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Berrell N, Monkman J, Donovan M, Blick T, O'Byrne K, Ladwa R, Tan CW, Kulasinghe A. Spatial resolution of the head and neck cancer tumor microenvironment to identify tumor and stromal features associated with therapy response. Immunol Cell Biol 2024. [PMID: 39048134 DOI: 10.1111/imcb.12811] [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: 02/20/2024] [Revised: 05/29/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
Abstract
Head and neck cancer (HNC) is the seventh most common cancer globally, resulting in 440 000 deaths per year. While there have been advancements in chemoradiotherapy and surgery, relapse occurs in more than half of HNCs, and these patients have a median survival of 10 months and a 2-year survival of < 20%. Only a subset of patients displays durable benefits from immunotherapies in metastatic and recurrent HNC, making it critical to understand the tumor microenvironment (TME) underpinning therapy responses in HNC. To recognize biological differences within the TME that may be predictive of immunotherapy response, we applied cutting-edge geospatial whole-transcriptome profiling (NanoString GeoMx Digital Spatial Profiler) and spatial proteomics profiling (Akoya PhenoCycler-Fusion) on a tumor microarray consisting of 25 cores from 12 patients that included 4 immunotherapy-unresponsive (8 cores) and 2 immunotherapy-responsive patients (5 cores), as well as 6 immunotherapy naïve patients (12 cores). Through high-plex, regional-based transcriptomic mapping of the tumor and TME, pathways involved with the complement system and hypoxia were identified to be differentially expressed in patients who went on to experience a poor immunotherapy response. Single-cell, targeted proteomic analysis found that immune cell infiltration of the cancer cell mass and interactions of CD8 T cells with tumor and other immune cells were associated with positive immunotherapy response. The relative abundance of specific tumor phenotypes and their interactions with various immune cells was identified to be different between response groups. This study demonstrates how spatial transcriptomics and proteomics can resolve novel alterations in the TME of HNC that may contribute to therapy sensitivity and resistance.
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Affiliation(s)
- Naomi Berrell
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Wesley Research Institute, Level 8 East Wing, The Wesley Hospital, Auchenflower, QLD, Australia
| | - James Monkman
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Meg Donovan
- Wesley Research Institute, Level 8 East Wing, The Wesley Hospital, Auchenflower, QLD, Australia
| | - Tony Blick
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Ken O'Byrne
- Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Rahul Ladwa
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Chin Wee Tan
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Wesley Research Institute, Level 8 East Wing, The Wesley Hospital, Auchenflower, QLD, Australia
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2
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Sadeghirad H, Monkman J, Tan CW, Liu N, Yunis J, Donovan ML, Moradi A, Jhaveri N, Perry C, Adams MN, O'Byrne K, Warkiani ME, Ladwa R, Hughes BGM, Kulasinghe A. Spatial dynamics of tertiary lymphoid aggregates in head and neck cancer: insights into immunotherapy response. J Transl Med 2024; 22:677. [PMID: 39049036 PMCID: PMC11267849 DOI: 10.1186/s12967-024-05409-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 06/17/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Recurrent/metastatic head and neck squamous cell carcinoma (R/M HNSCC) generally has a poor prognosis for patients with limited treatment options. While incorporating immune checkpoint inhibitors (ICIs) has now become the standard of care, the efficacy is variable, with only a subset of patients responding. The complexity of the tumor microenvironment (TME) and the role of tertiary lymphoid structures (TLS) have emerged as critical determinants for immunotherapeutic response. METHODS In this study, we analyzed two independently collected R/M HNSCC patient tissue cohorts to better understand the role of TLS in response to ICIs. Utilizing a multi-omics approach, we first performed targeted proteomic profiling using the Nanostring GeoMx Digital Spatial Profiler to quantify immune-related protein expression with spatial resolution. This was further characterized by spatially resolved whole transcriptome profiling of TLSs and germinal centers (GCs). Deeper single-cell resolved proteomic profiling of the TLSs was performed using the Akoya Biosciences Phenocycler Fusion platform. RESULTS Our proteomic analysis revealed the presence of T lymphocyte markers, including CD3, CD45, and CD8, expressing cells and upregulation of immune checkpoint marker PD-L1 within tumor compartments of patients responsive to ICIs, indicative of 'hot tumor' phenotypes. We also observed the presence of antigen-presenting cells marked by expression of CD40, CD68, CD11c, and CD163 with upregulation of antigen-presentation marker HLA-DR, in patients responding to ICIs. Transcriptome analysis of TLS and GCs uncovered a marked elevation in the expression of genes related to immune modulation, diverse immune cell recruitment, and a potent interferon response within the TLS structure. Notably, the distribution of TLS-tumor distance was found to be significantly different across response groups (H = 9.28, p = 0.026). The proximity of TLSs to tumor cells was found to be a critical indicator of ICI response, implying that patients with TLSs located further from tumor cells have worse outcomes. CONCLUSION The study underscores the multifaceted role of TLSs in modulating the immunogenic landscape of the TME in R/M HNSCC, likely influencing the efficacy of ICIs. Spatially resolved multi-omics approaches offer valuable insights into potential biomarkers for ICI response and highlight the importance of profiling the TME complexity when developing therapeutic strategies and patient stratification.
