1
|
Strum S, Andersen MH, Svane IM, Siu LL, Weber JS. State-Of-The-Art Advancements on Cancer Vaccines and Biomarkers. Am Soc Clin Oncol Educ Book 2024; 44:e438592. [PMID: 38669611 DOI: 10.1200/edbk_438592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The origins of cancer vaccines date back to the 1800s. Since then, there have been significant efforts to generate vaccines against solid and hematologic malignancies using a variety of platforms. To date, these efforts have generally been met with minimal success. However, in the era of improved methods and technological advancements, supported by compelling preclinical and clinical data, a wave of renewed interest in the field offers the promise of discovering field-changing paradigms in the management of established and resected disease using cancer vaccines. These include novel approaches to personalized neoantigen vaccine development, as well as innovative immune-modulatory vaccines (IMVs) that facilitate activation of antiregulatory T cells to limit immunosuppression caused by regulatory immune cells. This article will introduce some of the limitations that have affected cancer vaccine development over the past several decades, followed by an introduction to the latest advancements in neoantigen vaccine and IMV therapy, and then conclude with a discussion of some of the newest technologies and progress that are occurring across the cancer vaccine space. Cancer vaccines are among the most promising frontiers for breakthrough innovations and strategies poised to make a measurable impact in the ongoing fight against cancer.
Collapse
Affiliation(s)
- Scott Strum
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| | - Mads Hald Andersen
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Inge Marie Svane
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Lillian L Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| | - Jeffrey S Weber
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY
| |
Collapse
|
2
|
Desai N, Chavda V, Singh TRR, Thorat ND, Vora LK. Cancer Nanovaccines: Nanomaterials and Clinical Perspectives. Small 2024:e2401631. [PMID: 38693099 DOI: 10.1002/smll.202401631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/30/2024] [Indexed: 05/03/2024]
Abstract
Cancer nanovaccines represent a promising frontier in cancer immunotherapy, utilizing nanotechnology to augment traditional vaccine efficacy. This review comprehensively examines the current state-of-the-art in cancer nanovaccine development, elucidating innovative strategies and technologies employed in their design. It explores both preclinical and clinical advancements, emphasizing key studies demonstrating their potential to elicit robust anti-tumor immune responses. The study encompasses various facets, including integrating biomaterial-based nanocarriers for antigen delivery, adjuvant selection, and the impact of nanoscale properties on vaccine performance. Detailed insights into the complex interplay between the tumor microenvironment and nanovaccine responses are provided, highlighting challenges and opportunities in optimizing therapeutic outcomes. Additionally, the study presents a thorough analysis of ongoing clinical trials, presenting a snapshot of the current clinical landscape. By curating the latest scientific findings and clinical developments, this study aims to serve as a comprehensive resource for researchers and clinicians engaged in advancing cancer immunotherapy. Integrating nanotechnology into vaccine design holds immense promise for revolutionizing cancer treatment paradigms, and this review provides a timely update on the evolving landscape of cancer nanovaccines.
Collapse
Affiliation(s)
- Nimeet Desai
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi, Telangana, 502285, India
| | - Vivek Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad, 380009, India
| | | | - Nanasaheb D Thorat
- Limerick Digital Cancer Research Centre (LDCRC), University of Limerick, Castletroy, Limerick, V94T9PX, Ireland
- Department of Physics, Bernal Institute, Castletroy, Limerick, V94T9PX, Ireland
- Nuffield Department of Women's & Reproductive Health, Medical Science Division, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Lalitkumar K Vora
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| |
Collapse
|
3
|
Sun Z, Tan R, Wu H, Fang X. Commentary: Flow cytometry quantification of tumor-infiltrating lymphocytes to predict the survival of patients with diffuse large B-cell lymphoma. Front Immunol 2024; 15:1377221. [PMID: 38698842 PMCID: PMC11063292 DOI: 10.3389/fimmu.2024.1377221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Affiliation(s)
- Zhongling Sun
- Department of Neurology, Zhaoyuan People’s Hospital, Zhaoyuan, China
| | - Ran Tan
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Huanling Wu
- Department of Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Xiaosheng Fang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| |
Collapse
|
4
|
Sharma S, Singh N, Turk AA, Wan I, Guttikonda A, Dong JL, Zhang X, Opyrchal M. Molecular insights into clinical trials for immune checkpoint inhibitors in colorectal cancer: Unravelling challenges and future directions. World J Gastroenterol 2024; 30:1815-1835. [PMID: 38659481 PMCID: PMC11036501 DOI: 10.3748/wjg.v30.i13.1815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/22/2024] [Accepted: 03/13/2024] [Indexed: 04/03/2024] Open
Abstract
Colorectal cancer (CRC) is a complex disease with diverse etiologies and clinical outcomes. Despite considerable progress in development of CRC therapeutics, challenges remain regarding the diagnosis and management of advanced stage metastatic CRC (mCRC). In particular, the five-year survival rate is very low since mCRC is currently rarely curable. Over the past decade, cancer treatment has significantly improved with the introduction of cancer immunotherapies, specifically immune checkpoint inhibitors. Therapies aimed at blocking immune checkpoints such as PD-1, PD-L1, and CTLA-4 target inhibitory pathways of the immune system, and thereby enhance anti-tumor immunity. These therapies thus have shown promising results in many clinical trials alone or in combination. The efficacy and safety of immunotherapy, either alone or in combination with CRC, have been investigated in several clinical trials. Clinical trials, including KEYNOTE-164 and CheckMate 142, have led to Food and Drug Administration approval of the PD-1 inhibitors pembrolizumab and nivolumab, respectively, for the treatment of patients with unresectable or metastatic microsatellite instability-high or deficient mismatch repair CRC. Unfortunately, these drugs benefit only a small percentage of patients, with the benefits of immunotherapy remaining elusive for the vast majority of CRC patients. To this end, primary and secondary resistance to immunotherapy remains a significant issue, and further research is necessary to optimize the use of immunotherapy in CRC and identify biomarkers to predict the response. This review provides a comprehensive overview of the clinical trials involving immune checkpoint inhibitors in CRC. The underlying rationale, challenges faced, and potential future steps to improve the prognosis and enhance the likelihood of successful trials in this field are discussed.
Collapse
Affiliation(s)
- Samantha Sharma
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Naresh Singh
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Anita Ahmed Turk
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Isabella Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Akshay Guttikonda
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Julia Lily Dong
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Xinna Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Mateusz Opyrchal
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| |
Collapse
|
5
|
Vargas GM, Shafique N, Xu X, Karakousis G. Tumor-infiltrating lymphocytes as a prognostic and predictive factor for Melanoma. Expert Rev Mol Diagn 2024; 24:299-310. [PMID: 38314660 DOI: 10.1080/14737159.2024.2312102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/17/2024] [Indexed: 02/06/2024]
Abstract
INTRODUCTION Tumor-infiltrating lymphocytes (TILs) have been investigated as prognostic factors in melanoma. Recent advancements in assessing the tumor microenvironment in the setting of more widespread use of immune checkpoint blockade have reignited interest in identifying predictive biomarkers. This review examines the function and significance of TILs in cutaneous melanoma, evaluating their potential as prognostic and predictive markers. AREAS COVERED A literature search was conducted on papers covering tumor infiltrating lymphocytes in cutaneous melanoma available online in PubMed and Web of Science from inception to 1 December 2023, supplemented by citation searching. This article encompasses the assessment of TILs, the role of TILs in the immune microenvironment, TILs as a prognostic factor, TILs as a predictive factor for immunotherapy response, and clinical applications of TILs in the treatment of cutaneous melanoma. EXPERT OPINION Tumor-infiltrating lymphocytes play a heterogeneous role in cutaneous melanoma. While they have historically been associated with improved survival, their status as independent prognostic or predictive factors remains uncertain. Novel methods of TIL assessment, such as determination of TIL subtypes and molecular signaling, demonstrate potential for predicting therapeutic response. Further, while their clinical utility in risk-stratification in melanoma treatment shows promise, a lack of consensus data hinders standardized application.
Collapse
Affiliation(s)
| | - Neha Shafique
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaowei Xu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Giorgos Karakousis
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
6
|
Longhini ALF, Fernández-Maestre I, Kennedy MC, Wereski MG, Mowla S, Xiao W, Lowe SW, Levine RL, Gardner R. Development of a customizable mouse backbone spectral flow cytometry panel to delineate immune cell populations in normal and tumor tissues. Front Immunol 2024; 15:1374943. [PMID: 38605953 PMCID: PMC11008467 DOI: 10.3389/fimmu.2024.1374943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024] Open
Abstract
Introduction In vivo studies of cancer biology and assessment of therapeutic efficacy are critical to advancing cancer research and ultimately improving patient outcomes. Murine cancer models have proven to be an invaluable tool in pre-clinical studies. In this context, multi-parameter flow cytometry is a powerful method for elucidating the profile of immune cells within the tumor microenvironment and/or play a role in hematological diseases. However, designing an appropriate multi-parameter panel to comprehensively profile the increasing diversity of immune cells across different murine tissues can be extremely challenging. Methods To address this issue, we designed a panel with 13 fixed markers that define the major immune populations -referred to as the backbone panel- that can be profiled in different tissues but with the option to incorporate up to seven additional fluorochromes, including any marker specific to the study in question. Results This backbone panel maintains its resolution across different spectral flow cytometers and organs, both hematopoietic and non-hematopoietic, as well as tumors with complex immune microenvironments. Discussion Having a robust backbone that can be easily customized with pre-validated drop-in fluorochromes saves time and resources and brings consistency and standardization, making it a versatile solution for immuno-oncology researchers. In addition, the approach presented here can serve as a guide to develop similar types of customizable backbone panels for different research questions requiring high-parameter flow cytometry panels.
Collapse
Affiliation(s)
- Ana Leda F. Longhini
- Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, United States
| | - Inés Fernández-Maestre
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Margaret C. Kennedy
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Shoron Mowla
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Wenbin Xiao
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Scott W. Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Ross L. Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Rui Gardner
- Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, United States
| |
Collapse
|
7
|
Davoudi F, Moradi A, Sadeghirad H, Kulasinghe A. Tissue biomarkers of immune checkpoint inhibitor therapy. Immunol Cell Biol 2024; 102:179-193. [PMID: 38228572 DOI: 10.1111/imcb.12723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/19/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024]
Abstract
Cancer immunotherapy has been rejuvenated by the growing understanding of the immune system's role in tumor activity over the past two decades. During cancer initiation and progression, tumor cells employ various mechanisms that resemble peripheral immune tolerance to evade the antitumor responses of the immune system. Immune checkpoint molecules are the major mechanism of immune resistance that are exploited by tumor cells to inhibit T-cell activation and suppress immune responses. The targeting of immune checkpoint pathways has led to substantial improvements in survival rates in a number of solid cancers. However, a lack of understanding of the heterogeneity of the tumor microenvironment (TME) has resulted in inefficient therapy responses. A greater understanding of the TME is needed to identify patients likely to respond, and those that will have resistance to immune checkpoint inhibitors (ICIs). Advancement in spatial single-cell technologies has allowed deeper insight into the phenotypic and functional diversities of cells in the TME. In this review, we provide an overview of ICI biomarkers and highlight how high-dimensional spatially resolved, single-cell approaches provide deep molecular insights into the TME and allow for the discovery of biomarkers of clinical benefit.
Collapse
Affiliation(s)
- Fatemeh Davoudi
- Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Afshin Moradi
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Habib Sadeghirad
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
8
|
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, Acosta Haab G, Acs B, Adams S, Almeida JS, Alvarado-Cabrero I, Azmoudeh-Ardalan F, Badve S, Baharun NB, Bellolio ER, Bheemaraju V, Blenman KR, Botinelly Mendonça Fujimoto L, Burgues O, Chardas A, Cheang MCU, Ciompi F, Cooper LA, Coosemans A, Corredor G, Dantas Portela FL, 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 EA, Kataoka TR, Kawaguchi K, Khramtsov AI, Kiraz U, Kirtani P, Kodach LL, Korski K, Akturk G, Scott E, Kovács A, Laenkholm AV, Lang-Schwarz C, Larsimont D, Lennerz JK, Lerousseau M, Li X, Madabhushi A, Maley SK, Manur Narasimhamurthy V, 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, Specht Stovgaard E, 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 DOI: 10.1002/path.6238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [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.
