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Rodríguez-Bejarano OH, Roa L, Vargas-Hernández G, Botero-Espinosa L, Parra-López C, Patarroyo MA. Strategies for studying immune and non-immune human and canine mammary gland cancer tumour infiltrate. Biochim Biophys Acta Rev Cancer 2024; 1879:189064. [PMID: 38158026 DOI: 10.1016/j.bbcan.2023.189064] [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: 08/23/2023] [Revised: 12/11/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
The tumour microenvironment (TME) is usually defined as a cell environment associated with tumours or cancerous stem cells where conditions are established affecting tumour development and progression through malignant cell interaction with non-malignant cells. The TME is made up of endothelial, immune and non-immune cells, extracellular matrix (ECM) components and signalling molecules acting specifically on tumour and non-tumour cells. Breast cancer (BC) is the commonest malignant neoplasm worldwide and the main cause of mortality in women globally; advances regarding BC study and understanding it are relevant for acquiring novel, personalised therapeutic tools. Studying canine mammary gland tumours (CMGT) is one of the most relevant options for understanding BC using animal models as they share common epidemiological, clinical, pathological, biological, environmental, genetic and molecular characteristics with human BC. In-depth, detailed investigation regarding knowledge of human BC-related TME and in its canine model is considered extremely relevant for understanding changes in TME composition during tumour development. This review addresses important aspects concerned with different methods used for studying BC- and CMGT-related TME that are important for developing new and more effective therapeutic strategies for attacking a tumour during specific evolutionary stages.
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Affiliation(s)
- Oscar Hernán Rodríguez-Bejarano
- Health Sciences Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Calle 222#55-37, Bogotá 111166, Colombia; Molecular Biology and Immunology Department, Fundacion Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; PhD Programme in Biotechnology, Faculty of Sciences, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia
| | - Leonardo Roa
- Veterinary Clinic, Faculty of Agricultural Sciences, Universidad de La Salle, Carrera 7 #179-03, Bogotá 110141, Colombia
| | - Giovanni Vargas-Hernández
- Animal Health Department, Faculty of Veterinary Medicine and Zootechnics, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia
| | - Lucía Botero-Espinosa
- Animal Health Department, Faculty of Veterinary Medicine and Zootechnics, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia
| | - Carlos Parra-López
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia.
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundacion Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia.
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2
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Wang WJ, Chu LX, He LY, Zhang MJ, Dang KT, Gao C, Ge QY, Wang ZG, Zhao XW. Spatial transcriptomics: recent developments and insights in respiratory research. Mil Med Res 2023; 10:38. [PMID: 37592342 PMCID: PMC10433685 DOI: 10.1186/s40779-023-00471-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
The respiratory system's complex cellular heterogeneity presents unique challenges to researchers in this field. Although bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) have provided insights into cell types and heterogeneity in the respiratory system, the relevant specific spatial localization and cellular interactions have not been clearly elucidated. Spatial transcriptomics (ST) has filled this gap and has been widely used in respiratory studies. This review focuses on the latest iterative technology of ST in recent years, summarizing how ST can be applied to the physiological and pathological processes of the respiratory system, with emphasis on the lungs. Finally, the current challenges and potential development directions are proposed, including high-throughput full-length transcriptome, integration of multi-omics, temporal and spatial omics, bioinformatics analysis, etc. These viewpoints are expected to advance the study of systematic mechanisms, including respiratory studies.