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Affiliation(s)
- Habib Sadeghirad
- Frazer Institute, Faculty of Medicine, Translational Research Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - James Monkman
- Frazer Institute, Faculty of Medicine, Translational Research Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Chin Wee Tan
- Frazer Institute, Faculty of Medicine, Translational Research Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ning Liu
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
- South Australian immunoGENomics Cancer Institute, The University of Adelaide, SA, Australia
| | - Joseph Yunis
- Frazer Institute, Faculty of Medicine, Translational Research Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
- Ian Frazer Centre for Children's Immunotherapy Research, Children's Health Research Centre, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia
| | - Meg L Donovan
- Frazer Institute, Faculty of Medicine, Translational Research Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
- Queensland Spatial Biology Centre, Wesley Research Institute, The Wesley Hospital, Auchenflower, QLD, Australia
| | - Afshin Moradi
- Frazer Institute, Faculty of Medicine, Translational Research Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Niyati Jhaveri
- Discovery Applications, Akoya Biosciences, The Spatial Biology Company, Marlborough, MA, USA
| | - Chris Perry
- The Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Mark N Adams
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Ken O'Byrne
- The Princess Alexandra Hospital, Woolloongabba, QLD, Australia
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | | | - Rahul Ladwa
- Frazer Institute, Faculty of Medicine, Translational Research Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
- The Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Brett G M Hughes
- The Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- School of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, Translational Research Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
- Queensland Spatial Biology Centre, Wesley Research Institute, The Wesley Hospital, Auchenflower, QLD, Australia.
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Menéndez V, Solórzano JL, García-Cosío M, Cereceda L, Díaz E, Estévez M, Roncador G, Vega Z, Montalbán C, Kulasinghe A, García JF. Mapping the Spatial Dynamics of the CD4+ T Cell Spectrum in Classical Hodgkin Lymphoma. Mod Pathol 2024; 37:100551. [PMID: 38936478 DOI: 10.1016/j.modpat.2024.100551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/10/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
As around 25% to 30% of classical Hodgkin lymphoma (cHL) patients with advanced stages do not respond to standard therapies, the tumor microenvironment of cHL is one avenue that may be explored with the aim of improving risk stratification. CD4+ T cells are thought to be one of the main cell types in the tumor microenvironment. However, few immune signatures have been studied, and many of these lack related spatial data. Thus, our aim is to spatially resolve the CD4+ T cell subtypes that influence cHL outcome, depicting new immune signatures or transcriptional patterns that are in crosstalk with the tumor cells. This study was conducted using the NanoString GeoMx digital spatial profiling technology, based on the selection of distinct functional areas of patients' tissues followed by gene-expression profiling. The goals were to assess the differences in CD4+ T cell populations between tumor-rich and immune-predominant areas defined by different CD30 and PD-L1 expression levels and seek correlations with clinical metadata. Our results depict a complex map of CD4+ T cells with different functions and differentiation states that are enriched at distinct locations, the flux of cytokines and chemokines that could be related to these, and the specific relationships with the clinical outcome.
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Affiliation(s)
- Victoria Menéndez
- Translational Research, MD Anderson Cancer Center Foundation, Madrid, Spain
| | - José L Solórzano
- Translational Research, MD Anderson Cancer Center Foundation, Madrid, Spain; Pathology Department, MD Anderson Cancer Center Madrid, Madrid, Spain
| | - Mónica García-Cosío
- Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Laura Cereceda
- Translational Research, MD Anderson Cancer Center Foundation, Madrid, Spain; Pathology Department, MD Anderson Cancer Center Madrid, Madrid, Spain
| | - Eva Díaz
- Translational Research, MD Anderson Cancer Center Foundation, Madrid, Spain
| | - Mónica Estévez
- Department of Hematology, MD Anderson Cancer Center Madrid, Madrid, Spain
| | - Giovanna Roncador
- Monoclonal Antibodies and Histopathology Units, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Zaira Vega
- Monoclonal Antibodies and Histopathology Units, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Carlos Montalbán
- Translational Research, MD Anderson Cancer Center Foundation, Madrid, Spain
| | - Arutha Kulasinghe
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, Australia
| | - Juan F García
- Translational Research, MD Anderson Cancer Center Foundation, Madrid, Spain; Pathology Department, MD Anderson Cancer Center Madrid, Madrid, Spain.
