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Kim H, Kim BJ, Koh S, Cho HJ, Jin X, Kim BG, Choi JY. Analysis of the spatial and morphological characteristics of oligodendrocytes from images of in vitro culture. MethodsX 2024; 13:102781. [PMID: 38978971 PMCID: PMC11228796 DOI: 10.1016/j.mex.2024.102781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/27/2024] [Indexed: 07/10/2024] Open
Abstract
Oligodendrocytes (OLs) are glial cells responsible for the formation of myelin sheaths in the central nervous system. The characteristic features of the oligodendrocyte lineage, ranging from proliferative and migratory oligodendrocyte progenitor cells (OPC) to myelinating mature OLs, can be observed in vitro cultures of OL lineage cells. Here, we introduce a method for analyzing the spatial distribution of OPCs, which reflects their capacity for proliferation and migration, and the morphological complexity of mature OLs, which reflects their capacity for myelin formation, from immunostaining images of in vitro OL cultures. Through the methods described, we have demonstrated the tendency for OPCs to cluster in an environment with epidermal growth factor (EGF), and the differing morphological complexity of mature OLs according to culture medium and duration of differentiation.•The proliferative and migratory characteristics of OPCs can be evaluated by analyzing their spatial distribution.•The myelin-forming capacity of mature OLs can be measured by analyzing their morphological complexity.•Image-based analyses may be a substitute for more convoluted experiments to assess OL function.
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Affiliation(s)
- Hanki Kim
- Department of Brain Science, Ajou University School of Medicine, Suwon, 16499, Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Korea
| | - Bum Jun Kim
- Department of Brain Science, Ajou University School of Medicine, Suwon, 16499, Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Korea
| | - Seungyon Koh
- Department of Brain Science, Ajou University School of Medicine, Suwon, 16499, Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Korea
- Department of Neurology, Ajou University School of Medicine, Suwon, 16499, Korea
| | - Hyo Jin Cho
- Department of Brain Science, Ajou University School of Medicine, Suwon, 16499, Korea
| | - Xuelian Jin
- Department of Brain Science, Ajou University School of Medicine, Suwon, 16499, Korea
- Geriatrics Department, The Affiliated Suqian First People's Hospital of Nanjing Medical University, Suqian, 223800, China
| | - Byung Gon Kim
- Department of Brain Science, Ajou University School of Medicine, Suwon, 16499, Korea
- Department of Neurology, Ajou University School of Medicine, Suwon, 16499, Korea
| | - Jun Young Choi
- Department of Brain Science, Ajou University School of Medicine, Suwon, 16499, Korea
- Department of Neurology, Ajou University School of Medicine, Suwon, 16499, Korea
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2
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VanderDoes J, Marceaux C, Yokote K, Asselin-Labat ML, Rice G, Hywood JD. Using random forests to uncover the predictive power of distance-varying cell interactions in tumor microenvironments. PLoS Comput Biol 2024; 20:e1011361. [PMID: 38875302 PMCID: PMC11210873 DOI: 10.1371/journal.pcbi.1011361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 06/27/2024] [Accepted: 05/31/2024] [Indexed: 06/16/2024] Open
Abstract
Tumor microenvironments (TMEs) contain vast amounts of information on patient's cancer through their cellular composition and the spatial distribution of tumor cells and immune cell populations. Exploring variations in TMEs between patient groups, as well as determining the extent to which this information can predict outcomes such as patient survival or treatment success with emerging immunotherapies, is of great interest. Moreover, in the face of a large number of cell interactions to consider, we often wish to identify specific interactions that are useful in making such predictions. We present an approach to achieve these goals based on summarizing spatial relationships in the TME using spatial K functions, and then applying functional data analysis and random forest models to both predict outcomes of interest and identify important spatial relationships. This approach is shown to be effective in simulation experiments at both identifying important spatial interactions while also controlling the false discovery rate. We further used the proposed approach to interrogate two real data sets of Multiplexed Ion Beam Images of TMEs in triple negative breast cancer and lung cancer patients. The methods proposed are publicly available in a companion R package funkycells.
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Affiliation(s)
- Jeremy VanderDoes
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, Canada
| | - Claire Marceaux
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Kenta Yokote
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Marie-Liesse Asselin-Labat
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Gregory Rice
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, Canada
| | - Jack D. Hywood
- Department of Anatomical Pathology, Royal Melbourne Hospital, Parkville, Australia
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3
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Yang H, Li M, Deng Y, Wen H, Luo M, Zhang W. Roles and interactions of tumor microenvironment components in medulloblastoma with implications for novel therapeutics. Genes Chromosomes Cancer 2024; 63:e23233. [PMID: 38607297 DOI: 10.1002/gcc.23233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 03/16/2024] [Indexed: 04/13/2024] Open
Abstract
Medulloblastomas, the most common malignant pediatric brain tumors, can be classified into the wingless, sonic hedgehog (SHH), group 3, and group 4 subgroups. Among them, the SHH subgroup with the TP53 mutation and group 3 generally present with the worst patient outcomes due to their high rates of recurrence and metastasis. A novel and effective treatment for refractory medulloblastomas is urgently needed. To date, the tumor microenvironment (TME) has been shown to influence tumor growth, recurrence, and metastasis through immunosuppression, angiogenesis, and chronic inflammation. Treatments targeting TME components have emerged as promising approaches to the treatment of solid tumors. In this review, we summarize progress in research on medulloblastoma microenvironment components and their interactions. We also discuss challenges and future research directions for TME-targeting medulloblastoma therapy.
