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Kumar G, Pandurengan RK, Parra ER, Kannan K, Haymaker C. Spatial modelling of the tumor microenvironment from multiplex immunofluorescence images: methods and applications. Front Immunol 2023; 14:1288802. [PMID: 38179056 PMCID: PMC10765501 DOI: 10.3389/fimmu.2023.1288802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024] Open
Abstract
Spatial modelling methods have gained prominence with developments in high throughput imaging platforms. Multiplex immunofluorescence (mIF) provides the scope to examine interactions between tumor and immune compartment at single cell resolution using a panel of antibodies that can be chosen based on the cancer type or the clinical interest of the study. The markers can be used to identify the phenotypes and to examine cellular interactions at global and local scales. Several translational studies rely on key understanding of the tumor microenvironment (TME) to identify drivers of immune response in immunotherapy based clinical trials. To improve the success of ongoing trials, a number of retrospective approaches can be adopted to understand differences in response, recurrence and progression by examining the patient's TME from tissue samples obtained at baseline and at various time points along the treatment. The multiplex immunofluorescence (mIF) technique provides insight on patient specific cell populations and their relative spatial distribution as qualitative measures of a favorable treatment outcome. Spatial analysis of these images provides an understanding of the intratumoral heterogeneity and clustering among cell populations in the TME. A number of mathematical models, which establish clustering as a measure of deviation from complete spatial randomness, can be applied to the mIF images represented as spatial point patterns. These mathematical models, developed for landscape ecology and geographic information studies, can be applied to the TME after careful consideration of the tumor type (cold vs. hot) and the tumor immune landscape. The spatial modelling of mIF images can show observable engagement of T cells expressing immune checkpoint molecules and this can then be correlated with single-cell RNA sequencing data.
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Affiliation(s)
| | | | | | - Kasthuri Kannan
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, United States
| | - Cara Haymaker
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, United States
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Laberiano-Fernandez C, Baldavira CM, Machado-Rugolo J, Tamegnon A, Pandurengan RK, Ab’Saber AM, Balancin ML, Takagaki TY, Nagai MA, Capelozzi VL, Parra ER. The Immunological Landscape of M1 and M2 Macrophages and Their Spatial Distribution in Patients with Malignant Pleural Mesothelioma. Cancers (Basel) 2023; 15:5116. [PMID: 37958292 PMCID: PMC10650059 DOI: 10.3390/cancers15215116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/12/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Several tumor-associated macrophages (TAMs) have shown promise as prognosticators in cancer. Our aim was to validate the importance of TAMs in malignant pleural mesothelioma (MPM) using a two-stage design. METHODS We explored The Cancer Genome Atlas (TCGA-MESO) to select immune-relevant macrophage genes in MPM, including M1/M2 markers, as a discovery cohort. This computational cohort was used to create a multiplex immunofluorescence panel. Moreover, a cohort of 68 samples of MPM in paraffin blocks was used to validate the macrophage phenotypes and the co-localization and spatial distribution of these immune cells within the TME and the stromal or tumor compartments. RESULTS The discovery cohort revealed six immune-relevant macrophage genes (CD68, CD86, CD163, CD206, ARG1, CD274), and complementary genes were differentially expressed by M1 and M2 phenotypes with distinct roles in the tumor microenvironment and were associated with the prognosis. In addition, immune-suppressed MPMs with increased enrichment of CD68, CD86, and CD163 genes and high densities of M2 macrophages expressing CD163 and CD206 proteins were associated with worse overall survival (OS). Interestingly, below-median distances from malignant cells to specific M2a and M2c macrophages were associated with worse OS, suggesting an M2 macrophage-driven suppressive component in these tumors. CONCLUSIONS The interactions between TAMs in situ and, particularly, CD206+ macrophages are highly relevant to patient outcomes. High-resolution technology is important for identifying the roles of macrophage populations in tissue specimens and identifying potential therapeutic candidates in MPM.
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Affiliation(s)
- Caddie Laberiano-Fernandez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.L.-F.); (A.T.); (R.K.P.)
| | - Camila Machado Baldavira
- Department of Pathology, Medical School, University of Sao Paulo, Sao Paulo 01246-903, Brazil; (C.M.B.); (J.M.-R.); (A.M.A.); (M.L.B.); (V.L.C.)
| | - Juliana Machado-Rugolo
- Department of Pathology, Medical School, University of Sao Paulo, Sao Paulo 01246-903, Brazil; (C.M.B.); (J.M.-R.); (A.M.A.); (M.L.B.); (V.L.C.)
| | - Auriole Tamegnon
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.L.-F.); (A.T.); (R.K.P.)
| | - Renganayaki Krishna Pandurengan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.L.-F.); (A.T.); (R.K.P.)
| | - Alexandre Muxfeldt Ab’Saber
- Department of Pathology, Medical School, University of Sao Paulo, Sao Paulo 01246-903, Brazil; (C.M.B.); (J.M.-R.); (A.M.A.); (M.L.B.); (V.L.C.)
- Division of Pneumology, Instituto do Coração (Incor), Medical School, University of Sao Paulo, Sao Paulo 01246-903, Brazil;
| | - Marcelo Luiz Balancin
- Department of Pathology, Medical School, University of Sao Paulo, Sao Paulo 01246-903, Brazil; (C.M.B.); (J.M.-R.); (A.M.A.); (M.L.B.); (V.L.C.)
