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Li CC, Liu M, Lee HP, Wu W, Ma L. Heterogeneity in Liver Cancer Immune Microenvironment: Emerging Single-Cell and Spatial Perspectives. Semin Liver Dis 2024. [PMID: 38788780 DOI: 10.1055/s-0044-1787152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Primary liver cancer is a solid malignancy with a high mortality rate. The success of immunotherapy has shown great promise in improving patient care and highlights a crucial need to understand the complexity of the liver tumor immune microenvironment (TIME). Recent advances in single-cell and spatial omics technologies, coupled with the development of systems biology approaches, are rapidly transforming the landscape of tumor immunology. Here we review the cellular landscape of liver TIME from single-cell and spatial perspectives. We also discuss the cellular interaction networks within the tumor cell community in regulating immune responses. We further highlight the challenges and opportunities with implications for biomarker discovery, patient stratification, and combination immunotherapies.
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Affiliation(s)
- Caiyi Cherry Li
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Meng Liu
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Hsin-Pei Lee
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Wenqi Wu
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Lichun Ma
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
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2
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Wang Z, Santa-Maria CA, Popel AS, Sulam J. Bi-level Graph Learning Unveils Prognosis-Relevant Tumor Microenvironment Patterns from Breast Multiplexed Digital Pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590118. [PMID: 38712207 PMCID: PMC11071347 DOI: 10.1101/2024.04.22.590118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The tumor microenvironment is widely recognized for its central role in driving cancer progression and influencing prognostic outcomes. Despite extensive research efforts dedicated to characterizing this complex and heterogeneous environment, considerable challenges persist. In this study, we introduce a data-driven approach for identifying patterns of cell organizations in the tumor microenvironment that are associated with patient prognoses. Our methodology relies on the construction of a bi-level graph model: (i) a cellular graph, which models the intricate tumor microenvironment, and (ii) a population graph that captures inter-patient similarities, given their respective cellular graphs, by means of a soft Weisfeiler-Lehman subtree kernel. This systematic integration of information across different scales enables us to identify patient subgroups exhibiting unique prognoses while unveiling tumor microenvironment patterns that characterize them. We demonstrate our approach in a cohort of breast cancer patients, where the identified tumor microenvironment patterns result in a risk stratification system that provides complementary, new information with respect to alternative standards. Our results, which are validated in a completely independent cohort, allow for new insights into the prognostic implications of the breast tumor microenvironment, and this methodology could be applied to other cancer types more generally.
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Affiliation(s)
- Zhenzhen Wang
- Department of Biomedical Engineering, Johns Hopkins University
- Mathematical Institute for Data Science, Johns Hopkins University
| | - Cesar A Santa-Maria
- Department of Oncology, Johns Hopkins University
- Sidney Kimmel Comprehensive Cancer Center
| | | | - Jeremias Sulam
- Department of Biomedical Engineering, Johns Hopkins University
- Mathematical Institute for Data Science, Johns Hopkins University
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3
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Maestri E, Kedei N, Khatib S, Forgues M, Ylaya K, Hewitt SM, Wang L, Chaisaingmongkol J, Ruchirawat M, Ma L, Wang XW. Spatial proximity of tumor-immune interactions predicts patient outcome in hepatocellular carcinoma. Hepatology 2024; 79:768-779. [PMID: 37725716 PMCID: PMC10948323 DOI: 10.1097/hep.0000000000000600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND AND AIMS The fitness and viability of a tumor ecosystem are influenced by the spatial organization of its cells. We aimed to study the structure, architecture, and cell-cell dynamics of the heterogeneous liver cancer tumor microenvironment using spatially resolved multiplexed imaging. APPROACH AND RESULTS We performed co-detection by indexing multiplexed immunofluorescence imaging on 68 HCC biopsies from Thai patients [(Thailand Initiative in Genomics and Expression Research for Liver Cancer (TIGER-LC)] as a discovery cohort, and then validated the results in an additional 190 HCC biopsies from Chinese patients [Liver Cancer Institute (LCI)]. We segmented and annotated 117,270 and 465,632 cells from the TIGER-LC and LCI cohorts, respectively. We observed 4 patient groups of TIGER-LC (IC1, IC2, IC3, and IC4) with distinct tumor-immune cellular interaction patterns. In addition, patients from IC2 and IC4 had much better overall survival than those from IC1 and IC3. Noticeably, tumor and CD8 + T-cell interactions were strongly enriched in IC2, the group with the best patient outcomes. The close proximity between the tumor and CD8 + T cells was a strong predictor of patient outcome in both the TIGER-LC and the LCI cohorts. Bulk transcriptomic data from 51 of the 68 HCC cases were used to determine tumor-specific gene expression features of our classified subtypes. Moreover, we observed that the presence of immune spatial neighborhoods in HCC as a measure of overall immune infiltration is linked to better patient prognosis. CONCLUSIONS Highly multiplexed imaging analysis of liver cancer reveals tumor-immune cellular heterogeneity within spatial contexts, such as tumor and CD8 + T-cell interactions, which may predict patient survival.
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Affiliation(s)
- Evan Maestri
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Noemi Kedei
- Collaborative Protein Technology Resource, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Subreen Khatib
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Kris Ylaya
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Stephen M. Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Limin Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Jittiporn Chaisaingmongkol
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Thailand
| | - Mathuros Ruchirawat
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Thailand
| | - Lichun Ma
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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4
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Li M, Wang L, Cong L, Wong CC, Zhang X, Chen H, Zeng T, Li B, Jia X, Huo J, Huang Y, Ren X, Peng S, Fu G, Xu L, Sung JJ, Kuang M, Li X, Yu J. Spatial proteomics of immune microenvironment in nonalcoholic steatohepatitis-associated hepatocellular carcinoma. Hepatology 2024; 79:560-574. [PMID: 37733002 PMCID: PMC10871559 DOI: 10.1097/hep.0000000000000591] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/13/2023] [Indexed: 09/22/2023]
Abstract
BACKGROUND AND AIMS NASH-HCC is inherently resistant to immune checkpoint blockade, but its tumor immune microenvironment is largely unknown. APPROACH AND RESULTS We applied the imaging mass cytometry to construct a spatially resolved single-cell atlas from the formalin-fixed and paraffin-embedded tissue sections from patients with NASH-HCC, virus-HCC (HBV-HCC and HCV-HCC), and healthy donors. Based on 35 biomarkers, over 750,000 individual cells were categorized into 13 distinct cell types, together with the expression of key immune functional markers. Higher infiltration of T cells, myeloid-derived suppressor cell (MDSCs), and tumor-associated macrophages (TAMs) in HCC compared to controls. The distribution of immune cells in NASH-HCC is spatially heterogeneous, enriched at adjacent normal tissues and declined toward tumors. Cell-cell connections analysis revealed the interplay of MDSCs and TAMs with CD8 + T cells in NASH-HCC. In particular, exhausted programmed cell death 1 (PD-1 + )CD8 + T cells connected with programmed cell death-ligand 1 (PD-L1 + )/inducible T cell costimulator (ICOS + ) MDSCs and TAMs in NASH-HCC, but not in viral HCC. In contrast, CD4 + /CD8 + T cells with granzyme B positivity were reduced in NASH-HCC. Tumor cells expressed low PD-L1 and showed few connections with immune cells. CONCLUSIONS Our work provides the first detailed spatial map of single-cell phenotypes and multicellular connections in NASH-HCC. We demonstrate that interactions between MDSCs and TAMs with effector T cells underlie immunosuppression in NASH-HCC and are an actionable target.