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Affiliation(s)
- Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Liu-Xi Chu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Yong He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ming-Jing Zhang
- Orthopaedic Bioengineering Research Group, Division of Surgery and Interventional Science, University College London, London, HA7 4LP, UK
| | - Kai-Tong Dang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qin-Yu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Zhou-Guang Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Xiang-Wei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
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3
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Brožová K, Hantusch B, Kenner L, Kratochwill K. Spatial Proteomics for the Molecular Characterization of Breast Cancer. Proteomes 2023; 11:17. [PMID: 37218922 PMCID: PMC10204503 DOI: 10.3390/proteomes11020017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/30/2023] [Accepted: 04/23/2023] [Indexed: 05/24/2023] Open
Abstract
Breast cancer (BC) is a major global health issue, affecting a significant proportion of the female population and contributing to high rates of mortality. One of the primary challenges in the treatment of BC is the disease's heterogeneity, which can lead to ineffective therapies and poor patient outcomes. Spatial proteomics, which involves the study of protein localization within cells, offers a promising approach for understanding the biological processes that contribute to cellular heterogeneity within BC tissue. To fully leverage the potential of spatial proteomics, it is critical to identify early diagnostic biomarkers and therapeutic targets, and to understand protein expression levels and modifications. The subcellular localization of proteins is a key factor in their physiological function, making the study of subcellular localization a major challenge in cell biology. Achieving high resolution at the cellular and subcellular level is essential for obtaining an accurate spatial distribution of proteins, which in turn can enable the application of proteomics in clinical research. In this review, we present a comparison of current methods of spatial proteomics in BC, including untargeted and targeted strategies. Untargeted strategies enable the detection and analysis of proteins and peptides without a predetermined molecular focus, whereas targeted strategies allow the investigation of a predefined set of proteins or peptides of interest, overcoming the limitations associated with the stochastic nature of untargeted proteomics. By directly comparing these methods, we aim to provide insights into their strengths and limitations and their potential applications in BC research.
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Affiliation(s)
- Klára Brožová
- Core Facility Proteomics, Medical University of Vienna, 1090 Vienna, Austria
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
- Division of Molecular and Structural Preclinical Imaging, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1210 Vienna, Austria
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine, 1090 Vienna, Austria
| | - Brigitte Hantusch
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
| | - Lukas Kenner
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine, 1090 Vienna, Austria
- CBmed GmbH—Center for Biomarker Research in Medicine, 8010 Graz, Austria
- Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna, 1090 Vienna, Austria
| | - Klaus Kratochwill
- Core Facility Proteomics, Medical University of Vienna, 1090 Vienna, Austria
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
- Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
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4
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Wang N, Li X, Ding Z. High-Plex Spatial Profiling of RNA and Protein Using Digital Spatial Profiler. Methods Mol Biol 2023; 2660:69-83. [PMID: 37191791 DOI: 10.1007/978-1-0716-3163-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The rapid emergence of spatial multi-omics technologies in recent years has revolutionized biomedical research. Among these, the Digital Spatial Profiler (DSP, commercialized by nanoString) has become one of the dominant technologies in spatial transcriptomics and proteomics and has assisted in deconvoluting complex biological questions. Based on our practical experience in the past 3 years with DSP, we share here a detailed hands-on protocol and key handling notes that will allow the broader community to optimize their work procedure.
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Affiliation(s)
- Nan Wang
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd, Jinan City, Shandong Province, P. R. China
| | - Xia Li
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd, Jinan City, Shandong Province, P. R. China
| | - Zhiyong Ding
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd, Jinan City, Shandong Province, P. R. China.
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5
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Hu B, Sajid M, Lv R, Liu L, Sun C. A review of spatial profiling technologies for characterizing the tumor microenvironment in immuno-oncology. Front Immunol 2022; 13:996721. [PMID: 36389765 PMCID: PMC9659855 DOI: 10.3389/fimmu.2022.996721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/17/2022] [Indexed: 08/13/2023] Open
Abstract
Interpreting the mechanisms and principles that govern gene activity and how these genes work according to -their cellular distribution in organisms has profound implications for cancer research. The latest technological advancements, such as imaging-based approaches and next-generation single-cell sequencing technologies, have established a platform for spatial transcriptomics to systematically quantify the expression of all or most genes in the entire tumor microenvironment and explore an array of disease milieus, particularly in tumors. Spatial profiling technologies permit the study of transcriptional activity at the spatial or single-cell level. This multidimensional classification of the transcriptomic and proteomic signatures of tumors, especially the associated immune and stromal cells, facilitates evaluation of tumor heterogeneity, details of the evolutionary trajectory of each tumor, and multifaceted interactions between each tumor cell and its microenvironment. Therefore, spatial profiling technologies may provide abundant and high-resolution information required for the description of clinical-related features in immuno-oncology. From this perspective, the present review will highlight the importance of spatial transcriptomic and spatial proteomics analysis along with the joint use of other sequencing technologies and their implications in cancers and immune-oncology. In the near future, advances in spatial profiling technologies will undoubtedly expand our understanding of tumor biology and highlight possible precision therapeutic targets for cancer patients.