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Moutafi MK, Bates KM, Aung TN, Milian RG, Xirou V, Vathiotis IA, Gavrielatou N, Angelakis A, Schalper KA, Salichos L, Rimm DL. High-throughput transcriptome profiling indicates ribosomal RNAs to be associated with resistance to immunotherapy in non-small cell lung cancer (NSCLC). J Immunother Cancer 2024; 12:e009039. [PMID: 38857914 PMCID: PMC11168162 DOI: 10.1136/jitc-2024-009039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Despite the impressive outcomes with immune checkpoint inhibitor (ICI) in non-small cell lung cancer (NSCLC), only a minority of the patients show long-term benefits from ICI. In this study, we used retrospective cohorts of ICI treated patients with NSCLC to discover and validate spatially resolved protein markers associated with resistance to programmed cell death protein-1 (PD-1) axis inhibition. METHODS Pretreatment samples from 56 patients with NSCLC treated with ICI were collected and analyzed in a tissue microarray (TMA) format in including four different tumor regions per patient using the GeoMx platform for spatially informed transcriptomics. 34 patients had assessable tissue with tumor compartment in all 4 TMA spots, 22 with leukocyte compartment and 12 with CD68 compartment. The patients' tissue that was not assessable in fourfold redundancy in each compartment was designated as the validation cohort; cytokeratin (CK) (N=22), leukocytes CD45 (N=31), macrophages, CD68 (N=43). The human whole transcriptome, represented by~18,000 individual genes assessed by oligonucleotide-tagged in situ hybridization, was sequenced on the NovaSeq platform to quantify the RNAs present in each region of interest. RESULTS 54,000 gene variables were generated per case, from them 25,740 were analyzed after removing targets with expression lower than a prespecified frequency. Cox proportional-hazards model analysis was performed for overall and progression-free survival (OS, PFS, respectively). After identifying genes significantly associated with limited survival benefit (HR>1)/progression per spot per patient, we used the intersection of them across the four TMA spots per patient. This resulted in a list of 12 genes in the tumor-cell compartment (RPL13A, GNL3, FAM83A, CYBA, ACSL4, SLC25A6, EPAS1, RPL5, APOL1, HSPD1, RPS4Y1, ADI1). RPL13A, GNL3 in tumor-cell compartment were also significantly associated with OS and PFS, respectively, in the validation cohort (CK: HR, 2.48; p=0.02 and HR, 5.33; p=0.04). In CD45 compartment, secreted frizzled-related protein 2, was associated with OS in the discovery cohort but not in the validation cohort. Similarly, in the CD68 compartment ARHGAP and PNN interacting serine and arginine rich protein were significantly associated with PFS and OS, respectively, in the majority but not all four spots per patient. CONCLUSION This work highlights RPL13A and GNL3 as potential indicative biomarkers of resistance to PD-1 axis blockade that might help to improve precision immunotherapy strategies for lung cancer.
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Affiliation(s)
- Myrto K Moutafi
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Katherine M Bates
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Thazin Nwe Aung
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
- Yale School of Medicine, New Haven, Connecticut, USA
| | - Rolando Garcia Milian
- Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale School of Medicine, New Haven, Connecticut, USA
| | - Vasiliki Xirou
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
- Yale School of Medicine, New Haven, Connecticut, USA
| | - Ioannis A Vathiotis
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Niki Gavrielatou
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
- Yale School of Medicine, New Haven, Connecticut, USA
| | - Athanasios Angelakis
- Epidemiology and Data Science, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
- Department of Methodology, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Kurt A Schalper
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Leonidas Salichos
- Biomedical Data Science Center Director, Center for Cancer Research, Department of Computational Biology at New York Institute of Technology, New York Institute of Technology, Old Westbury, New York, USA
| | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
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5
