1
|
Sutanto H, Pradana FR, Adytia GJ, Ansharullah BA, Waitupu A, Bramantono B, Fetarayani D. Memory T Cells in Respiratory Virus Infections: Protective Potential and Persistent Vulnerabilities. Med Sci (Basel) 2025; 13:48. [PMID: 40407543 PMCID: PMC12101432 DOI: 10.3390/medsci13020048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2025] [Revised: 04/19/2025] [Accepted: 04/25/2025] [Indexed: 05/26/2025] Open
Abstract
Respiratory virus infections, such as those caused by influenza viruses, respiratory syncytial virus (RSV), and coronaviruses, pose a significant global health burden. While the immune system's adaptive components, including memory T cells, are critical for recognizing and combating these pathogens, recurrent infections and variable disease outcomes persist. Memory T cells are a key element of long-term immunity, capable of responding swiftly upon re-exposure to pathogens. They play diverse roles, including cross-reactivity to conserved viral epitopes and modulation of inflammatory responses. However, the protective efficacy of these cells is influenced by several factors, including viral evolution, host age, and immune system dynamics. This review explores the dichotomy of memory T cells in respiratory virus infections: their potential to confer robust protection and the limitations that allow for breakthrough infections. Understanding the underlying mechanisms governing the formation, maintenance, and functional deployment of memory T cells in respiratory mucosa is critical for improving immunological interventions. We highlight recent advances in vaccine strategies aimed at bolstering T cell-mediated immunity and discuss the challenges posed by viral immune evasion. Addressing these gaps in knowledge is pivotal for designing effective therapeutics and vaccines to mitigate the global burden of respiratory viruses.
Collapse
Affiliation(s)
- Henry Sutanto
- Internal Medicine Study Program, Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia; (H.S.); (F.R.P.); (G.J.A.); (B.A.A.); (A.W.)
- Department of Internal Medicine, Dr. Soetomo General Academic Hospital, Surabaya 60286, Indonesia
| | - Febrian Ramadhan Pradana
- Internal Medicine Study Program, Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia; (H.S.); (F.R.P.); (G.J.A.); (B.A.A.); (A.W.)
- Department of Internal Medicine, Dr. Soetomo General Academic Hospital, Surabaya 60286, Indonesia
| | - Galih Januar Adytia
- Internal Medicine Study Program, Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia; (H.S.); (F.R.P.); (G.J.A.); (B.A.A.); (A.W.)
- Department of Internal Medicine, Dr. Soetomo General Academic Hospital, Surabaya 60286, Indonesia
| | - Bagus Aditya Ansharullah
- Internal Medicine Study Program, Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia; (H.S.); (F.R.P.); (G.J.A.); (B.A.A.); (A.W.)
- Department of Internal Medicine, Dr. Soetomo General Academic Hospital, Surabaya 60286, Indonesia
| | - Alief Waitupu
- Internal Medicine Study Program, Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia; (H.S.); (F.R.P.); (G.J.A.); (B.A.A.); (A.W.)
