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Cerapio JP, Gravelle P, Quillet-Mary A, Valle C, Martins F, Franchini DM, Syrykh C, Brousset P, Traverse-Glehen A, Ysebaert L, Fournie JJ, Laurent C. Integrated spatial and multimodal single-cell transcriptomics reveal patient-dependent cell heterogeneity in splenic marginal zone lymphoma. J Pathol 2024. [PMID: 38828498 DOI: 10.1002/path.6296] [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: 09/20/2023] [Revised: 12/22/2023] [Accepted: 04/17/2024] [Indexed: 06/05/2024]
Abstract
Biological hallmarks of splenic marginal zone lymphoma (SMZL) remain poorly described. Herein, we performed in-depth SMZL characterization through multimodal single-cell analyses of paired blood/spleen samples. The 3'-single-cell RNA-sequencing, Cellular Indexing of Transcriptomes and Epitopes by sequencing, and 5'-V(D)J single-cell RNA-sequencing datasets were integrated to characterize SMZL transcriptome profiles, including B-cell receptor and T-cell receptor repertoires. Hyperexpanded B-cell clones in the spleen were at a memory-like stage, whereas recirculating tumor B-cells in blood encompassed multiple differentiation stages, indicating an unexpected desynchronization of the B-cell maturation program in SMZL cells. Spatial transcriptomics showed the enrichment of T-effector and T-follicular helper (TFH) signatures in the nodular subtype of SMZL. This latter also exhibited gene-based cell-cell interactions suggestive of dynamic crosstalk between TFH and cancer cells in transcriptomics, further substantiated by using imaging mass cytometry. Our findings provide a comprehensive high-resolution description of SMZL biological hallmarks and characterize, for the first time in situ, inter- and intra-patient heterogeneity at both transcriptomic and protein levels. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Juan Pablo Cerapio
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
| | - Pauline Gravelle
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
- Institut Carnot Lymphome - ADREP CALYM, Paris, France
- Centre Hospitalier Universitaire, Toulouse, France
| | - Anne Quillet-Mary
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
- Institut Carnot Lymphome - ADREP CALYM, Paris, France
| | - Carine Valle
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
| | - Frederic Martins
- Institut Maladies Metaboliques et Cardiovasculaires, INSERM UMR1297, Toulouse, France
| | - Don-Marc Franchini
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
- Institut Carnot Lymphome - ADREP CALYM, Paris, France
- Centre Hospitalier Universitaire, Toulouse, France
| | - Charlotte Syrykh
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Centre Hospitalier Universitaire, Toulouse, France
| | - Pierre Brousset
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
- Institut Carnot Lymphome - ADREP CALYM, Paris, France
- Centre Hospitalier Universitaire, Toulouse, France
| | | | - Loic Ysebaert
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
- Institut Carnot Lymphome - ADREP CALYM, Paris, France
- Centre Hospitalier Universitaire, Toulouse, France
| | - Jean-Jacques Fournie
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
- Institut Carnot Lymphome - ADREP CALYM, Paris, France
| | - Camille Laurent
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
- Institut Carnot Lymphome - ADREP CALYM, Paris, France
- Centre Hospitalier Universitaire, Toulouse, France
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Røgenes H, Finne K, Winge I, Akslen LA, Östman A, Milosevic V. Development of 42 marker panel for in-depth study of cancer associated fibroblast niches in breast cancer using imaging mass cytometry. Front Immunol 2024; 15:1325191. [PMID: 38711512 PMCID: PMC11070582 DOI: 10.3389/fimmu.2024.1325191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/05/2024] [Indexed: 05/08/2024] Open
Abstract
Imaging Mass Cytometry (IMC) is a novel, and formidable high multiplexing imaging method emerging as a promising tool for in-depth studying of tissue architecture and intercellular communications. Several studies have reported various IMC antibody panels mainly focused on studying the immunological landscape of the tumor microenvironment (TME). With this paper, we wanted to address cancer associated fibroblasts (CAFs), a component of the TME very often underrepresented and not emphasized enough in present IMC studies. Therefore, we focused on the development of a comprehensive IMC panel that can be used for a thorough description of the CAF composition of breast cancer TME and for an in-depth study of different CAF niches in relation to both immune and breast cancer cell communication. We established and validated a 42 marker panel using a variety of control tissues and rigorous quantification methods. The final panel contained 6 CAF-associated markers (aSMA, FAP, PDGFRa, PDGFRb, YAP1, pSMAD2). Breast cancer tissues (4 cases of luminal, 5 cases of triple negative breast cancer) and a modified CELESTA pipeline were used to demonstrate the utility of our IMC panel for detailed profiling of different CAF, immune and cancer cell phenotypes.
