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Luo X, Gong Y, Gong Z, Fan K, Suo T, Liu H, Ni X, Ni X, Abudureyimu M, Liu H. Liver and bile duct organoids and tumoroids. Biomed Pharmacother 2024; 178:117104. [PMID: 39024834 DOI: 10.1016/j.biopha.2024.117104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/23/2024] [Accepted: 07/07/2024] [Indexed: 07/20/2024] Open
Abstract
Organoids refer to 3D cultures established to recapitulate histology, pathology, architecture, and genetic traits of various organs and tissues in the body, thereby replacing 2D cell cultures, xenograft, and animal models. Organoids form a 3D in vitro mimic of original tissues like the liver and are derived from embryonic or adult tissue stem cells. Liver and bile duct tumor organoids, also called, tumoroids capture genetic diversity, cellular, and pathophysiological properties of original tumors. Moreover, co-culture techniques along with genetic modulation of organoids allow for using tumoroids in liver and bile duct cancer research and drug screening/testing. Therefore, tumoroids are promising platforms for studying liver and bile duct cancer, which paves the way for the new era of personalized therapies. In the current review, we aimed to discuss liver and bile duct organoids with special emphasis on tumoroids and their applications, advantages, and shortcomings.
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Affiliation(s)
- Xuanming Luo
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Center of Zhongshan Hospital, Fudan University, China; Cancer Center, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Institute, Fudan University, China; Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, China; Department of General Surgery, Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
| | - Yuda Gong
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Center of Zhongshan Hospital, Fudan University, China; Cancer Center, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Institute, Fudan University, China; Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, China
| | - Zijun Gong
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Center of Zhongshan Hospital, Fudan University, China; Cancer Center, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Institute, Fudan University, China; Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, China
| | - Kun Fan
- Department of General Surgery, Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
| | - Tao Suo
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Center of Zhongshan Hospital, Fudan University, China; Cancer Center, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Institute, Fudan University, China; Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, China
| | - Han Liu
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Center of Zhongshan Hospital, Fudan University, China; Cancer Center, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Institute, Fudan University, China; Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, China
| | - Xiaoling Ni
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Center of Zhongshan Hospital, Fudan University, China; Cancer Center, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Institute, Fudan University, China; Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, China
| | - Xiaojian Ni
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Center of Zhongshan Hospital, Fudan University, China; Cancer Center, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Institute, Fudan University, China; Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, China
| | - Miyesaier Abudureyimu
- Cardiovascular Department, Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.
| | - Houbao Liu
- Department of Biliary Surgery, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Center of Zhongshan Hospital, Fudan University, China; Cancer Center, Zhongshan Hospital, Fudan University, China; Biliary Tract Disease Institute, Fudan University, China; Shanghai Engineering Research Center of Biliary Tract Minimal Invasive Surgery and Materials, China; Department of General Surgery, Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.
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Hu X, Wei J, Liu P, Zheng Q, Zhang Y, Zhang Q, Yao J, Ni J. Organoid as a promising tool for primary liver cancer research: a comprehensive review. Cell Biosci 2024; 14:107. [PMID: 39192365 DOI: 10.1186/s13578-024-01287-5] [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: 04/07/2024] [Accepted: 08/15/2024] [Indexed: 08/29/2024] Open
Abstract
Primary liver cancer (PLC) is one of the most common malignant gastrointestinal tumors worldwide. Limited by the shortage of liver transplantation donors and the heterogeneity of tumors, patients with liver cancer lack effective treatment options, which leads to rapid progression and metastasis. Currently, preclinical models of PLC fall short of clinical reality and are limited in their response to disease progression and the effectiveness of drug therapy. Organoids are in vitro three-dimensional cultured preclinical models with a high degree of heterogeneity that preserve the histomorphological and genomic features of primary tumors. Liver cancer organoids have been widely used for drug screening, new target discovery, and precision medicine; thus representing a promising tool to study PLC. Here, we summarize the progress of research on liver cancer organoids and their potential application as disease models. This review provides a comprehensive introduction to this emerging technology and offers new ideas for researchers to explore in the field of precision medicine.
