboratory Medicine, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael J. Birrer
- Winthrop P. Rockefelle Cancer Institute, The University of Arkanasas for Medical Sciences, Little Rock, AR 72205, USA
| | - Karen H. Lu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA (K.H.L.)
| | - Samuel C. Mok
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA (K.H.L.)
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34
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Hou D, Wan H, Katz JL, Wang S, Castro BA, Vazquez-Cervantes GI, Arrieta VA, Dhiantravan S, Najem H, Rashidi A, Chia TY, Arjmandi T, Collado J, Billingham L, Lopez-Rosas A, Han Y, Sonabend AM, Heimberger AB, Zhang P, Miska J, Lee-Chang C. Antigen-presenting B cells promote TCF-1 + PD1 - stem-like CD8 + T-cell proliferation in glioblastoma. Front Immunol 2024; 14:1295218. [PMID: 38268923 PMCID: PMC10806106 DOI: 10.3389/fimmu.2023.1295218] [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: 09/15/2023] [Accepted: 11/27/2023] [Indexed: 01/26/2024] Open
Abstract
Understanding the spatial relationship and functional interaction of immune cells in glioblastoma (GBM) is critical for developing new therapeutics that overcome the highly immunosuppressive tumor microenvironment. Our study showed that B and T cells form clusters within the GBM microenvironment within a 15-μm radius, suggesting that B and T cells could form immune synapses within the GBM. However, GBM-infiltrating B cells suppress the activation of CD8+ T cells. To overcome this immunosuppression, we leveraged B-cell functions by activating them with CD40 agonism, IFNγ, and BAFF to generate a potent antigen-presenting B cells named BVax. BVax had improved antigen cross-presentation potential compared to naïve B cells and were primed to use the IL15-IL15Ra mechanism to enhance T cell activation. Compared to naïve B cells, BVax could improve CD8 T cell activation and proliferation. Compared to dendritic cells (DCs), which are the current gold standard professional antigen-presenting cell, BVax promoted highly proliferative T cells in-vitro that had a stem-like memory T cell phenotype characterized by CD62L+CD44- expression, high TCF-1 expression, and low PD-1 and granzyme B expression. Adoptive transfer of BVax-activated CD8+ T cells into tumor-bearing brains led to T cell reactivation with higher TCF-1 expression and elevated granzyme B production compared to DC-activated CD8+ T cells. Adoptive transfer of BVax into an irradiated immunocompetent tumor-bearing host promoted more CD8+ T cell proliferation than adoptive transfer of DCs. Moreover, highly proliferative CD8+ T cells in the BVax group had less PD-1 expression than those highly proliferative CD8+ T cells in the DC group. The findings of this study suggest that BVax and DC could generate distinctive CD8+ T cells, which potentially serve multiple purposes in cellular vaccine development.
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Affiliation(s)
- David Hou
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Hanxiao Wan
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Joshua L. Katz
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Si Wang
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Brandyn A. Castro
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Department of Neurological Surgery, University of Illinois Chicago, Chicago, IL, United States
| | - Gustavo I. Vazquez-Cervantes
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Victor A. Arrieta
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Silpol Dhiantravan
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Hinda Najem
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Aida Rashidi
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Tzu-yi Chia
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Tarlan Arjmandi
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Department of Biotechnology, McCormick School of Engineering, Northwestern University, Evanston, IL, United States
| | - Jimena Collado
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Leah Billingham
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Aurora Lopez-Rosas
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Yu Han
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Adam M. Sonabend
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Lou and Jean Malnati Brain Tumor Institute, Chicago, IL, United States
| | - Amy B. Heimberger
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Lou and Jean Malnati Brain Tumor Institute, Chicago, IL, United States
| | - Peng Zhang
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Lou and Jean Malnati Brain Tumor Institute, Chicago, IL, United States
| | - Jason Miska
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Lou and Jean Malnati Brain Tumor Institute, Chicago, IL, United States
| | - Catalina Lee-Chang
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Lou and Jean Malnati Brain Tumor Institute, Chicago, IL, United States
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