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Affiliation(s)
- Hanna Røgenes
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Kenneth Finne
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Ingeborg Winge
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Lars A. Akslen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Arne Östman
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Oncology and Pathology, Karolinska Institutet, Solna, Sweden
| | - Vladan Milosevic
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
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Stepanenko AA, Sosnovtseva AO, Valikhov MP, Chernysheva AA, Abramova OV, Pavlov KA, Chekhonin VP. Systemic and local immunosuppression in glioblastoma and its prognostic significance. Front Immunol 2024; 15:1326753. [PMID: 38481999 PMCID: PMC10932993 DOI: 10.3389/fimmu.2024.1326753] [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: 10/23/2023] [Accepted: 02/06/2024] [Indexed: 04/07/2024] Open
Abstract
The effectiveness of tumor therapy, especially immunotherapy and oncolytic virotherapy, critically depends on the activity of the host immune cells. However, various local and systemic mechanisms of immunosuppression operate in cancer patients. Tumor-associated immunosuppression involves deregulation of many components of immunity, including a decrease in the number of T lymphocytes (lymphopenia), an increase in the levels or ratios of circulating and tumor-infiltrating immunosuppressive subsets [e.g., macrophages, microglia, myeloid-derived suppressor cells (MDSCs), and regulatory T cells (Tregs)], as well as defective functions of subsets of antigen-presenting, helper and effector immune cell due to altered expression of various soluble and membrane proteins (receptors, costimulatory molecules, and cytokines). In this review, we specifically focus on data from patients with glioblastoma/glioma before standard chemoradiotherapy. We discuss glioblastoma-related immunosuppression at baseline and the prognostic significance of different subsets of circulating and tumor-infiltrating immune cells (lymphocytes, CD4+ and CD8+ T cells, Tregs, natural killer (NK) cells, neutrophils, macrophages, MDSCs, and dendritic cells), including neutrophil-to-lymphocyte ratio (NLR), focus on the immune landscape and prognostic significance of isocitrate dehydrogenase (IDH)-mutant gliomas, proneural, classical and mesenchymal molecular subtypes, and highlight the features of immune surveillance in the brain. All attempts to identify a reliable prognostic immune marker in glioblastoma tissue have led to contradictory results, which can be explained, among other things, by the unprecedented level of spatial heterogeneity of the immune infiltrate and the significant phenotypic diversity and (dys)functional states of immune subpopulations. High NLR is one of the most repeatedly confirmed independent prognostic factors for shorter overall survival in patients with glioblastoma and carcinoma, and its combination with other markers of the immune response or systemic inflammation significantly improves the accuracy of prediction; however, more prospective studies are needed to confirm the prognostic/predictive power of NLR. We call for the inclusion of dynamic assessment of NLR and other blood inflammatory markers (e.g., absolute/total lymphocyte count, platelet-to-lymphocyte ratio, lymphocyte-to-monocyte ratio, systemic immune-inflammation index, and systemic immune response index) in all neuro-oncology studies for rigorous evaluation and comparison of their individual and combinatorial prognostic/predictive significance and relative superiority.
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Affiliation(s)
- Aleksei A. Stepanenko
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Moscow, Russia
- Department of Medical Nanobiotechnology, Institute of Translational Medicine, N. I. Pirogov Russian National Research Medical University, The Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anastasiia O. Sosnovtseva
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Marat P. Valikhov
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Moscow, Russia
- Department of Medical Nanobiotechnology, Institute of Translational Medicine, N. I. Pirogov Russian National Research Medical University, The Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anastasia A. Chernysheva
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Olga V. Abramova
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Konstantin A. Pavlov
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vladimir P. Chekhonin
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Moscow, Russia
- Department of Medical Nanobiotechnology, Institute of Translational Medicine, N. I. Pirogov Russian National Research Medical University, The Ministry of Health of the Russian Federation, Moscow, Russia
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Erreni M, Fumagalli MR, Zanini D, Candiello E, Tiberi G, Parente R, D’Anna R, Magrini E, Marchesi F, Cappello P, Doni A. Multiplexed Imaging Mass Cytometry Analysis in Preclinical Models of Pancreatic Cancer. Int J Mol Sci 2024; 25:1389. [PMID: 38338669 PMCID: PMC10855072 DOI: 10.3390/ijms25031389] [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: 12/28/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers. PDAC is characterized by a complex tumor microenvironment (TME), that plays a pivotal role in disease progression and resistance to therapy. Investigating the spatial distribution and interaction of TME cells with the tumor is the basis for understanding the mechanisms underlying disease progression and represents a current challenge in PDAC research. Imaging mass cytometry (IMC) is the major multiplex imaging technology for the spatial analysis of tumor heterogeneity. However, there is a dearth of reports of multiplexed IMC panels for different preclinical mouse models, including pancreatic cancer. We addressed this gap by utilizing two preclinical models of PDAC: the genetically engineered, bearing KRAS-TP53 mutations in pancreatic cells, and the orthotopic, and developed a 28-marker panel for single-cell IMC analysis to assess the abundance, distribution and phenotypes of cells involved in PDAC progression and their reciprocal functional interactions. Herein, we provide an unprecedented definition of the distribution of TME cells in PDAC and compare the diversity between transplanted and genetic disease models. The results obtained represent an important and customizable tool for unraveling the complexities of PDAC and deciphering the mechanisms behind therapy resistance.
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Affiliation(s)
- Marco Erreni
- Unit of Multiscale and Nanostructural Imaging, IRCCS Humanitas Research Hospital -, via Manzoni 56, 20089 Rozzano, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
| | - Maria Rita Fumagalli
- Unit of Multiscale and Nanostructural Imaging, IRCCS Humanitas Research Hospital -, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Damiano Zanini
- Unit of Multiscale and Nanostructural Imaging, IRCCS Humanitas Research Hospital -, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Ermes Candiello
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Piazza Nizza 44b, 10126 Torino, Italy
| | - Giorgia Tiberi
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Piazza Nizza 44b, 10126 Torino, Italy
| | - Raffaella Parente
- Unit of Multiscale and Nanostructural Imaging, IRCCS Humanitas Research Hospital -, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Raffaella D’Anna
- Unit of Multiscale and Nanostructural Imaging, IRCCS Humanitas Research Hospital -, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Elena Magrini
- IRCCS Humanitas Research Hospital -, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Federica Marchesi
- IRCCS Humanitas Research Hospital -, via Manzoni 56, 20089 Rozzano, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20133 Milan, Italy
| | - Paola Cappello
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Piazza Nizza 44b, 10126 Torino, Italy
| | - Andrea Doni
- Unit of Multiscale and Nanostructural Imaging, IRCCS Humanitas Research Hospital -, via Manzoni 56, 20089 Rozzano, Milan, Italy
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