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Affiliation(s)
- Hanjie Yang
- Department of Pediatric Neurosurgery, Neurosurgery Center, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Min Li
- Department of Pediatric Neurosurgery, Neurosurgery Center, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yuhao Deng
- Department of Pediatric Neurosurgery, Neurosurgery Center, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Huantao Wen
- Department of Pediatric Neurosurgery, Neurosurgery Center, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Minjie Luo
- Department of Pediatric Neurosurgery, Neurosurgery Center, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Wangming Zhang
- Department of Pediatric Neurosurgery, Neurosurgery Center, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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4
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Zeng Z, Du W, Yang F, Hui Z, Wang Y, Zhang P, Zhang X, Yu W, Ren X, Wei F. The spatial landscape of T cells in the microenvironment of stage III lung adenocarcinoma. J Pathol 2024; 262:517-528. [PMID: 38361487 DOI: 10.1002/path.6254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 02/17/2024]
Abstract
This study aimed to provide more information for prognostic stratification for patients through an analysis of the T-cell spatial landscape. It involved analyzing stained tissue sections of 80 patients with stage III lung adenocarcinoma (LUAD) using multiplex immunofluorescence and exploring the spatial landscape of T cells and their relationship with prognosis in the center of the tumor (CT) and invasive margin (IM). In this study, multivariate regression suggested that the relative clustering of CT CD4+ conventional T cell (Tconv) to inducible Treg (iTreg), natural regulatory T cell (nTreg) to Tconv, terminal CD8+ T cell (tCD8) to helper T cell (Th), and IM Treg to tCD8 and the relative dispersion of CT nTreg to iTreg, IM nTreg to nTreg were independent risk factors for DFS. Finally, we constructed a spatial immunological score named the GT score, which had stronger prognostic correlation than IMMUNOSCORE® based on CD3/CD8 cell densities. The spatial layout of T cells in the tumor microenvironment and the proposed GT score can reflect the prognosis of patients with stage III LUAD more effectively than T-cell density. The exploration of the T-cell spatial landscape may suggest potential cell-cell interactions and therapeutic targets and better guide clinical decision-making. © 2024 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Ziqing Zeng
- Department of Nuclear Medicine, State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals (National Medical Products Administration), Peking University Cancer Hospital & Institute, Beijing, PR China
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
- National Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, PR China
- Tianjin's Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, PR China
| | - Weijiao Du
- National Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, PR China
- Tianjin's Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, PR China
- Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
| | - Fan Yang
- National Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, PR China
- Tianjin's Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, PR China
- Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
| | - Zhenzhen Hui
- National Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, PR China
- Tianjin's Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, PR China
- Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
| | - Yunliang Wang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
- National Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, PR China
- Tianjin's Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, PR China
- Department of Oncology, First Central Hospital of Baoding of Hebei Province, Baoding, PR China
| | - Peng Zhang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
- National Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, PR China
- Tianjin's Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, PR China
| | - Xiying Zhang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
- National Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, PR China
- Tianjin's Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, PR China
| | - Wenwen Yu
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
- National Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, PR China
- Tianjin's Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, PR China
| | - Xiubao Ren
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
- National Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, PR China
- Tianjin's Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, PR China
- Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
- Haihe Laboratory of Cell Ecosystem, Tianjin, PR China
| | - Feng Wei
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
- National Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, PR China
- Tianjin's Clinical Research Center for Cancer, Tianjin, PR China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, PR China
- Haihe Laboratory of Cell Ecosystem, Tianjin, PR China
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5
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Gil-Jimenez A, van Dijk N, Vos JL, Lubeck Y, van Montfoort ML, Peters D, Hooijberg E, Broeks A, Zuur CL, van Rhijn BWG, Vis DJ, van der Heijden MS, Wessels LFA. Spatial relationships in the urothelial and head and neck tumor microenvironment predict response to combination immune checkpoint inhibitors. Nat Commun 2024; 15:2538. [PMID: 38514623 PMCID: PMC10957922 DOI: 10.1038/s41467-024-46450-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 02/28/2024] [Indexed: 03/23/2024] Open
Abstract
Immune checkpoint inhibitors (ICI) can achieve remarkable responses in urothelial cancer (UC), which may depend on tumor microenvironment (TME) characteristics. However, the relationship between the TME, usually characterized by immune cell density, and response to ICI is unclear. Here, we quantify the TME immune cell densities and spatial relationships (SRs) of 24 baseline UC samples, obtained before pre-operative combination ICI treatment, using multiplex immunofluorescence. We describe SRs by approximating the first nearest-neighbor distance distribution with a Weibull distribution and evaluate the association between TME metrics and ipilimumab+nivolumab response. Immune cell density does not discriminate between response groups. However, the Weibull SR metrics of CD8+ T cells or macrophages to their closest cancer cell positively associate with response. CD8+ T cells close to B cells are characteristic of non-response. We validate our SR response associations in a combination ICI cohort of head and neck tumors. Our data confirm that SRs, in contrast to density metrics, are strong biomarkers of response to pre-operative combination ICIs.
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Affiliation(s)
- Alberto Gil-Jimenez
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Nick van Dijk
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joris L Vos
- Department of Head and Neck Surgery and Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Yoni Lubeck
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Dennis Peters
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Erik Hooijberg
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Charlotte L Zuur
- Department of Head and Neck Surgery and Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Otorhinolaryngology Head and Neck Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Bas W G van Rhijn
- Department of Urology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Urology, Caritas St. Josef Medical Centre, University of Regensburg, Regensburg, Germany
| | - Daniel J Vis
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Michiel S van der Heijden
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
- Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands.
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6
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Scheuermann S, Kristmann B, Engelmann F, Nuernbergk A, Scheuermann D, Koloseus M, Abed T, Solass W, Seitz CM. Unveiling spatial complexity in solid tumor immune microenvironments through multiplexed imaging. Front Immunol 2024; 15:1383932. [PMID: 38566984 PMCID: PMC10985204 DOI: 10.3389/fimmu.2024.1383932] [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: 02/08/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Deciphering cellular components and the spatial interaction network of the tumor immune microenvironment (TIME) of solid tumors is pivotal for understanding biologically relevant cross-talks and, ultimately, advancing therapies. Multiplexed tissue imaging provides a powerful tool to elucidate spatial complexity in a holistic manner. We established and cross-validated a comprehensive immunophenotyping panel comprising over 121 markers for multiplexed tissue imaging using MACSima™ imaging cyclic staining (MICS) alongside an end-to-end analysis workflow. Applying this panel and workflow to primary cancer tissues, we characterized tumor heterogeneity, investigated potential therapeutical targets, conducted in-depth profiling of cell types and states, sub-phenotyped T cells within the TIME, and scrutinized cellular neighborhoods of diverse T cell subsets. Our findings highlight the advantage of spatial profiling, revealing immunosuppressive molecular signatures of tumor-associated myeloid cells interacting with neighboring exhausted, PD1high T cells in the TIME of hepatocellular carcinoma (HCC). This study establishes a robust framework for spatial exploration of TIMEs in solid tumors and underscores the potency of multiplexed tissue imaging and ultra-deep cell phenotyping in unraveling clinically relevant tumor components.