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Affiliation(s)
- Meiyi Li
- State Key Laboratory of Digestive Disease, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lina Wang
- Center of Hepato-Pancreato-Biliary Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Liang Cong
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chi Chun Wong
- State Key Laboratory of Digestive Disease, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiang Zhang
- State Key Laboratory of Digestive Disease, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Huarong Chen
- State Key Laboratory of Digestive Disease, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tao Zeng
- Guangzhou Laboratory, Guangzhou, China
| | - Bin Li
- Clinical Trial Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xian Jia
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, School of Medicine, Xiamen University, Xiamen, China
| | - Jihui Huo
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuhua Huang
- State Key Laboratory of Oncology in South China, Department of Pathology, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xiaoxue Ren
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Sui Peng
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Clinical Trial Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Guo Fu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, School of Medicine, Xiamen University, Xiamen, China
| | - Lixia Xu
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Oncology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Joseph J.Y. Sung
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Ming Kuang
- Center of Hepato-Pancreato-Biliary Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoxing Li
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jun Yu
- State Key Laboratory of Digestive Disease, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Zhou Z, Lin T, Chen S, Zhang G, Xu Y, Zou H, Zhou A, Zhang Y, Weng S, Han X, Liu Z. Omics-based molecular classifications empowering in precision oncology. Cell Oncol (Dordr) 2024:10.1007/s13402-023-00912-8. [PMID: 38294647 DOI: 10.1007/s13402-023-00912-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND In the past decades, cancer enigmatical heterogeneity at distinct expression levels could interpret disparities in therapeutic response and prognosis. It built hindrances to precision medicine, a tactic to tailor customized treatment informed by the tumors' molecular profile. Single-omics analysis dissected the biological features associated with carcinogenesis to some extent but still failed to revolutionize cancer treatment as expected. Integrated omics analysis incorporated tumor biological networks from diverse layers and deciphered a holistic overview of cancer behaviors, yielding precise molecular classification to facilitate the evolution and refinement of precision medicine. CONCLUSION This review outlined the biomarkers at multiple expression layers to tutor molecular classification and pinpoint tumor diagnosis, and explored the paradigm shift in precision therapy: from single- to multi-omics-based subtyping to optimize therapeutic regimens. Ultimately, we firmly believe that by parsing molecular characteristics, omics-based typing will be a powerful assistant for precision oncology.
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Affiliation(s)
- Zhaokai Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Ting Lin
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Shuang Chen
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yudi Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Haijiao Zou
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Aoyang Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan, 450052, China.
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan, 450052, China.
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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6
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Duan Y, Zhang H, Tan T, Ye W, Yin K, Yu Y, Kang M, Yang J, Liao R. The immune response of hepatocellular carcinoma after locoregional and systemic therapies: The available combination option for immunotherapy. Biosci Trends 2024; 17:427-444. [PMID: 37981319 DOI: 10.5582/bst.2023.01275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Hepatocellular carcinoma (HCC) is associated with a highly heterogeneous immune environment that produces an immune response to various locoregional treatments (LRTs), which in turn affects the effectiveness of immunotherapy. Although LRTs still dominate HCC therapies, 50-60% of patients will ultimately be treated with systemic therapies and might receive those treatments for the rest of their life. TACE, SIRT, and thermal ablation can dramatically increase the immunosuppressive state of HCC, a condition that can be addressed by combination with immunotherapy to restore the activity of lymphocytes and the secretion of cellular immune factors. Immune treatment with locoregional and systemic treatments has dramatically changed the management of HCC. In this review, we examine the research on the changes in the immune microenvironment after locoregional or systemic treatment. We also summarize the regulation of various immune cells and immune factors in the tumor microenvironment and discuss the different infiltration degrees of immune cells and factors on the prognosis of HCC to better compare the efficacy between different treatment methods from the perspective of the tumor microenvironment. This information can be used to help develop treatment options for the upcoming new era of HCC treatment in the future.
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Affiliation(s)
- Yuxin Duan
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hua Zhang
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tao Tan
- Chongqing Health Statistics Information Center, Chongqing, China
| | - Wentao Ye
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Kunli Yin
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yanxi Yu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Meiqing Kang
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jian Yang
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Rui Liao
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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7
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Lee S, Kim G, Lee J, Lee AC, Kwon S. Mapping cancer biology in space: applications and perspectives on spatial omics for oncology. Mol Cancer 2024; 23:26. [PMID: 38291400 PMCID: PMC10826015 DOI: 10.1186/s12943-024-01941-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024] Open
Abstract
Technologies to decipher cellular biology, such as bulk sequencing technologies and single-cell sequencing technologies, have greatly assisted novel findings in tumor biology. Recent findings in tumor biology suggest that tumors construct architectures that influence the underlying cancerous mechanisms. Increasing research has reported novel techniques to map the tissue in a spatial context or targeted sampling-based characterization and has introduced such technologies to solve oncology regarding tumor heterogeneity, tumor microenvironment, and spatially located biomarkers. In this study, we address spatial technologies that can delineate the omics profile in a spatial context, novel findings discovered via spatial technologies in oncology, and suggest perspectives regarding therapeutic approaches and further technological developments.
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Affiliation(s)
- Sumin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Meteor Biotech,, Co. Ltd, Seoul, 08826, Republic of Korea
| | - Gyeongjun Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - JinYoung Lee
- Division of Engineering Science, University of Toronto, Toronto, Ontario, ON, M5S 3H6, Canada
| | - Amos C Lee
- Meteor Biotech,, Co. Ltd, Seoul, 08826, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, 08826, Republic of Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
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8
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Sverchkova A, Burkholz S, Rubsamen R, Stratford R, Clancy T. Integrative HLA typing of tumor and adjacent normal tissue can reveal insights into the tumor immune response. BMC Med Genomics 2024; 17:37. [PMID: 38281021 PMCID: PMC10821267 DOI: 10.1186/s12920-024-01808-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND The HLA complex is the most polymorphic region of the human genome, and its improved characterization can help us understand the genetics of human disease as well as the interplay between cancer and the immune system. The main function of HLA genes is to recognize "non-self" antigens and to present them on the cell surface to T cells, which instigate an immune response toward infected or transformed cells. While sequence variation in the antigen-binding groove of HLA may modulate the repertoire of immunogenic antigens presented to T cells, alterations in HLA expression can significantly influence the immune response to pathogens and cancer. METHODS RNA sequencing was used here to accurately genotype the HLA region and quantify and compare the level of allele-specific HLA expression in tumors and patient-matched adjacent normal tissue. The computational approach utilized in the study types classical and non-classical Class I and Class II HLA alleles from RNA-seq while simultaneously quantifying allele-specific or personalized HLA expression. The strategy also uses RNA-seq data to infer immune cell infiltration into tumors and the corresponding immune cell composition of matched normal tissue, to reveal potential insights related to T cell and NK cell interactions with tumor HLA alleles. RESULTS The genotyping method outperforms existing RNA-seq-based HLA typing tools for Class II HLA genotyping. Further, we demonstrate its potential for studying tumor-immune interactions by applying the method to tumor samples from two different subtypes of breast cancer and their matched normal breast tissue controls. CONCLUSIONS The integrative RNA-seq-based HLA typing approach described in the study, coupled with HLA expression analysis, neoantigen prediction and immune cell infiltration, may help increase our understanding of the interplay between a patient's tumor and immune system; and provide further insights into the immune mechanisms that determine a positive or negative outcome following treatment with immunotherapy such as checkpoint blockade.