- Department of Internal Medicine, Dr. Soetomo General Academic Hospital, Surabaya 60286, Indonesia
| | - Bramantono Bramantono
- Department of Internal Medicine, Dr. Soetomo General Academic Hospital, Surabaya 60286, Indonesia
- Division of Tropical and Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Deasy Fetarayani
- Department of Internal Medicine, Dr. Soetomo General Academic Hospital, Surabaya 60286, Indonesia
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| |
Collapse
|
2
|
Vo T, Prakrithi P, Jones K, Yoon S, Lam PY, Kao Y, Ma N, Tan SX, Jin X, Zhou C, Crawford J, Walters S, Gupta I, Soyer PH, Khosrotehrani K, Stark MS, Nguyen Q. Assessing spatial sequencing and imaging approaches to capture the molecular and pathological heterogeneity of archived cancer tissues. J Pathol 2025; 265:274-288. [PMID: 39846232 PMCID: PMC11794982 DOI: 10.1002/path.6383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 10/10/2024] [Accepted: 11/22/2024] [Indexed: 01/24/2025]
Abstract
Spatial transcriptomics (ST) offers enormous potential to decipher the biological and pathological heterogeneity in precious archival cancer tissues. Traditionally, these tissues have rarely been used and only examined at a low throughput, most commonly by histopathological staining. ST adds thousands of times as many molecular features to histopathological images, but critical technical issues and limitations require more assessment of how ST performs on fixed archival tissues. In this work, we addressed this in a cancer-heterogeneity pipeline, starting with an exploration of the whole transcriptome by two sequencing-based ST protocols capable of measuring coding and non-coding RNAs. We optimised the two protocols to work with challenging formalin-fixed paraffin-embedded (FFPE) tissues, derived from skin. We then assessed alternative imaging methods, including multiplex RNAScope single-molecule imaging and multiplex protein imaging (CODEX). We evaluated the methods' performance for tissues stored from 4 to 14 years ago, covering a range of RNA qualities, allowing us to assess variation. In addition to technical performance metrics, we determined the ability of these methods to quantify tumour heterogeneity. We integrated gene expression profiles with pathological information, charting a new molecular landscape on the pathologically defined tissue regions. Together, this work provides important and comprehensive experimental technical perspectives to consider the applications of ST in deciphering the cancer heterogeneity in archived tissues. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Tuan Vo
- The Institute for Molecular BioscienceThe University of QueenslandSt LuciaQueenslandAustralia
- Queensland Institute of Medical ResearchHerstonQueenslandAustralia
- School of Biomedical Sciences and PharmacyUniversity of NewcastleCallaghanNew South WalesAustralia
- Precision Medicine Research ProgramHunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
| | - P Prakrithi
- The Institute for Molecular BioscienceThe University of QueenslandSt LuciaQueenslandAustralia
- Queensland Institute of Medical ResearchHerstonQueenslandAustralia
- University of Queensland – IIT Delhi Research Academy (UQIDRA)New DelhiIndia
- Department of Biochemical Engineering and BiotechnologyIndian Institute of Technology DelhiNew DelhiIndia
| | - Kahli Jones
- The Institute for Molecular BioscienceThe University of QueenslandSt LuciaQueenslandAustralia
| | - Sohye Yoon
- Genome Innovation HubThe University of QueenslandSt LuciaQueenslandAustralia
| | - Pui Yeng Lam
- The Institute for Molecular BioscienceThe University of QueenslandSt LuciaQueenslandAustralia
| | - Yung‐Ching Kao
- Dermatology Research CentreThe Frazer Institute, The University of QueenslandWoolloongabbaQueenslandAustralia
| | - Ning Ma
- Akoya Biosciences IncMarlboroughMassachusettsUSA
| | - Samuel X Tan
- Dermatology Research CentreThe Frazer Institute, The University of QueenslandWoolloongabbaQueenslandAustralia
| | - Xinnan Jin
- The Institute for Molecular BioscienceThe University of QueenslandSt LuciaQueenslandAustralia
- Queensland Institute of Medical ResearchHerstonQueenslandAustralia
| | - Chenhao Zhou
- Dermatology Research CentreThe Frazer Institute, The University of QueenslandWoolloongabbaQueenslandAustralia
| | - Joanna Crawford
- The Institute for Molecular BioscienceThe University of QueenslandSt LuciaQueenslandAustralia
| | - Shaun Walters
- School of Biomedical SciencesThe University of QueenslandSt LuciaQueenslandAustralia
| | - Ishaan Gupta
- University of Queensland – IIT Delhi Research Academy (UQIDRA)New DelhiIndia
- Department of Biochemical Engineering and BiotechnologyIndian Institute of Technology DelhiNew DelhiIndia
| | - Peter H Soyer
- Dermatology Research CentreThe Frazer Institute, The University of QueenslandWoolloongabbaQueenslandAustralia
| | - Kiarash Khosrotehrani
- Dermatology Research CentreThe Frazer Institute, The University of QueenslandWoolloongabbaQueenslandAustralia
| | - Mitchell S Stark
- Dermatology Research CentreThe Frazer Institute, The University of QueenslandWoolloongabbaQueenslandAustralia