Collapse
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 PA2, 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, MI, 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/Incliva, 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 PA2, 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
- Instituto Universitario de Investigación 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/Onc, 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
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
- 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 Laenkholm
- 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 "Iuliu 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
- AI 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 Warwick, 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-Isenburg, 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 PA2, 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
| |
Collapse
|
9
|
Shuman JHB, Lin AS, Westland MD, Bryant KN, Piazuelo MB, Reyzer ML, Judd AM, McDonald WH, McClain MS, Schey KL, Algood HMS, Cover TL. Remodeling of the gastric environment in Helicobacter pylori-induced atrophic gastritis. mSystems 2024; 9:e0109823. [PMID: 38059647 PMCID: PMC10805037 DOI: 10.1128/msystems.01098-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 12/08/2023] Open
Abstract
Helicobacter pylori colonization of the human stomach is a strong risk factor for gastric cancer. To investigate H. pylori-induced gastric molecular alterations, we used a Mongolian gerbil model of gastric carcinogenesis. Histologic evaluation revealed varying levels of atrophic gastritis (a premalignant condition characterized by parietal and chief cell loss) in H. pylori-infected animals, and transcriptional profiling revealed a loss of markers for these cell types. We then assessed the spatial distribution and relative abundance of proteins in the gastric tissues using imaging mass spectrometry and liquid chromatography with tandem mass spectrometry. We detected striking differences in the protein content of corpus and antrum tissues. Four hundred ninety-two proteins were preferentially localized to the corpus in uninfected animals. The abundance of 91 of these proteins was reduced in H. pylori-infected corpus tissues exhibiting atrophic gastritis compared with infected corpus tissues exhibiting non-atrophic gastritis or uninfected corpus tissues; these included numerous proteins with metabolic functions. Fifty proteins localized to the corpus in uninfected animals were diffusely delocalized throughout the stomach in infected tissues with atrophic gastritis; these included numerous proteins with roles in protein processing. The corresponding alterations were not detected in animals infected with a H. pylori ∆cagT mutant (lacking Cag type IV secretion system activity). These results indicate that H. pylori can cause loss of proteins normally localized to the gastric corpus as well as diffuse delocalization of corpus-specific proteins, resulting in marked changes in the normal gastric molecular partitioning into distinct corpus and antrum regions.IMPORTANCEA normal stomach is organized into distinct regions known as the corpus and antrum, which have different functions, cell types, and gland architectures. Previous studies have primarily used histologic methods to differentiate these regions and detect H. pylori-induced alterations leading to stomach cancer. In this study, we investigated H. pylori-induced gastric molecular alterations in a Mongolian gerbil model of carcinogenesis. We report the detection of numerous proteins that are preferentially localized to the gastric corpus but not the antrum in a normal stomach. We show that stomachs with H. pylori-induced atrophic gastritis (a precancerous condition characterized by the loss of specialized cell types) exhibit marked changes in the abundance and localization of proteins normally localized to the gastric corpus. These results provide new insights into H. pylori-induced gastric molecular alterations that are associated with the development of stomach cancer.
Collapse
Affiliation(s)
- Jennifer H. B. Shuman
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Aung Soe Lin
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mandy D. Westland
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kaeli N. Bryant
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M. Blanca Piazuelo
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Michelle L. Reyzer
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Audra M. Judd
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - W. Hayes McDonald
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Mark S. McClain
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kevin L. Schey
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Holly M. S. Algood
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
| | - Timothy L. Cover
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
| |
Collapse
|
10
|
Basher ARMA, Hallinan C, Lee K. Heterogeneity-Preserving Discriminative Feature Selection for Subtype Discovery. bioRxiv 2023:2023.05.14.540686. [PMID: 38187596 PMCID: PMC10769187 DOI: 10.1101/2023.05.14.540686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The discovery of subtypes is pivotal for disease diagnosis and targeted therapy, considering the diverse responses of different cells or patients to specific treatments. Exploring the heterogeneity within disease or cell states provides insights into disease progression mechanisms and cell differentiation. The advent of high-throughput technologies has enabled the generation and analysis of various molecular data types, such as single-cell RNA-seq, proteomic, and imaging datasets, at large scales. While presenting opportunities for subtype discovery, these datasets pose challenges in finding relevant signatures due to their high dimensionality. Feature selection, a crucial step in the analysis pipeline, involves choosing signatures that reduce the feature size for more efficient downstream computational analysis. Numerous existing methods focus on selecting signatures that differentiate known diseases or cell states, yet they often fall short in identifying features that preserve heterogeneity and reveal subtypes. To identify features that can capture the diversity within each class while also maintaining the discrimination of known disease states, we employed deep metric learning-based feature embedding to conduct a detailed exploration of the statistical properties of features essential in preserving heterogeneity. Our analysis revealed that features with a significant difference in interquartile range (IQR) between classes possess crucial subtype information. Guided by this insight, we developed a robust statistical method, termed PHet (Preserving Heterogeneity) that performs iterative subsampling differential analysis of IQR and Fisher's method between classes, identifying a minimal set of heterogeneity-preserving discriminative features to optimize subtype clustering quality. Validation using public single-cell RNA-seq and microarray datasets showcased PHet's effectiveness in preserving sample heterogeneity while maintaining discrimination of known disease/cell states, surpassing the performance of previous outlier-based methods. Furthermore, analysis of a single-cell RNA-seq dataset from mouse tracheal epithelial cells revealed, through PHet-based features, the presence of two distinct basal cell subtypes undergoing differentiation toward a luminal secretory phenotype. Notably, one of these subtypes exhibited high expression of BPIFA1. Interestingly, previous studies have linked BPIFA1 secretion to the emergence of secretory cells during mucociliary differentiation of airway epithelial cells. PHet successfully pinpointed the basal cell subtype associated with this phenomenon, a distinction that pre-annotated markers and dispersion-based features failed to make due to their admixed feature expression profiles. These findings underscore the potential of our method to deepen our understanding of the mechanisms underlying diseases and cell differentiation and contribute significantly to personalized medicine.
Collapse
Affiliation(s)
- Abdur Rahman M. A. Basher
- Vascular Biology Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Caleb Hallinan
- Vascular Biology Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Kwonmoo Lee
- Vascular Biology Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
11
|
Sharma NS, Choudhary B. Good Cop, Bad Cop: Profiling the Immune Landscape in Multiple Myeloma. Biomolecules 2023; 13:1629. [PMID: 38002311 PMCID: PMC10669790 DOI: 10.3390/biom13111629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/26/2023] Open
Abstract
Multiple myeloma (MM) is a dyscrasia of plasma cells (PCs) characterized by abnormal immunoglobulin (Ig) production. The disease remains incurable due to a multitude of mutations and structural abnormalities in MM cells, coupled with a favorable microenvironment and immune suppression that eventually contribute to the development of drug resistance. The bone marrow microenvironment (BMME) is composed of a cellular component comprising stromal cells, endothelial cells, osteoclasts, osteoblasts, and immune cells, and a non-cellular component made of the extracellular matrix (ECM) and the liquid milieu, which contains cytokines, growth factors, and chemokines. The bone marrow stromal cells (BMSCs) are involved in the adhesion of MM cells, promote the growth, proliferation, invasion, and drug resistance of MM cells, and are also crucial in angiogenesis and the formation of lytic bone lesions. Classical immunophenotyping in combination with advanced immune profiling using single-cell sequencing technologies has enabled immune cell-specific gene expression analysis in MM to further elucidate the roles of specific immune cell fractions from peripheral blood and bone marrow (BM) in myelomagenesis and progression, immune evasion and exhaustion mechanisms, and development of drug resistance and relapse. The review describes the role of BMME components in MM development and ongoing clinical trials using immunotherapeutic approaches.
Collapse
Affiliation(s)
- Niyati Seshagiri Sharma
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Electronic City, Bengaluru 560100, India
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Electronic City, Bengaluru 560100, India
| |
Collapse
|
12
|
Thomsen LCV, Kleinmanns K, Anandan S, Gullaksen SE, Abdelaal T, Iversen GA, Akslen LA, McCormack E, Bjørge L. Combining Mass Cytometry Data by CyTOFmerge Reveals Additional Cell Phenotypes in the Heterogeneous Ovarian Cancer Tumor Microenvironment: A Pilot Study. Cancers (Basel) 2023; 15:5106. [PMID: 37894472 PMCID: PMC10605295 DOI: 10.3390/cancers15205106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
The prognosis of high-grade serous ovarian carcinoma (HGSOC) is poor, and treatment selection is challenging. A heterogeneous tumor microenvironment (TME) characterizes HGSOC and influences tumor growth, progression, and therapy response. Better characterization with multidimensional approaches for simultaneous identification and categorization of the various cell populations is needed to map the TME complexity. While mass cytometry allows the simultaneous detection of around 40 proteins, the CyTOFmerge MATLAB algorithm integrates data sets and extends the phenotyping. This pilot study explored the potential of combining two datasets for improved TME phenotyping by profiling single-cell suspensions from ten chemo-naïve HGSOC tumors by mass cytometry. A 35-marker pan-tumor dataset and a 34-marker pan-immune dataset were analyzed separately and combined with the CyTOFmerge, merging 18 shared markers. While the merged analysis confirmed heterogeneity across patients, it also identified a main tumor cell subset, additionally to the nine identified by the pan-tumor panel. Furthermore, the expression of traditional immune cell markers on tumor and stromal cells was revealed, as were marker combinations that have rarely been examined on individual cells. This study demonstrates the potential of merging mass cytometry data to generate new hypotheses on tumor biology and predictive biomarker research in HGSOC that could improve treatment effectiveness.
Collapse
Affiliation(s)
- Liv Cecilie Vestrheim Thomsen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, 5021 Bergen, Norway
- Norwegian Institute of Public Health, 5015 Bergen, Norway
| | - Katrin Kleinmanns
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Shamundeeswari Anandan
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Stein-Erik Gullaksen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Tamim Abdelaal
- Delft Bioinformatics Laboratory, Delft University of Technology, 2628XE Delft, The Netherlands
- Department of Radiology, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Grete Alrek Iversen
- Department of Obstetrics and Gynecology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Lars Andreas Akslen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway
- Department of Pathology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Emmet McCormack
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Centre for Pharmacy, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Line Bjørge
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, 5021 Bergen, Norway
| |
Collapse
|
13
|
Chatziioannou E, Roßner J, Aung TN, Rimm DL, Niessner H, Keim U, Serna-Higuita LM, Bonzheim I, Kuhn Cuellar L, Westphal D, Steininger J, Meier F, Pop OT, Forchhammer S, Flatz L, Eigentler T, Garbe C, Röcken M, Amaral T, Sinnberg T. Deep learning-based scoring of tumour-infiltrating lymphocytes is prognostic in primary melanoma and predictive to PD-1 checkpoint inhibition in melanoma metastases. EBioMedicine 2023; 93:104644. [PMID: 37295047 PMCID: PMC10363450 DOI: 10.1016/j.ebiom.2023.104644] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 05/15/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Recent advances in digital pathology have enabled accurate and standardised enumeration of tumour-infiltrating lymphocytes (TILs). Here, we aim to evaluate TILs as a percentage electronic TIL score (eTILs) and investigate its prognostic and predictive relevance in cutaneous melanoma. METHODS We included stage I to IV cutaneous melanoma patients and used hematoxylin-eosin-stained slides for TIL analysis. We assessed eTILs as a continuous and categorical variable using the published cut-off of 16.6% and applied Cox regression models to evaluate associations of eTILs with relapse-free, distant metastasis-free, and overall survival. We compared eTILs of the primaries with matched metastasis. Moreover, we assessed the predictive relevance of eTILs in therapy-naïve metastases according to the first-line therapy. FINDINGS We analysed 321 primary cutaneous melanomas and 191 metastatic samples. In simple Cox regression, tumour thickness (p < 0.0001), presence of ulceration (p = 0.0001) and eTILs ≤16.6% (p = 0.0012) were found to be significant unfavourable prognostic factors for RFS. In multiple Cox regression, eTILs ≤16.6% (p = 0.0161) remained significant and downgraded the current staging. Lower eTILs in the primary tissue was associated with unfavourable relapse-free (p = 0.0014) and distant metastasis-free survival (p = 0.0056). In multiple Cox regression adjusted for tumour thickness and ulceration, eTILs as continuous remained significant (p = 0.019). When comparing TILs in primary tissue and corresponding metastasis of the same patient, eTILs in metastases was lower than in primary melanomas (p < 0.0001). In therapy-naïve metastases, an eTILs >12.2% was associated with longer progression-free survival (p = 0.037) and melanoma-specific survival (p = 0.0038) in patients treated with anti-PD-1-based immunotherapy. In multiple Cox regression, lactate dehydrogenase (p < 0.0001) and eTILs ≤12.2% (p = 0.0130) were significantly associated with unfavourable melanoma-specific survival. INTERPRETATION Assessment of TILs is prognostic in primary melanoma samples, and the eTILs complements staging. In therapy-naïve metastases, eTILs ≤12.2% is predictive of unfavourable survival outcomes in patients receiving anti-PD-1-based therapy. FUNDING See a detailed list of funding bodies in the Acknowledgements section at the end of the manuscript.