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Affiliation(s)
- Xuekai Hu
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Jiayun Wei
- The First school of Clinical Medicine, Lanzhou University, Lanzhou, 730000, China
- The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Pinyan Liu
- The First school of Clinical Medicine, Lanzhou University, Lanzhou, 730000, China
- The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Qiuxia Zheng
- The First school of Clinical Medicine, Lanzhou University, Lanzhou, 730000, China
| | - Yue Zhang
- The First school of Clinical Medicine, Lanzhou University, Lanzhou, 730000, China
| | - Qichen Zhang
- The First school of Clinical Medicine, Lanzhou University, Lanzhou, 730000, China
| | - Jia Yao
- The First school of Clinical Medicine, Lanzhou University, Lanzhou, 730000, China.
- The First Hospital of Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Biotherapy and Regenerative Medicine, First Hospital of Lanzhou University, Lanzhou, 730000, China.
- The First Hospital of Lanzhou University, No. 1 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China.
| | - Jingman Ni
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China.
- School of Basic Medical Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou, China.
- School of Pharmacy, Lanzhou University, No. 199 West Donggang Road, Lanzhou, Gansu, 730000, P. R. China.
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3
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Liu S, Cheng C, Zhu L, Zhao T, Wang Z, Yi X, Yan F, Wang X, Li C, Cui T, Yang B. Liver organoids: updates on generation strategies and biomedical applications. Stem Cell Res Ther 2024; 15:244. [PMID: 39113154 PMCID: PMC11304926 DOI: 10.1186/s13287-024-03865-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/27/2024] [Indexed: 08/10/2024] Open
Abstract
The liver is the most important metabolic organ in the body. While mouse models and cell lines have further deepened our understanding of liver biology and related diseases, they are flawed in replicating key aspects of human liver tissue, particularly its complex structure and metabolic functions. The organoid model represents a major breakthrough in cell biology that revolutionized biomedical research. Organoids are in vitro three-dimensional (3D) physiological structures that recapitulate the morphological and functional characteristics of tissues in vivo, and have significant advantages over traditional cell culture methods. In this review, we discuss the generation strategies and current advances in the field focusing on their application in regenerative medicine, drug discovery and modeling diseases.
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Affiliation(s)
- Sen Liu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016, China
- State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin Institute of Pharmaceutical Research, Tianjin, 300301, China
| | | | - Liuyang Zhu
- First Central Clinical College of Tianjin Medical University, Tianjin, 300192, China
| | - Tianyu Zhao
- State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin Institute of Pharmaceutical Research, Tianjin, 300301, China
| | - Ze Wang
- State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin Institute of Pharmaceutical Research, Tianjin, 300301, China
- Research Unit for Drug Metabolism, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiulin Yi
- State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin Institute of Pharmaceutical Research, Tianjin, 300301, China
- Research Unit for Drug Metabolism, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Fengying Yan
- State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin Institute of Pharmaceutical Research, Tianjin, 300301, China
- Research Unit for Drug Metabolism, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiaoliang Wang
- State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin Institute of Pharmaceutical Research, Tianjin, 300301, China
| | - Chunli Li
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Tao Cui
- State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin Institute of Pharmaceutical Research, Tianjin, 300301, China.
- Research Unit for Drug Metabolism, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Baofeng Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016, China.
- School of Pharmacy, Harbin Medical University, Harbin, 150081, China.
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Polak R, Zhang ET, Kuo CJ. Cancer organoids 2.0: modelling the complexity of the tumour immune microenvironment. Nat Rev Cancer 2024; 24:523-539. [PMID: 38977835 DOI: 10.1038/s41568-024-00706-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/09/2024] [Indexed: 07/10/2024]
Abstract
The development of neoplasia involves a complex and continuous interplay between malignantly transformed cells and the tumour microenvironment (TME). Cancer immunotherapies targeting the immune TME have been increasingly validated in clinical trials but response rates vary substantially between tumour histologies and are often transient, idiosyncratic and confounded by resistance. Faithful experimental models of the patient-specific tumour immune microenvironment, capable of recapitulating tumour biology and immunotherapy effects, would greatly improve patient selection, target identification and definition of resistance mechanisms for immuno-oncology therapeutics. In this Review, we discuss currently available and rapidly evolving 3D tumour organoid models that capture important immune features of the TME. We highlight diverse opportunities for organoid-based investigations of tumour immunity, drug development and precision medicine.