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Affiliation(s)
- Sophia Scheuermann
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
- iFIT Cluster of Excellence EXC 2180 ‘Image-Guided and Functionally Instructed Tumor Therapies’, University of Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK), partner site Tuebingen, a partnership between German Cancer Research Center (DKFZ) and University Hospital Tuebingen, Tuebingen, Germany
| | - Beate Kristmann
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
| | - Fabienne Engelmann
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
| | - Alice Nuernbergk
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
| | - David Scheuermann
- School of Business and Economics, Faculty of Economics and Social Sciences, University of Tuebingen, Tuebingen, Germany
| | - Marie Koloseus
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
| | - Tayeb Abed
- Institute of Pathology and Neuropathology, University Hospital Tuebingen and Comprehensive Cancer Center, Tuebingen, Germany
| | - Wiebke Solass
- Institute of Tissue Medicine and Pathology (ITMP), University of Bern, Bern, Switzerland
| | - Christian M. Seitz
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
- iFIT Cluster of Excellence EXC 2180 ‘Image-Guided and Functionally Instructed Tumor Therapies’, University of Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK), partner site Tuebingen, a partnership between German Cancer Research Center (DKFZ) and University Hospital Tuebingen, Tuebingen, Germany
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7
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Jahangir CA, Page DB, Broeckx G, Gonzalez CA, Burke C, Murphy C, Reis-Filho JS, Ly A, Harms PW, Gupta RR, Vieth M, Hida AI, Kahila M, Kos Z, van Diest PJ, Verbandt S, Thagaard J, Khiroya R, Abduljabbar K, Haab GA, Acs B, Adams S, Almeida JS, Alvarado-Cabrero I, Azmoudeh-Ardalan F, Badve S, Baharun NB, Bellolio ER, Bheemaraju V, Blenman KRM, Fujimoto LBM, Burgues O, Chardas A, Cheang MCU, Ciompi F, Cooper LAD, Coosemans A, Corredor G, Portela FLD, Deman F, Demaria S, Dudgeon SN, Elghazawy M, Fernandez-Martín C, Fineberg S, Fox SB, Giltnane JM, Gnjatic S, Gonzalez-Ericsson PI, Grigoriadis A, Halama N, Hanna MG, Harbhajanka A, Hart SN, Hartman J, Hewitt S, Horlings HM, Husain Z, Irshad S, Janssen EAM, Kataoka TR, Kawaguchi K, Khramtsov AI, Kiraz U, Kirtani P, Kodach LL, Korski K, Akturk G, Scott E, Kovács A, Lænkholm AV, Lang-Schwarz C, Larsimont D, Lennerz JK, Lerousseau M, Li X, Madabhushi A, Maley SK, Narasimhamurthy VM, Marks DK, McDonald ES, Mehrotra R, Michiels S, Kharidehal D, Minhas FUAA, Mittal S, Moore DA, Mushtaq S, Nighat H, Papathomas T, Penault-Llorca F, Perera RD, Pinard CJ, Pinto-Cardenas JC, Pruneri G, Pusztai L, Rajpoot NM, Rapoport BL, Rau TT, Ribeiro JM, Rimm D, Vincent-Salomon A, Saltz J, Sayed S, Hytopoulos E, Mahon S, Siziopikou KP, Sotiriou C, Stenzinger A, Sughayer MA, Sur D, Symmans F, Tanaka S, Taxter T, Tejpar S, Teuwen J, Thompson EA, Tramm T, Tran WT, van der Laak J, Verghese GE, Viale G, Wahab N, Walter T, Waumans Y, Wen HY, Yang W, Yuan Y, Bartlett J, Loibl S, Denkert C, Savas P, Loi S, Stovgaard ES, Salgado R, Gallagher WM, Rahman A. Image-based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno-oncology Biomarker Working Group on Breast Cancer. J Pathol 2024; 262:271-288. [PMID: 38230434 PMCID: PMC11288342 DOI: 10.1002/path.6238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/17/2023] [Indexed: 01/18/2024]
Abstract
Recent advances in the field of immuno-oncology have brought transformative changes in the management of cancer patients. The immune profile of tumours has been found to have key value in predicting disease prognosis and treatment response in various cancers. Multiplex immunohistochemistry and immunofluorescence have emerged as potent tools for the simultaneous detection of multiple protein biomarkers in a single tissue section, thereby expanding opportunities for molecular and immune profiling while preserving tissue samples. By establishing the phenotype of individual tumour cells when distributed within a mixed cell population, the identification of clinically relevant biomarkers with high-throughput multiplex immunophenotyping of tumour samples has great potential to guide appropriate treatment choices. Moreover, the emergence of novel multi-marker imaging approaches can now provide unprecedented insights into the tumour microenvironment, including the potential interplay between various cell types. However, there are significant challenges to widespread integration of these technologies in daily research and clinical practice. This review addresses the challenges and potential solutions within a structured framework of action from a regulatory and clinical trial perspective. New developments within the field of immunophenotyping using multiplexed tissue imaging platforms and associated digital pathology are also described, with a specific focus on translational implications across different subtypes of cancer. © 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)
- Chowdhury Arif Jahangir
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - David B Page
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - Glenn Broeckx
- Department of Pathology PA, GZA-ZNA Hospitals, Antwerp, Belgium
- Centre for Oncological Research (CORE), MIPPRO, Faculty of Medicine, Antwerp University, Antwerp, Belgium
| | - Claudia A Gonzalez
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Caoimbhe Burke
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Clodagh Murphy
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amy Ly
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Paul W Harms
- Departments of Pathology and Dermatology, University of Michigan, Ann Arbor, Ml, USA
| | - Rajarsi R Gupta
- Department of Biomedical informatics, Stony Brook University, Stony Brook, NY, USA
| | - Michael Vieth
- Institute of Pathology, Klinikum Bayreuth GmbH, Friedrich-Alexander-University Erlangen-Nuremberg, Bayreuth, Germany
| | - Akira I Hida
- Department of Pathology, Matsuyama Shimin Hospital, Matsuyama, Japan
| | - Mohamed Kahila
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Zuzana Kos
- Department of Pathology and Laboratory Medicine, University of British Columbia, BC Cancer, Vancouver, British Columbia, Canada
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
- Johns Hopkins Oncology Center, Baltimore, MD, USA
| | - Sara Verbandt
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jeppe Thagaard
- Technical University of Denmark, Kgs. Lyngby, Denmark
- Visiopharm A/S, Hørsholm, Denmark
| | - Reena Khiroya
- Department of Cellular Pathology, University College Hospital, London, UK
| | - Khalid Abduljabbar
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | | | - Balazs Acs
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Sylvia Adams
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, Manhattan, NY, USA
| | - Jonas S Almeida
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), Rockville, MD, USA
| | | | | | - Sunil Badve
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory University Winship Cancer Institute, Atlanta, GA, USA
| | | | - Enrique R Bellolio
- Departamento de Anatomía Patológica, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | | | - Kim RM Blenman
- Department of internal Medicine Section of Medical Oncology and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Computer Science, Yale School of Engineering and Applied Science, New Haven, CT, USA
| | | | - Octavio Burgues
- Pathology Department, Hospital Cliníco Universitario de Valencia/lncliva, Valencia, Spain
| | - Alexandros Chardas
- Department of Pathobiology & Population Sciences, The Royal Veterinary College, London, UK
| | - Maggie Chon U Cheang
- Head of Integrative Genomics Analysis in Clinical Trials, ICR-CTSU, Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Francesco Ciompi
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lee AD Cooper
- Department of Pathology, Northwestern Feinberg School of Medicine, Chicago, IL, USA
| | - An Coosemans
- Department of Oncology, Laboratory of Tumor Immunology and Immunotherapy, KU Leuven, Leuven, Belgium
| | - Germán Corredor
- Biomedical Engineering Department, Emory University, Atlanta, GA, USA
| | | | - Frederik Deman
- Department of Pathology PA, GZA-ZNA Hospitals, Antwerp, Belgium
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Department of Pathology, Weill Cornell Medicine, New York NY, USA
| | - Sarah N Dudgeon
- Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Mahmoud Elghazawy
- University of Surrey, Guildford, UK
- Ain Shams University, Cairo, Egypt
| | - Claudio Fernandez-Martín
- Institute Universitario de Investigatión en Tecnología Centrada en el Ser Humano, HUMAN-tech, Universitat Politècnica de València, Valencia, Spain
| | - Susan Fineberg
- Montefiore Medical Center and the Albert Einstein College of Medicine, New York, NY, USA
| | - Stephen B Fox
- Pathology, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Sacha Gnjatic
- Department of Oncological Sciences, Medicine Hem/One, and Pathology, Tisch Cancer Institute – Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | | | - Anita Grigoriadis
- Cancer Bioinformatics, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, King’s College London, London, UK
- The Breast Cancer Now Research Unit Faculty of Life Sciences and Medicine, School of Cancer and Pharmaceutical Sciences, King’s College London, London, UK
| | - Niels Halama
- Department of Translational Immunotherapy, German Cancer Research Center, Heidelberg, Germany
| | | | | | - Steven N Hart
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Johan Hartman
- Tehran University of Medical Sciences, Tehran, Iran
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Stephen Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hugo M Horlings