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Affiliation(s)
- Angelina Sverchkova
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Scott Burkholz
- Flow Pharma, Inc, Warrensville Heights, Galaxy Parkway, OH, 4829, USA
| | - Reid Rubsamen
- Flow Pharma, Inc, Warrensville Heights, Galaxy Parkway, OH, 4829, USA
- University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
- Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Richard Stratford
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway
| | - Trevor Clancy
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway.
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Saldarriaga OA, Wanninger TG, Arroyave E, Gosnell J, Krishnan S, Oneka M, Bao D, Millian DE, Kueht ML, Moghe A, Jiao J, Sanchez JI, Spratt H, Beretta L, Rao A, Burks JK, Stevenson HL. Heterogeneity in intrahepatic macrophage populations and druggable target expression in patients with steatotic liver disease-related fibrosis. JHEP Rep 2024; 6:100958. [PMID: 38162144 PMCID: PMC10757256 DOI: 10.1016/j.jhepr.2023.100958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/18/2023] [Accepted: 09/25/2023] [Indexed: 01/03/2024] Open
Abstract
Background & Aims Clinical trials for reducing fibrosis in steatotic liver disease (SLD) have targeted macrophages with variable results. We evaluated intrahepatic macrophages in patients with SLD to determine if activity scores or fibrosis stages influenced phenotypes and expression of druggable targets, such as CCR2 and galectin-3. Methods Liver biopsies from controls or patients with minimal or advanced fibrosis were subject to gene expression analysis using nCounter to determine differences in macrophage-related genes (n = 30). To investigate variability among individual patients, we compared additional biopsies by staining them with multiplex antibody panels (CD68/CD14/CD16/CD163/Mac387 or CD163/CCR2/galectin-3/Mac387) followed by spectral imaging and spatial analysis. Algorithms that utilize deep learning/artificial intelligence were applied to create cell cluster plots, phenotype profile maps, and to determine levels of protein expression (n = 34). Results Several genes known to be pro-fibrotic (e.g. CD206, TREM2, CD163, and ARG1) showed either no significant differences or significantly decreased with advanced fibrosis. Although marked variability in gene expression was observed in individual patients with cirrhosis, several druggable targets and their ligands (e.g. CCR2, CCR5, CCL2, CCL5, and LGALS3) were significantly increased when compared to patients with minimal fibrosis. Antibody panels identified populations that were significantly increased (e.g. Mac387+), decreased (e.g. CD14+), or enriched (e.g. interactions of Mac387) in patients that had progression of disease or advanced fibrosis. Despite heterogeneity in patients with SLD, several macrophage phenotypes and druggable targets showed a positive correlation with increasing NAFLD activity scores and fibrosis stages. Conclusions Patients with SLD have markedly varied macrophage- and druggable target-related gene and protein expression in their livers. Several patients had relatively high expression, while others were like controls. Overall, patients with more advanced disease had significantly higher expression of CCR2 and galectin-3 at both the gene and protein levels. Impact and implications Appreciating individual differences within the hepatic microenvironment of patients with SLD may be paramount to developing effective treatments. These results may explain why such a small percentage of patients have responded to macrophage-targeting therapies and provide additional support for precision medicine-guided treatment of chronic liver diseases.
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Affiliation(s)
- Omar A. Saldarriaga
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Timothy G. Wanninger
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Esteban Arroyave
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Joseph Gosnell
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Santhoshi Krishnan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Morgan Oneka
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Daniel Bao
- School of Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Daniel E. Millian
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Michael L. Kueht
- Department of Surgery, University of Texas Medical Branch, Galveston, TX, USA
| | - Akshata Moghe
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Jingjing Jiao
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jessica I. Sanchez
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heidi Spratt
- Department of Biostatistics and Data Science, University of Texas Medical Branch, Galveston, TX, USA
| | - Laura Beretta
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Arvind Rao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
- Departmen of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, Rice University, Ann Arbor, MI, USA
| | - Jared K. Burks
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Lurje I, Hammerich L. The suppressive tumor microenvironment of AFP-positive hepatocellular carcinoma and its therapeutic implications. Transl Gastroenterol Hepatol 2023; 9:1. [PMID: 38317743 PMCID: PMC10838608 DOI: 10.21037/tgh-23-81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/04/2023] [Indexed: 02/07/2024] Open
Affiliation(s)
- Isabella Lurje
- Department of Hepatology and Gastroenterology, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Linda Hammerich
- Department of Hepatology and Gastroenterology, Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, Germany
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11
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Mi H, Varadhan R, Cimino-Mathews AM, Emens LA, Santa-Maria CA, Popel AS. Spatial and Compositional Biomarkers in Tumor Microenvironment Predicts Clinical Outcomes in Triple-Negative Breast Cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572234. [PMID: 38187696 PMCID: PMC10769235 DOI: 10.1101/2023.12.18.572234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited treatment options, which warrants identification of novel therapeutic targets. Deciphering nuances in the tumor microenvironment (TME) may unveil insightful links between anti-tumor immunity and clinical outcomes, yet such connections remain underexplored. Here we employed a dataset derived from imaging mass cytometry of 58 TNBC patient specimens at single-cell resolution and performed in-depth quantifications with a suite of multi-scale computational algorithms. We detected distinct cell distribution patterns among clinical subgroups, potentially stemming from different infiltration related to tumor vasculature and fibroblast heterogeneity. Spatial analysis also identified ten recurrent cellular neighborhoods (CNs) - a collection of local TME characteristics with unique cell components. Coupling of the prevalence of pan-immune and perivasculature immune hotspot CNs, enrichment of inter-CN interactions was associated with improved survival. Using a deep learning model trained on engineered spatial data, we can with high accuracy (mean AUC of 5-fold cross-validation = 0.71) how a separate cohort of patients in the NeoTRIP clinical trial will respond to treatment based on baseline TME features. These data reinforce that the TME architecture is structured in cellular compositions, spatial organizations, vasculature biology, and molecular profiles, and suggest novel imaging-based biomarkers for treatment development in the context of TNBC.