| | - Quan Nguyen
- The Institute for Molecular BioscienceThe University of QueenslandSt LuciaQueenslandAustralia
- Queensland Institute of Medical ResearchHerstonQueenslandAustralia
| |
Collapse
|
3
|
Jiang S, Mantri M, Maymi V, Leddon SA, Schweitzer P, Bhandari S, Holdener C, Ntekas I, Vollmers C, Flyak AI, Fowell DJ, Rudd BD, De Vlaminck I. A Temporal and Spatial Atlas of Adaptive Immune Responses in the Lymph Node Following Viral Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.31.635509. [PMID: 39975238 PMCID: PMC11838507 DOI: 10.1101/2025.01.31.635509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
The spatial organization of adaptive immune cells within lymph nodes is critical for understanding immune responses during infection and disease. Here, we introduce AIR-SPACE, an integrative approach that combines high-resolution spatial transcriptomics with paired, high-fidelity long-read sequencing of T and B cell receptors. This method enables the simultaneous analysis of cellular transcriptomes and adaptive immune receptor (AIR) repertoires within their native spatial context. We applied AIR-SPACE to mouse popliteal lymph nodes at five distinct time points after Vaccinia virus footpad infection and constructed a comprehensive map of the developing adaptive immune response. Our analysis revealed heterogeneous activation niches, characterized by Interferon-gamma (IFN-γ) production, during the early stages of infection. At later stages, we delineated sub-anatomical structures within the germinal center (GC) and observed evidence that antibody-producing plasma cells differentiate and exit the GC through the dark zone. Furthermore, by combining clonotype data with spatial lineage tracing, we demonstrate that B cell clones are shared among multiple GCs within the same lymph node, reinforcing the concept of a dynamic, interconnected network of GCs. Overall, our study demonstrates how AIR-SPACE can be used to gain insight into the spatial dynamics of infection responses within lymphoid organs.
Collapse
Affiliation(s)
- Shaowen Jiang
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Madhav Mantri
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Viviana Maymi
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Scott A Leddon
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Peter Schweitzer
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Subash Bhandari
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Chase Holdener
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Ioannis Ntekas
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Andrew I Flyak
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Deborah J Fowell
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| |
Collapse
|
4
|
Miranda-Hernandez S, Kumar M, Henderson A, Graham E, Tan X, Taylor J, Meehan M, Ceja Z, Del Pozo-Ramos L, Pan Y, Tsui E, Donovan ML, Rentería ME, Flores-Valdez MA, Blumenthal A, Nguyen Q, Subbian S, Field MA, Kupz A. CD8 + T cells mediate vaccination-induced lymphatic containment of latent Mycobacterium tuberculosis infection following immunosuppression, while B cells are dispensable. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.23.634479. [PMID: 39896630 PMCID: PMC11785187 DOI: 10.1101/2025.01.23.634479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
Abstract
It is estimated that two billion people are latently infected with Mycobacterium tuberculosis ( Mtb ), the causative agent of tuberculosis (TB). Latent Mtb infection (LTBI) can occur in multiple organs, including the lymphatics. The risk of LTBI reactivation increases in immunocompromised conditions, such as coinfection with human immunodeficiency virus (HIV), and during treatment of autoimmune diseases and organ transplantation. The immunological correlates of protection against TB, including against reactivation of LTBI, remain largely elusive. Here, we used a mouse model of latent lymphatic Mtb infection to dissect the immunological mechanisms underlying LTBI containment versus reactivation. We show that immunosuppression-mediated reactivation of lymphatic LTBI and the subsequent spread to non-lymphatic organs can be prevented by vaccination with multiple recombinant BCG (rBCG) strains despite the deficiency of CD4 + T cells. Using spatial transcriptomics, multi-parameter imaging, network analysis and bioinformatic integration of histopathological images, we reveal that immunosuppression is associated with a distinct repositioning of non-CD4 immune cells at the edge of TB lesions within the infection-draining cervical lymph nodes. While B cells increased in numbers, they are dispensable for the containment of LTBI. Lymphatic Mtb infection in different immune cell-deficient mouse strains, antibody-mediated cell depletion and adoptive transfer experiments into highly susceptible mice unequivocally show that vaccination-mediated prevention of LTBI reactivation is critically dependent on CD8 + T cells. These findings have profound implications for our understanding of immunity to TB and the management of LTBI.