- Division of Pathology, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | | | - Sheeba Irshad
- King's College London & Guys & St Thomas NHS Trust London, UK
| | - Emiel AM Janssen
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
| | | | - Kosuke Kawaguchi
- Department of Breast Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Andrey I Khramtsov
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA
| | - Umay Kiraz
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
| | - Pawan Kirtani
- Histopathology, Aakash Healthcare Super Speciality Hospital, New Delhi, India
| | - Liudmila L Kodach
- Department of Pathology, Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Konstanty Korski
- Data, Analytics and Imaging, Product Development, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Guray Akturk
- Translational Molecular Biomarkers, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Ely Scott
- Translational Medicine, Bristol Myers Squibb, Princeton, NJ, USA
| | - Anikó Kovács
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anne-Vibeke Lænkholm
- Department of Surgical Pathology, Zealand University Hospital, Roskilde, Denmark
- Department of Surgical Pathology, University of Copenhagen, Copenhagen, Denmark
| | - Corinna Lang-Schwarz
- Institute of Pathology, Klinikum Bayreuth GmbH, Friedrich-Alexander-University Erlangen-Nuremberg, Bayreuth, Germany
| | - Denis Larsimont
- Institut Jules Bordet Université Libre de Bruxelles, Brussels, Belgium
| | - Jochen K Lennerz
- Center for Integrated Diagnostics, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Marvin Lerousseau
- Centre for Computational Biology (CBIO), Mines Paris, PSL University, Paris, France
- Institut Curie, PSL University, Paris, France
- INSERM U900, Paris, France
| | - Xiaoxian Li
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Anant Madabhushi
- Department of Biomedical Engineering, Radiology and Imaging Sciences, Biomedical Informatics, Pathology, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Sai K Maley
- NRG Oncology/NSABP Foundation, Pittsburgh, PA, USA
| | | | - Douglas K Marks
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Elizabeth S McDonald
- Breast Cancer Translational Research Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Ravi Mehrotra
- Indian Cancer Genomic Atlas, Pune, India
- Centre for Health, Innovation and Policy Foundation, Noida, India
| | - Stefan Michiels
- Office of Biostatistics and Epidemiology, Gustave Roussy, Oncostat U1018, Inserm, University Paris-Saclay, Ligue Contre le Cancer labeled Team, Villejuif France
| | - Durga Kharidehal
- Department of Pathology, Narayana Medical College and Hospital, Nellore, India
| | - Fayyaz ul Amir Afsar Minhas
- Tissue Image Analytics Centre, Warwick Cancer Research Centre, PathLAKE Consortium, Department of Computer Science, University of Warwick, Coventry, UK
| | - Shachi Mittal
- Department of Chemical Engineering, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - David A Moore
- CRUK Lung Cancer Centre of Excellence, UCL and Cellular Pathology Department UCLH, London, UK
| | - Shamim Mushtaq
- Department of Biochemistry, Ziauddin University, Karachi, Pakistan
| | - Hussain Nighat
- Pathology and Laboratory Medicine, All India Institute of Medical Sciences, Raipur, India
| | - Thomas Papathomas
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
- Department of Clinical Pathology, Drammen Sykehus, Vestre Viken HF, Drammen, Norway
| | - Frederique Penault-Llorca
- Service de Pathologie et Biopathologie, Centre Jean PERRIN, INSERM U1240 Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Rashindrie D Perera
- School of Electrical, Mechanical and Infrastructure Engineering, University of Melbourne, Melbourne, Victoria, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Christopher J Pinard
- Radiogenomics Laboratory, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- Department of Oncology, Lakeshore Animal Health Partners, Mississauga, Ontario, Canada
- Centre for Advancing Responsible and Ethical Artificial Intelligence (CARE-AI), University of Guelph, Guelph, Ontario, Canada
| | | | - Giancarlo Pruneri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Faculty of Medicine and Surgery, University of Milan, Milan, Italy
| | - Lajos Pusztai
- Yale Cancer Center, Yale University, New Haven, CT, USA
- Department of Medical Oncology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | | | - Bernardo Leon Rapoport
- The Medical Oncology Centre of Rosebank Johannesburg South Africa
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Tilman T Rau
- Institute of Pathology, University Hospital Düsseldorf and Heinrich-Heine-University, Düsseldorf Germany
| | | | - David Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Anne Vincent-Salomon
- Department of Diagnostic and Theranostic Medicine, Institut Curie, University Paris-Sciences et Lettres, Paris, France
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook Medicine, New York NY, USA
| | - Shahin Sayed
- Department of Pathology, Aga Khan University, Nairobi, Kenya
| | - Evangelos Hytopoulos
- Department of Pathology, Aga Khan University, Nairobi, Kenya
- iRhythm Technologies Inc., San Francisco, CA, USA
| | - Sarah Mahon
- Mater Misericordiae University Hospital, Dublin, Ireland
| | - Kalliopi P Siziopikou
- Department of Pathology, Section of Breast Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory J.-C. Heuson, Institut Jules Bordet Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium
- Medical Oncology Department Institut Jules Bordet Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Centers for Personalized Medicine (ZPM), Heidelberg, Germany
| | | | - Daniel Sur
- Department of Medical Oncology, University of Medicine and Pharmacy “luliu Hatieganu ”, Cluj-Napoca, Romania
| | - Fraser Symmans
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Sabine Tejpar
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jonas Teuwen
- Al for Oncology Lab, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Trine Tramm
- Department of Pathology, Institute of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - William T Tran
- Department of Radiation Oncology, University of Toronto and Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Jeroen van der Laak
- Head of Integrative Genomics Analysis in Clinical Trials, ICR-CTSU, Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Gregory E Verghese
- Cancer Bioinformatics, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, King’s College London, London, UK
- The Breast Cancer Now Research Unit Faculty of Life Sciences and Medicine, School of Cancer and Pharmaceutical Sciences, King’s College London, London, UK
| | - Giuseppe Viale
- Department of Pathology, European Institute of Oncology & University of Milan, Milan, Italy
| | - Noorul Wahab
- Tissue Image Analytics Centre, Department of Computer Science, University of Wanwick Coventry, UK
| | - Thomas Walter
- Centre for Computational Biology (CBIO), Mines Paris, PSL University, Paris, France
- Institut Curie, PSL University, Paris, France
- INSERM U900, Paris, France
| | | | - Hannah Y Wen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wentao Yang
- Fudan Medical University Shanghai Cancer Center, Shanghai, PR China
| | - Yinyin Yuan
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Sibylle Loibl
- Department of Medicine and Research, German Breast Group, Neu-lsenburg Germany
| | - Carsten Denkert
- Institut für Pathologie, Philipps-Universität Marburg und Universitätsklinikum Marburg, Marburg, Germany
| | - Peter Savas
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sherene Loi
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Roberto Salgado
- Department of Pathology PA, GZA-ZNA Hospitals, Antwerp, Belgium
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - William M Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Arman Rahman
- UCD School of Medicine, UCD Conway Institute, University College Dublin, Dublin, Ireland
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8
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Kim MK, Park J, Tak S, Paek K, Bang G, Woo SM, Ravichandran NK, Hong WG, Kang HW, Kim H, Bae JY, Kim JA. A long-term storable gel-laden chip composite built in a multi-well plate enabling in situcell encapsulation for high-throughput liver model. Biofabrication 2024; 16:025020. [PMID: 38390723 DOI: 10.1088/1758-5090/ad28ef] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
Hydrogels are widely used as scaffold materials for constructingin vitrothree-dimensional microphysiological systems. However, their high sensitivity to various external cues hinders the development of hydrogel-laden, microscale, and high-throughput chips. Here, we have developed a long-term storable gel-laden chip composite built in a multi-well plate, which enablesin situcell encapsulation and facilitates high-throughput analysis. Through optimized chemical crosslinking and freeze-drying method (C/FD), we have achieved a high-quality of gel-laden chip composite with excellent transparency, uniform porosity, and appropriate swelling and mechanical characteristics. Besides collagen, decellularized extracellular matrix with tissue-specific biochemical compound has been applied as chip composite. As a ready-to-use platform,in situcell encapsulation within the gel has been achieved through capillary force generated during gel reswelling. The liver-mimetic chip composite, comprising HepG2 cells or primary hepatocytes, has demonstrated favorable hepatic functionality and high sensitivity in drug testing. The developed fabrication process with improved stability of gels and storability allows chip composites to be stored at a wide range of temperatures for up to 28 d without any deformation, demonstrating off-the-shelf products. Consequently, this provides an exceptionally simple and long-term storable platform that can be utilized for an efficient tissue-specific modeling and various biomedical applications.