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Affiliation(s)
- Haoyang Mi
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ravi Varadhan
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ashley M. Cimino-Mathews
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, MD, United States
| | | | - Cesar A. Santa-Maria
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Aleksander S. Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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12
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Kumar G, Pandurengan RK, Parra ER, Kannan K, Haymaker C. Spatial modelling of the tumor microenvironment from multiplex immunofluorescence images: methods and applications. Front Immunol 2023; 14:1288802. [PMID: 38179056 PMCID: PMC10765501 DOI: 10.3389/fimmu.2023.1288802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024] Open
Abstract
Spatial modelling methods have gained prominence with developments in high throughput imaging platforms. Multiplex immunofluorescence (mIF) provides the scope to examine interactions between tumor and immune compartment at single cell resolution using a panel of antibodies that can be chosen based on the cancer type or the clinical interest of the study. The markers can be used to identify the phenotypes and to examine cellular interactions at global and local scales. Several translational studies rely on key understanding of the tumor microenvironment (TME) to identify drivers of immune response in immunotherapy based clinical trials. To improve the success of ongoing trials, a number of retrospective approaches can be adopted to understand differences in response, recurrence and progression by examining the patient's TME from tissue samples obtained at baseline and at various time points along the treatment. The multiplex immunofluorescence (mIF) technique provides insight on patient specific cell populations and their relative spatial distribution as qualitative measures of a favorable treatment outcome. Spatial analysis of these images provides an understanding of the intratumoral heterogeneity and clustering among cell populations in the TME. A number of mathematical models, which establish clustering as a measure of deviation from complete spatial randomness, can be applied to the mIF images represented as spatial point patterns. These mathematical models, developed for landscape ecology and geographic information studies, can be applied to the TME after careful consideration of the tumor type (cold vs. hot) and the tumor immune landscape. The spatial modelling of mIF images can show observable engagement of T cells expressing immune checkpoint molecules and this can then be correlated with single-cell RNA sequencing data.
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Affiliation(s)
| | | | | | - Kasthuri Kannan
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, United States
| | - Cara Haymaker
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, United States
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13
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Zhang S, Yuan L, Danilova L, Mo G, Zhu Q, Deshpande A, Bell ATF, Elisseeff J, Popel AS, Anders RA, Jaffee EM, Yarchoan M, Fertig EJ, Kagohara LT. Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence. Genome Med 2023; 15:72. [PMID: 37723590 PMCID: PMC10506285 DOI: 10.1186/s13073-023-01218-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/04/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Novel immunotherapy combination therapies have improved outcomes for patients with hepatocellular carcinoma (HCC), but responses are limited to a subset of patients. Little is known about the inter- and intra-tumor heterogeneity in cellular signaling networks within the HCC tumor microenvironment (TME) that underlie responses to modern systemic therapy. METHODS We applied spatial transcriptomics (ST) profiling to characterize the tumor microenvironment in HCC resection specimens from a prospective clinical trial of neoadjuvant cabozantinib, a multi-tyrosine kinase inhibitor that primarily blocks VEGF, and nivolumab, a PD-1 inhibitor in which 5 out of 15 patients were found to have a pathologic response at the time of resection. RESULTS ST profiling demonstrated that the TME of responding tumors was enriched for immune cells and cancer-associated fibroblasts (CAF) with pro-inflammatory signaling relative to the non-responders. The enriched cancer-immune interactions in responding tumors are characterized by activation of the PAX5 module, a known regulator of B cell maturation, which colocalized with spots with increased B cell marker expression suggesting strong activity of these cells. HCC-CAF interactions were also enriched in the responding tumors and were associated with extracellular matrix (ECM) remodeling as there was high activation of FOS and JUN in CAFs adjacent to the tumor. The ECM remodeling is consistent with proliferative fibrosis in association with immune-mediated tumor regression. Among the patients with major pathologic responses, a single patient experienced early HCC recurrence. ST analysis of this clinical outlier demonstrated marked tumor heterogeneity, with a distinctive immune-poor tumor region that resembles the non-responding TME across patients and was characterized by HCC-CAF interactions and expression of cancer stem cell markers, potentially mediating early tumor immune escape and recurrence in this patient. CONCLUSIONS These data show that responses to modern systemic therapy in HCC are associated with distinctive molecular and cellular landscapes and provide new targets to enhance and prolong responses to systemic therapy in HCC.
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Affiliation(s)
- Shuming Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Long Yuan
- Department of Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ludmila Danilova
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Guanglan Mo
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Qingfeng Zhu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Atul Deshpande
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Alexander T F Bell
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer Elisseeff
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert A Anders
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth M Jaffee
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Mark Yarchoan
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Elana J Fertig
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA.
- Department of Applied Mathematics and Statistics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Luciane T Kagohara
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA.
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14
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Wu CS, Chien YC, Yen CJ, Wu JY, Bai LY, Yu YL. EZH2-mediated epigenetic silencing of tumor-suppressive let-7c/miR-99a cluster by hepatitis B virus X antigen enhances hepatocellular carcinoma progression and metastasis. Cancer Cell Int 2023; 23:199. [PMID: 37689710 PMCID: PMC10493019 DOI: 10.1186/s12935-023-03002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/25/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV)-encoded X antigen, HBx, assists in the development of hepatocellular carcinoma (HCC) through complex mechanisms. Our results provide new insights into the EZH2 epigenetic repression of let-7c that promotes HCC migration induced by HBx. Thus, let-7c and HMGA2 represent key diagnostic markers and potential therapeutic targets for the treatment of HBV-related HCC. RESULTS We investigated the epigenetic regulation of let-7c, an important representative miRNA in liver tumor metastasis, in human HCC cells to verify the effect of HBx. Based on quantitative PCR (qPCR) of mRNA isolated from tumor and adjacent non-tumor liver tissues of 24 patients with HBV-related HCC, EZH2 expression was significantly overexpressed in most HCC tissues (87.5%). We executed a miRNA microarray analysis in paired HBV-related HCC tumor and adjacent non-tumorous liver tissue from six of these patients and identified let-7c, miR-199a-3p, and miR-99a as being downregulated in the tumor tissue. Real-time PCR analysis verified significant downregulation of let-7c and miR-99a in both HepG2X and Hep3BX cells, which stably overexpress HBx, relative to parental cells. HBX enhanced EZH2 expression and attenuated let-7c expression to induce HMGA2 expression in the HCC cells. Knockdown of HMGA2 significantly downregulated the metastatic potential of HCC cells induced by HBx. CONCLUSIONS The deregulation of let-7c expression by HBx may indicate a potential novel pathway through deregulating cell metastasis and imply that HMGA2 might be used as a new prognostic marker and/or as an effective therapeutic target for HCC.
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Affiliation(s)
- Chen-Shiou Wu
- Institute of Translational Medicine and New Drug Development, Taichung, 40402, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, 40402, Taiwan
| | - Yi-Chung Chien
- Institute of Translational Medicine and New Drug Development, Taichung, 40402, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, 40402, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan
| | - Chia-Jui Yen
- Division of Hematology and Oncology, Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, 70403, Taiwan
| | - Jia-Yan Wu
- Institute of Translational Medicine and New Drug Development, Taichung, 40402, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, 40402, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan
| | - Li-Yuan Bai
- Division of Hematology and Oncology, China Medical University Hospital, Taichung, 40402, Taiwan.
| | - Yung-Luen Yu
- Institute of Translational Medicine and New Drug Development, Taichung, 40402, Taiwan.