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Affiliation(s)
- Bian Hu
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Muhammad Sajid
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Rong Lv
- Blood Transfusion Laboratory, Anhui Blood Center, Hefei, China
| | - Lianxin Liu
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Cheng Sun
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, University of Science and Technology of China, Hefei, China
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6
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Yu Q, Jiang M, Wu L. Spatial transcriptomics technology in cancer research. Front Oncol 2022; 12:1019111. [PMID: 36313703 PMCID: PMC9606570 DOI: 10.3389/fonc.2022.1019111] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/21/2022] [Indexed: 08/25/2023] Open
Abstract
In recent years, spatial transcriptomics (ST) technologies have developed rapidly and have been widely used in constructing spatial tissue atlases and characterizing spatiotemporal heterogeneity of cancers. Currently, ST has been used to profile spatial heterogeneity in multiple cancer types. Besides, ST is a benefit for identifying and comprehensively understanding special spatial areas such as tumor interface and tertiary lymphoid structures (TLSs), which exhibit unique tumor microenvironments (TMEs). Therefore, ST has also shown great potential to improve pathological diagnosis and identify novel prognostic factors in cancer. This review presents recent advances and prospects of applications on cancer research based on ST technologies as well as the challenges.
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Affiliation(s)
- Qichao Yu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Miaomiao Jiang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Liang Wu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
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7
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Kumar V, Randhawa P, Bilodeau R, Mercola D, McClelland M, Agrawal A, Nguyen J, Castro P, Ittmann MM, Rahmatpanah F. Spatial Profiling of the Prostate Cancer Tumor Microenvironment Reveals Multiple Differences in Gene Expression and Correlation with Recurrence Risk. Cancers (Basel) 2022; 14:cancers14194923. [PMID: 36230846 PMCID: PMC9562240 DOI: 10.3390/cancers14194923] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/03/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022] Open
Abstract
The tumor microenvironment plays a crucial role in both the development and progression of prostate cancer. Furthermore, identifying protein and gene expression differences between different regions is valuable for treatment development. We applied Digital Spatial Profiling multiplex analysis to formalin-fixed paraffin embedded prostatectomy tissue blocks to investigate protein and transcriptome differences between tumor, tumor-adjacent stroma (TAS), CD45+ tumor, and CD45+ TAS tissue. Differential expression of an immunology/oncology protein panel (n = 58) was measured. OX40L and CTLA4 were expressed at higher levels while 22 other proteins, including CD11c, were expressed at lower levels (FDR < 0.2 and p-value < 0.05) in TAS as compared to tumor epithelia. A tissue microarray analysis of 97 patients with 1547 cores found positive correlations between high expression of CD11c and increased time to recurrence in tumor and TAS, and inverse relationships for CTLA4 and OX40L, where higher expression in tumor correlated with lower time to recurrence, but higher time to recurrence in TAS. Spatial transcriptomic analysis using a Cancer Transcriptome Atlas panel (n = 1825 genes) identified 162 genes downregulated and 69 upregulated in TAS versus tumor, 26 downregulated and 6 upregulated in CD45+ TAS versus CD45+ tumor. We utilized CIBERSORTx to estimate the relative immune cell fractions using CD45+ gene expression and found higher average fractions for memory B, naïve B, and T cells in TAS. In summary, the combination of protein expression differences, immune cell fractions, and correlations of protein expression with time to recurrence suggest that closely examining the tumor microenvironment provides valuable data that can improve prognostication and treatment techniques.