Collapse
Affiliation(s)
- Eftychia Chatziioannou
- Department of Dermatology, University of Tübingen, Liebermeisterstr. 25, 72076 Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Tübingen, Germany
| | - Jana Roßner
- Department of Dermatology, University of Heidelberg, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany
| | - Thazin New Aung
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Heike Niessner
- Department of Dermatology, University of Tübingen, Liebermeisterstr. 25, 72076 Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Tübingen, Germany
| | - Ulrike Keim
- Department of Dermatology, University of Tübingen, Liebermeisterstr. 25, 72076 Tübingen, Germany
| | - Lina Maria Serna-Higuita
- Department of Clinical Epidemiology and Applied Biostatistics, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
| | - Irina Bonzheim
- Institute of Pathology and Neuropathology, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
| | - Luis Kuhn Cuellar
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Dana Westphal
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Skin Cancer Center at the University Cancer Center and National Center for Tumor Diseases, Technical University Dresden, 01307 Dresden, Germany
| | - Julian Steininger
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Skin Cancer Center at the University Cancer Center and National Center for Tumor Diseases, Technical University Dresden, 01307 Dresden, Germany
| | - Friedegund Meier
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Skin Cancer Center at the University Cancer Center and National Center for Tumor Diseases, Technical University Dresden, 01307 Dresden, Germany
| | - Oltin Tiberiu Pop
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Stephan Forchhammer
- Department of Dermatology, University of Tübingen, Liebermeisterstr. 25, 72076 Tübingen, Germany
| | - Lukas Flatz
- Department of Dermatology, University of Tübingen, Liebermeisterstr. 25, 72076 Tübingen, Germany; Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Thomas Eigentler
- Department of Dermatology, Venereology and Allergology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Claus Garbe
- Department of Dermatology, University of Tübingen, Liebermeisterstr. 25, 72076 Tübingen, Germany
| | - Martin Röcken
- Department of Dermatology, University of Tübingen, Liebermeisterstr. 25, 72076 Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Tübingen, Germany
| | - Teresa Amaral
- Department of Dermatology, University of Tübingen, Liebermeisterstr. 25, 72076 Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Tübingen, Germany
| | - Tobias Sinnberg
- Department of Dermatology, University of Tübingen, Liebermeisterstr. 25, 72076 Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Tübingen, Germany; Department of Dermatology, Venereology and Allergology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| |
Collapse
|
14
|
Shen K, Ke S, Chen B, Zhang T, Wang H, Lv J, Gao W. Identification and validation of biomarkers for epithelial-mesenchymal transition-related cells to estimate the prognosis and immune microenvironment in primary gastric cancer by the integrated analysis of single-cell and bulk RNA sequencing data. Math Biosci Eng 2023; 20:13798-13823. [PMID: 37679111 DOI: 10.3934/mbe.2023614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
BACKGROUND The epithelial-mesenchymal transition (EMT) is associated with gastric cancer (GC) progression and immune microenvironment. To better understand the heterogeneity underlying EMT, we integrated single-cell RNA-sequencing (scRNA-seq) data and bulk sequencing data from GC patients to evaluate the prognostic utility of biomarkers for EMT-related cells (ERCs), namely, cancer-associated fibroblasts (CAFs) and epithelial cells (ECs). METHODS scRNA-seq data from primary GC tumor samples were obtained from the Gene Expression Omnibus (GEO) database to identify ERC marker genes. Bulk GC datasets from the Cancer Genome Atlas (TCGA) and GEO were used as training and validation sets, respectively. Differentially expressed markers were identified from the TCGA database. Univariate Cox, least-absolute shrinkage, and selection operator regression analyses were performed to identify EMT-related cell-prognostic genes (ERCPGs). Kaplan-Meier, Cox regression, and receiver-operating characteristic (ROC) curve analyses were adopted to evaluate the prognostic utility of the ERCPG signature. An ERCPG-based nomogram was constructed by integrating independent prognostic factors. Finally, we evaluated the correlations between the ERCPG signature and immune-cell infiltration and verified the expression of ERCPG prognostic signature genes by in vitro cellular assays. RESULTS The ERCPG signature was comprised of seven genes (COL4A1, F2R, MMP11, CAV1, VCAN, FKBP10, and APOD). Patients were divided into high- and low-risk groups based on the ERCPG risk scores. Patients in the high-risk group showed a poor prognosis. ROC and calibration curves suggested that the ERCPG signature and nomogram had a good prognostic utility. An immune cell-infiltration analysis suggested that the abnormal expression of ERCPGs induced the formation of an unfavorable tumor immune microenvironment. In vitro cellular assays showed that ERCPGs were more abundantly expressed in GC cell lines compared to normal gastric tissue cell lines. CONCLUSIONS We constructed and validated an ERCPG signature using scRNA-seq and bulk sequencing data from ERCs of GC patients. Our findings support the estimation of patient prognosis and tumor treatment in future clinical practice.
Collapse
Affiliation(s)
- Kaiyu Shen
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Shuaiyi Ke
- Department of Internal Medicine, XianJu People's Hospital, XianJu 317399, China
| | - Binyu Chen
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Tiantian Zhang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Hongtai Wang
- Department of General Surgery, XianJu People' Hospital, XianJu 317399, China
| | - Jianhui Lv
- Department of General Surgery, XianJu People' Hospital, XianJu 317399, China
| | - Wencang Gao
- Department of Oncology, Zhejiang Chinese Medical University, Hangzhou 310005, China
| |
Collapse
|
15
|
Geras A, Darvish Shafighi S, Domżał K, Filipiuk I, Rączkowska A, Szymczak P, Toosi H, Kaczmarek L, Koperski Ł, Lagergren J, Nowis D, Szczurek E. Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data. Genome Biol 2023; 24:120. [PMID: 37198601 PMCID: PMC10190053 DOI: 10.1186/s13059-023-02951-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 04/21/2023] [Indexed: 05/19/2023] Open
Abstract
Spatial transcriptomics maps gene expression across tissues, posing the challenge of determining the spatial arrangement of different cell types. However, spatial transcriptomics spots contain multiple cells. Therefore, the observed signal comes from mixtures of cells of different types. Here, we propose an innovative probabilistic model, Celloscope, that utilizes established prior knowledge on marker genes for cell type deconvolution from spatial transcriptomics data. Celloscope outperforms other methods on simulated data, successfully indicates known brain structures and spatially distinguishes between inhibitory and excitatory neuron types based in mouse brain tissue, and dissects large heterogeneity of immune infiltrate composition in prostate gland tissue.
Collapse
Affiliation(s)
- Agnieszka Geras
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw, Poland
| | - Shadi Darvish Shafighi
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw, Poland
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR, Paris, France
| | - Kacper Domżał
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw, Poland
| | - Igor Filipiuk
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw, Poland
| | - Alicja Rączkowska
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw, Poland
| | - Paulina Szymczak
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw, Poland
| | - Hosein Toosi
- KTH Royal Institute of Technology, Stockholm, Sweden
| | - Leszek Kaczmarek
- BRAINCITY, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Łukasz Koperski
- Department of Pathology, Medical University of Warsaw, Warsaw, Poland
| | | | - Dominika Nowis
- Laboratory of Experimental Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Szczurek
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw, Poland.
| |
Collapse
|
16
|
Mahdavi Sharif P, Pastaki Khoshbin A, Nasrollahzadeh E, Keshavarz-fathi M, Rezaei N. Tumor immunology. Clin Immunol 2023. [DOI: 10.1016/b978-0-12-818006-8.00003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
17
|
Venkatesiah SS, Augustine D, Mishra D, Gujjar N, Haragannavar VC, Awan KH, Patil S. Immunology of Oral Squamous Cell Carcinoma-A Comprehensive Insight with Recent Concepts. Life (Basel) 2022; 12:1807. [PMID: 36362963 PMCID: PMC9695443 DOI: 10.3390/life12111807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/30/2022] [Accepted: 11/02/2022] [Indexed: 09/28/2023] Open
Abstract
This review aims to understand the concept of oral cancer immunology through the notion of immune profiling, immunoediting and immunotherapy, and to gain knowledge regarding its application for the management of oral cancer patients. Oral cancer is an immunogenic tumor where the cells of the tumor microenvironment play an important role in tumorigenesis. Understanding the mechanism of these modulations can help design immunotherapeutic strategies in oral cancer patients. This article gives an overview of immunomodulation in the oral cancer tumor microenvironment, with concepts of immune profiling, immunoediting and immunotherapy. English literature searches via Google Scholar, Web of Science, EBSCO, Scopus, and PubMed database were performed with the key words immunology, tumor microenvironment, cells, cross talk, immune profiling, biomarkers, inflammation, gene expression, techniques, immunoediting, immunosurveillance, tumor escape, immunotherapy, immune checkpoint inhibitors, vaccines in cancer, oral cancer, and head and neck cancer. Original research articles, reviews, and case reports published from 2016-2021 (n = 81) were included to appraise different topics, and were discussed under the following subsections. Literature published on oral cancer immunology reveals that oral cancer immune profiling with appropriate markers and techniques and knowledge on immunoediting concepts can help design and play an effective role in immunotherapeutic management of oral cancer patients. An evaluation of oral cancer immunology helps to determine its role in tumorigenesis, and immunotherapy could be the emerging drift in the effective management of oral cancer.
Collapse
Affiliation(s)
- Sowmya Samudrala Venkatesiah
- Department of Oral Pathology & Microbiology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, MSR Nagar, Bengaluru 560054, India
| | - Dominic Augustine
- Department of Oral Pathology & Microbiology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, MSR Nagar, Bengaluru 560054, India
| | - Deepika Mishra
- Department of Oral Pathology & Microbiology, Centre for Dental Education and Research, All India Institute of Medical Sciences (AIIMS), Delhi 110608, India
| | - Neethi Gujjar
- Department of Oral Pathology & Microbiology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, MSR Nagar, Bengaluru 560054, India
| | - Vanishri C. Haragannavar
- Department of Oral Pathology & Microbiology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, MSR Nagar, Bengaluru 560054, India
| | - Kamran Habib Awan
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UT 84095, USA
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UT 84095, USA
- Centre of Molecular Medicine and Diagnostics (COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences University, Chennai 600077, India
| |
Collapse
|
18
|
So JY, Ohm J, Lipkowitz S, Yang L. Triple negative breast cancer (TNBC): Non-genetic tumor heterogeneity and immune microenvironment: Emerging treatment options. Pharmacol Ther 2022; 237:108253. [PMID: 35872332 PMCID: PMC9378710 DOI: 10.1016/j.pharmthera.2022.108253] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/01/2022] [Accepted: 07/18/2022] [Indexed: 12/17/2022]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by extensive intra-tumoral heterogeneity, and frequently develops resistance to therapies. Tumor heterogeneity and lack of biomarkers are thought to be some of the most difficult challenges driving therapeutic resistance and relapse. This review will summarize current therapy for TNBC, studies in treatment resistance and relapse, including data from recent single cell sequencing. We will discuss changes in both the transcriptome and epigenome of TNBC, and we will review mechanisms regulating the immune microenvironment. Lastly, we will provide new perspective in patient stratification, and treatment options targeting transcriptome dysregulation and the immune microenvironment of TNBC patients.
Collapse
Affiliation(s)
- Jae Young So
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joyce Ohm
- Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Stan Lipkowitz
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Yang
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
19
|
Lee JY, Kannan B, Lim BY, Li Z, Lim AH, Loh JW, Ko TK, Ng CCY, Chan JY. The Multi-Dimensional Biomarker Landscape in Cancer Immunotherapy. Int J Mol Sci 2022; 23:7839. [PMID: 35887186 PMCID: PMC9323480 DOI: 10.3390/ijms23147839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/10/2022] [Accepted: 07/14/2022] [Indexed: 02/04/2023] Open
Abstract
The field of immuno-oncology is now at the forefront of cancer care and is rapidly evolving. The immune checkpoint blockade has been demonstrated to restore antitumor responses in several cancer types. However, durable responses can be observed only in a subset of patients, highlighting the importance of investigating the tumor microenvironment (TME) and cellular heterogeneity to define the phenotypes that contribute to resistance as opposed to those that confer susceptibility to immune surveillance and immunotherapy. In this review, we summarize how some of the most widely used conventional technologies and biomarkers may be useful for the purpose of predicting immunotherapy outcomes in patients, and discuss their shortcomings. We also provide an overview of how emerging single-cell spatial omics may be applied to further advance our understanding of the interactions within the TME, and how these technologies help to deliver important new insights into biomarker discovery to improve the prediction of patient response.
Collapse
Affiliation(s)
- Jing Yi Lee
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Bavani Kannan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Boon Yee Lim
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Zhimei Li
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Abner Herbert Lim
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Jui Wan Loh
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Tun Kiat Ko
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Cedric Chuan-Young Ng
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Jason Yongsheng Chan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore 169857, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| |
Collapse
|
20
|
Hingorani DV, Allevato MM, Camargo MF, Lesperance J, Quraishi MA, Aguilera J, Franiak-Pietryga I, Scanderbeg DJ, Wang Z, Molinolo AA, Alvarado D, Sharabi AB, Bui JD, Cohen EEW, Adams SR, Gutkind JS, Advani SJ. Monomethyl auristatin antibody and peptide drug conjugates for trimodal cancer chemo-radio-immunotherapy. Nat Commun 2022; 13:3869. [PMID: 35790753 PMCID: PMC9256669 DOI: 10.1038/s41467-022-31601-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 06/24/2022] [Indexed: 12/20/2022] Open
Abstract
Locally advanced cancers remain therapeutically challenging to eradicate. The most successful treatments continue to combine decades old non-targeted chemotherapies with radiotherapy that unfortunately increase normal tissue damage in the irradiated field and have systemic toxicities precluding further treatment intensification. Therefore, alternative molecularly guided systemic therapies are needed to improve patient outcomes when applied with radiotherapy. In this work, we report a trimodal precision cytotoxic chemo-radio-immunotherapy paradigm using spatially targeted auristatin warheads. Tumor-directed antibodies and peptides conjugated to radiosensitizing monomethyl auristatin E (MMAE) specifically produce CD8 T cell dependent durable tumor control of irradiated tumors and immunologic memory. In combination with ionizing radiation, MMAE sculpts the tumor immune infiltrate to potentiate immune checkpoint inhibition. Here, we report therapeutic synergies of targeted cytotoxic auristatin radiosensitization to stimulate anti-tumor immune responses providing a rationale for clinical translational of auristatin antibody drug conjugates with radio-immunotherapy combinations to improve tumor control.