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Affiliation(s)
- Min Kyeong Kim
- Center for Scientific Instrumentation, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
| | - Jubin Park
- Center for Scientific Instrumentation, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
- Program in Biomicro System Technology, Korea University, Seoul 02841, Republic of Korea
| | - Sungho Tak
- Center for Bio-Imaging and Translational Research, Korea Basic Science Institute, Cheongju 28119, Chungbuk, Republic of Korea
| | - Kyurim Paek
- Center for Scientific Instrumentation, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
- Program in Biomicro System Technology, Korea University, Seoul 02841, Republic of Korea
| | - Geul Bang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Chungbuk, Republic of Korea
| | - Sang-Mi Woo
- Center for Scientific Instrumentation, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
| | - Naresh Kumar Ravichandran
- Center for Scientific Instrumentation, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
| | - Won Gi Hong
- Research Center for Materials Analysis, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
| | - Hyun-Wook Kang
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulju-gun 44919, Ulsan, Republic of Korea
| | - Hyang Kim
- Institute of New Horizon Regenerative Medicine, Myongji Hospital, Goyang 10475, Republic of Korea
| | - Ji Yong Bae
- Center for Scientific Instrumentation, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
| | - Jeong Ah Kim
- Center for Scientific Instrumentation, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
- Department of Bio-Analytical Science, University of Science and Technology, Daejeon 34113, Republic of Korea
- Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
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9
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Schwarze S, Schaadt NS, Sobotta VMG, Spicher N, Skripuletz T, Esmaeilzadeh M, Krauss JK, Hartmann C, Deserno TM, Feuerhake F. Task design for crowdsourced glioma cell annotation in microscopy images. Sci Rep 2024; 14:1965. [PMID: 38263411 PMCID: PMC10805723 DOI: 10.1038/s41598-024-51995-8] [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: 09/06/2023] [Accepted: 01/12/2024] [Indexed: 01/25/2024] Open
Abstract
Crowdsourcing has been used in computational pathology to generate cell and cell nuclei annotations for machine learning. Herein, we broaden its scope to the previously unsolved challenging task of glioma cell detection. This requires multiplexed immunofluorescence microscopy due to diffuse invasiveness and exceptional similarity between glioma cells and reactive astrocytes. In four pilot experiments, we iteratively developed a task design enabling high-quality annotations by crowdworkers on Amazon Mechanical Turk. We applied majority or weighted vote and validated them against ground truth in the final setting. On the base of a YOLO convolutional neural network architecture, we used these consensus labels for training with different image representations regarding colors, intensities, and immmunohistochemical marker combinations. A crowd of 712 workers defined aggregated point annotations in 235 images with an average [Formula: see text] score of 0.627 for majority vote. The networks resulted in acceptable [Formula: see text] scores up to 0.69 for YOLOv8 on average and indicated first evidence for transferability to images lacking tumor markers, especially in IDH-wildtype glioblastoma. Our work confirms feasibility of crowdsourcing to generate labels suitable for training of machine learning tools in the challenging and clinically relevant use case of glioma microenvironment.
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Affiliation(s)
- Svea Schwarze
- Department of Neuropathology, Institute for Pathology, Hannover Medical School, Hannover, Germany
| | - Nadine S Schaadt
- Department of Neuropathology, Institute for Pathology, Hannover Medical School, Hannover, Germany
| | - Viktor M G Sobotta
- Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Braunschweig, Germany
| | - Nicolai Spicher
- Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Braunschweig, Germany
| | | | | | - Joachim K Krauss
- Department of Neurosurgery, Hannover Medical School, Hannover, Germany
| | - Christian Hartmann
- Department of Neuropathology, Institute for Pathology, Hannover Medical School, Hannover, Germany
| | - Thomas M Deserno
- Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Braunschweig, Germany
| | - Friedrich Feuerhake
- Department of Neuropathology, Institute for Pathology, Hannover Medical School, Hannover, Germany.
- Institute of Neuropathology, University Clinic Freiburg, Freiburg, Germany.
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10
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Ionescu F, Nguyen J, Segura CM, Paravathaneni M, Grass GD, Johnstone P, Zacharias NM, Pettaway CA, Lu X, Kim Y, Whiting J, Dhillon J, Eschrich SA, Chadha J, Gullapalli K, Roman Souza G, Miyagi H, Manley BJ, Spiess PE, Chahoud J. Multiplex Immunofluorescence Captures Progressive Immune Exhaustion with Advancing Penile Squamous Cell Cancer Stage. Cancers (Basel) 2024; 16:303. [PMID: 38275860 PMCID: PMC10814242 DOI: 10.3390/cancers16020303] [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: 12/04/2023] [Revised: 12/25/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
Penile squamous cell carcinoma (PSCC) is a rare and deadly malignancy. Therapeutic advances have been stifled by a poor understanding of disease biology. Specifically, the immune microenvironment is an underexplored component in PSCC and the activity of immune checkpoint inhibitors observed in a subset of patients suggests immune escape may play an important role in tumorigenesis. Herein, we explored for the first time the immune microenvironment of 57 men with PSCC and how it varies with the presence of human papillomavirus (HPV) infection and across tumor stages using multiplex immunofluorescence of key immune cell markers. We observed an increase in the density of immune effector cells in node-negative tumors and a progressive rise in inhibitory immune players such as type 2 macrophages and upregulation of the PD-L1 checkpoint in men with N1 and N2-3 disease. There were no differences in immune cell densities with HPV status.
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Affiliation(s)
- Filip Ionescu
- Genitourinary Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (F.I.); (M.P.); (J.C.); (P.E.S.)
| | - Jonathan Nguyen
- Pathology Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | | | - Mahati Paravathaneni
- Genitourinary Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (F.I.); (M.P.); (J.C.); (P.E.S.)
| | - G. Daniel Grass
- Radiation Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Peter Johnstone
- Radiation Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Niki M. Zacharias
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Curtis A. Pettaway
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xin Lu
- Department of Biological Sciences, University of Notre Dame, Norte Dame, IN 46556, USA;
| | - Youngchul Kim
- Biostatistics and Bioinformatics Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Junmin Whiting
- Biostatistics and Bioinformatics Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Jasreman Dhillon
- Pathology Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Steven A. Eschrich
- Biostatistics and Bioinformatics Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Juskaran Chadha
- Genitourinary Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (F.I.); (M.P.); (J.C.); (P.E.S.)
| | - Keerthi Gullapalli
- Genitourinary Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (F.I.); (M.P.); (J.C.); (P.E.S.)
| | - Gabriel Roman Souza
- Genitourinary Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (F.I.); (M.P.); (J.C.); (P.E.S.)
| | - Hiroko Miyagi
- Genitourinary Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (F.I.); (M.P.); (J.C.); (P.E.S.)
| | - Brandon J. Manley
- Genitourinary Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (F.I.); (M.P.); (J.C.); (P.E.S.)
| | - Philippe E. Spiess
- Genitourinary Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (F.I.); (M.P.); (J.C.); (P.E.S.)
| | - Jad Chahoud
- Genitourinary Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (F.I.); (M.P.); (J.C.); (P.E.S.)