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Affiliation(s)
- Vinay Kumar
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Pavneet Randhawa
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Robert Bilodeau
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Dan Mercola
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Michael McClelland
- Department of Molecular and Microbiology, University of California, Irvine, CA 92697, USA
| | - Anshu Agrawal
- Department of Medicine, University of California, Irvine, CA 92697, USA
| | - James Nguyen
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Patricia Castro
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael M. Ittmann
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Farah Rahmatpanah
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
- Correspondence:
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Dissecting Tumor-Immune Microenvironment in Breast Cancer at a Spatial and Multiplex Resolution. Cancers (Basel) 2022; 14:cancers14081999. [PMID: 35454904 PMCID: PMC9026731 DOI: 10.3390/cancers14081999] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023] Open
Abstract
The tumor immune microenvironment (TIME) is an important player in breast cancer pathophysiology. Surrogates for antitumor immune response have been explored as predictive biomarkers to immunotherapy, though with several limitations. Immunohistochemistry for programmed death ligand 1 suffers from analytical problems, immune signatures are devoid of spatial information and histopathological evaluation of tumor infiltrating lymphocytes exhibits interobserver variability. Towards improved understanding of the complex interactions in TIME, several emerging multiplex in situ methods are being developed and gaining much attention for protein detection. They enable the simultaneous evaluation of multiple targets in situ, detection of cell densities/subpopulations as well as estimations of functional states of immune infiltrate. Furthermore, they can characterize spatial organization of TIME—by cell-to-cell interaction analyses and the evaluation of distribution within different regions of interest and tissue compartments—while digital imaging and image analysis software allow for reproducibility of the various assays. In this review, we aim to provide an overview of the different multiplex in situ methods used in cancer research with special focus on breast cancer TIME at the neoadjuvant, adjuvant and metastatic setting. Spatial heterogeneity of TIME and importance of longitudinal evaluation of TIME changes under the pressure of therapy and metastatic progression are also addressed.
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Cheung AMY, Wang D, Liu K, Hope T, Murray M, Ginty F, Nofech-Mozes S, Martel AL, Yaffe MJ. Quantitative single-cell analysis of immunofluorescence protein multiplex images illustrates biomarker spatial heterogeneity within breast cancer subtypes. Breast Cancer Res 2021; 23:114. [PMID: 34922607 PMCID: PMC8684264 DOI: 10.1186/s13058-021-01475-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/11/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The extent of cellular heterogeneity in breast cancer could have potential impact on diagnosis and long-term outcome. However, pathology evaluation is limited to biomarker immunohistochemical staining and morphology of the bulk cancer. Inter-cellular heterogeneity of biomarkers is not usually assessed. As an initial evaluation of the extent of breast cancer cellular heterogeneity, we conducted quantitative and spatial imaging of Estrogen Receptor (ER), Progesterone Receptor (PR), Epidermal Growth Factor Receptor-2 (HER2), Ki67, TP53, CDKN1A (P21/WAF1), CDKN2A (P16INK4A), CD8 and CD20 of a tissue microarray (TMA) representing subtypes defined by St. Gallen surrogate classification. METHODS Quantitative, single cell-based imaging was conducted using an Immunofluorescence protein multiplexing platform (MxIF) to study protein co-expression signatures and their spatial localization patterns. The range of MxIF intensity values of each protein marker was compared to the respective IHC score for the TMA core. Extent of heterogeneity in spatial neighborhoods was analyzed using co-occurrence matrix and Diversity Index measures. RESULTS On the 101 cores from 59 cases studied, diverse expression levels and distributions were observed in MxIF measures of ER and PR among the hormonal receptor-positive tumor cores. As expected, Luminal A-like cancers exhibit higher proportions of cell groups that co-express ER and PR, while Luminal B-like (HER2-negative) cancers were composed of ER+, PR- groups. Proliferating cells defined by Ki67 positivity were mainly found in groups with PR-negative cells. Triple-Negative Breast Cancer (TNBC) exhibited the highest proliferative fraction and incidence of abnormal P53 and P16 expression. Among the tumors exhibiting P53 overexpression by immunohistochemistry, a group of TNBC was found with much higher MxIF-measured P53 signal intensity compared to HER2+, Luminal B-like and other TNBC cases. Densities of CD8 and CD20 cells were highest in HER2+ cancers. Spatial analysis demonstrated variability in heterogeneity in cellular neighborhoods in the cancer and the tumor microenvironment. CONCLUSIONS Protein marker multiplexing and quantitative image analysis demonstrated marked heterogeneity in protein co-expression signatures and cellular arrangement within each breast cancer subtype. These refined descriptors of biomarker expressions and spatial patterns could be valuable in the development of more informative tools to guide diagnosis and treatment.