Collapse
|
5
|
de Oliveira G, Costa-Rocha IA, Oliveira-Carvalho N, dos Santos TMAF, Campi-Azevedo AC, Peruhype-Magalhães V, Miranda VHS, Prado RO, Pereira AAS, Alves CC, Brito-de-Sousa JP, Reis LR, Costa-Pereira C, da Mata CPSM, Almeida VES, dos Santos LM, Almeida GG, Antonelli LRDV, Coelho-dos-Reis JG, Teixeira-Carvalho A, Martins-Filho OA. Phenotypic Timeline Kinetics, Integrative Networks, and Performance of T- and B-Cell Subsets Associated with Distinct Clinical Outcome of Severe COVID-19 Patients. Microorganisms 2024; 12:2272. [PMID: 39597661 PMCID: PMC11596994 DOI: 10.3390/microorganisms12112272] [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: 05/29/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 11/29/2024] Open
Abstract
The present study aimed to evaluate the kinetics of the phenotypic profile and integrative networks of T/B-cells in severe COVID-19 patients, categorized according to disease outcome, during the circulation of the B.1.1.28 and B.1.1.33 SARS-CoV-2 strains in Brazil. Peripheral blood obtained at distinct time points (baseline/D0; D7; D14-28) was used for ex vivo flow cytometry immunophenotyping. The data demonstrated a decrease at D0 in the frequency of CD3+ T-cells and CD4+ T-cells and an increase in B-cells with mixed activation/exhaustion profiles. Higher changes in B-cell and CD4+ T-cells at D7 were associated with discharge/death outcomes, respectively. Regardless of the lower T/B-cell connectivity at D0, distinct profiles from D7/D14-28 revealed that, while discharge was associated with increasing connectivity for B-cells, CD4+ and CD8+ T-cells death was related to increased connectivity involving B-cells, but with lower connections mediated by CD4+ T-cells. The CD4+CD38+ and CD8+CD69+ subsets accurately classified COVID-19 vs. healthy controls throughout the kinetic analysis. Binary logistic regression identified CD4+CD107a+, CD4+T-bet+, CD8+CD69+, and CD8+T-bet+ at D0 and CD4+CD45RO+CD27+ at D7 as subsets associated with disease outcomes. Results showed that distinct phenotypic timeline kinetics and integrative networks of T/B-cells are associated with COVID-19 outcomes that may subsidize the establishment of applicable biomarkers for clinical/therapeutic monitoring.
Collapse
Affiliation(s)
- Gabriela de Oliveira
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| | - Ismael Artur Costa-Rocha
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| | - Nani Oliveira-Carvalho
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| | - Tâmilla Mayane Alves Fidelis dos Santos
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| | - Ana Carolina Campi-Azevedo
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| | - Vanessa Peruhype-Magalhães
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| | - Vitor Hugo Simões Miranda
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| | - Roberta Oliveira Prado
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| | - Agnes Antônia Sampaio Pereira
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| | - Clarice Carvalho Alves
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| | - Joaquim Pedro Brito-de-Sousa
- Departamento de Imunologia e Parasitologia, Universidade Federal de Uberlândia, Uberlândia 38408-100, MG, Brazil;
| | - Laise Rodrigues Reis
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| | - Christiane Costa-Pereira
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| | | | | | - Liliane Martins dos Santos
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| | - Gregório Guilherme Almeida
- Biologia e Imunologia de Doenças Infecciosas e Parasitárias, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.G.A.); (L.R.d.V.A.)
| | - Lis Ribeiro do Valle Antonelli
- Biologia e Imunologia de Doenças Infecciosas e Parasitárias, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.G.A.); (L.R.d.V.A.)
| | - Jordana Grazziela Coelho-dos-Reis
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Andréa Teixeira-Carvalho
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| | - Olindo Assis Martins-Filho
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ-Minas, Belo Horizonte 30190-002, MG, Brazil; (G.d.O.); (I.A.C.-R.); (N.O.-C.); (T.M.A.F.d.S.); (A.C.C.-A.); (V.P.-M.); (V.H.S.M.); (R.O.P.); (A.A.S.P.); (C.C.A.); (L.R.R.); (C.C.-P.); (L.M.d.S.); (J.G.C.-d.-R.); (A.T.-C.)