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Affiliation(s)
- Roel Polak
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Elisa T Zhang
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA.
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5
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Cigliano A, Liao W, Deiana GA, Rizzo D, Chen X, Calvisi DF. Preclinical Models of Hepatocellular Carcinoma: Current Utility, Limitations, and Challenges. Biomedicines 2024; 12:1624. [PMID: 39062197 PMCID: PMC11274649 DOI: 10.3390/biomedicines12071624] [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: 06/14/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC), the predominant primary liver tumor, remains one of the most lethal cancers worldwide, despite the advances in therapy in recent years. In addition to the traditional chemically and dietary-induced HCC models, a broad spectrum of novel preclinical tools have been generated following the advent of transgenic, transposon, organoid, and in silico technologies to overcome this gloomy scenario. These models have become rapidly robust preclinical instruments to unravel the molecular pathogenesis of liver cancer and establish new therapeutic approaches against this deadly disease. The present review article aims to summarize and discuss the commonly used preclinical models for HCC, evaluating their strengths and weaknesses.
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Affiliation(s)
- Antonio Cigliano
- Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy; (A.C.); (G.A.D.); (D.R.)
| | - Weiting Liao
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, CA 94143, USA; (W.L.); (X.C.)
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Giovanni A. Deiana
- Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy; (A.C.); (G.A.D.); (D.R.)
| | - Davide Rizzo
- Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy; (A.C.); (G.A.D.); (D.R.)
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, CA 94143, USA; (W.L.); (X.C.)
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Diego F. Calvisi
- Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy; (A.C.); (G.A.D.); (D.R.)
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Sturgill IR, Raab JR, Hoadley KA. Expanded detection and impact of BAP1 alterations in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.21.568094. [PMID: 38045292 PMCID: PMC10690206 DOI: 10.1101/2023.11.21.568094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Aberrant expression of the BAP1 tumor suppressor gene is a prominent risk factor for several tumor types and is important in tumor evolution and progression. Here we performed integrated multi-omic analyses using data from The Cancer Genome Atlas (TCGA) for 33 cancer types and over 10,000 individuals to identify alterations leading to BAP1 disruption. We combined existing variant calls and new calls derived from a de novo local realignment pipeline across multiple independent variant callers, increasing somatic variant detection by 41% from 182 to 257, including 11 indels ≥40bp. The expanded detection of mutations highlights the power of new tools to uncover longer indels and impactful mutations. We developed an expression-based BAP1 activity score and identified a transcriptional profile associated with BAP1 disruption in cancer. BAP1 has been proposed to play a critical role in controlling tumor plasticity and normal cell fate. Leveraging human and mouse liver datasets, BAP1 loss in normal cells resulted in lower BAP1 activity scores and lower scores were associated with a less-differentiated phenotype in embryonic cells. Together, our expanded BAP1 mutant samples revealed a transcriptional signature in cancer cells, supporting BAP1's influences on cellular plasticity and cell identity maintenance.
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Hu Y, Geng Q, Wang L, Wang Y, Huang C, Fan Z, Kong D. Research progress and application of liver organoids for disease modeling and regenerative therapy. J Mol Med (Berl) 2024; 102:859-874. [PMID: 38802517 PMCID: PMC11213763 DOI: 10.1007/s00109-024-02455-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 04/19/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]
Abstract
The liver is a major metabolic organ of the human body and has a high incidence of diseases. In recent years, the annual incidence of liver disease has increased, seriously endangering human life and health. The study of the occurrence and development mechanism of liver diseases, discovery of new therapeutic targets, and establishment of new methods of medical treatment are major issues related to the national economy and people's livelihood. The development of stable and effective research models is expected to provide new insights into the pathogenesis of liver diseases and the search for more effective treatment options. Organoid technology is a new in vitro culture system, and organoids constructed by human cells can simulate the morphological structure, gene expression, and glucose and lipid metabolism of organs in vivo, providing a new model for related research on liver diseases. This paper reviews the latest research progress on liver organoids from the establishment of cell sources and application of liver organoids and discusses their application potential in the field of liver disease research.