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Affiliation(s)
- Alison Min-Yan Cheung
- Biomarker Imaging Research Lab (BIRL), Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - Dan Wang
- Biomarker Imaging Research Lab (BIRL), Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - Kela Liu
- Biomarker Imaging Research Lab (BIRL), Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - Tyna Hope
- Biomarker Imaging Research Lab (BIRL), Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - Mayan Murray
- Biomarker Imaging Research Lab (BIRL), Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - Fiona Ginty
- Biosciences, GE Research (GER), Niskayuna, NY, USA
| | - Sharon Nofech-Mozes
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Anne Louise Martel
- Biomarker Imaging Research Lab (BIRL), Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Martin Joel Yaffe
- Biomarker Imaging Research Lab (BIRL), Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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10
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Ahmed R, Augustine R, Valera E, Ganguli A, Mesaeli N, Ahmad IS, Bashir R, Hasan A. Spatial mapping of cancer tissues by OMICS technologies. Biochim Biophys Acta Rev Cancer 2021; 1877:188663. [PMID: 34861353 DOI: 10.1016/j.bbcan.2021.188663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/15/2021] [Accepted: 11/26/2021] [Indexed: 12/14/2022]
Abstract
Spatial mapping of heterogeneity in gene expression in cancer tissues can improve our understanding of cancers and help in the rapid detection of cancers with high accuracy and reliability. Significant advancements have been made in recent years in OMICS technologies, which possess the strong potential to be applied in the spatial mapping of biopsy tissue samples and their molecular profiling to a single-cell level. The clinical application of OMICS technologies in spatial profiling of cancer tissues is also advancing. The current review presents recent advancements and prospects of applying OMICS technologies to the spatial mapping of various analytes in cancer tissues. We benchmark the current state of the art in the field to advance existing OMICS technologies for high throughput spatial profiling. The factors taken into consideration include spatial resolution, types of biomolecules, number of different biomolecules that can be detected from the same assay, labeled versus label-free approaches, and approximate time required for each assay. Further advancements are still needed for the widespread application of OMICs technologies in performing fast and high throughput spatial mapping of cancer tissues as well as their effective use in research and clinical applications.
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Affiliation(s)
- Rashid Ahmed
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar; Biomedical Research Center (BRC), Qatar University, Doha 2713, Qatar; Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA
| | - Robin Augustine
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar; Biomedical Research Center (BRC), Qatar University, Doha 2713, Qatar
| | - Enrique Valera
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA; Department of Bioengineering, University of Illinois at Urbana Champaign, IL, USA
| | - Anurup Ganguli
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA; Department of Bioengineering, University of Illinois at Urbana Champaign, IL, USA
| | - Nasrin Mesaeli
- Department of Biochemistry, Weill Cornell Medicine in Qatar, Qatar Foundation, Doha, Qatar
| | - Irfan S Ahmad
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA
| | - Rashid Bashir
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA; Department of Bioengineering, University of Illinois at Urbana Champaign, IL, USA; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar; Biomedical Research Center (BRC), Qatar University, Doha 2713, Qatar.