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11
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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] [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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12
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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] [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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13
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Sereda S, Shankar A, Weber L, Ramsay AD, Hall GW, Hayward J, Wallace WHB, Landman-Parker J, Braeuninger A, Hasenclever D, Schneider A, Mauz-Koerholz C, Koerholz D, Gattenloehner S. Digital pathology in pediatric nodular lymphocyte-predominant Hodgkin lymphoma: correlation with treatment response. Blood Adv 2023; 7:6285-6289. [PMID: 37611165 PMCID: PMC10589766 DOI: 10.1182/bloodadvances.2023010652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/04/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023] Open
Affiliation(s)
- Sergej Sereda
- Department of Pathology, University Hospital Giessen and Marburg GmbH, Giessen, Germany
| | - Ananth Shankar
- Children and Young People’s Cancer Services, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Luise Weber
- Department of Pathology, University Hospital Giessen and Marburg GmbH, Giessen, Germany
| | - Alan D. Ramsay
- Department of Cellular Pathology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Georgina W. Hall
- Paediatric and Adolescent Haematology & Oncology Unit, Children’s Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Janis Hayward
- School of Cancer Sciences, Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, United Kingdom
| | | | - Judith Landman-Parker
- Sorbonne University, Assistance Publique–Hôpitaux de Paris, Hôpital Armand-Trousseau, Paris, France
| | - Andreas Braeuninger
- Department of Pathology, University Hospital Giessen and Marburg GmbH, Giessen, Germany
| | - Dirk Hasenclever
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Astrid Schneider
- Pediatric Hematology and Oncology, University Hospital Giessen and Marburg GmbH, Giessen, Germany
| | - Christine Mauz-Koerholz
- Pediatric Hematology and Oncology, University Hospital Giessen and Marburg GmbH, Giessen, Germany
- Medical Faculty of the Martin-Luther-University of Halle-Wittenberg, Halle, Germany
| | - Dieter Koerholz
- Pediatric Hematology and Oncology, University Hospital Giessen and Marburg GmbH, Giessen, Germany
| | - Stefan Gattenloehner
- Department of Pathology, University Hospital Giessen and Marburg GmbH, Giessen, Germany
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14
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Khanduri I, Maru DM, Parra ER. Exploratory study of macrophage polarization and spatial distribution in colorectal cancer liver metastasis: a pilot study. Front Immunol 2023; 14:1223864. [PMID: 37637998 PMCID: PMC10449458 DOI: 10.3389/fimmu.2023.1223864] [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: 05/18/2023] [Accepted: 07/27/2023] [Indexed: 08/29/2023] Open
Abstract
Background The liver is the most typical site of metastatic disease for patients with colorectal cancer (CRC), and up to half the patients with CRC will develop colorectal liver metastasis (CLM). Studying the tumor microenvironment, particularly macrophages and their spatial distribution, can give us critical insight into treatment. Methods Ten CLMs (five treatment-naïve and five post-neoadjuvant chemotherapy) were stained with multiplex immunofluorescence panels against cytokeratins, CD68, Arg1, CD206, CD86, CD163, PD-L1, and MRP8-14. Densities of cell phenotypes and their spatial distribution in the tumor center and the normal liver-tumor interface were correlated with clinicopathological variables. Results M2 macrophages were the predominant subtype in both the tumor center and the periphery, with a relatively higher density at the periphery. The larger tumors, more than 3.9 cm, were associated with higher densities of total CD68+ macrophages and CD68+CD163+ CD206neg and CD68+CD206+ CD163neg M2 macrophage subtypes. Total macrophages in the tumor periphery demonstrated significantly greater proximity to malignant cells than did those in the tumor center (p=0.0371). The presence of higher than median CD68+MRP8-14+CD86neg M1 macrophages in the tumor center was associated with poor overall survival (median 2.34 years) compared to cases with lower than median M1 macrophages at the tumor center (median 6.41 years) in univariate analysis. Conclusion The dominant polarization of the M2 macrophage subtype could drive new therapeutic approaches in CLM patients.
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Affiliation(s)
- Isha Khanduri
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Dipen M. Maru
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Edwin R. Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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15
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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: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [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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16
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Locke D, Hoyt CC. Companion diagnostic requirements for spatial biology using multiplex immunofluorescence and multispectral imaging. Front Mol Biosci 2023; 10:1051491. [PMID: 36845550 PMCID: PMC9948403 DOI: 10.3389/fmolb.2023.1051491] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Immunohistochemistry has long been held as the gold standard for understanding the expression patterns of therapeutically relevant proteins to identify prognostic and predictive biomarkers. Patient selection for targeted therapy in oncology has successfully relied upon standard microscopy-based methodologies, such as single-marker brightfield chromogenic immunohistochemistry. As promising as these results are, the analysis of one protein, with few exceptions, no longer provides enough information to draw effective conclusions about the probability of treatment response. More multifaceted scientific queries have driven the development of high-throughput and high-order technologies to interrogate biomarker expression patterns and spatial interactions between cell phenotypes in the tumor microenvironment. Such multi-parameter data analysis has been historically reserved for technologies that lack the spatial context that is provided by immunohistochemistry. Over the past decade, technical developments in multiplex fluorescence immunohistochemistry and discoveries made with improving image data analysis platforms have highlighted the importance of spatial relationships between certain biomarkers in understanding a patient's likelihood to respond to, typically, immune checkpoint inhibitors. At the same time, personalized medicine has instigated changes in both clinical trial design and its conduct in a push to make drug development and cancer treatment more efficient, precise, and economical. Precision medicine in immuno-oncology is being steered by data-driven approaches to gain insight into the tumor and its dynamic interaction with the immune system. This is particularly necessary given the rapid growth in the number of trials involving more than one immune checkpoint drug, and/or using those in combination with conventional cancer treatments. As multiplex methods, like immunofluorescence, push the boundaries of immunohistochemistry, it becomes critical to understand the foundation of this technology and how it can be deployed for use as a regulated test to identify the prospect of response from mono- and combination therapies. To that end, this work will focus on: 1) the scientific, clinical, and economic requirements for developing clinical multiplex immunofluorescence assays; 2) the attributes of the Akoya Phenoptics workflow to support predictive tests, including design principles, verification, and validation needs; 3) regulatory, safety and quality considerations; 4) application of multiplex immunohistochemistry through lab-developed-tests and regulated in vitro diagnostic devices.
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Affiliation(s)
- Darren Locke
- Clinical Assay Development, Akoya Biosciences, Marlborough, MA, United States,*Correspondence: Darren Locke,
| | - Clifford C. Hoyt
- Translational and Scientific Affairs, Akoya Biosciences, Marlborough, MA, United States
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17
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Wisniewski L, Braak S, Klamer Z, Gao C, Shi C, Allen P, Haab BB. Heterogeneity of Glycan Biomarker Clusters as an Indicator of Recurrence in Pancreatic Cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522607. [PMID: 36711795 PMCID: PMC9881915 DOI: 10.1101/2023.01.05.522607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Outcomes following tumor resection vary dramatically among patients with pancreatic cancer. A challenge in defining predictive biomarkers is to discern within the complex tumor tissue the specific subpopulations and relationships that drive recurrence. Multiplexed immunofluorescence is valuable for such studies when supplied with markers of relevant subpopulations and analysis methods to sort out the intra-tumor relationships that are informative of tumor behavior. We hypothesized that the glycan biomarkers CA19-9 and STRA, which detect separate subpopulations of cancer cells, define intra-tumoral features associated with recurrence. We probed this question using automated signal thresholding and spatial cluster analysis applied to the immunofluorescence images of the STRA and CA19-9 glycan biomarkers in whole-block tumor sections. The tumors (N = 22) displayed extreme diversity between them in the amounts of the glycans and in the levels of spatial clustering, but neither the amounts nor the clusters of the individual and combined glycans associated with recurrence. The combined glycans, however, marked divergent types of spatial clusters, alternatively only STRA, only CA19-9, or both. The co-occurrence of more than one cluster type within a tumor associated significantly with disease recurrence, in contrast to the independent occurrence of each type of cluster. In addition, intra-tumoral regions with heterogeneity in biomarker clusters spatially aligned with pathology-confirmed cancer cells, whereas regions with homogeneous biomarker clusters aligned with various non-cancer cells. Thus, the STRA and CA19-9 glycans are markers of distinct and co-occurring subpopulations of cancer cells that in combination are associated with recurrence. Furthermore, automated signal thresholding and spatial clustering provides a tool for quantifying intra-tumoral subpopulations that are informative of outcome.