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Affiliation(s)
- Yang Hu
- Chinese Medicine Modernization and Big Data Research Center, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, 210022, Jiangsu, China
| | - Qiao Geng
- Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, China
| | - Lu Wang
- Department of Angioenterology, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, 157 Daming Avenue, Nanjing, 210022, Jiangsu, China
| | - Yi Wang
- Department of Angioenterology, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, 157 Daming Avenue, Nanjing, 210022, Jiangsu, China
| | - Chuyue Huang
- Department of Angioenterology, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, 157 Daming Avenue, Nanjing, 210022, Jiangsu, China
| | - Zhimin Fan
- Department of Angioenterology, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, 157 Daming Avenue, Nanjing, 210022, Jiangsu, China.
| | - Desong Kong
- Chinese Medicine Modernization and Big Data Research Center, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, 210022, Jiangsu, China.
- Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, 210023, China.
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Love JR, Karthaus WR. Next-Generation Modeling of Cancer Using Organoids. Cold Spring Harb Perspect Med 2024; 14:a041380. [PMID: 37734867 PMCID: PMC11146310 DOI: 10.1101/cshperspect.a041380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
In the last decade, organoid technology has become a cornerstone in cancer research. Organoids are long-term primary cell cultures, usually of epithelial origin, grown in a three-dimensional (3D) protein matrix and a fully defined medium. Organoids can be derived from many organs and cancer types and sites, encompassing both murine and human tissues. Importantly, they can be established from various stages during tumor evolution and recapitulate with high accuracy patient genomics and phenotypes in vitro, offering a platform for personalized medicine. Additionally, organoids are remarkably amendable for experimental manipulation. Taken together, these features make organoids a powerful tool with applications in basic cancer research and personalized medicine. Here, we will discuss the origins of organoid culture, applications in cancer research, and how cancer organoids can synergize with other models of cancer to drive basic discoveries as well as to translate these toward clinical solutions.
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Affiliation(s)
- Jillian R Love
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, 1015 Lausanne, Switzerland
| | - Wouter R Karthaus
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, 1015 Lausanne, Switzerland
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Afonso MB, Marques V, van Mil SW, Rodrigues CM. Human liver organoids: From generation to applications. Hepatology 2024; 79:1432-1451. [PMID: 36815360 PMCID: PMC11095893 DOI: 10.1097/hep.0000000000000343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/11/2022] [Accepted: 12/19/2022] [Indexed: 02/24/2023]
Abstract
In the last decade, research into human hepatology has been revolutionized by the development of mini human livers in a dish. These liver organoids are formed by self-organizing stem cells and resemble their native counterparts in cellular content, multicellular architecture, and functional features. Liver organoids can be derived from the liver tissue or pluripotent stem cells generated from a skin biopsy, blood cells, or renal epithelial cells present in urine. With the development of liver organoids, a large part of previous hurdles in modeling the human liver is likely to be solved, enabling possibilities to better model liver disease, improve (personalized) drug testing, and advance bioengineering options. In this review, we address strategies to generate and use organoids in human liver disease modeling, followed by a discussion of their potential application in drug development and therapeutics, as well as their strengths and limitations.