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11
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Schlam I, Church SE, Hether TD, Chaldekas K, Hudson BM, White AM, Maisonet E, Harris BT, Swain SM. The tumor immune microenvironment of primary and metastatic HER2- positive breast cancers utilizing gene expression and spatial proteomic profiling. J Transl Med 2021; 19:480. [PMID: 34838031 PMCID: PMC8626906 DOI: 10.1186/s12967-021-03113-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/10/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The characterization of the immune component of the tumor microenvironment (TME) of human epidermal growth factor receptor 2 positive (HER2+) breast cancer has been limited. Molecular and spatial characterization of HER2+ TME of primary, recurrent, and metastatic breast tumors has the potential to identify immune mediated mechanisms and biomarker targets that could be used to guide selection of therapies. METHODS We examined 15 specimens from eight patients with HER2+ breast cancer: 10 primary breast tumors (PBT), two soft tissue, one lung, and two brain metastases (BM). Using molecular profiling by bulk gene expression TME signatures, including the Tumor Inflammation Signature (TIS) and PAM50 subtyping, as well as spatial characterization of immune hot, warm, and cold regions in the stroma and tumor epithelium using 64 protein targets on the GeoMx Digital Spatial Profiler. RESULTS PBT had higher infiltration of immune cells relative to metastatic sites and higher protein and gene expression of immune activation markers when compared to metastatic sites. TIS scores were lower in metastases, particularly in BM. BM also had less immune infiltration overall, but in the stromal compartment with the highest density of immune infiltration had similar levels of T cells that were less activated than PBT stromal regions suggesting immune exclusion in the tumor epithelium. CONCLUSIONS Our findings show stromal and tumor localized immune cells in the TME are more active in primary versus metastatic disease. This suggests patients with early HER2+ breast cancer could have more benefit from immune-targeting therapies than patients with advanced disease.
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Affiliation(s)
- Ilana Schlam
- Department of Hematology-Oncology, MedStar Washington Hospital Center, Washington, DC USA
- Present Address: Department of Hematology and Oncology, Tufts Medical Center, 800 Washington St, 245, Boston, MA 02111 USA
| | | | | | - Krysta Chaldekas
- MedStar Georgetown University Hospital, 4000 Reservoir road NW, 120 Building D, Washington, DC 20057 USA
- Lombardi Comprehensive Cancer Center, Washington, DC USA
| | - Briana M. Hudson
- Present Address: Department of Hematology and Oncology, Tufts Medical Center, 800 Washington St, 245, Boston, MA 02111 USA
| | | | - Emily Maisonet
- MedStar Georgetown University Hospital, 4000 Reservoir road NW, 120 Building D, Washington, DC 20057 USA
- Lombardi Comprehensive Cancer Center, Washington, DC USA
| | - Brent T. Harris
- MedStar Georgetown University Hospital, 4000 Reservoir road NW, 120 Building D, Washington, DC 20057 USA
- Lombardi Comprehensive Cancer Center, Washington, DC USA
| | - Sandra M. Swain
- MedStar Georgetown University Hospital, 4000 Reservoir road NW, 120 Building D, Washington, DC 20057 USA
- Lombardi Comprehensive Cancer Center, Washington, DC USA
- MedStar Health, Washington, DC USA
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12
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Bergholtz H, Carter JM, Cesano A, Cheang MCU, Church SE, Divakar P, Fuhrman CA, Goel S, Gong J, Guerriero JL, Hoang ML, Hwang ES, Kuasne H, Lee J, Liang Y, Mittendorf EA, Perez J, Prat A, Pusztai L, Reeves JW, Riazalhosseini Y, Richer JK, Sahin Ö, Sato H, Schlam I, Sørlie T, Stover DG, Swain SM, Swarbrick A, Thompson EA, Tolaney SM, Warren SE, On Behalf Of The GeoMx Breast Cancer Consortium. Best Practices for Spatial Profiling for Breast Cancer Research with the GeoMx ® Digital Spatial Profiler. Cancers (Basel) 2021; 13:4456. [PMID: 34503266 PMCID: PMC8431590 DOI: 10.3390/cancers13174456] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 01/07/2023] Open
Abstract
Breast cancer is a heterogenous disease with variability in tumor cells and in the surrounding tumor microenvironment (TME). Understanding the molecular diversity in breast cancer is critical for improving prediction of therapeutic response and prognostication. High-plex spatial profiling of tumors enables characterization of heterogeneity in the breast TME, which can holistically illuminate the biology of tumor growth, dissemination and, ultimately, response to therapy. The GeoMx Digital Spatial Profiler (DSP) enables researchers to spatially resolve and quantify proteins and RNA transcripts from tissue sections. The platform is compatible with both formalin-fixed paraffin-embedded and frozen tissues. RNA profiling was developed at the whole transcriptome level for human and mouse samples and protein profiling of 100-plex for human samples. Tissue can be optically segmented for analysis of regions of interest or cell populations to study biology-directed tissue characterization. The GeoMx Breast Cancer Consortium (GBCC) is composed of breast cancer researchers who are developing innovative approaches for spatial profiling to accelerate biomarker discovery. Here, the GBCC presents best practices for GeoMx profiling to promote the collection of high-quality data, optimization of data analysis and integration of datasets to advance collaboration and meta-analyses. Although the capabilities of the platform are presented in the context of breast cancer research, they can be generalized to a variety of other tumor types that are characterized by high heterogeneity.