- Center for Molecular Medicine, China Medical University Hospital, Taichung, 40402, Taiwan.
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan.
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, 41354, Taiwan.
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15
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Yuan Y, Wu D, Li J, Huang D, Zhao Y, Gao T, Zhuang Z, Cui Y, Zheng DY, Tang Y. Mechanisms of tumor-associated macrophages affecting the progression of hepatocellular carcinoma. Front Pharmacol 2023; 14:1217400. [PMID: 37663266 PMCID: PMC10470150 DOI: 10.3389/fphar.2023.1217400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/23/2023] [Indexed: 09/05/2023] Open
Abstract
Tumor-associated macrophages (TAMs) are essential components of the immune cell stroma of hepatocellular carcinoma. TAMs originate from monocytic myeloid-derived suppressor cells, peripheral blood monocytes, and kupffer cells. The recruitment of monocytes to the HCC tumor microenvironment is facilitated by various factors, leading to their differentiation into TAMs with unique phenotypes. TAMs can directly activate or inhibit the nuclear factor-κB, interleukin-6/signal transducer and signal transducer and activator of transcription 3, Wnt/β-catenin, transforming growth factor-β1/bone morphogenetic protein, and extracellular signal-regulated kinase 1/2 signaling pathways in tumor cells and interact with other immune cells via producing cytokines and extracellular vesicles, thus affecting carcinoma cell proliferation, invasive and migratory, angiogenesis, liver fibrosis progression, and other processes to participate in different stages of tumor progression. In recent years, TAMs have received much attention as a prospective treatment target for HCC. This review describes the origin and characteristics of TAMs and their mechanism of action in the occurrence and development of HCC to offer a theoretical foundation for further clinical research of TAMs.
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Affiliation(s)
- Yi Yuan
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Dailin Wu
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Jing Li
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Dan Huang
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Yan Zhao
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Tianqi Gao
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhenjie Zhuang
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Ying Cui
- Department of Psychiatry, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Da-Yong Zheng
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, Guangdong, China
- Department of Hepatopancreatobiliary, Cancer Center, Southern Medical University, Guangzhou, Guangdong, China
| | - Ying Tang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
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16
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Chen X, Xu Y, Wang M, Ren C. Elucidating the Role of Pyroptosis in Lower-Grade Glioma: Development of a Novel Scoring System to Enhance Personalized Therapeutic Approaches. J Mol Neurosci 2023; 73:649-663. [PMID: 37566191 DOI: 10.1007/s12031-023-02147-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023]
Abstract
Pyroptosis, an orchestrated cellular death pathway, has gained attention due to its role in the pathophysiology and evolution of numerous malignancies. Despite this, no robust quantitative measure of pyroptosis activity in lower-grade glioma (LGG) exists currently. We scrutinized the transcriptomic data of LGG specimens acquired from TCGA and CGGA repositories, juxtaposed with the expression patterns of healthy brain tissues from the GTEx database. A register of pyroptosis-associated genes was extracted from the GSEA database. Utilizing unsupervised clustering algorithms on the expression patterns of these genes, we stratified LGG samples into unique subgroups. We implemented the Boruta machine learning algorithm to discern representative variables for each pyroptosis subtype and applied principal component analysis (PCA) to condense the dimensionality of the feature gene expression data, which led to the formulation of a pyroptosis scoring system (P score) to estimate pyroptosis activity in LGG. Furthermore, we affirmed the capacity of the P score to discriminate diverse cell subpopulations within a single-cell database and explored the correlations between the P score and clinical attributes, prognostic implications, and the tumor immune microenvironment in LGG. We identified three distinctive pyroptosis patterns with significant correlations to patient survival, clinicopathological properties, and characteristics of the tumor immune microenvironment (TIME). Two gene clusters, associated with unique prognostic and TIME attributes, emerged from differentially expressed genes (DEGs) across the pyroptosis patterns. The P score was formulated and authenticated as an autonomous prognostic determinant for overall survival in the TCGA and CGGA cohorts. Additionally, the P score demonstrated its competency to quantitatively represent pyroptosis activity across different cellular subpopulations in single-cell data. Notably, the P score in LGG was found to be indicative of tumor stemness and could serve as a predictive biomarker for the efficacy of temozolomide treatment and immunotherapy, underscoring its potential clinical utility. Our investigation pioneers a novel pyroptosis-centric scoring system with significant prognostic implications. The P score holds promise as a potential predictive biomarker for the response to chemotherapy and immunotherapy, facilitating the development of personalized therapeutic approaches in LGG patients.
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Affiliation(s)
- Xiao Chen
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an JiaotongUniversity, Xi'an, 710061, Shaanxi, China
- Center for Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Ying Xu
- Health Information Services, The First Affiliated Hospital of Xi'an Jiaotong, Xi'an, 710061, Shaanxi, China
| | - Maode Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an JiaotongUniversity, Xi'an, 710061, Shaanxi, China.
- Center for Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
| | - Chunying Ren
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an JiaotongUniversity, Xi'an, 710061, Shaanxi, China.
- Gamma Knife Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
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17
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Zhang D, Ni Y, Wang Y, Feng J, Zhuang N, Li J, Liu L, Shen W, Zheng J, Zheng W, Qian C, Shan J, Zhou Z. Spatial heterogeneity of tumor microenvironment influences the prognosis of clear cell renal cell carcinoma. J Transl Med 2023; 21:489. [PMID: 37474942 PMCID: PMC10360235 DOI: 10.1186/s12967-023-04336-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 07/09/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is an immunologically and histologically diverse tumor. However, how the structural heterogeneity of tumor microenvironment (TME) affects cancer progression and treatment response remains unclear. Hence, we characterized the TME architectures of ccRCC tissues using imaging mass cytometry (IMC) and explored their associations with clinical outcome and therapeutic response. METHODS Using IMC, we profiled the TME landscape of ccRCC and paracancerous tissue by measuring 17 markers involved in tissue architecture, immune cell and immune activation. In the ccRCC tissue, we identified distinct immune architectures of ccRCC tissue based on the mix score and performed cellular neighborhood (CN) analysis to subdivide TME phenotypes. Moreover, we assessed the relationship between the different TME phenotypes and ccRCC patient survival, clinical features and treatment response. RESULTS We found that ccRCC tissues had higher levels of CD8+ T cells, CD163- macrophages, Treg cells, endothelial cells, and fibroblasts than paracancerous tissues. Immune infiltrates in ccRCC tissues distinctly showed clustered and scattered patterns. Within the clustered pattern, we identified two subtypes with different clinical outcomes based on CN analysis. The TLS-like phenotype had cell communities resembling tertiary lymphoid structures, characterized by cell-cell interactions of CD8+ T cells-B cells and GZMB+CD8+ T cells-B cells, which exhibited anti-tumor features and favorable outcomes, while the Macrophage/T-clustered phenotype with macrophage- or T cell-dominated cell communities had a poor prognosis. Patients with scattered immune architecture could be further divided into scattered-CN-hot and scattered-CN-cold phenotypes based on the presence or absence of immune CNs, but both had a better prognosis than the macrophage/T-clustered phenotype. We further analyzed the relationship between the TME phenotypes and treatment response in five metastatic ccRCC patients treated with sunitinib, and found that all three responders were scattered-CN-hot phenotype while both non-responders were macrophage/T-clustered phenotype. CONCLUSION Our study revealed the structural heterogeneity of TME in ccRCC and its impact on clinical outcome and personalized treatment. These findings highlight the potential of IMC and CN analysis for characterizing TME structural units in cancer research.