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18
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Wisniewski L, Braak S, Klamer Z, Gao C, Shi C, Allen P, Haab BB. Heterogeneity of glycan biomarker clusters as an indicator of recurrence in pancreatic cancer. Front Oncol 2023; 13:1135405. [PMID: 37124496 PMCID: PMC10130372 DOI: 10.3389/fonc.2023.1135405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/17/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Outcomes following tumor resection vary dramatically among patients with pancreatic ductal adenocarcinoma (PDAC). A challenge in defining predictive biomarkers is to discern within the complex tumor tissue the specific subpopulations and relationships that drive recurrence. Multiplexed immunofluorescence is valuable for such studies when supplied with markers of relevant subpopulations and analysis methods to sort out the intra-tumor relationships that are informative of tumor behavior. We hypothesized that the glycan biomarkers CA19-9 and STRA, which detect separate subpopulations of cancer cells, define intra-tumoral features associated with recurrence. Methods We probed this question using automated signal thresholding and spatial cluster analysis applied to the immunofluorescence images of the STRA and CA19-9 glycan biomarkers in whole-block sections of PDAC tumors collected from curative resections. Results The tumors (N = 22) displayed extreme diversity between them in the amounts of the glycans and in the levels of spatial clustering, but neither the amounts nor the clusters of the individual and combined glycans associated with recurrence. The combined glycans, however, marked divergent types of spatial clusters, alternatively only STRA, only CA19-9, or both. The co-occurrence of more than one cluster type within a tumor associated significantly with disease recurrence, in contrast to the independent occurrence of each type of cluster. In addition, intra-tumoral regions with heterogeneity in biomarker clusters spatially aligned with pathology-confirmed cancer cells, whereas regions with homogeneous biomarker clusters aligned with various non-cancer cells. Conclusion Thus, the STRA and CA19-9 glycans are markers of distinct and co-occurring subpopulations of cancer cells that in combination are associated with recurrence. Furthermore, automated signal thresholding and spatial clustering provides a tool for quantifying intra-tumoral subpopulations that are informative of outcome.
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Affiliation(s)
- Luke Wisniewski
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - Samuel Braak
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - Zachary Klamer
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - ChongFeng Gao
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - Chanjuan Shi
- Department of Pathology, Duke University School of Medicine, Durham, NC, United States
| | - Peter Allen
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Brian B. Haab
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, United States
- *Correspondence: Brian B. Haab,
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19
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Kuswanto W, Nolan G, Lu G. Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease. Semin Immunopathol 2023; 45:145-157. [PMID: 36414691 PMCID: PMC9684921 DOI: 10.1007/s00281-022-00974-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/06/2022] [Indexed: 11/23/2022]
Abstract
Multiplexed imaging, which enables spatial localization of proteins and RNA to cells within tissues, complements existing multi-omic technologies and has deepened our understanding of health and disease. CODEX, a multiplexed single-cell imaging technology, utilizes a microfluidics system that incorporates DNA barcoded antibodies to visualize 50 + cellular markers at the single-cell level. Here, we discuss the latest applications of CODEX to studies of cancer, autoimmunity, and infection as well as current bioinformatics approaches for analysis of multiplexed imaging data from preprocessing to cell segmentation and marker quantification to spatial analysis techniques. We conclude with a commentary on the challenges and future developments for multiplexed spatial profiling.
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Affiliation(s)
- Wilson Kuswanto
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, 94304, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Garry Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94304, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Guolan Lu
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94304, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94304, USA.
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, 94304, USA.
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20
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Antoranz A, Van Herck Y, Bolognesi MM, Lynch SM, Rahman A, Gallagher WM, Boecxstaens V, Marine JC, Cattoretti G, van den Oord JJ, De Smet F, Bechter O, Bosisio FM. Mapping the Immune Landscape in Metastatic Melanoma Reveals Localized Cell-Cell Interactions That Predict Immunotherapy Response. Cancer Res 2022; 82:3275-3290. [PMID: 35834277 PMCID: PMC9478533 DOI: 10.1158/0008-5472.can-22-0363] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/30/2022] [Accepted: 07/07/2022] [Indexed: 01/07/2023]
Abstract
While immune checkpoint-based immunotherapy (ICI) shows promising clinical results in patients with cancer, only a subset of patients responds favorably. Response to ICI is dictated by complex networks of cellular interactions between malignant and nonmalignant cells. Although insights into the mechanisms that modulate the pivotal antitumoral activity of cytotoxic T cells (Tcy) have recently been gained, much of what has been learned is based on single-cell analyses of dissociated tumor samples, resulting in a lack of critical information about the spatial distribution of relevant cell types. Here, we used multiplexed IHC to spatially characterize the immune landscape of metastatic melanoma from responders and nonresponders to ICI. Such high-dimensional pathology maps showed that Tcy gradually evolve toward an exhausted phenotype as they approach and infiltrate the tumor. Moreover, a key cellular interaction network functionally linked Tcy and PD-L1+ macrophages. Mapping the respective spatial distributions of these two cell populations predicted response to anti-PD-1 immunotherapy with high confidence. These results suggest that baseline measurements of the spatial context should be integrated in the design of predictive biomarkers to identify patients likely to benefit from ICI. SIGNIFICANCE This study shows that spatial characterization can address the challenge of finding efficient biomarkers, revealing that localization of macrophages and T cells in melanoma predicts patient response to ICI. See related commentary by Smalley and Smalley, p. 3198.
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Affiliation(s)
- Asier Antoranz
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Belgium, Leuven
| | - Yannick Van Herck
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Belgium, Leuven
| | - Maddalena M. Bolognesi
- Pathology, Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Seodhna M. Lynch
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Arman Rahman
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - William M. Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Veerle Boecxstaens
- Department of Surgical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB/KU Leuven Center for Cancer Biology, Leuven, Belgium.,Laboratory for Molecular Cancer Biology, Oncology Department, KU Leuven, Leuven, Belgium
| | - Giorgio Cattoretti
- Pathology, Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Joost J. van den Oord
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Belgium, Leuven
| | - Frederik De Smet
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Belgium, Leuven
| | - Oliver Bechter
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Belgium, Leuven
| | - Francesca M. Bosisio
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Belgium, Leuven.,Corresponding Author: Francesca M Bosisio, Laboratory of Translational Cell and Tissue Research, KU Leuven, Herestraat 49, Leuven 3000, Belgium. Phone: 321-632-9965; E-mail:
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21
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Marsh-Wakefield F, Ferguson AL, Liu K, Santhakumar C, McCaughan G, Palendira U. Approaches to spatially resolving the tumour immune microenvironment of hepatocellular carcinoma. Ther Adv Med Oncol 2022; 14:17588359221113270. [PMID: 35898965 PMCID: PMC9310213 DOI: 10.1177/17588359221113270] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/27/2022] [Indexed: 12/15/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a common and deadly cancer worldwide. Many factors contribute to mortality and place an individual at high risk of developing HCC, including viral infection, alcohol intake, metabolic-associated disease, autoimmunity and genetic liver disorders. Although there are many therapeutics available, much about this disease remains to be understood. This is most evident when investigating the tumour microenvironment (TME). Both innate and adaptive immune cells have been associated with carcinogenesis within the TME of HCC patients. The ability to interrogate the TME more thoroughly with spatial technologies continues to improve, both at the experimental and analytical stages. This review provides insight into technologies available to investigate the TME, and how such technologies are beneficial for improving our understanding of HCC carcinogenesis.