| |
Collapse
|
6
|
Fan X, Sun AR, Young RSE, Afara IO, Hamilton BR, Ong LJY, Crawford R, Prasadam I. Spatial analysis of the osteoarthritis microenvironment: techniques, insights, and applications. Bone Res 2024; 12:7. [PMID: 38311627 PMCID: PMC10838951 DOI: 10.1038/s41413-023-00304-6] [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: 09/05/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 02/06/2024] Open
Abstract
Osteoarthritis (OA) is a debilitating degenerative disease affecting multiple joint tissues, including cartilage, bone, synovium, and adipose tissues. OA presents diverse clinical phenotypes and distinct molecular endotypes, including inflammatory, metabolic, mechanical, genetic, and synovial variants. Consequently, innovative technologies are needed to support the development of effective diagnostic and precision therapeutic approaches. Traditional analysis of bulk OA tissue extracts has limitations due to technical constraints, causing challenges in the differentiation between various physiological and pathological phenotypes in joint tissues. This issue has led to standardization difficulties and hindered the success of clinical trials. Gaining insights into the spatial variations of the cellular and molecular structures in OA tissues, encompassing DNA, RNA, metabolites, and proteins, as well as their chemical properties, elemental composition, and mechanical attributes, can contribute to a more comprehensive understanding of the disease subtypes. Spatially resolved biology enables biologists to investigate cells within the context of their tissue microenvironment, providing a more holistic view of cellular function. Recent advances in innovative spatial biology techniques now allow intact tissue sections to be examined using various -omics lenses, such as genomics, transcriptomics, proteomics, and metabolomics, with spatial data. This fusion of approaches provides researchers with critical insights into the molecular composition and functions of the cells and tissues at precise spatial coordinates. Furthermore, advanced imaging techniques, including high-resolution microscopy, hyperspectral imaging, and mass spectrometry imaging, enable the visualization and analysis of the spatial distribution of biomolecules, cells, and tissues. Linking these molecular imaging outputs to conventional tissue histology can facilitate a more comprehensive characterization of disease phenotypes. This review summarizes the recent advancements in the molecular imaging modalities and methodologies for in-depth spatial analysis. It explores their applications, challenges, and potential opportunities in the field of OA. Additionally, this review provides a perspective on the potential research directions for these contemporary approaches that can meet the requirements of clinical diagnoses and the establishment of therapeutic targets for OA.
Collapse
Affiliation(s)
- Xiwei Fan
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Antonia Rujia Sun
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Reuben S E Young
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Isaac O Afara
- Department of Technical Physics, University of Eastern Finland, Kuopio, Finland
- School of Electrical Engineering and Computer Science, Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, QLD, Australia
| | - Brett R Hamilton
- Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, QLD, Australia
| | - Louis Jun Ye Ong
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Ross Crawford
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Indira Prasadam
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia.
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia.
| |
Collapse
|
7
|
Tu C, Kulasinghe A, Barbour A, Souza-Fonseca-Guimaraes F. Leveraging spatial omics for the development of precision sarcoma treatments. Trends Pharmacol Sci 2024; 45:134-144. [PMID: 38212196 DOI: 10.1016/j.tips.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/13/2024]
Abstract
Sarcomas are rare and heterogeneous cancers that arise from bone or soft tissue, and are the second most prevalent solid cancer in children and adolescents. Owing to the complex nature of pediatric sarcomas, the development of therapeutics for pediatric sarcoma has seen little progress in the past decades. Existing treatments are largely limited to chemotherapy, radiation, and surgery. Limited knowledge of the sarcoma tumor microenvironment (TME) and of well-defined target antigens in the different subtypes necessitates an alternative investigative approach to improve treatments. Recent advances in spatial omics technologies have enabled a more comprehensive study of the TME in multiple cancers. In this opinion article we discuss advances in our understanding of the TME of some cancers enabled by spatial omics technologies, and we explore how these technologies might advance the development of precision treatments for sarcoma, especially pediatric sarcoma.
Collapse
Affiliation(s)
- Cui Tu
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Andrew Barbour
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia; Department of Surgery, Princess Alexandra Hospital, Brisbane, QLD 4102, Australia
| | | |
Collapse
|