- Division of Pneumology, Instituto do Coração (Incor), Medical School, University of Sao Paulo, Sao Paulo 01246-903, Brazil;
| | - Teresa Yae Takagaki
- Division of Pneumology, Instituto do Coração (Incor), Medical School, University of Sao Paulo, Sao Paulo 01246-903, Brazil;
| | - Maria Aparecida Nagai
- Department of Radiology and Oncology, Medical School, University of Sao Paulo, Sao Paulo 01246-903, Brazil;
- Laboratory of Molecular Genetics, Center for Translational Research in Oncology, Cancer Institute of Sao Paulo, Sao Paulo 01246-903, Brazil
| | - Vera Luiza Capelozzi
- Department of Pathology, Medical School, University of Sao Paulo, Sao Paulo 01246-903, Brazil; (C.M.B.); (J.M.-R.); (A.M.A.); (M.L.B.); (V.L.C.)
- Division of Pneumology, Instituto do Coração (Incor), Medical School, University of Sao Paulo, Sao Paulo 01246-903, Brazil;
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.L.-F.); (A.T.); (R.K.P.)
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Parra ER, Zhang J, Jiang M, Tamegnon A, Pandurengan RK, Behrens C, Solis L, Haymaker C, Heymach JV, Moran C, Lee JJ, Gibbons D, Wistuba II. Immune cellular patterns of distribution affect outcomes of patients with non-small cell lung cancer. Nat Commun 2023; 14:2364. [PMID: 37185575 PMCID: PMC10130161 DOI: 10.1038/s41467-023-37905-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
Studying the cellular geographic distribution in non-small cell lung cancer is essential to understand the roles of cell populations in this type of tumor. In this study, we characterize the spatial cellular distribution of immune cell populations using 23 makers placed in five multiplex immunofluorescence panels and their associations with clinicopathologic variables and outcomes. Our results demonstrate two cellular distribution patterns-an unmixed pattern mostly related to immunoprotective cells and a mixed pattern mostly related to immunosuppressive cells. Distance analysis shows that T-cells expressing immune checkpoints are closer to malignant cells than other cells. Combining the cellular distribution patterns with cellular distances, we can identify four groups related to inflamed and not-inflamed tumors. Cellular distribution patterns and distance are associated with survival in univariate and multivariable analyses. Spatial distribution is a tool to better understand the tumor microenvironment, predict outcomes, and may can help select therapeutic interventions.
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Affiliation(s)
- Edwin Roger Parra
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Jiexin Zhang
- Departments of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mei Jiang
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Auriole Tamegnon
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Carmen Behrens
- Departments of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luisa Solis
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cara Haymaker
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Victor Heymach
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cesar Moran
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jack J Lee
- Departments of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Don Gibbons
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Departments of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio Ivan Wistuba
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Pandurengan RK, Dumont AG, Araujo DM, Ludwig JA, Ravi V, Patel S, Garber J, Benjamin RS, Strom SS, Trent JC. Survival of patients with multiple primary malignancies: a study of 783 patients with gastrointestinal stromal tumor. Ann Oncol 2010; 21:2107-2111. [PMID: 20348145 DOI: 10.1093/annonc/mdq078] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND We sought to investigate the characteristics and survival rate of patients with gastrointestinal stromal tumor (GIST) associated with other primary malignancies. PATIENTS AND METHODS A total of 783 patients with GIST were identified from 1995 to 2007. Additional primaries included tumors not considered metastasis, invasion, or recurrence of GIST, nor non-melanoma skin cancer. Data on gender, age at diagnosis, follow-up time after diagnosis, and death were collected. RESULTS Of the 783 patients with GIST, 153(20%) were identified with at least one additional primary. Patients with additional primaries were more often men (M : F 1.5 versus 1.3) and older (66 versus 53 years). More patients had another cancer diagnosed before (134) than after (52) GIST. Primaries observed before GIST were cancers of the prostate (25), breast (12), esophagus (9), and kidney (7) and melanoma (6). Lung (5) and kidney (5) primaries were the most frequent after GIST. The 5-year survival was 68% for patients with primaries before GIST, 61% for patients with primaries after GIST, 58% for patients with GIST only, and 49% for patients with two or more primaries in addition to GIST (P = 0.002). CONCLUSIONS Approximately 20% of patients with GIST develop other cancers. Inferior median 5-year survival was observed in patients with GIST with two or more other cancers. The etiology and clinical implications of other malignancies in patients with GIST should be investigated.
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Affiliation(s)
| | - A G Dumont
- Department of Sarcoma Medical Oncology; The Adult Sarcoma Research Center, The University of Texas, M. D. Anderson Cancer Center, Houston, TX
| | | | - J A Ludwig
- Department of Sarcoma Medical Oncology; The Adult Sarcoma Research Center, The University of Texas, M. D. Anderson Cancer Center, Houston, TX
| | - V Ravi
- Department of Sarcoma Medical Oncology
| | - S Patel
- Department of Sarcoma Medical Oncology
| | - J Garber
- Cancer Risk and Prevention Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - J C Trent
- Department of Sarcoma Medical Oncology; The Adult Sarcoma Research Center, The University of Texas, M. D. Anderson Cancer Center, Houston, TX.
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