Collapse
Affiliation(s)
- Dina V Hingorani
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michael M Allevato
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Maria F Camargo
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jacqueline Lesperance
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Maryam A Quraishi
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Joseph Aguilera
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ida Franiak-Pietryga
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniel J Scanderbeg
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Zhiyong Wang
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alfredo A Molinolo
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA
- UC San Diego, Moores Cancer Center, La Jolla, CA, 92093, USA
| | | | - Andrew B Sharabi
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- UC San Diego, Moores Cancer Center, La Jolla, CA, 92093, USA
| | - Jack D Bui
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA
- UC San Diego, Moores Cancer Center, La Jolla, CA, 92093, USA
| | - Ezra E W Cohen
- UC San Diego, Moores Cancer Center, La Jolla, CA, 92093, USA
- Department of Medicine, Division of Hematology and Oncology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Stephen R Adams
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | - J Silvio Gutkind
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
- UC San Diego, Moores Cancer Center, La Jolla, CA, 92093, USA
| | - Sunil J Advani
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
- UC San Diego, Moores Cancer Center, La Jolla, CA, 92093, USA.
| |
Collapse
|
21
|
Hamilton AM, Hurson AN, Olsson LT, Walens A, Nsonwu-Farley J, Kirk EL, Abdou Y, Downs-Canner SM, Serody JS, Perou CM, Calhoun BC, Troester MA, Hoadley KA. The Landscape of Immune Microenvironments in Racially Diverse Breast Cancer Patients. Cancer Epidemiol Biomarkers Prev 2022; 31:1341-1350. [PMID: 35437570 PMCID: PMC9292136 DOI: 10.1158/1055-9965.epi-21-1312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/01/2022] [Accepted: 04/12/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Immunotherapy is a rapidly evolving treatment option in breast cancer; However, the breast cancer immune microenvironment is understudied in Black and younger (<50 years) patients. METHODS We used histologic and RNA-based immunoprofiling methods to characterize the breast cancer immune landscape in 1,952 tumors from the Carolina Breast Cancer Study (CBCS), a population-based study that oversampled Black (n = 1,030) and young women (n = 1,039). We evaluated immune response leveraging markers for 10 immune cell populations, compared profiles to those in The Cancer Genome Atlas (TCGA) Project [n = 1,095 tumors, Black (n = 183), and young women (n = 295)], and evaluated in association with clinical and demographic variables, including recurrence. RESULTS Consensus clustering identified three immune clusters in CBCS (adaptive-enriched, innate-enriched, or immune-quiet) that varied in frequency by race, age, tumor grade and subtype; however, only two clusters were identified in TCGA, which were predominantly comprised of adaptive-enriched and innate-enriched tumors. In CBCS, the strongest adaptive immune response was observed for basal-like, HER2-positive (HER2+), triple-negative breast cancer (TNBC), and high-grade tumors. Younger patients had higher proportions of adaptive-enriched tumors, particularly among estrogen receptor (ER)-negative (ER-) cases. Black patients had higher frequencies of both adaptive-enriched and innate-enriched tumors. Immune clusters were associated with recurrence among ER- tumors, with adaptive-enriched showing the best and innate-enriched showing the poorest 5-year recurrence-free survival. CONCLUSIONS These data suggest that immune microenvironments are intricately related to race, age, tumor subtype, and grade. IMPACT Given higher mortality among Black and young women, more defined immune classification using cell-type-specific panels could help explain higher recurrence and ultimately lead to targetable interventions.
Collapse
Affiliation(s)
- Alina M. Hamilton
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Amber N. Hurson
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Linnea T. Olsson
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Andrea Walens
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Joseph Nsonwu-Farley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Erin L. Kirk
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yara Abdou
- Department of Medicine, Division of Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephanie M. Downs-Canner
- Department of Surgery, Division of Surgical Oncology and Endocrine Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Jonathan S. Serody
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Charles M. Perou
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Benjamin C. Calhoun
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Melissa A. Troester
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Katherine A. Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| |
Collapse
|
22
|
Abstract
Historically, non-small-cell lung cancer (NSCLC) has been regarded as a nonimmunogenic tumor; however, recent studies have shown that NSCLCs are among the most responsive cancers to monoclonal antibody immune checkpoint inhibitors (ICIs). ICIs have dramatically improved clinical outcomes for a subset of patients (∼20%) with locally advanced and metastatic NSCLC, and they have also demonstrated promise as neoadjuvant therapy for early-stage resectable disease. Nevertheless, the majority of patients with NSCLC are refractory to ICIs for reasons that are poorly understood. Thus, major questions are: how do we initially identify the patients most likely to derive significant clinical benefit from these therapies; how can we increase the number of patients benefiting; what are the mechanisms of primary and acquired resistance to immune-based therapies; are there additional immune checkpoints besides PD-1/PD-L1 and CTLA-4 that can be targeted to provide greater clinical benefit to patients; and how do we best combine ICI therapy with surgery, radiotherapy, chemotherapy, and targeted therapy? To answer these questions, we need to deploy the latest technologies to study tumors and their microenvironment and how they interact with components of the innate and adaptive immune systems. There is also a need for new preclinical model systems to investigate the molecular mechanisms of resistance to treatment and identify novel therapeutic targets. Recent advances in technology are beginning to shed new light on the immune landscape of NSCLC that may uncover biomarkers of response and maximize the clinical benefit of immune-based therapies. Identification of the mechanisms of resistance should lead to the identification of novel targets and the generation of new therapeutic strategies that improve outcomes for a greater number of patients. In the sections below, we discuss the results of studies examining the immune microenvironment in NSCLC, summarize the clinical experience with immunotherapy for NSCLC, and review candidate biomarkers of response to these agents in NSCLC.
Collapse
Affiliation(s)
- Tina Cascone
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jared Fradette
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Monika Pradhan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| |
Collapse
|
23
|
Ahmed AA, Strong MJ, Zhou X, Robinson T, Rocco S, Siegel GW, Clines GA, Moore BB, Keller ET, Szerlip NJ. Differential immune landscapes in appendicular versus axial skeleton. PLoS One 2022; 17:e0267642. [PMID: 35476843 PMCID: PMC9045623 DOI: 10.1371/journal.pone.0267642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
Roughly 400,000 people in the U.S. are living with bone metastases, the vast majority occurring in the spine. Metastases to the spine result in fractures, pain, paralysis, and significant health care costs. This predilection for cancer to metastasize to the bone is seen across most cancer histologies, with the greatest incidence seen in prostate, breast, and lung cancer. The molecular process involved in this predilection for axial versus appendicular skeleton is not fully understood, although it is likely that a combination of tumor and local micro-environmental factors plays a role. Immune cells are an important constituent of the bone marrow microenvironment and many of these cells have been shown to play a significant role in tumor growth and progression in soft tissue and bone disease. With this in mind, we sought to examine the differences in immune landscape between axial and appendicular bones in the normal noncancerous setting in order to obtain an understanding of these landscapes. To accomplish this, we utilized mass cytometry by time-of-flight (CyTOF) to examine differences in the immune cell landscapes between the long bone and vertebral body bone marrow from patient clinical samples and C57BL/6J mice. We demonstrate significant differences between immune populations in both murine and human marrow with a predominance of myeloid progenitor cells in the spine. Additionally, cytokine analysis revealed differences in concentrations favoring a more myeloid enriched population of cells in the vertebral body bone marrow. These differences could have clinical implications with respect to the distribution and permissive growth of bone metastases.
Collapse
Affiliation(s)
- Aqila A. Ahmed
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Michael J. Strong
- Department of Neurosurgery, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Xiaofeng Zhou
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tyler Robinson
- Department of Urology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sabrina Rocco
- Department of Neurosurgery, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Geoffrey W. Siegel
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gregory A. Clines
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Veterans Affairs Medical Center, Ann Arbor, Michigan, United States of America
| | - Bethany B. Moore
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Evan T. Keller
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Urology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nicholas J. Szerlip
- Department of Neurosurgery, University of Michigan, Ann Arbor, Michigan, United States of America
- Veterans Affairs Medical Center, Ann Arbor, Michigan, United States of America
- * E-mail:
| |
Collapse
|
24
|
Zhang X, Moore CM, Harmacek LD, Domenico J, Rangaraj VR, Ideozu JE, Knapp JR, Woods KJ, Jump S, Jia S, Prokop JW, Bowler R, Hessner MJ, Gelfand EW, Levy H. CFTR-mediated monocyte/macrophage dysfunction revealed by cystic fibrosis proband-parent comparisons. JCI Insight 2022; 7:152186. [PMID: 35315363 PMCID: PMC8986072 DOI: 10.1172/jci.insight.152186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 02/02/2022] [Indexed: 12/23/2022] Open
Abstract
Cystic fibrosis (CF) is an inherited disorder caused by biallelic mutations of the CF transmembrane conductance regulator (CFTR) gene. Converging evidence suggests that CF carriers with only 1 defective CFTR copy are at increased risk for CF-related conditions and pulmonary infections, but the molecular mechanisms underpinning this effect remain unknown. We performed transcriptomic profiling of peripheral blood mononuclear cells (PBMCs) of CF child-parent trios (proband, father, and mother) and healthy control (HC) PBMCs or THP-1 cells incubated with the plasma of these participants. Transcriptomic analyses revealed suppression of cytokine-enriched immune-related genes (IL-1β, CXCL8, CREM), implicating lipopolysaccharide tolerance in innate immune cells (monocytes) of CF probands and their parents. These data suggest that a homozygous as well as a heterozygous CFTR mutation can modulate the immune/inflammatory system. This conclusion is further supported by the finding of lower numbers of circulating monocytes in CF probands and their parents, compared with HCs, and the abundance of mononuclear phagocyte subsets, which correlated with Pseudomonas aeruginosa infection, lung disease severity, and CF progression in the probands. This study provides insight into demonstrated CFTR-related innate immune dysfunction in individuals with CF and carriers of a CFTR mutation that may serve as a target for personalized therapy.
Collapse
Affiliation(s)
- Xi Zhang
- Data Science program, Weinberg College of Arts and Sciences, Northwestern University, Evanston, Illinois, USA.,Division of Pediatric Pulmonary Medicine, Department of Pediatrics, and
| | - Camille M Moore
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Laura D Harmacek
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Joanne Domenico
- Division of Pediatric Pulmonary Medicine, Department of Pediatrics, and
| | - Vittobai Rashika Rangaraj
- Division of Pulmonary & Sleep Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Justin E Ideozu
- Genomic Medicine, Genomics Research Center, AbbVie, North Chicago, Illinois, USA
| | - Jennifer R Knapp
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Katherine J Woods
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Stephanie Jump
- Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
| | - Shuang Jia
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Max McGee Center for Juvenile Diabetes, Children's Research Institute, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Russell Bowler
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Martin J Hessner
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Max McGee Center for Juvenile Diabetes, Children's Research Institute, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, USA
| | - Erwin W Gelfand
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA.,Division of Immunology, Microbiology and Pediatrics, Department of Pediatrics, University of Colorado School of Medicine, Denver, Colorado, USA
| | - Hara Levy
- Division of Pediatric Pulmonary Medicine, Department of Pediatrics, and
| |
Collapse
|
25
|
Capobianco E. High-dimensional role of AI and machine learning in cancer research. Br J Cancer 2022; 126:523-32. [PMID: 35013580 DOI: 10.1038/s41416-021-01689-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 11/23/2021] [Accepted: 12/23/2021] [Indexed: 01/12/2023] Open
Abstract
The role of Artificial Intelligence and Machine Learning in cancer research offers several advantages, primarily scaling up the information processing and increasing the accuracy of the clinical decision-making. The key enabling tools currently in use in Precision, Digital and Translational Medicine, here named as 'Intelligent Systems' (IS), leverage unprecedented data volumes and aim to model their underlying heterogeneous influences and variables correlated with patients' outcomes. As functionality and performance of IS are associated with complex diagnosis and therapy decisions, a rich spectrum of patterns and features detected in high-dimensional data may be critical for inference purposes. Many challenges are also present in such discovery task. First, the generation of interpretable model results from a mix of structured and unstructured input information. Second, the design, and implementation of automated clinical decision processes for drawing disease trajectories and patient profiles. Ultimately, the clinical impacts depend on the data effectively subjected to steps such as harmonisation, integration, validation, etc. The aim of this work is to discuss the transformative value of IS applied to multimodal data acquired through various interrelated cancer domains (high-throughput genomics, experimental biology, medical image processing, radiomics, patient electronic records, etc.).
Collapse
|
26
|
Li J, Sheng Q, Shyr Y, Liu Q. scMRMA: single cell multiresolution marker-based annotation. Nucleic Acids Res 2022; 50:e7. [PMID: 34648021 PMCID: PMC8789072 DOI: 10.1093/nar/gkab931] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/10/2021] [Accepted: 09/28/2021] [Indexed: 01/22/2023] Open
Abstract
Single-cell RNA sequencing has become a powerful tool for identifying and characterizing cellular heterogeneity. One essential step to understanding cellular heterogeneity is determining cell identities. The widely used strategy predicts identities by projecting cells or cell clusters unidirectionally against a reference to find the best match. Here, we develop a bidirectional method, scMRMA, where a hierarchical reference guides iterative clustering and deep annotation with enhanced resolutions. Taking full advantage of the reference, scMRMA greatly improves the annotation accuracy. scMRMA achieved better performance than existing methods in four benchmark datasets and successfully revealed the expansion of CD8 T cell populations in squamous cell carcinoma after anti-PD-1 treatment.
Collapse
Affiliation(s)
- Jia Li
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yu Shyr
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| |
Collapse
|
27
|
Kou Y, Li Z, Sun Q, Yang S, Wang Y, Hu C, Gu H, Wang H, Xu H, Li Y, Kou Y, Han B. Prognostic value and predictive biomarkers of phenotypes of tumor-associated macrophages in colorectal cancer. Scand J Immunol 2021; 95:e13137. [PMID: 34964155 PMCID: PMC9286461 DOI: 10.1111/sji.13137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 10/29/2021] [Accepted: 12/26/2021] [Indexed: 12/09/2022]
Abstract
BACKGROUND The roles of different subtypes of tumor-associated macrophages (TAMs) in predicting the prognosis of colorectal cancer (CRC) remain controversial. In this study, different subtypes of TAMs were investigated as prognostic and predictive biomarkers for CRC. METHODS Expressions of CD68, CD86 and CD163 were investigated by immunohistochemistry (IHC) and immunofluorescence (IF), and the correlation between the expression of CD86 and CD163 was calculated in colorectal cancer tissues from 64 CRC patients. RESULTS The results showed that high expressions of CD86+ and CD68+ CD86+ TAMs as well as low expression of CD163+ and CD68+ CD163+ TAMs were significantly associated with favorable overall survival (OS). The level of CD86 protein expression showed a negative correlation with CD163 protein expression. In addition, CD86 protein expression remarkably negative correlated with tumor differentiation and tumor node metastasis (TNM) stage, while CD163 protein expression significantly positive correlated with tumor differentiation and tumor size. As an independent risk factor, high expression of CD86 TAMs had prominently favorable prognostic efficacy while high expression of CD68+ CD163+ TAMs had significantly poor prognostic efficacy. CONCLUSIONS These results indicate that CD86+ and CD68+ CD163+ TAMs as prognostic and predictive biomarkers for CRC.