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Affiliation(s)
- Helga Bergholtz
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway
| | - Jodi M Carter
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Maggie Chon U Cheang
- ICR Clinical Trials and Statistics Unit, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK
| | | | | | | | - Shom Goel
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jingjing Gong
- NanoString® Technologies Inc., Seattle, WA 98109, USA
| | - Jennifer L Guerriero
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - E Shelley Hwang
- Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Hellen Kuasne
- Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3A 0G4, Canada
| | - Jinho Lee
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Yan Liang
- NanoString® Technologies Inc., Seattle, WA 98109, USA
| | - Elizabeth A Mittendorf
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
- Breast Oncology Program, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Jessica Perez
- NanoString® Technologies Inc., Seattle, WA 98109, USA
| | - Aleix Prat
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute, 08036 Barcelona, Spain
| | - Lajos Pusztai
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Yasser Riazalhosseini
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada
- McGill University Genome Centre, McGill University, Montreal, QC H3A 0G4, Canada
| | - Jennifer K Richer
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Özgür Sahin
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Hiromi Sato
- NanoString® Technologies Inc., Seattle, WA 98109, USA
| | - Ilana Schlam
- MedStar Washington Hospital Center, Washington, DC 20010, USA
- Tufts Medical Center, Boston, MA 02111, USA
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, 0315 Oslo, Norway
| | - Daniel G Stover
- Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Sandra M Swain
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC 20057, USA
- Georgetown University Medical Center, Washington, DC 20057, USA
- MedStar Health, Washington, DC 20057, USA
| | - Alexander Swarbrick
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney NSW 2052, Australia
| | - E Aubrey Thompson
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Sara M Tolaney
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
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13
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Tien TZ, Lee JNLW, Lim JCT, Chen XY, Thike AA, Tan PH, Yeong JPS. Delineating the breast cancer immune microenvironment in the era of multiplex immunohistochemistry/immunofluorescence. Histopathology 2021; 79:139-159. [PMID: 33400265 DOI: 10.1111/his.14328] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Breast cancer is the most common malignancy and the leading cause of cancer death in females worldwide. Treatment is challenging, especially for those who are triple-negative. Increasing evidence suggests that diverse immune populations are present in the breast tumour microenvironment, which opens up avenues for personalised drug targets. Historically, our investigations into the immune constitution of breast tumours have been restricted to analyses of one or two markers at a given time. Recent technological advances have allowed simultaneous labelling of more than 35 markers and detailed profiling of tumour-immune infiltrates at the single-cell level, as well as determining the cellular composition and spatial analysis of the entire tumour architecture. In this review, we describe emerging technologies that have contributed to the field of breast cancer diagnosis, and discuss how to interpret the vast data sets obtained in order to effectively translate them for clinically relevant use.