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Affiliation(s)
- Marta B. Afonso
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - Vanda Marques
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - Saskia W.C. van Mil
- Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, The Netherlands
| | - Cecilia M.P. Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
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Park S, Cho SW. Bioengineering toolkits for potentiating organoid therapeutics. Adv Drug Deliv Rev 2024; 208:115238. [PMID: 38447933 DOI: 10.1016/j.addr.2024.115238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/28/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Organoids are three-dimensional, multicellular constructs that recapitulate the structural and functional features of specific organs. Because of these characteristics, organoids have been widely applied in biomedical research in recent decades. Remarkable advancements in organoid technology have positioned them as promising candidates for regenerative medicine. However, current organoids still have limitations, such as the absence of internal vasculature, limited functionality, and a small size that is not commensurate with that of actual organs. These limitations hinder their survival and regenerative effects after transplantation. Another significant concern is the reliance on mouse tumor-derived matrix in organoid culture, which is unsuitable for clinical translation due to its tumor origin and safety issues. Therefore, our aim is to describe engineering strategies and alternative biocompatible materials that can facilitate the practical applications of organoids in regenerative medicine. Furthermore, we highlight meaningful progress in organoid transplantation, with a particular emphasis on the functional restoration of various organs.
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Affiliation(s)
- Sewon Park
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Seung-Woo Cho
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea; Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea; Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea.
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11
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Boretto M, Geurts MH, Gandhi S, Ma Z, Staliarova N, Celotti M, Lim S, He GW, Millen R, Driehuis E, Begthel H, Smabers L, Roodhart J, van Es J, Wu W, Clevers H. Epidermal growth factor receptor (EGFR) is a target of the tumor-suppressor E3 ligase FBXW7. Proc Natl Acad Sci U S A 2024; 121:e2309902121. [PMID: 38483988 PMCID: PMC10962967 DOI: 10.1073/pnas.2309902121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/08/2024] [Indexed: 03/19/2024] Open
Abstract
FBXW7 is an E3 ubiquitin ligase that targets proteins for proteasome-mediated degradation and is mutated in various cancer types. Here, we use CRISPR base editors to introduce different FBXW7 hotspot mutations in human colon organoids. Functionally, FBXW7 mutation reduces EGF dependency of organoid growth by ~10,000-fold. Combined transcriptomic and proteomic analyses revealed increased EGFR protein stability in FBXW7 mutants. Two distinct phosphodegron motifs reside in the cytoplasmic tail of EGFR. Mutations in these phosphodegron motifs occur in human cancer. CRISPR-mediated disruption of the phosphodegron motif at T693 reduced EGFR degradation and EGF growth factor dependency. FBXW7 mutant organoids showed reduced sensitivity to EGFR-MAPK inhibitors. These observations were further strengthened in CRC-derived organoid lines and validated in a cohort of patients treated with panitumumab. Our data imply that FBXW7 mutations reduce EGF dependency by disabling EGFR turnover.
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Affiliation(s)
- Matteo Boretto
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Maarten H. Geurts
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Shashank Gandhi
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
- Department of Molecular and Cellular Biology, Miller Institute for Basic Research in Science, University of California, Berkeley, CA94720
| | - Ziliang Ma
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore138648, Singapore
- Department of Pharmacy, National University of Singapore, Singapore117543, Singapore
- Department of Biomolecular Mass Spectrometry and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CHUtrecht, the Netherlands
| | - Nadzeya Staliarova
- Department of Biomolecular Mass Spectrometry and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CHUtrecht, the Netherlands
| | - Martina Celotti
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Sangho Lim
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Gui-Wei He
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Rosemary Millen
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Else Driehuis
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Harry Begthel
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Lidwien Smabers
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CXUtrecht, the Netherlands
| | - Jeanine Roodhart
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CXUtrecht, the Netherlands
| | - Johan van Es
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Wei Wu
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore138648, Singapore
- Department of Pharmacy, National University of Singapore, Singapore117543, Singapore
- Department of Biomolecular Mass Spectrometry and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CHUtrecht, the Netherlands
| | - Hans Clevers
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
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12
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Schene IF, Ardisasmita AI, Fuchs SA. Misidentification of neural cell identity in liver-derived organoid systems. Stem Cell Reports 2024; 19:315-316. [PMID: 38335964 PMCID: PMC10937148 DOI: 10.1016/j.stemcr.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/02/2024] [Accepted: 01/12/2024] [Indexed: 02/12/2024] Open
Affiliation(s)
- Imre F Schene
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Arif I Ardisasmita
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Sabine A Fuchs
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands.