Collapse
Affiliation(s)
- Yu Kou
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medcine for Prevention and Treatment of Senile Diseases, Medical College of Yangzhou University, 225000, Jiangsu, China.,Department of Traditional Chinese Medicine Affiliated Hospital, Yangzhou University, 225000, Jiangsu, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, 225000, Jiangsu, China
| | - Zhuoqun Li
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medcine for Prevention and Treatment of Senile Diseases, Medical College of Yangzhou University, 225000, Jiangsu, China.,Department of Traditional Chinese Medicine Affiliated Hospital, Yangzhou University, 225000, Jiangsu, China
| | - Qidi Sun
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medcine for Prevention and Treatment of Senile Diseases, Medical College of Yangzhou University, 225000, Jiangsu, China.,Department of Traditional Chinese Medicine Affiliated Hospital, Yangzhou University, 225000, Jiangsu, China
| | - Shengnan Yang
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medcine for Prevention and Treatment of Senile Diseases, Medical College of Yangzhou University, 225000, Jiangsu, China.,Department of Traditional Chinese Medicine Affiliated Hospital, Yangzhou University, 225000, Jiangsu, China
| | - Yunshuai Wang
- Department of General Surgery, Luoyang Central Hospital Affiliated of Zhengzhou University, 471000, Henan, China
| | - Chen Hu
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medcine for Prevention and Treatment of Senile Diseases, Medical College of Yangzhou University, 225000, Jiangsu, China.,Department of Traditional Chinese Medicine Affiliated Hospital, Yangzhou University, 225000, Jiangsu, China
| | - Huijie Gu
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medcine for Prevention and Treatment of Senile Diseases, Medical College of Yangzhou University, 225000, Jiangsu, China.,Department of Traditional Chinese Medicine Affiliated Hospital, Yangzhou University, 225000, Jiangsu, China
| | - Huangjian Wang
- Department of General Surgery, Luoyang Central Hospital Affiliated of Zhengzhou University, 471000, Henan, China
| | - Hairong Xu
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medcine for Prevention and Treatment of Senile Diseases, Medical College of Yangzhou University, 225000, Jiangsu, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, 225000, Jiangsu, China
| | - Yan Li
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medcine for Prevention and Treatment of Senile Diseases, Medical College of Yangzhou University, 225000, Jiangsu, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, 225000, Jiangsu, China
| | - Yu Kou
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medcine for Prevention and Treatment of Senile Diseases, Medical College of Yangzhou University, 225000, Jiangsu, China.,Department of Traditional Chinese Medicine Affiliated Hospital, Yangzhou University, 225000, Jiangsu, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, 225000, Jiangsu, China
| | - Baowei Han
- Department of General Surgery, Luoyang Central Hospital Affiliated of Zhengzhou University, 471000, Henan, China
| |
Collapse
|
28
|
Kishi M, Asgarova A, Desterke C, Chaker D, Artus J, Turhan AG, Bennaceur-Griscelli A, Griscelli F. Evidence of Antitumor and Antimetastatic Potential of Induced Pluripotent Stem Cell-Based Vaccines in Cancer Immunotherapy. Front Med (Lausanne) 2021; 8:729018. [PMID: 34957134 PMCID: PMC8702815 DOI: 10.3389/fmed.2021.729018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/18/2021] [Indexed: 12/27/2022] Open
Abstract
Cancer is maintained by the activity of a rare population of self-renewing "cancer stem cells" (CSCs), which are resistant to conventional therapies. CSCs over-express several proteins shared with induced pluripotent stem cells (iPSCs). We show here that allogenic or autologous murine iPSCs, combined with a histone deacetylase inhibitor (HDACi), are able to elicit major anti-tumor responses in a highly aggressive triple-negative breast cancer, as a relevant cancer stemness model. This immunotherapy strategy was effective in preventing tumor establishment and efficiently targeted CSCs by inducing extensive modifications of the tumor microenvironment. The anti-tumoral effect was correlated with the generation of CD4+, CD8+ T cells, and CD44+ CD62L- CCR7low CD127low T-effector memory cells, and the reduction of CD4+ CD25+FoxP3+ Tregs, Arg1+ CD11b+ Gr1+, and Arg1+ and CD11b+ Ly6+ myeloid-derived suppressor cell populations within the tumor. The anti-tumoral effect was associated with a reduction in metastatic dissemination and an improvement in the survival rate. These results demonstrate for the first time the clinical relevance of using an off-the-shelf allogeneic iPSC-based vaccine combined with an HDACi as a novel pan-cancer anti-cancer immunotherapy strategy against aggressive tumors harboring stemness features with high metastatic potential.
Collapse
Affiliation(s)
- Masae Kishi
- Institut National de la Santé et de la Recherche Médicale (INSERM) UA9-Human Pluripotent Stem Cell Core Facility, CITHERA Infrastructure-INGESTEM, Villejuif, France
| | - Afag Asgarova
- Institut National de la Santé et de la Recherche Médicale (INSERM) UA9-Human Pluripotent Stem Cell Core Facility, CITHERA Infrastructure-INGESTEM, Villejuif, France
| | - Christophe Desterke
- Institut National de la Santé et de la Recherche Médicale (INSERM) UA9-Human Pluripotent Stem Cell Core Facility, CITHERA Infrastructure-INGESTEM, Villejuif, France.,Université Paris-Saclay, Faculté de Médecine, Kremlin Bicêtre, France
| | - Diana Chaker
- Institut National de la Santé et de la Recherche Médicale (INSERM) UA9-Human Pluripotent Stem Cell Core Facility, CITHERA Infrastructure-INGESTEM, Villejuif, France
| | - Jérôme Artus
- Institut National de la Santé et de la Recherche Médicale (INSERM) UA9-Human Pluripotent Stem Cell Core Facility, CITHERA Infrastructure-INGESTEM, Villejuif, France.,Université Paris-Saclay, Faculté de Médecine, Kremlin Bicêtre, France
| | - Ali G Turhan
- Institut National de la Santé et de la Recherche Médicale (INSERM) UA9-Human Pluripotent Stem Cell Core Facility, CITHERA Infrastructure-INGESTEM, Villejuif, France.,Université Paris-Saclay, Faculté de Médecine, Kremlin Bicêtre, France.,APHP Paris-Saclay Service d'Hématologie, Hôpital Universitaire Paris Sud (AP-HP), Kremlin Bicêtre, France
| | - Annelise Bennaceur-Griscelli
- Institut National de la Santé et de la Recherche Médicale (INSERM) UA9-Human Pluripotent Stem Cell Core Facility, CITHERA Infrastructure-INGESTEM, Villejuif, France.,Université Paris-Saclay, Faculté de Médecine, Kremlin Bicêtre, France.,APHP Paris-Saclay Service d'Hématologie, Hôpital Universitaire Paris Sud (AP-HP), Kremlin Bicêtre, France
| | - Frank Griscelli
- Institut National de la Santé et de la Recherche Médicale (INSERM) UA9-Human Pluripotent Stem Cell Core Facility, CITHERA Infrastructure-INGESTEM, Villejuif, France.,Université Paris Descartes, Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France.,Département de Biologie Médicale et Pathologie Médicales, Gustave Roussy Cancer Campus, Villejuif, France
| |
Collapse
|
29
|
Zhou H, Gao Y, Li X, Shang S, Wang P, Zhi H, Guo S, Sun D, Liu H, Li X, Zhang Y, Ning S. Identifying and characterizing lincRNA genomic clusters reveals its cooperative functions in human cancer. J Transl Med 2021; 19:509. [PMID: 34906173 PMCID: PMC8672572 DOI: 10.1186/s12967-021-03179-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/03/2021] [Indexed: 02/01/2023] Open
Abstract
Background Emerging evidence has revealed that some long intergenic non-coding RNAs (lincRNAs) are likely to form clusters on the same chromosome, and lincRNA genomic clusters might play critical roles in the pathophysiological mechanism. However, the comprehensive investigation of lincRNA clustering is rarely studied, particularly the characterization of their functional significance across different cancer types. Methods In this study, we firstly constructed a computational method basing a sliding window approach for systematically identifying lincRNA genomic clusters. We then dissected these lincRNA genomic clusters to identify common characteristics in cooperative expression, conservation among divergent species, targeted miRNAs, and CNV frequency. Next, we performed comprehensive analyses in differentially-expressed patterns and overall survival outcomes for patients from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx) across multiple cancer types. Finally, we explored the underlying mechanisms of lincRNA genomic clusters by functional enrichment analysis, pathway analysis, and drug-target interaction. Results We identified lincRNA genomic clusters according to the algorithm. Clustering lincRNAs tended to be co-expressed, highly conserved, targeted by more miRNAs, and with similar deletion and duplication frequency, suggesting that lincRNA genomic clusters may exert their effects by acting in combination. We further systematically explored conserved and cancer-specific lincRNA genomic clusters, indicating they were involved in some important mechanisms of disease occurrence through diverse approaches. Furthermore, lincRNA genomic clusters can serve as biomarkers with potential clinical significance and involve in specific pathological processes in the development of cancer. Moreover, a lincRNA genomic cluster named Cluster127 in DLK1-DIO3 imprinted locus was discovered, which contained MEG3, MEG8, MEG9, MIR381HG, LINC02285, AL132709.5, and AL132709.1. Further analysis indicated that Cluster127 may have the potential for predicting prognosis in cancer and could play their roles by participating in the regulation of PI3K-AKT signaling pathway. Conclusions Clarification of the lincRNA genomic clusters specific roles in human cancers could be beneficial for understanding the molecular pathogenesis of different cancer types. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03179-5.
Collapse
Affiliation(s)
- Hanxiao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Shuang Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Dailin Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Hongjia Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| |
Collapse
|
30
|
Moore J, Ma L, Lazar AA, Barcellos-Hoff MH. Mammary tumor-derived transplants as breast cancer models to evaluate tumor-immune interactions and therapeutic responses. Cancer Res 2021; 82:365-376. [PMID: 34903599 DOI: 10.1158/0008-5472.can-21-0253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/25/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022]
Abstract
In breast cancer, the type and distribution of infiltrating immune cells are associated with clinical outcome. Moreover, infiltrated cancers with abundant tumor infiltrating lymphocytes (TIL) are more likely to respond to immunotherapy, while those in which CD8+ T cells are completely absent (deserts) or excluded are less likely to respond. Detailed understanding of this biology is limited by a lack of preclinical breast cancer models that recapitulate TIL distributions and their associated biology. Here we established mammary tumor-derived transplants (mTDT) from 12 Trp53 null mammary tumors in syngeneic BALB/cJ mice and examined the stability of their growth rate, TIL distribution, and transcriptomic profiles. All mTDT were estrogen receptor negative. Half of the parental tumors were classified as infiltrated, and the rest were divided between excluded and desert phenotypes. After two orthotopic passages, most (70%) mTDT from infiltrated parents recapitulated this pattern, whereas the desert or excluded parental patterns were maintained in about half of daughter mTDT. Approximately 30% of mTDT gave rise to lung or liver metastases, but metastasis was not associated with a TIL phenotype. Unsupervised transcriptomic analysis clustered mTDT according to their TIL spatial patterns. Infiltrated mTDT transplanted subcutaneously and orthotopically were resistant to anti-PD-L1. Profiling implicated prolonged antigen stimulation and loss of effector function of lymphocytes rather than T cell exhaustion in the lack of response of infiltrated mTDT to checkpoint blockade. In summary, the molecular diversity and immune complexity of mTDT will facilitate the dissection of mechanisms of breast cancer response to immunotherapies.
Collapse
Affiliation(s)
- Jade Moore
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Lin Ma
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Ann A Lazar
- Department of Oral Epidemiology, School of Dentistry, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco School of Medicine, San Francisco, California
| | - Mary Helen Barcellos-Hoff
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.
| |
Collapse
|
31
|
Qi X, Wang XQ, Jin L, Gao LX, Guo HF. Uncovering potential single nucleotide polymorphisms, copy number variations and related signaling pathways in primary Sjogren's syndrome. Bioengineered 2021; 12:9313-9331. [PMID: 34723755 PMCID: PMC8809958 DOI: 10.1080/21655979.2021.2000245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Primary Sjogren’s syndrome (pSS) is a complex systemic autoimmune disease, which is difficult to accurately diagnose due to symptom diversity in patients, especially at earlier stages. We tried to find potential single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and related signaling pathways. Genomic DNA was extracted from peripheral blood of 12 individuals (7 individuals from 3 pSS pedigrees and 5 sporadic cases) for whole-exome sequencing (WES) analysis. SNPs and CNVs were identified, followed by functional annotation of genes with SNPs and CNVs. Gene expression profile (involving 64 normal controls and 166 cases) was downloaded from the Gene Expression Omnibus database (GEO) dataset for differentially expression analysis. Sanger sequencing and in vitro validation was used to validate the identified SNPs and differentially expressed genes, respectively. A total of 5 SNPs were identified in both pedigrees and sporadic cases, such as FES, PPM1J, and TRAPPC9. A total of 3402 and 19 CNVs were identified in pedigrees and sporadic cases, respectively. Fifty-one differentially expressed genes were associated with immunity, such as BATF3, LAP3, BATF2, PARP9, and IL15RA. AMPK signaling pathway and cell adhesion molecules (CAMs) were the most significantly enriched signaling pathways of identified SNPs. Identified CNVs were associated with systemic lupus erythematosus, mineral absorption, and HTLV-I infection. IL2-STAT5 signaling, interferon-gamma response, and interferon-alpha response were significantly enriched immune related signaling pathways of identified differentially expressed genes. In conclusion, our study found some potential SNPs, CNVs, and related signaling pathways, which could be useful in understanding the pathological mechanism of pSS.