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Affiliation(s)
- Tracy Z Tien
- Integrative Biology for Theranostics, Institute of Molecular Cell Biology, Agency of Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Justina N L W Lee
- Integrative Biology for Theranostics, Institute of Molecular Cell Biology, Agency of Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jeffrey C T Lim
- Integrative Biology for Theranostics, Institute of Molecular Cell Biology, Agency of Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Xiao-Yang Chen
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore.,Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Aye Aye Thike
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Puay Hoon Tan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore.,Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore.,Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Joe P S Yeong
- Integrative Biology for Theranostics, Institute of Molecular Cell Biology, Agency of Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
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14
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Kalita-de Croft P, Sadeghi Rad H, Gasper H, O'Byrne K, Lakhani SR, Kulasinghe A. Spatial profiling technologies and applications for brain cancers. Expert Rev Mol Diagn 2021; 21:323-332. [PMID: 33685321 DOI: 10.1080/14737159.2021.1900735] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Malignant primary and secondary brain tumors pose a major health challenge, and the incidence of these tumors is rising. The brain tumor microenvironment (TME) is highly complex and thought to impact treatment resistance and failure. To enable a greater understanding of the milieu of cells in the brain TME, advances in imaging and sequential profiling of proteins/mRNA have given rise to the field of spatial transcriptomics. These technologies provide a greater depth of understanding of the tissue architecture, cellular and spatial profiles, including cellular activation status, which may provide insights into effective therapies for brain cancers. AREAS COVERED In this review, we provide an overview of spatial profiling technologies at the forefront in the field and describe the applications for brain cancer. EXPERT OPINION Brain tumors are often resistant to treatment, and display both an immunosuppressive and heterogeneous tumor microenvironment. Next-generation imaging and multi-omics technologies are providing a tool for intricately characterizing their tissue biology. This information will aid in the design of effective therapies and begin to provide an understanding of therapy resistance.
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Affiliation(s)
- Priyakshi Kalita-de Croft
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Habib Sadeghi Rad
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Harry Gasper
- Department of Medical Oncology, Royal Brisbane and Women's Hospital, Herston, Australia.,School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Ken O'Byrne
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University ofTechnology, Woolloongabba, Queensland, Australia.,Translational Research Institute, Brisbane, Queensland, Australia.,Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Sunil R Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia.,Pathology Queensland, The Royal Brisbane and Women's Hospital Herston, Queensland, Australia
| | - Arutha Kulasinghe
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University ofTechnology, Woolloongabba, Queensland, Australia.,Translational Research Institute, Brisbane, Queensland, Australia
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15
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Nerurkar SN, Goh D, Cheung CCL, Nga PQY, Lim JCT, Yeong JPS. Transcriptional Spatial Profiling of Cancer Tissues in the Era of Immunotherapy: The Potential and Promise. Cancers (Basel) 2020; 12:E2572. [PMID: 32917035 PMCID: PMC7563386 DOI: 10.3390/cancers12092572] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/05/2020] [Accepted: 09/06/2020] [Indexed: 12/18/2022] Open
Abstract
Intratumoral heterogeneity poses a major challenge to making an accurate diagnosis and establishing personalized treatment strategies for cancer patients. Moreover, this heterogeneity might underlie treatment resistance, disease progression, and cancer relapse. For example, while immunotherapies can confer a high success rate, selective pressures coupled with dynamic evolution within a tumour can drive the emergence of drug-resistant clones that allow tumours to persist in certain patients. To improve immunotherapy efficacy, researchers have used transcriptional spatial profiling techniques to identify and subsequently block the source of tumour heterogeneity. In this review, we describe and assess the different technologies available for such profiling within a cancer tissue. We first outline two well-known approaches, in situ hybridization and digital spatial profiling. Then, we highlight the features of an emerging technology known as Visium Spatial Gene Expression Solution. Visium generates quantitative gene expression data and maps them to the tissue architecture. By retaining spatial information, we are well positioned to identify novel biomarkers and perform computational analyses that might inform on novel combinatorial immunotherapies.
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Affiliation(s)
- Sanjna Nilesh Nerurkar
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore;
| | - Denise Goh
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | | | - Pei Qi Yvonne Nga
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | - Jeffrey Chun Tatt Lim
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | - Joe Poh Sheng Yeong
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), Singapore 138648, Singapore
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