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Affiliation(s)
- Felix Marsh-Wakefield
- Liver Injury & Cancer Program, Centenary Institute, Royal Prince Alfred Hospital, Missenden Road, Sydney, NSW, 2050, Australia
| | - Angela L Ferguson
- Liver Injury & Cancer Program, Centenary Institute, Sydney, NSW, Australia
| | - Ken Liu
- Liver Injury & Cancer Program, Centenary Institute, Sydney, NSW, Australia
| | | | - Geoffrey McCaughan
- Liver Injury & Cancer Program, Centenary Institute, Sydney, NSW, Australia
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22
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Bright-Field Multiplex Immunohistochemistry Assay for Tumor Microenvironment Evaluation in Melanoma Tissues. Cancers (Basel) 2022; 14:cancers14153682. [PMID: 35954345 PMCID: PMC9367593 DOI: 10.3390/cancers14153682] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Bright-field (BF) immunohistochemistry (IHC) remains the gold standard for histopathological evaluations. The development of new BF multiplex IHC could be very useful for the study and characterization of the tumor microenvironment (TME) in melanoma samples. We herein compared different BF IHC multiplex protocols for the study of TME in primary cutaneous melanoma tissues and offered the best optimized protocol for visualization and evaluation. These methodologies are studied to maximize the quality of staining considering the tissue characteristics under examination, maintaining a high level of standardization and reproducibility. Abstract The tumor microenvironment (TME) plays a crucial role in melanoma development, progression and response to treatment. As many of the most relevant TME cell phenotypes are defined by the simultaneous detection of more than two markers, the bright-field (BF) multiplex immunohistochemistry (IHC) technique has been introduced for the quantitative assessment and evaluation of the relative spatial distances between immune cells and melanoma cells. In the current study, we aimed to validate BF multiplex IHC techniques in the Ventana Discovery Ultra Immunostainer to be applied to the evaluation of the TME in variably pigmented melanoma tissues. The BF multiplex IHC staining was performed using different combinations of six immune-cell markers—CD3, CD4, CD8, CD20, CD68 and CD163—and the melanoma cell marker SOX10. Our results show that the BF double IHC Yellow/Purple protocol guarantees the maximum contrast in all the cell populations tested and the combination SOX10 (Green), CD8 (Yellow) and CD163 (Purple) of the BF triple IHC protocol ensures the best contrast and discrimination between the three stained cell populations. Furthermore, the labeled cells were clearly distinct and easily identifiable using the image analysis software. Our standardized BF IHC multiplex protocols can be used to better assess the immune contexts of melanoma patients with potential applications to drive therapeutic decisions within clinical trials.
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23
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Casagrande N, Borghese C, Aldinucci D. Current and Emerging Approaches to Study Microenvironmental Interactions and Drug Activity in Classical Hodgkin Lymphoma. Cancers (Basel) 2022; 14:cancers14102427. [PMID: 35626032 PMCID: PMC9139207 DOI: 10.3390/cancers14102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary In classical Hodgkin Lymphoma (cHL), the tumor microenvironment (TME) plays an important role in tumor progression and treatment response, making its evaluation critical for determining prognosis, treatment strategies and predicting an increase in drug toxicity. Therefore, there is a need to utilize more complex systems to study the cHL-TME and its interplay with tumor cells. To evaluate new anticancer drugs and to find the mechanisms of drug resistance, this review summarizes emerging approaches for the analysis of the TME composition and to identify the state of the disease; the in vitro techniques used to determine the mechanisms involved in the building of an immunosuppressive and protective TME; new 3-dimensional (3D) models, the heterospheroids (HS), developed to mimic TME interactions. Here, we describe the present and likely future clinical applications indicated by the results of these studies and propose a classification for the in vitro culture methods used to study TME interactions in cHL. Abstract Classic Hodgkin lymphoma is characterized by a few tumor cells surrounded by a protective and immunosuppressive tumor microenvironment (TME) composed by a wide variety of noncancerous cells that are an active part of the disease. Therefore, new techniques to study the cHL-TME and new therapeutic strategies targeting specifically tumor cells, reactivating the antitumor immunity, counteracting the protective effects of the TME, were developed. Here, we describe new methods used to study the cell composition, the phenotype, and the spatial distribution of Hodgkin and Reed–Sternberg (HRS) cells and of noncancerous cells in tumor tissues. Moreover, we propose a classification, with increasing complexity, of the in vitro functional studies used to clarify the interactions leading not only to HRS cell survival, growth and drug resistance, but also to the immunosuppressive tumor education of monocytes, T lymphocytes and fibroblasts. This classification also includes new 3-dimensional (3D) models, obtained by cultivating HRS cells in extracellular matrix scaffolds or in sponge scaffolds, under non-adherent conditions with noncancerous cells to form heterospheroids (HS), implanted in developing chick eggs (ovo model). We report results obtained with these approaches and their applications in clinical setting.
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Vasiukov G, Novitskaya T, Senosain MF, Camai A, Menshikh A, Massion P, Zijlstra A, Novitskiy S. Integrated Cells and Collagen Fibers Spatial Image Analysis. FRONTIERS IN BIOINFORMATICS 2021; 1. [PMID: 35813245 PMCID: PMC9268206 DOI: 10.3389/fbinf.2021.758775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Modern technologies designed for tissue structure visualization like brightfield microscopy, fluorescent microscopy, mass cytometry imaging (MCI) and mass spectrometry imaging (MSI) provide large amounts of quantitative and spatial information about cells and tissue structures like vessels, bronchioles etc. Many published reports have demonstrated that the structural features of cells and extracellular matrix (ECM) and their interactions strongly predict disease development and progression. Computational image analysis methods in combination with spatial analysis and machine learning can reveal novel structural patterns in normal and diseased tissue. Here, we have developed a Python package designed for integrated analysis of cells and ECM in a spatially dependent manner. The package performs segmentation, labeling and feature analysis of ECM fibers, combines this information with pre-generated single-cell based datasets and realizes cell-cell and cell-fiber spatial analysis. To demonstrate performance and compatibility of our computational tool, we integrated it with a pipeline designed for cell segmentation, classification, and feature analysis in the KNIME analytical platform. For validation, we used a set of mouse mammary gland tumors and human lung adenocarcinoma tissue samples stained for multiple cellular markers and collagen as the main ECM protein. The developed package provides sufficient performance and precision to be used as a novel method to investigate cell-ECM relationships in the tissue, as well as detect structural patterns correlated with specific disease outcomes.
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Affiliation(s)
- Georgii Vasiukov
- Department of Medicine, Division of Allergy, Pulmonary, Critical Care Medicine, Vanderbilt, University Medical Center, Nashville, TN, United States
- *Correspondence: Georgii Vasiukov,
| | - Tatiana Novitskaya
- Department of Pathology, Microbiology, And Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Maria-Fernanda Senosain
- Department of Medicine, Division of Allergy, Pulmonary, Critical Care Medicine, Vanderbilt, University Medical Center, Nashville, TN, United States
| | - Alex Camai
- Department of Medicine, Division of Allergy, Pulmonary, Critical Care Medicine, Vanderbilt, University Medical Center, Nashville, TN, United States
| | - Anna Menshikh
- Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Pierre Massion
- Department of Medicine, Division of Allergy, Pulmonary, Critical Care Medicine, Vanderbilt, University Medical Center, Nashville, TN, United States
| | - Andries Zijlstra
- Department of Pathology, Microbiology, And Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Sergey Novitskiy
- Department of Medicine, Division of Allergy, Pulmonary, Critical Care Medicine, Vanderbilt, University Medical Center, Nashville, TN, United States
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Laberiano-Fernández C, Hernández-Ruiz S, Rojas F, Parra ER. Best Practices for Technical Reproducibility Assessment of Multiplex Immunofluorescence. Front Mol Biosci 2021; 8:660202. [PMID: 34532339 PMCID: PMC8438151 DOI: 10.3389/fmolb.2021.660202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/11/2021] [Indexed: 11/22/2022] Open
Abstract
Multiplex immunofluorescence (mIF) tyramide signal amplification is a new and useful tool for the study of cancer that combines the staining of multiple markers in a single slide. Several technical requirements are important to performing high-quality staining and analysis and to obtaining high internal and external reproducibility of the results. This review manuscript aimed to describe the mIF panel workflow and discuss the challenges and solutions for ensuring that mIF panels have the highest reproducibility possible. Although this platform has shown high flexibility in cancer studies, it presents several challenges in pre-analytic, analytic, and post-analytic evaluation, as well as with external comparisons. Adequate antibody selection, antibody optimization and validation, panel design, staining optimization and validation, analysis strategies, and correct data generation are important for reproducibility and to minimize or identify possible issues during the mIF staining process that sometimes are not completely under our control, such as the tissue fixation process, storage, and cutting procedures.
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Affiliation(s)
- Caddie Laberiano-Fernández
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sharia Hernández-Ruiz
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Frank Rojas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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