Collapse
Affiliation(s)
- Xuan Qi
- Department of Rheumatism and Immunology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xi-Qin Wang
- Internal Medicine, Yuhua Yunfang Integrated Traditional Chinese and Western Medicine Clinic, Shijiazhuang, Hebei, China
| | - Lu Jin
- Department of Rheumatism and Immunology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Li-Xia Gao
- Department of Rheumatism and Immunology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Hui-Fang Guo
- Department of Rheumatism and Immunology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| |
Collapse
|
32
|
Abstract
Immunotherapy is a rapidly growing field for cancer treatment. In contrast to conventional cancer therapies, immunotherapeutic strategies focus on reactivating the immune system to mount an antitumor response. Despite the encouraging outcome in clinical trials, a large proportion of patients still do not respond to treatment and many experience different degrees of immune-related adverse events. Furthermore, it is now increasingly appreciated that even many conventional cancer therapies such as radiotherapy could have a positive impact on the host immune system for better clinical response. Hence, there is a need to better understand tumor immunity in order to design immunotherapeutic strategies, especially evidence-based combination therapies, for improved clinical outcomes. With this aim, cancer research turned its attention to profiling the immune contexture of either the tumor microenvironment (TME) or peripheral blood to uncover mechanisms and biomarkers which might aid in precision immunotherapeutics. Conventional technologies used for this purpose were limited by the depth and dimensionality of the data. Advances in newer techniques have, however, greatly improved the breadth and depth, as well as the quantity and quality of data that can be obtained. The result of these advances is a wealth of new information and insights on how the TME could be affected by various immune cell-types, and how this might in turn impact the clinical outcome of cancer patients . We highlight herein some of the high-dimensional technologies currently employed in immune profiling in cancer and summarize the insights and potential benefits they could bring in designing better cancer immunotherapies.
Collapse
Affiliation(s)
- Samuel Chuah
- Translational Immunology Institute (TII), SingHealth-DukeNUS Academic Medical Centre, Singapore, Singapore
| | - Valerie Chew
- Translational Immunology Institute (TII), SingHealth-DukeNUS Academic Medical Centre, Singapore, Singapore
| |
Collapse
|
33
|
Maestri E, Duszka K, Kuznetsov VA. Immunity Depletion, Telomere Imbalance, and Cancer-Associated Metabolism Pathway Aberrations in Intestinal Mucosa upon Short-Term Caloric Restriction. Cancers (Basel) 2021; 13:cancers13133180. [PMID: 34202278 PMCID: PMC8267928 DOI: 10.3390/cancers13133180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 11/16/2022] Open
Abstract
Systems cancer biology analysis of calorie restriction (CR) mechanisms and pathways has not been carried out, leaving therapeutic benefits unclear. Using metadata analysis, we studied gene expression changes in normal mouse duodenum mucosa (DM) response to short-term (2-weeks) 25% CR as a biological model. Our results indicate cancer-associated genes consist of 26% of 467 CR responding differential expressed genes (DEGs). The DEGs were enriched with over-expressed cell cycle, oncogenes, and metabolic reprogramming pathways that determine tissue-specific tumorigenesis, cancer, and stem cell activation; tumor suppressors and apoptosis genes were under-expressed. DEG enrichments suggest telomeric maintenance misbalance and metabolic pathway activation playing dual (anti-cancer and pro-oncogenic) roles. The aberrant DEG profile of DM epithelial cells is found within CR-induced overexpression of Paneth cells and is coordinated significantly across GI tract tissues mucosa. Immune system genes (ISGs) consist of 37% of the total DEGs; the majority of ISGs are suppressed, including cell-autonomous immunity and tumor-immune surveillance. CR induces metabolic reprogramming, suppressing immune mechanics and activating oncogenic pathways. We introduce and argue for our network pro-oncogenic model of the mucosa multicellular tissue response to CR leading to aberrant transcription and pre-malignant states. These findings change the paradigm regarding CR's anti-cancer role, initiating specific treatment target development. This will aid future work to define critical oncogenic pathways preceding intestinal lesion development and biomarkers for earlier adenoma and colorectal cancer detection.
Collapse
Affiliation(s)
- Evan Maestri
- Department of Biochemistry and Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA;
- Department of Biology, SUNY University at Buffalo, Buffalo, NY 14260, USA
| | - Kalina Duszka
- Department of Nutritional Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria;
| | - Vladimir A. Kuznetsov
- Department of Biochemistry and Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA;
- Bioinformatics Institute, Biomedical Sciences Institutes A*STAR, Singapore 13867, Singapore
- Correspondence:
| |
Collapse
|
34
|
Aaes TL, Vandenabeele P. The intrinsic immunogenic properties of cancer cell lines, immunogenic cell death, and how these influence host antitumor immune responses. Cell Death Differ 2021; 28:843-860. [PMID: 33214663 PMCID: PMC7937679 DOI: 10.1038/s41418-020-00658-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 01/30/2023] Open
Abstract
Modern cancer therapies often involve the combination of tumor-directed cytotoxic strategies and generation of a host antitumor immune response. The latter is unleashed by immunotherapies that activate the immune system generating a more immunostimulatory tumor microenvironment and a stronger tumor antigen-specific immune response. Studying the interaction between antitumor cytotoxic therapies, dying cancer cells, and the innate and adaptive immune system requires appropriate experimental tumor models in mice. In this review, we discuss the immunostimulatory and immunosuppressive properties of cancer cell lines commonly used in immunogenic cell death (ICD) studies being apoptosis or necroptosis. We will especially focus on the antigenic component of immunogenicity. While in several cancer cell lines the epitopes of endogenously expressed tumor antigens are known, these intrinsic epitopes are rarely determined in experimental apoptotic or necroptotic ICD settings. Instead by far the most ICD research studies investigate the antigenic response against exogenously expressed model antigens such as ovalbumin or retroviral epitopes (e.g., AH1). In this review, we will argue that the immune response against endogenous tumor antigens and the immunopeptidome profile of cancer cell lines affect the eventual biological readouts in the typical prophylactic tumor vaccination type of experiments used in ICD research, and we will propose additional methods involving immunopeptidome profiling, major histocompatibility complex molecule expression, and identification of tumor-infiltrating immune cells to document intrinsic immunogenicity following different cell death modalities.
Collapse
Affiliation(s)
- Tania Løve Aaes
- grid.11486.3a0000000104788040Unit for Cell Clearance in Health and Disease, VIB Center for Inflammation Research, Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium ,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Peter Vandenabeele
- grid.5342.00000 0001 2069 7798Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium ,Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.11486.3a0000000104788040Unit of Molecular Signaling and Cell Death, VIB Center for Inflammation Research, Ghent, Belgium
| |
Collapse
|
35
|
Khella CA, Mehta GA, Mehta RN, Gatza ML. Recent Advances in Integrative Multi-Omics Research in Breast and Ovarian Cancer. J Pers Med 2021; 11:149. [PMID: 33669749 PMCID: PMC7922242 DOI: 10.3390/jpm11020149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 02/07/2023] Open
Abstract
The underlying molecular heterogeneity of cancer is responsible for the dynamic clinical landscape of this disease. The combination of genomic and proteomic alterations, including both inherited and acquired mutations, promotes tumor diversity and accounts for variable disease progression, therapeutic response, and clinical outcome. Recent advances in high-throughput proteogenomic profiling of tumor samples have resulted in the identification of novel oncogenic drivers, tumor suppressors, and signaling networks; biomarkers for the prediction of drug sensitivity and disease progression; and have contributed to the development of novel and more effective treatment strategies. In this review, we will focus on the impact of historical and recent advances in single platform and integrative proteogenomic studies in breast and ovarian cancer, which constitute two of the most lethal forms of cancer for women, and discuss the molecular similarities of these diseases, the impact of these findings on our understanding of tumor biology as well as the clinical applicability of these discoveries.
Collapse
Affiliation(s)
- Christen A Khella
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Gaurav A Mehta
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Rushabh N Mehta
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Michael L Gatza
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| |
Collapse
|
36
|
Wei C, Liu X, Wang Q, Li Q, Xie M. Identification of Hypoxia Signature to Assess the Tumor Immune Microenvironment and Predict Prognosis in Patients with Ovarian Cancer. Int J Endocrinol 2021; 2021:4156187. [PMID: 34950205 PMCID: PMC8692015 DOI: 10.1155/2021/4156187] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The 5-year overall survival rate of ovarian cancer (OC) patients is less than 40%. Hypoxia promotes the proliferation of OC cells and leads to the decline of cell immunity. It is crucial to find potential predictors or risk model related to OC prognosis. This study aimed at establishing the hypoxia-associated gene signature to assess tumor immune microenvironment and predicting the prognosis of OC. METHODS The gene expression data of 378 OC patients and 370 OC patients were downloaded from datasets. The hypoxia risk model was constructed to reflect the immune microenvironment in OC and predict prognosis. RESULTS 8 genes (AKAP12, ALDOC, ANGPTL4, CITED2, ISG20, PPP1R15A, PRDX5, and TGFBI) were included in the hypoxic gene signature. Patients in the high hypoxia risk group showed worse survival. Hypoxia signature significantly related to clinical features and may serve as an independent prognostic factor for OC patients. 2 types of immune cells, plasmacytoid dendritic cell and regulatory T cell, showed a significant infiltration in the tissues of the high hypoxia risk group patients. Most of the immunosuppressive genes (such as ARG1, CD160, CD244, CXCL12, DNMT1, and HAVCR1) and immune checkpoints (such as CD80, CTLA4, and CD274) were upregulated in the high hypoxia risk group. Gene sets related to the high hypoxia risk group were associated with signaling pathways of cell cycle, MAPK, mTOR, PI3K-Akt, VEGF, and AMPK. CONCLUSION The hypoxia risk model could serve as an independent prognostic indicator and reflect overall immune response intensity in the OC microenvironment.
Collapse
Affiliation(s)
- Chunyan Wei
- Department of Gynaecology and Obstetrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoqing Liu
- Department of Gynaecology and Obstetrics, Maternal and Child Health Hospital of Shangzhou District, Shangluo, Shanxi Province, China
| | - Qin Wang
- Department of Gynaecology and Obstetrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qipei Li
- Department of Gynaecology and Obstetrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Min Xie
- Department of Gynaecology and Obstetrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
37
|
Lee K, Han MR, Yeon JW, Kim B, Kim TH. Whole Transcriptome Analysis of Myeloid Dendritic Cells Reveals Distinct Genetic Regulation in Patients with Allergies. Int J Mol Sci 2020; 21:ijms21228640. [PMID: 33207814 PMCID: PMC7697962 DOI: 10.3390/ijms21228640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/23/2022] Open
Abstract
Dendritic cells (DCs) play critical roles in atopic diseases, orchestrating both innate and adaptive immune systems. Nevertheless, limited information is available regarding the mechanism through which DCs induce hyperresponsiveness in patients with allergies. This study aims to reveal novel genetic alterations and future therapeutic target molecules in the DCs from patients with allergies using whole transcriptome sequencing. Transcriptome sequencing of human BDCA-3+/CD11c+ DCs sorted from peripheral blood monocytes obtained from six patients with allergies and four healthy controls was conducted. Gene expression profile data were analyzed, and an ingenuity pathway analysis was performed. A total of 1638 differentially expressed genes were identified at p-values < 0.05, with 11 genes showing a log2-fold change ≥1.5. The top gene network was associated with cell death/survival and organismal injury/abnormality. In validation experiments, amphiregulin (AREG) showed consistent results with transcriptome sequencing data, with increased mRNA expression in THP-1-derived DCs after Der p 1 stimulation and higher protein expression in myeloid DCs obtained from patients with allergies. This study suggests an alteration in the expression of DCs in patients with allergies, proposing related altered functions and intracellular mechanisms. Notably, AREG might play a crucial role in DCs by inducing the Th2 immune response.
Collapse
Affiliation(s)
- Kijeong Lee
- Department of Otorhinolaryngology-Head & Neck Surgery, College of Medicine, Korea University, Seoul 02841, Korea; (K.L.); (J.W.Y.); (B.K.)
| | - Mi-Ryung Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea;
| | - Ji Woo Yeon
- Department of Otorhinolaryngology-Head & Neck Surgery, College of Medicine, Korea University, Seoul 02841, Korea; (K.L.); (J.W.Y.); (B.K.)
| | - Byoungjae Kim
- Department of Otorhinolaryngology-Head & Neck Surgery, College of Medicine, Korea University, Seoul 02841, Korea; (K.L.); (J.W.Y.); (B.K.)
| | - Tae Hoon Kim
- Department of Otorhinolaryngology-Head & Neck Surgery, College of Medicine, Korea University, Seoul 02841, Korea; (K.L.); (J.W.Y.); (B.K.)