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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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Yeo YY, Qiu H, Bai Y, Zhu B, Chang Y, Yeung J, Michel HA, Wright K, Shaban M, Sadigh S, Nkosi D, Shanmugam V, Rock P, Tung Yiu SP, Cramer P, Paczkowska J, Stephan P, Liao G, Huang AY, Wang H, Chen H, Frauenfeld L, Mitra B, Gewurz BE, Schürch CM, Zhao B, Nolan GP, Zhang B, Shalek AK, Angelo M, Mahmood F, Ma Q, Burack WR, Shipp MA, Rodig SJ, Jiang S. Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.583586. [PMID: 38496566 PMCID: PMC10942289 DOI: 10.1101/2024.03.05.583586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Classic Hodgkin Lymphoma (cHL) is a tumor composed of rare malignant Hodgkin and Reed-Sternberg (HRS) cells nested within a T-cell rich inflammatory immune infiltrate. cHL is associated with Epstein-Barr Virus (EBV) in 25% of cases. The specific contributions of EBV to the pathogenesis of cHL remain largely unknown, in part due to technical barriers in dissecting the tumor microenvironment (TME) in high detail. Herein, we applied multiplexed ion beam imaging (MIBI) spatial pro-teomics on 6 EBV-positive and 14 EBV-negative cHL samples. We identify key TME features that distinguish between EBV-positive and EBV-negative cHL, including the relative predominance of memory CD8 T cells and increased T-cell dysfunction as a function of spatial proximity to HRS cells. Building upon a larger multi-institutional cohort of 22 EBV-positive and 24 EBV-negative cHL samples, we orthogonally validated our findings through a spatial multi-omics approach, coupling whole transcriptome capture with antibody-defined cell types for tu-mor and T-cell populations within the cHL TME. We delineate contrasting transcriptomic immunological signatures between EBV-positive and EBV-negative cases that differently impact HRS cell proliferation, tumor-immune interactions, and mecha-nisms of T-cell dysregulation and dysfunction. Our multi-modal framework enabled a comprehensive dissection of EBV-linked reorganization and immune evasion within the cHL TME, and highlighted the need to elucidate the cellular and molecular fac-tors of virus-associated tumors, with potential for targeted therapeutic strategies.
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Tan CW, Chen J, Liu N, Bhuva DD, Blick T, Monkman J, Cooper C, Kharbanda M, Feher K, Phipson B, Killingbeck EE, Pan L, Kim Y, Liang Y, Nam A, Leon M, Souza-Fonseca-Guimaraes P, Nagashima S, Camargo Martins AP, Machado-Souza C, de Noronha L, Tang B, Short K, Fraser J, Belz GT, Souza-Fonseca-Guimaraes F, Kulasinghe A, Davis MJ. In situ single-cell profiling sheds light on IFI27 localisation during SARS-CoV-2 infection. EBioMedicine 2024; 101:105016. [PMID: 38377798 PMCID: PMC10884333 DOI: 10.1016/j.ebiom.2024.105016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/02/2024] [Accepted: 02/03/2024] [Indexed: 02/22/2024] Open
Abstract
The utilization of single-cell resolved spatial transcriptomics to delineate immune responses during SARS-CoV-2 infection was able to identify M1 macrophages to have elevated expression of IFI27 in areas of infection.
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Affiliation(s)
- Chin Wee Tan
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Jinjin Chen
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ning Liu
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia; South Australian ImmunoGENomics Cancer Institute, The University of Adelaide, SA, Australia
| | - Dharmesh D Bhuva
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia; South Australian ImmunoGENomics Cancer Institute, The University of Adelaide, SA, Australia
| | - Tony Blick
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - James Monkman
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Caroline Cooper
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia; Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Malvika Kharbanda
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia; South Australian ImmunoGENomics Cancer Institute, The University of Adelaide, SA, Australia
| | - Kristen Feher
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia; South Australian ImmunoGENomics Cancer Institute, The University of Adelaide, SA, Australia
| | - Belinda Phipson
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Liuliu Pan
- Nanostring Technologies, Inc, Seattle, WA, USA
| | - Youngmi Kim
- Nanostring Technologies, Inc, Seattle, WA, USA
| | - Yan Liang
- Nanostring Technologies, Inc, Seattle, WA, USA
| | - Andy Nam
- Nanostring Technologies, Inc, Seattle, WA, USA
| | | | | | - Seigo Nagashima
- Laboratório de Patologia Experimental, PPGCS da PUCPR, Curitiba, Brazil
| | | | - Cleber Machado-Souza
- Faculdades Pequeno Príncipe (FPP), Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), R. Silva Jardim, 1632-ÁguaVerde, Curitiba, 80230-020, PR, Brazil
| | - Lucia de Noronha
- Laboratório de Patologia Experimental, PPGCS da PUCPR, Curitiba, Brazil
| | - Benjamin Tang
- Westmead Institute for Medical Research, Sydney, Australia
| | - Kirsty Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - John Fraser
- Critical Care Research Group, The Prince Charles Hospital, Brisbane, Australia; Faculty of Medicine University of Queensland, Brisbane, QLD, Australia; St Andrew's War Memorial Hospital, UnitingCare, Spring Hill, QLD, Australia
| | - Gabrielle T Belz
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | | | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
| | - Melissa J Davis
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia; South Australian ImmunoGENomics Cancer Institute, The University of Adelaide, SA, Australia; Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
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