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Affiliation(s)
- Dawei Zhang
- Department of Urology, The Southwest Hospital, Army Medical University, No. 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Yuanli Ni
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, No. 181 Hanyu Road, Shapingba District, Chongqing, 400030, China
| | - Yongquan Wang
- Department of Urology, The Southwest Hospital, Army Medical University, No. 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Juan Feng
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, No. 181 Hanyu Road, Shapingba District, Chongqing, 400030, China
| | - Na Zhuang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, No. 181 Hanyu Road, Shapingba District, Chongqing, 400030, China
| | - Jiatao Li
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, No. 181 Hanyu Road, Shapingba District, Chongqing, 400030, China
| | - Limei Liu
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, No. 181 Hanyu Road, Shapingba District, Chongqing, 400030, China
| | - Wenhao Shen
- Department of Urology, The Southwest Hospital, Army Medical University, No. 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Ji Zheng
- Department of Urology, The Southwest Hospital, Army Medical University, No. 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Wei Zheng
- Anesthesiology Department, The 80th Army Hospital of Chinese PLA, Weifang, 261021, Shandong, China
| | - Cheng Qian
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, No. 181 Hanyu Road, Shapingba District, Chongqing, 400030, China.
| | - Juanjuan Shan
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, No. 181 Hanyu Road, Shapingba District, Chongqing, 400030, China.
| | - Zhansong Zhou
- Department of Urology, The Southwest Hospital, Army Medical University, No. 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China.
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18
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Jing Q, Yuan C, Zhou C, Jin W, Wang A, Wu Y, Shang W, Zhang G, Ke X, Du J, Li Y, Shao F. Comprehensive analysis identifies CLEC1B as a potential prognostic biomarker in hepatocellular carcinoma. Cancer Cell Int 2023; 23:113. [PMID: 37308868 DOI: 10.1186/s12935-023-02939-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/06/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND C-type lectin domain family 1 member B (CLEC1B, encoding the CLEC-2 protein), a member of the C-type lectin superfamily, is a type II transmembrane receptor involved in platelet activation, angiogenesis, and immune and inflammatory responses. However, data regarding its function and clinical prognostic value in hepatocellular carcinoma (HCC) remain scarce. METHODS The expression of CLEC1B was explored using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. RT-qPCR, western blot, and immunohistochemistry assays were employed to validate the downregulation of CLEC1B. Univariate Cox regression and survival analyses were used to evaluate the prognostic value of CLEC1B. Gene Set Enrichment Analysis (GSEA) was conducted to investigate the potential association between cancer hallmarks and CLEC1B expression. The TISIDB database was applied to search for the correlation between immune cell infiltration levels and CLEC1B expression. The association between CLEC1B and immunomodulators was conducted by Spearman correlation analysis based on the Sangerbox platform. Annexin V-FITC/PI apoptosis kit was used for the detection of cell apoptosis. RESULTS The expression of CLEC1B was low in various tumors and exhibited a promising clinical prognostic value for HCC patients. The expression level of CLEC1B was tightly associated with the infiltration of various immune cells in the HCC tumor microenvironment (TME) and positively correlated with a bulk of immunomodulators. In addition, CLEC1B and its related genes or interacting proteins are implicated in multiple immune-related processes and signaling pathways. Moreover, overexpression of CLEC1B significantly influenced the treatment effects of sorafenib on HCC cells. CONCLUSIONS Our results reveal that CLEC1B could serve as a potential prognostic biomarker and may be a novel immunoregulator for HCC. However, its function in immune regulation should be further explored.
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Grants
- 2021KY077, 2022KY503, 2022KY046, 2022KY074, 2022KY290 Medical and Health Science and Technology Project of Zhejiang Province
- 2021KY077, 2022KY503, 2022KY046, 2022KY074, 2022KY290 Medical and Health Science and Technology Project of Zhejiang Province
- 2021KY077, 2022KY503, 2022KY046, 2022KY074, 2022KY290 Medical and Health Science and Technology Project of Zhejiang Province
- 2020ZA098, 2021ZB245 Traditional Chinese Medicine Science and Technology Project of Zhejiang Province
- 2020ZA098, 2021ZB245 Traditional Chinese Medicine Science and Technology Project of Zhejiang Province
- LGF21H010008, LGF20H080005, LBY23H080004, LGF22H080008 Zhejiang Provincial Natural Science Foundation of China
- LGF21H010008, LGF20H080005, LBY23H080004, LGF22H080008 Zhejiang Provincial Natural Science Foundation of China
- LGF21H010008, LGF20H080005, LBY23H080004, LGF22H080008 Zhejiang Provincial Natural Science Foundation of China
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Affiliation(s)
- Qiangan Jing
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Department of Central Laboratory, Affiliated Hangzhou first people's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Chen Yuan
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Chaoting Zhou
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Weidong Jin
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Aiwei Wang
- Department of Hematology, The first people's Hospital of Fuyang Hangzhou, Hangzhou, Zhejiang, China
| | - Yanfang Wu
- Department of Hematology, The first people's Hospital of Fuyang Hangzhou, Hangzhou, Zhejiang, China
| | - Wenzhong Shang
- Department of Hematology, The first people's Hospital of Fuyang Hangzhou, Hangzhou, Zhejiang, China
| | - Guibing Zhang
- Department of Hematology, The first people's Hospital of Fuyang Hangzhou, Hangzhou, Zhejiang, China
| | - Xia Ke
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Jing Du
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China.
| | - Yanchun Li
- Department of Central Laboratory, Affiliated Hangzhou first people's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Fangchun Shao
- Cancer Center, Department of Pulmonary and Critical Care Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China.
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19
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Wang H, Arulraj T, Kimko H, Popel AS. Generating immunogenomic data-guided virtual patients using a QSP model to predict response of advanced NSCLC to PD-L1 inhibition. NPJ Precis Oncol 2023; 7:55. [PMID: 37291190 DOI: 10.1038/s41698-023-00405-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
Generating realistic virtual patients from a limited amount of patient data is one of the major challenges for quantitative systems pharmacology modeling in immuno-oncology. Quantitative systems pharmacology (QSP) is a mathematical modeling methodology that integrates mechanistic knowledge of biological systems to investigate dynamics in a whole system during disease progression and drug treatment. In the present analysis, we parameterized our previously published QSP model of the cancer-immunity cycle to non-small cell lung cancer (NSCLC) and generated a virtual patient cohort to predict clinical response to PD-L1 inhibition in NSCLC. The virtual patient generation was guided by immunogenomic data from iAtlas portal and population pharmacokinetic data of durvalumab, a PD-L1 inhibitor. With virtual patients generated following the immunogenomic data distribution, our model predicted a response rate of 18.6% (95% bootstrap confidence interval: 13.3-24.2%) and identified CD8/Treg ratio as a potential predictive biomarker in addition to PD-L1 expression and tumor mutational burden. We demonstrated that omics data served as a reliable resource for virtual patient generation techniques in immuno-oncology using QSP models.