- Correspondence: ; Tel.: +82-02-920-5486
| |
Collapse
|
38
|
Biswas N, Chakrabarti S. Artificial Intelligence (AI)-Based Systems Biology Approaches in Multi-Omics Data Analysis of Cancer. Front Oncol 2020; 10:588221. [PMID: 33154949 PMCID: PMC7591760 DOI: 10.3389/fonc.2020.588221] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022] Open
Abstract
Cancer is the manifestation of abnormalities of different physiological processes involving genes, DNAs, RNAs, proteins, and other biomolecules whose profiles are reflected in different omics data types. As these bio-entities are very much correlated, integrative analysis of different types of omics data, multi-omics data, is required to understanding the disease from the tumorigenesis to the disease progression. Artificial intelligence (AI), specifically machine learning algorithms, has the ability to make decisive interpretation of "big"-sized complex data and, hence, appears as the most effective tool for the analysis and understanding of multi-omics data for patient-specific observations. In this review, we have discussed about the recent outcomes of employing AI in multi-omics data analysis of different types of cancer. Based on the research trends and significance in patient treatment, we have primarily focused on the AI-based analysis for determining cancer subtypes, disease prognosis, and therapeutic targets. We have also discussed about AI analysis of some non-canonical types of omics data as they have the capability of playing the determiner role in cancer patient care. Additionally, we have briefly discussed about the data repositories because of their pivotal role in multi-omics data storing, processing, and analysis.
Collapse
Affiliation(s)
- Nupur Biswas
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, IICB TRUE Campus, Kolkata, India
| | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, IICB TRUE Campus, Kolkata, India
| |
Collapse
|
39
|
Tuit S, Salvagno C, Kapellos TS, Hau CS, Seep L, Oestreich M, Klee K, de Visser KE, Ulas T, Schultze JL. Transcriptional Signature Derived from Murine Tumor-Associated Macrophages Correlates with Poor Outcome in Breast Cancer Patients. Cell Rep 2020; 29:1221-1235.e5. [PMID: 31665635 PMCID: PMC7057267 DOI: 10.1016/j.celrep.2019.09.067] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/23/2019] [Accepted: 09/20/2019] [Indexed: 12/20/2022] Open
Abstract
Tumor-associated macrophages (TAMs) are frequently the most abundant immune cells in cancers and are associated with poor survival. Here, we generated TAM molecular signatures from K14cre;Cdh1flox/flox;Trp53flox/flox (KEP) and MMTV-NeuT (NeuT) transgenic mice that resemble human invasive lobular carcinoma (ILC) and HER2+ tumors, respectively. Determination of TAM-specific signatures requires comparison with healthy mammary tissue macrophages to avoid overestimation of gene expression differences. TAMs from the two models feature a distinct transcriptomic profile, suggesting that the cancer subtype dictates their phenotype. The KEP-derived signature reliably correlates with poor overall survival in ILC but not in triple-negative breast cancer patients, indicating that translation of murine TAM signatures to patients is cancer subtype dependent. Collectively, we show that a transgenic mouse tumor model can yield a TAM signature relevant for human breast cancer outcome prognosis and provide a generalizable strategy for determining and applying immune cell signatures provided the murine model reflects the human disease. Murine TAM signatures prognosticate outcomes in corresponding cancer patients TAM signatures are robust when they are compared with healthy tissue macrophages TAM transcriptome is dictated by tissue and tumor subtype-related signals Murine TAM signatures can be translated only when a suitable model is chosen
Collapse
Affiliation(s)
- Sander Tuit
- Genomics and Immunoregulation, LIMES Institute, University of Bonn, 53113 Bonn, Germany; Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Camilla Salvagno
- Division of Tumor Biology & Immunology, Oncode Institute, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Theodore S Kapellos
- Genomics and Immunoregulation, LIMES Institute, University of Bonn, 53113 Bonn, Germany
| | - Cheei-Sing Hau
- Division of Tumor Biology & Immunology, Oncode Institute, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Lea Seep
- Genomics and Immunoregulation, LIMES Institute, University of Bonn, 53113 Bonn, Germany
| | - Marie Oestreich
- Genomics and Immunoregulation, LIMES Institute, University of Bonn, 53113 Bonn, Germany
| | - Kathrin Klee
- Genomics and Immunoregulation, LIMES Institute, University of Bonn, 53113 Bonn, Germany
| | - Karin E de Visser
- Division of Tumor Biology & Immunology, Oncode Institute, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
| | - Thomas Ulas
- Genomics and Immunoregulation, LIMES Institute, University of Bonn, 53113 Bonn, Germany
| | - Joachim L Schultze
- Genomics and Immunoregulation, LIMES Institute, University of Bonn, 53113 Bonn, Germany; Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany.
| |
Collapse
|
40
|
Maibach F, Sadozai H, Seyed Jafari SM, Hunger RE, Schenk M. Tumor-Infiltrating Lymphocytes and Their Prognostic Value in Cutaneous Melanoma. Front Immunol 2020; 11:2105. [PMID: 33013886 PMCID: PMC7511547 DOI: 10.3389/fimmu.2020.02105] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/04/2020] [Indexed: 12/17/2022] Open
Abstract
Recent breakthroughs in tumor immunotherapy such as immune checkpoint blockade (ICB) antibodies, have demonstrated the capacity of the immune system to fight cancer in a number of malignancies such as melanoma and lung cancer. The numbers, localization and phenotypes of tumor-infiltrating lymphocytes (TIL) are not only predictive of response to immunotherapy but also key modulators of disease progression. In this review, we focus on TIL profiling in cutaneous melanoma using histopathological approaches and highlight the observed prognostic value of the primary TIL subsets. The quantification of TIL in formalin-fixed tumor samples ranges from visual scoring of lymphocytic infiltrates in H&E to multiplex immunohistochemistry and immunofluorescence followed by enumeration using image analysis software. Nevertheless, TIL enumeration in the current literature primarily relies upon single marker immunohistochemistry analyses of major lymphocyte subsets such as conventional T cells (CD3, CD4, CD8), regulatory T cells (FOXP3) and B cells (CD20). We review key studies in the literature on associations between TIL subsets and patient survival. We also cover recent findings with respect to the existence of ectopic lymphoid aggregates found in the TME which are termed tertiary lymphoid structures (TLS) and are generally a positive prognostic feature. In addition to their prognostic significance, the existence of various TIL sub-populations has also been reported to predict a patient's response to ICB. Thus, the literature on the predictive potential of TIL subsets in melanoma patients receiving ICB has also been discussed. Finally, we describe recently developed state-of-the-art profiling approaches for tumor infiltrating immune cells such as digital pathology scoring algorithms (e.g., Immunoscore) and multiplex proteomics-based immunophenotyping platforms (e.g., imaging mass cytometry). Translating these novel technologies have the potential to revolutionize tumor immunopathology leading to altering our current understanding of cancer immunology and dramatically improving outcomes for patients.
Collapse
Affiliation(s)
- Fabienne Maibach
- Institute of Pathology, Experimental Pathology, University of Bern, Bern, Switzerland
| | - Hassan Sadozai
- Institute of Pathology, Experimental Pathology, University of Bern, Bern, Switzerland
| | | | - Robert E. Hunger
- Department of Dermatology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Mirjam Schenk
- Institute of Pathology, Experimental Pathology, University of Bern, Bern, Switzerland
| |
Collapse
|
41
|
Affiliation(s)
- Amanda J Oliver
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Phillip K Darcy
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Michael H Kershaw
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Clare Y Slaney
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
42
|
Kim HK, Joung JG, Choi YL, Lee SH, Park BJ, Choi YS, Ryu D, Nam JY, Lee MS, Park WY, Hwang S, Cha H, Kim HS, Lee S, Jung Y, Lee JE, Doh J, Paik S, Kang JH, Lee J, Kim J. Earlier-Phased Cancer Immunity Cycle Strongly Influences Cancer Immunity in Operable Never-Smoker Lung Adenocarcinoma. iScience 2020; 23:101386. [PMID: 32795913 DOI: 10.1016/j.isci.2020.101386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 04/17/2020] [Accepted: 07/16/2020] [Indexed: 12/31/2022] Open
Abstract
Exome and transcriptome analyses of clinically homogeneous early-stage never-smoker female patients with lung adenocarcinoma were performed to understand tumor-T cell interactions and immune escape points. Using our novel gene panels of eight functional categories in the cancer-immunity cycle, three distinct subgroups were identified in this immune checkpoint blockade-refractory cohort by defective gene expression in two major domains, i.e., type I interferon production/signaling pathway and antigen-presenting machinery. Our approach could play a critical role in understanding immune evasion mechanisms, developing a method for effective selection of rare immune checkpoint blockade responders, and finding new treatment strategies.
Collapse
|
43
|
Abstract
Pediatric cancers, particularly high-risk solid tumors, urgently need effective and specific therapies. Their outlook has not appreciably improved in decades. Immunotherapies such as immune checkpoint inhibitors offer much promise, but most are only approved for use in adults. Though several hundred clinical trials have tested immune-based approaches in childhood cancers, few have been guided by biomarkers or clinical-grade assays developed to predict patient response and, ultimately, to help select those most likely to benefit. There is extensive evidence in adults to show that immune profiling has substantial predictive value, but few studies focus on childhood tumors, because of the relatively small disease population and restricted use of immune-based therapies. For instance, only one published study has retrospectively examined the immune profiles of pediatric brain tumors after immunotherapy. Furthermore, application and integration of advanced multiplex techniques has been extremely limited. Here, we review the current status of immune profiling of pediatric solid tumors, with emphasis on tumor types that represent enormous unmet clinical need, primarily in the context of immune checkpoint inhibitor therapy. Translating optimized and informative immune profiling into standard practice and access to personalized combination therapy will be critical if childhood cancers are to be treated effectively and affordably.
Collapse
Affiliation(s)
- Rachael L. Terry
- Children’s Cancer Institute, Randwick, New South Wales, Australia
| | - Deborah Meyran
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Université de Paris, Inserm, U976 HIPI Unit, Institut de Recherche Saint-Louis, Paris, France
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - David S. Ziegler
- Children’s Cancer Institute, Randwick, New South Wales, Australia
- Kids Cancer Center, Sydney Children’s Hospital, Randwick, New South Wales, Australia
| | - Michelle Haber
- Children’s Cancer Institute, Randwick, New South Wales, Australia
| | - Paul G. Ekert
- Children’s Cancer Institute, Randwick, New South Wales, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
| | - Joseph A. Trapani
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Paul J. Neeson
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
44
|
Kremenovic M, Rombini N, Chan AA, Gruber T, Bäriswyl L, Lee DJ, Schenk M. Characterization of a Myeloid Activation Signature that Correlates with Survival in Melanoma Patients. Cancers (Basel) 2020; 12:E1431. [PMID: 32486450 PMCID: PMC7352688 DOI: 10.3390/cancers12061431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 12/31/2022] Open
Abstract
Understanding the cellular interactions within the tumor microenvironment (TME) of melanoma paved the way for novel therapeutic modalities, such as T cell-targeted immune checkpoint inhibitors (ICI). However, only a limited fraction of patients benefits from such therapeutic modalities, highlighting the need for novel predictive and prognostic biomarkers. As myeloid cells orchestrate the tumor-specific immune response and influence the efficacy of ICI, assessing their activation state within the TME is of clinical relevance. Here, we characterized a myeloid activation (MA) signature, comprising the three genes Cxcl11, Gbp1, and Ido1, from gene expression data of human myeloid cells stimulated with poly(I:C) or cGAMP. This MA signature positively correlated to overall survival in melanoma. In addition, increased expression of the MA signature was observed in melanoma patients responding to ICI (anti-PD-1), as compared to non-responders. Furthermore, the MA signature was validated in the murine B16F10 melanoma model where it was induced and associated with decreased tumor growth upon intratumoral administration of poly(I:C) and cGAMP. Finally, we were able to visualize co-expression of the MA signature genes in myeloid cells of human melanoma tissues using RNAscope in situ hybridization. In conclusion, the MA signature indicates the activation state of myeloid cells and represents a prognostic biomarker for the overall survival in melanoma patients.