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Affiliation(s)
- Hanwen Wang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Theinmozhi Arulraj
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Holly Kimko
- Clinical Pharmacology & Quantitative Pharmacology, AstraZeneca, Gaithersburg, MD, USA
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Oncology, and the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
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20
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Nikfar M, Mi H, Gong C, Kimko H, Popel AS. Quantifying Intratumoral Heterogeneity and Immunoarchitecture Generated In-Silico by a Spatial Quantitative Systems Pharmacology Model. Cancers (Basel) 2023; 15:2750. [PMID: 37345087 DOI: 10.3390/cancers15102750] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 06/23/2023] Open
Abstract
Spatial heterogeneity is a hallmark of cancer. Tumor heterogeneity can vary with time and location. The tumor microenvironment (TME) encompasses various cell types and their interactions that impart response to therapies. Therefore, a quantitative evaluation of tumor heterogeneity is crucial for the development of effective treatments. Different approaches, such as multiregional sequencing, spatial transcriptomics, analysis of autopsy samples, and longitudinal analysis of biopsy samples, can be used to analyze the intratumoral heterogeneity (ITH) and temporal evolution and to reveal the mechanisms of therapeutic response. However, because of the limitations of these data and the uncertainty associated with the time points of sample collection, having a complete understanding of intratumoral heterogeneity role is challenging. Here, we used a hybrid model that integrates a whole-patient compartmental quantitative-systems-pharmacology (QSP) model with a spatial agent-based model (ABM) describing the TME; we applied four spatial metrics to quantify model-simulated intratumoral heterogeneity and classified the TME immunoarchitecture for representative cases of effective and ineffective anti-PD-1 therapy. The four metrics, adopted from computational digital pathology, included mixing score, average neighbor frequency, Shannon's entropy and area under the curve (AUC) of the G-cross function. A fifth non-spatial metric was used to supplement the analysis, which was the ratio of the number of cancer cells to immune cells. These metrics were utilized to classify the TME as "cold", "compartmentalized" and "mixed", which were related to treatment efficacy. The trends in these metrics for effective and ineffective treatments are in qualitative agreement with the clinical literature, indicating that compartmentalized immunoarchitecture is likely to result in more efficacious treatment outcomes.
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Affiliation(s)
- Mehdi Nikfar
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Haoyang Mi
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Chang Gong
- Clinical Pharmacology & Quantitative Pharmacology, AstraZeneca, Waltham, MA 02451, USA
| | - Holly Kimko
- Clinical Pharmacology & Quantitative Pharmacology, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Aleksander S Popel
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
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21
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Wang H, Arulraj T, Kimko H, Popel AS. Generating immunogenomic data-guided virtual patients using a QSP model to predict response of advanced NSCLC to PD-L1 inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538191. [PMID: 37162938 PMCID: PMC10168221 DOI: 10.1101/2023.04.25.538191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Generating realistic virtual patients from a limited amount of patient data is one of the major challenges for quantitative systems pharmacology modeling in immuno-oncology. Quantitative systems pharmacology (QSP) is a mathematical modeling methodology that integrates mechanistic knowledge of biological systems to investigate dynamics in a whole system during disease progression and drug treatment. In the present analysis, we parameterized our previously published QSP model of the cancer-immunity cycle to non-small cell lung cancer (NSCLC) and generated a virtual patient cohort to predict clinical response to PD-L1 inhibition in NSCLC. The virtual patient generation was guided by immunogenomic data from iAtlas portal and population pharmacokinetic data of durvalumab, a PD-L1 inhibitor. With virtual patients generated following the immunogenomic data distribution, our model predicted a response rate of 18.6% (95% bootstrap confidence interval: 13.3-24.2%) and identified CD8/Treg ratio as a potential predictive biomarker in addition to PD-L1 expression and tumor mutational burden. We demonstrated that omics data served as a reliable resource for virtual patient generation techniques in immuno-oncology using QSP models.
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22
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Saldarriaga OA, Krishnan S, Wanninger TG, Oneka M, Rao A, Bao D, Arroyave E, Gosnell J, Kueht M, Moghe A, Millian D, Jiao J, Sanchez JI, Spratt H, Beretta L, Stevenson HL. Patients with fibrosis from non-alcoholic steatohepatitis have heterogeneous intrahepatic macrophages and therapeutic targets. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.16.23285924. [PMID: 36865099 PMCID: PMC9980226 DOI: 10.1101/2023.02.16.23285924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Background and Aims In clinical trials for reducing fibrosis in NASH patients, therapeutics that target macrophages have had variable results. We evaluated intrahepatic macrophages in patients with non-alcoholic steatohepatitis to determine if fibrosis influenced phenotypes and expression of CCR2 and Galectin-3. Approach & Results We used nCounter to analyze liver biopsies from well-matched patients with minimal (n=12) or advanced (n=12) fibrosis to determine which macrophage-related genes would be significantly different. Known therapy targets (e.g., CCR2 and Galectin-3) were significantly increased in patients with cirrhosis.However, several genes (e.g., CD68, CD16, and CD14) did not show significant differences, and CD163, a marker of pro-fibrotic macrophages was significantly decreased with cirrhosis. Next, we analyzed patients with minimal (n=6) or advanced fibrosis (n=5) using approaches that preserved hepatic architecture by multiplex-staining with anti-CD68, Mac387, CD163, CD14, and CD16. Spectral data were analyzed using deep learning/artificial intelligence to determine percentages and spatial relationships. This approach showed patients with advanced fibrosis had increased CD68+, CD16+, Mac387+, CD163+, and CD16+CD163+ populations. Interaction of CD68+ and Mac387+ populations was significantly increased in patients with cirrhosis and enrichment of these same phenotypes in individuals with minimal fibrosis correlated with poor outcomes. Evaluation of a final set of patients (n=4) also showed heterogenous expression of CD163, CCR2, Galectin-3, and Mac387, and significant differences were not dependent on fibrosis stage or NAFLD activity. Conclusions Approaches that leave hepatic architecture intact, like multispectral imaging, may be paramount to developing effective treatments for NASH. In addition, understanding individual differences in patients may be required for optimal responses to macrophage-targeting therapies.