Collapse
Affiliation(s)
- Mirela Kremenovic
- Institute of Pathology, Experimental Pathology, University of Bern, 3008 Bern, Switzerland; (M.K.); (N.R.); (T.G.); (L.B.))
| | - Nives Rombini
- Institute of Pathology, Experimental Pathology, University of Bern, 3008 Bern, Switzerland; (M.K.); (N.R.); (T.G.); (L.B.))
| | - Alfred A. Chan
- Division of Dermatology, Department of Medicine, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA; (A.A.C.); (D.J.L.)
| | - Thomas Gruber
- Institute of Pathology, Experimental Pathology, University of Bern, 3008 Bern, Switzerland; (M.K.); (N.R.); (T.G.); (L.B.))
| | - Lukas Bäriswyl
- Institute of Pathology, Experimental Pathology, University of Bern, 3008 Bern, Switzerland; (M.K.); (N.R.); (T.G.); (L.B.))
| | - Delphine J. Lee
- Division of Dermatology, Department of Medicine, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA; (A.A.C.); (D.J.L.)
| | - Mirjam Schenk
- Institute of Pathology, Experimental Pathology, University of Bern, 3008 Bern, Switzerland; (M.K.); (N.R.); (T.G.); (L.B.))
| |
Collapse
|
45
|
Zhang X, Pan A, Jia S, Ideozu JE, Woods K, Murkowski K, Hessner MJ, Simpson PM, Levy H. Cystic Fibrosis Plasma Blunts the Immune Response to Bacterial Infection. Am J Respir Cell Mol Biol 2020; 61:301-311. [PMID: 30848661 DOI: 10.1165/rcmb.2018-0114oc] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cystic fibrosis (CF) is caused by mutations of the gene encoding the CF transmembrane conductance regulator. It remains unclear whether the abnormal immune response in CF involves extrinsic signals released from the external or internal environment. We sought to characterize the peripheral immune signatures in CF and its association with clinical phenotypes. Healthy peripheral blood mononuclear cells (PBMCs) were cultured with plasma from CF probands (CFPs) or healthy control subjects (HCs) followed by nCounter gene and microRNA (miRNA) profiling. A discovery cohort of 12 CFPs and 12 HCs and a validation cohort of 103 CFPs and 31 HCs (our previous microarray data [GSE71799]) were analyzed to characterize the composition of cultured immune cells and establish a miRNA‒mRNA network. Cell compositions and miRNA profiles were associated with clinical characteristics of the cohorts. Significantly differentially expressed genes and abundance of myeloid cells were downregulated in PMBCs after culture with CF plasma (P < 0.05). Top-ranked miRNAs that increased in response to CF plasma (adjusted P < 0.05) included miR-155 and miR-146a, which target many immune-related genes, such as IL-8. Pseudomonas aeruginosa infection was negatively associated with abundance of monocytes and the presence of those regulatory miRNAs. Extrinsic signals in plasma from patients with CF led to monocyte inactivation and miRNA upregulation in PBMCs. An improved understanding of the immune effects of extrinsic factors in CF holds great promise for integrating immunomodulatory cell therapies into current treatment strategies in CF.
Collapse
Affiliation(s)
- Xi Zhang
- Division of Pulmonary Medicine, Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Human Molecular Genetics Program, Stanley Manne Children's Research Institute of Chicago, Chicago, Illinois
| | - Amy Pan
- Children's Research Institute of the Children's Hospital of Wisconsin, Wauwatosa, Wisconsin; and.,Division of Quantitative Health Sciences, Department of Pediatrics
| | - Shuang Jia
- Division of Endocrinology, Department of Pediatrics.,Department of Pediatrics, Max McGee National Research Center for Juvenile Diabetes, and
| | - Justin E Ideozu
- Division of Pulmonary Medicine, Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Human Molecular Genetics Program, Stanley Manne Children's Research Institute of Chicago, Chicago, Illinois
| | - Katherine Woods
- Division of Pediatric Critical Care Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Kathleen Murkowski
- Division of Pediatric Critical Care Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Martin J Hessner
- Children's Research Institute of the Children's Hospital of Wisconsin, Wauwatosa, Wisconsin; and.,Division of Endocrinology, Department of Pediatrics.,Department of Pediatrics, Max McGee National Research Center for Juvenile Diabetes, and
| | - Pippa M Simpson
- Children's Research Institute of the Children's Hospital of Wisconsin, Wauwatosa, Wisconsin; and.,Division of Quantitative Health Sciences, Department of Pediatrics
| | - Hara Levy
- Division of Pulmonary Medicine, Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Human Molecular Genetics Program, Stanley Manne Children's Research Institute of Chicago, Chicago, Illinois
| |
Collapse
|
46
|
Das K, Urbiola C, Spiesschaert B, Mueller P, Wollmann G. Analysis of Immunological Treatment Effects of Virotherapy in Tumor Tissue. Methods Mol Biol 2020; 2058:155-77. [PMID: 31486037 DOI: 10.1007/978-1-4939-9794-7_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In addition of being directly tumoricidal, oncolytic viruses have emerged as potent partners for established and investigational immunotherapies due to their immune-stimulatory effects. The shifting focus on virus-mediated immune modulation calls for a comprehensive analysis of the tumor microenvironment (TME) and the factors orchestrating the antiviral and antitumor immune response. The oncolytic VSV-GP studied in our lab is a safe and potent antitumor agent with a fast replication cycle and killing of a broad range of different cancer types. It induces a robust local inflammatory conversion of the TME and drives a strong adaptive immune response toward the tumor. Here we present our multidisciplinary approach to study VSV-GP treatment effects in tumors by assessing both immune cells (tumor-infiltrating lymphocytes and tumor-associated macrophages) and immune-regulatory factors (cytokines) as well as characterizing immune signatures using an immune-targeted NanoString gene expression system.
Collapse
|
47
|
de Kanter JK, Lijnzaad P, Candelli T, Margaritis T, Holstege FCP. CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing. Nucleic Acids Res 2019; 47:e95. [PMID: 31226206 PMCID: PMC6895264 DOI: 10.1093/nar/gkz543] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/05/2019] [Accepted: 06/08/2019] [Indexed: 01/06/2023] Open
Abstract
Cell type identification is essential for single-cell RNA sequencing (scRNA-seq) studies, currently transforming the life sciences. CHETAH (CHaracterization of cEll Types Aided by Hierarchical classification) is an accurate cell type identification algorithm that is rapid and selective, including the possibility of intermediate or unassigned categories. Evidence for assignment is based on a classification tree of previously available scRNA-seq reference data and includes a confidence score based on the variance in gene expression per cell type. For cell types represented in the reference data, CHETAH’s accuracy is as good as existing methods. Its specificity is superior when cells of an unknown type are encountered, such as malignant cells in tumor samples which it pinpoints as intermediate or unassigned. Although designed for tumor samples in particular, the use of unassigned and intermediate types is also valuable in other exploratory studies. This is exemplified in pancreas datasets where CHETAH highlights cell populations not well represented in the reference dataset, including cells with profiles that lie on a continuum between that of acinar and ductal cell types. Having the possibility of unassigned and intermediate cell types is pivotal for preventing misclassification and can yield important biological information for previously unexplored tissues.
Collapse
Affiliation(s)
- Jurrian K de Kanter
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Philip Lijnzaad
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Tito Candelli
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Thanasis Margaritis
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| |
Collapse
|
48
|
Anoveros-Barrera A, Bhullar AS, Stretch C, Dunichand-Hoedl AR, Martins KJB, Rieger A, Bigam D, McMullen T, Bathe OF, Putman CT, Field CJ, Baracos VE, Mazurak VC. Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression. Skelet Muscle 2019; 9:24. [PMID: 31521204 PMCID: PMC6744687 DOI: 10.1186/s13395-019-0209-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/16/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Inflammation is a recognized contributor to muscle wasting. Research in injury and myopathy suggests that interactions between the skeletal muscle and immune cells confer a pro-inflammatory environment that influences muscle loss through several mechanisms; however, this has not been explored in the cancer setting. This study investigated the local immune environment of the muscle by identifying the phenotype of immune cell populations in the muscle and their relationship to muscle mass in cancer patients. METHODS Intraoperative muscle biopsies were collected from cancer patients (n = 30, 91% gastrointestinal malignancies). Muscle mass was assessed histologically (muscle fiber cross-sectional area, CSA; μm2) and radiologically (lumbar skeletal muscle index, SMI; cm2/m2 by computed tomography, CT). T cells (CD4 and CD8) and granulocytes/phagocytes (CD11b, CD14, and CD15) were assessed by immunohistochemistry. Microarray analysis was conducted in the muscle of a second cancer patient cohort. RESULTS T cells (CD3+), granulocytes/phagocytes (CD11b+), and CD3-CD4+ cells were identified. Muscle fiber CSA (μm2) was positively correlated (Spearman's r = > 0.45; p = < 0.05) with the total number of T cells, CD4, and CD8 T cells and granulocytes/phagocytes. In addition, patients with the smallest SMI exhibited fewer CD8 T cells within their muscle. Consistent with this, further exploration with gene correlation analyses suggests that the presence of CD8 T cells is negatively associated (Pearson's r = ≥ 0.5; p = <0.0001) with key genes within muscle catabolic pathways for signaling (ACVR2B), ubiquitin proteasome (FOXO4, TRIM63, FBXO32, MUL1, UBC, UBB, UBE2L3), and apoptosis/autophagy (CASP8, BECN1, ATG13, SIVA1). CONCLUSION The skeletal muscle immune environment of cancer patients is comprised of immune cell populations from the adaptive and innate immunity. Correlations of T cells, granulocyte/phagocytes, and CD3-CD4+ cells with muscle mass measurements indicate a positive relationship between immune cell numbers and muscle mass status in cancer patients. Further exploration with gene correlation analyses suggests that the presence of CD8 T cells is negatively correlated with components of muscle catabolism.
Collapse
Affiliation(s)
- Ana Anoveros-Barrera
- Department of Agricultural, Food & Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, 4-002 Li Ka Shing Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Amritpal S Bhullar
- Department of Agricultural, Food & Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, 4-002 Li Ka Shing Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Cynthia Stretch
- Department of Oncology, University of Calgary, Calgary, Alberta, Canada
| | - Abha R Dunichand-Hoedl
- Department of Agricultural, Food & Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, 4-002 Li Ka Shing Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Karen J B Martins
- Department of Agricultural, Food & Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, 4-002 Li Ka Shing Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Aja Rieger
- Flow Cytometry Facility, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - David Bigam
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Todd McMullen
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Oliver F Bathe
- Department of Oncology and Department of Surgery, University of Calgary, Calgary, Alberta, Canada
| | - Charles T Putman
- Faculty of Kinesiology, Sport, and Recreation, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Catherine J Field
- Department of Agricultural, Food & Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, 4-002 Li Ka Shing Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Vickie E Baracos
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Vera C Mazurak
- Department of Agricultural, Food & Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, 4-002 Li Ka Shing Centre, Edmonton, Alberta, T6G 2P5, Canada.
| |
Collapse
|
49
|
Fox JJ, Navarro HI, Hashimoto T, Garcia AJ, Goldstein AS. Mass cytometry reveals species-specific differences and a new level of complexity for immune cells in the prostate. Am J Clin Exp Urol 2019; 7:281-296. [PMID: 31511834 PMCID: PMC6734036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
Chronic inflammation in the benign prostate has been associated with a higher risk of developing prostate cancer. While a range of immune lineages is found in the prostate including T cells, B cells and myeloid cells, the specific subsets of immune cells with each major lineage have not been well described. In this study, we use mass cytometry (CyTOF) to comprehensively and reproducibly profile immune cells in mouse and human prostate. Using 4 myeloid markers (CD11b, CD11c, F4/80, Ly6C) in the mouse, we identified 8 phenotypically-distinct myeloid populations, demonstrating considerable heterogeneity within the immune compartment of the mouse prostate. We then profiled the prostate immune microenvironment from 9 human patients. Unlike the mouse prostate which is myeloid-dominant, the immune compartment in the benign human prostate is consistently T-lymphocyte-dominant. Using the X-shift algorithm to identify individual immune subsets based on marker expression, we found 57 phenotypically-distinct immune cell types in the human prostate. Despite similar proportions of T, B and myeloid lineage cells in the benign human prostate of all patients evaluated, we observed considerable interpatient heterogeneity in the abundance of more specific immune subsets. These findings highlight the importance of studying the immune compartment in the prostate at a granular level and will lead to future studies addressing the functional role of specific immune subsets in prostate epithelial transformation.
Collapse
Affiliation(s)
- Jonathan J Fox
- Department of Molecular, Cell and Developmental Biology, University of CaliforniaLos Angeles, Los Angeles, CA, USA
| | - Héctor I Navarro
- Molecular Biology Interdepartmental Program, University of CaliforniaLos Angeles, Los Angeles, CA, USA
| | - Takao Hashimoto
- Department of Molecular, Cell and Developmental Biology, University of CaliforniaLos Angeles, Los Angeles, CA, USA
| | - Alejandro J Garcia
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of CaliforniaLos Angeles, Los Angeles, CA, USA
| | - Andrew S Goldstein
- Department of Molecular, Cell and Developmental Biology, University of CaliforniaLos Angeles, Los Angeles, CA, USA
- Department of Urology, David Geffen School of Medicine, University of CaliforniaLos Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of CaliforniaLos Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of CaliforniaLos Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of CaliforniaLos Angeles, Los Angeles, CA, USA
| |
Collapse
|
50
|
Romero-Cordoba S, Meneghini E, Sant M, Iorio MV, Sfondrini L, Paolini B, Agresti R, Tagliabue E, Bianchi F. Decoding Immune Heterogeneity of Triple Negative Breast Cancer and Its Association with Systemic Inflammation. Cancers (Basel) 2019; 11:E911. [PMID: 31261762 DOI: 10.3390/cancers11070911] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023] Open
Abstract
Triple negative breast cancer (TNBC) is an aggressive subtype with limited therapeutic options. New opportunities are emerging from current comprehensive characterization of tumor immune infiltration and fitness. Therefore, effectiveness of current chemotherapies and novel immunotherapies are partially dictated by host inflammatory and immune profiles. However, further progress in breast cancer immuno-oncology is required to reach a detailed awareness of the immune infiltrate landscape and to determine additional reliable and easily detectable biomarkers. In this study, by analyzing gene expression profiles of 54 TNBC cases we identified three TNBC clusters displaying unique immune features. Deep molecular characterization of immune cells cytolytic-activity and tumor-inflammation status reveled variability in the local composition of the immune infiltrate in the TNBC clusters, reconciled by tumor-infiltrating lymphocytes counts. Platelet-to-lymphocyte ratio (PLR), a blood systemic parameter of inflammation evaluated using pre-surgical blood test data, resulted negatively correlated with local tumoral cytolytic activity and T cell–inflamed microenvironment, whereas tumor aggressiveness score signature positively correlated with PLR values. These data highlighted that systemic inflammation parameters may represent reliable and informative markers of the local immune tumor microenvironment in TNBC patients and could be exploited to decipher tumor infiltrate properties and consequently to select the most appropriate therapies.
Collapse
|