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23
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Zhang S, Yuan L, Danilova L, Mo G, Zhu Q, Deshpande A, Bell AT, Elisseeff J, Popel AS, Anders RA, Jaffee EM, Yarchoan M, Fertig EJ, Kagohara LT. Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523481. [PMID: 36712023 PMCID: PMC9882076 DOI: 10.1101/2023.01.10.523481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Novel immunotherapy combination therapies have improved outcomes for patients with hepatocellular carcinoma (HCC), but responses are limited to a subset of patients and recurrence can also occur. Little is known about the inter- and intra-tumor heterogeneity in cellular signaling networks within the HCC tumor microenvironment (TME) that underlie responses to modern systemic therapy. We applied spatial transcriptomics (ST) profiling to characterize the tumor microenvironment in HCC resection specimens from a clinical trial of neoadjuvant cabozantinib, a multi-tyrosine kinase inhibitor that primarily blocks VEGF, and nivolumab, a PD-1 inhibitor in which 5 out of 15 patients were found to have a pathologic response. ST profiling demonstrated that the TME of responding tumors was enriched for immune cells and cancer associated fibroblasts (CAF) with pro-inflammatory signaling relative to the non-responders. The enriched cancer-immune interactions in responding tumors are characterized by activation of the PAX5 module, a known regulator of B cell maturation, which colocalized with spots with increased B cell markers expression suggesting strong activity of these cells. Cancer-CAF interactions were also enriched in the responding tumors and were associated with extracellular matrix (ECM) remodeling as there was high activation of FOS and JUN in CAFs adjacent to tumor. The ECM remodeling is consistent with proliferative fibrosis in association with immune-mediated tumor regression. Among the patients with major pathologic response, a single patient experienced early HCC recurrence. ST analysis of this clinical outlier demonstrated marked tumor heterogeneity, with a distinctive immune-poor tumor region that resembles the non-responding TME across patients and was characterized by cancer-CAF interactions and expression of cancer stem cell markers, potentially mediating early tumor immune escape and recurrence in this patient. These data show that responses to modern systemic therapy in HCC are associated with distinctive molecular and cellular landscapes and provide new targets to enhance and prolong responses to systemic therapy in HCC.
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Affiliation(s)
- Shuming Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Long Yuan
- Department of Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ludmila Danilova
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Guanglan Mo
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Qingfeng Zhu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Atul Deshpande
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Alexander T.F. Bell
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer Elisseeff
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aleksander S. Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert A. Anders
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth M. Jaffee
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Mark Yarchoan
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Elana J. Fertig
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Luciane T. Kagohara
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
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24
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Mi H, Sivagnanam S, Betts CB, Liudahl SM, Jaffee EM, Coussens LM, Popel AS. Quantitative Spatial Profiling of Immune Populations in Pancreatic Ductal Adenocarcinoma Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers. Cancer Res 2022; 82:4359-4372. [PMID: 36112643 PMCID: PMC9716253 DOI: 10.1158/0008-5472.can-22-1190] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/04/2022] [Accepted: 09/12/2022] [Indexed: 01/24/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with poor 5-year survival rates, necessitating identification of novel therapeutic targets. Elucidating the biology of the tumor immune microenvironment (TiME) can provide vital insights into mechanisms of tumor progression. In this study, we developed a quantitative image processing platform to analyze sequential multiplexed IHC data from archival PDAC tissue resection specimens. A 27-plex marker panel was employed to simultaneously phenotype cell populations and their functional states, followed by a computational workflow to interrogate the immune contextures of the TiME in search of potential biomarkers. The PDAC TiME reflected a low-immunogenic ecosystem with both high intratumoral and intertumoral heterogeneity. Spatial analysis revealed that the relative distance between IL10+ myelomonocytes, PD-1+ CD4+ T cells, and granzyme B+ CD8+ T cells correlated significantly with survival, from which a spatial proximity signature termed imRS was derived that correlated with PDAC patient survival. Furthermore, spatial enrichment of CD8+ T cells in lymphoid aggregates was also linked to improved survival. Altogether, these findings indicate that the PDAC TiME, generally considered immuno-dormant or immunosuppressive, is a spatially nuanced ecosystem orchestrated by ordered immune hierarchies. This new understanding of spatial complexity may guide novel treatment strategies for PDAC. SIGNIFICANCE Quantitative image analysis of PDAC specimens reveals intertumoral and intratumoral heterogeneity of immune populations and identifies spatial immune architectures that are significantly associated with disease prognosis.
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Affiliation(s)
- Haoyang Mi
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Corresponding Authors: Haoyang Mi, Johns Hopkins University, Baltimore, MD 21205. Phone: 410-528-3768; E-mail: ; and Lisa M. Coussens,
| | | | - Courtney B. Betts
- Department of Cell, Development, and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Shannon M. Liudahl
- Department of Cell, Development, and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Elizabeth M. Jaffee
- Skip Viragh Center for Pancreatic Cancer, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medicine, Baltimore, Maryland.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lisa M. Coussens
- Department of Cell, Development, and Cancer Biology, Oregon Health and Science University, Portland, Oregon.,Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, Oregon.,Knight Cancer Institute, Portland, Oregon.,Corresponding Authors: Haoyang Mi, Johns Hopkins University, Baltimore, MD 21205. Phone: 410-528-3768; E-mail: ; and Lisa M. Coussens,
| | - Aleksander S. Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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25
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Sové RJ, Verma BK, Wang H, Ho WJ, Yarchoan M, Popel AS. Virtual clinical trials of anti-PD-1 and anti-CTLA-4 immunotherapy in advanced hepatocellular carcinoma using a quantitative systems pharmacology model. J Immunother Cancer 2022; 10:e005414. [PMID: 36323435 PMCID: PMC9639136 DOI: 10.1136/jitc-2022-005414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the most common form of primary liver cancer and is the third-leading cause of cancer-related death worldwide. Most patients with HCC are diagnosed at an advanced stage, and the median survival for patients with advanced HCC treated with modern systemic therapy is less than 2 years. This leaves the advanced stage patients with limited treatment options. Immune checkpoint inhibitors (ICIs) targeting programmed cell death protein 1 (PD-1) or its ligand, are widely used in the treatment of HCC and are associated with durable responses in a subset of patients. ICIs targeting cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) also have clinical activity in HCC. Combination therapy of nivolumab (anti-PD-1) and ipilimumab (anti-CTLA-4) is the first treatment option for HCC to be approved by Food and Drug Administration that targets more than one immune checkpoints. METHODS In this study, we used the framework of quantitative systems pharmacology (QSP) to perform a virtual clinical trial for nivolumab and ipilimumab in HCC patients. Our model incorporates detailed biological mechanisms of interactions of immune cells and cancer cells leading to antitumor response. To conduct virtual clinical trial, we generate virtual patient from a cohort of 5,000 proposed patients by extending recent algorithms from literature. The model was calibrated using the data of the clinical trial CheckMate 040 (ClinicalTrials.gov number, NCT01658878). RESULTS Retrospective analyses were performed for different immune checkpoint therapies as performed in CheckMate 040. Using machine learning approach, we predict the importance of potential biomarkers for immune blockade therapies. CONCLUSIONS This is the first QSP model for HCC with ICIs and the predictions are consistent with clinically observed outcomes. This study demonstrates that using a mechanistic understanding of the underlying pathophysiology, QSP models can facilitate patient selection and design clinical trials with improved success.
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Affiliation(s)
- Richard J Sové
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Babita K Verma
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hanwen Wang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Won Jin Ho
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark Yarchoan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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