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13
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Xue Y, Xue C, Song W. Emerging roles of deubiquitinating enzymes in actin cytoskeleton and tumor metastasis. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00923-z. [PMID: 38324230 DOI: 10.1007/s13402-024-00923-z] [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: 01/25/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Metastasis accounts for the majority of cancer-related deaths. Actin dynamics and actin-based cell migration and invasion are important factors in cancer metastasis. Metastasis is characterized by actin polymerization and depolymerization, which are precisely regulated by molecular changes involving a plethora of actin regulators, including actin-binding proteins (ABPs) and signalling pathways, that enable cancer cell dissemination from the primary tumour. Research on deubiquitinating enzymes (DUBs) has revealed their vital roles in actin dynamics and actin-based migration and invasion during cancer metastasis. CONCLUSION Here, we review how DUBs drive tumour metastasis by participating in actin rearrangement and actin-based migration and invasion. We summarize the well-characterized and essential actin cytoskeleton signalling molecules related to DUBs, including Rho GTPases, Src kinases, and ABPs such as cofilin and cortactin. Other DUBs that modulate actin-based migration signalling pathways are also discussed. Finally, we discuss and address therapeutic opportunities and ongoing challenges related to DUBs with respect to actin dynamics.
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Affiliation(s)
- Ying Xue
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, PR China.
| | - Cong Xue
- School of Stomatology, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, PR China
| | - Wei Song
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, PR China.
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14
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Hendriks D, Pagliaro A, Andreatta F, Ma Z, van Giessen J, Massalini S, López-Iglesias C, van Son GJF, DeMartino J, Damen JMA, Zoutendijk I, Staliarova N, Bredenoord AL, Holstege FCP, Peters PJ, Margaritis T, Chuva de Sousa Lopes S, Wu W, Clevers H, Artegiani B. Human fetal brain self-organizes into long-term expanding organoids. Cell 2024; 187:712-732.e38. [PMID: 38194967 DOI: 10.1016/j.cell.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 09/27/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024]
Abstract
Human brain development involves an orchestrated, massive neural progenitor expansion while a multi-cellular tissue architecture is established. Continuously expanding organoids can be grown directly from multiple somatic tissues, yet to date, brain organoids can solely be established from pluripotent stem cells. Here, we show that healthy human fetal brain in vitro self-organizes into organoids (FeBOs), phenocopying aspects of in vivo cellular heterogeneity and complex organization. FeBOs can be expanded over long time periods. FeBO growth requires maintenance of tissue integrity, which ensures production of a tissue-like extracellular matrix (ECM) niche, ultimately endowing FeBO expansion. FeBO lines derived from different areas of the central nervous system (CNS), including dorsal and ventral forebrain, preserve their regional identity and allow to probe aspects of positional identity. Using CRISPR-Cas9, we showcase the generation of syngeneic mutant FeBO lines for the study of brain cancer. Taken together, FeBOs constitute a complementary CNS organoid platform.
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Affiliation(s)
- Delilah Hendriks
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands.
| | - Anna Pagliaro
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Ziliang Ma
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Immunos, Singapore 138648, Singapore; Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Joey van Giessen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Simone Massalini
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Carmen López-Iglesias
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Gijs J F van Son
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Jeff DeMartino
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - J Mirjam A Damen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Iris Zoutendijk
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Nadzeya Staliarova
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Annelien L Bredenoord
- Erasmus School of Philosophy, Erasmus University Rotterdam, Rotterdam, the Netherlands
| | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | | | | | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Immunos, Singapore 138648, Singapore; Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Hans Clevers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands.
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15
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Fujii M, Sekine S, Sato T. Decoding the basis of histological variation in human cancer. Nat Rev Cancer 2024; 24:141-158. [PMID: 38135758 DOI: 10.1038/s41568-023-00648-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
Molecular abnormalities that shape human neoplasms dissociate their phenotypic landscape from that of the healthy counterpart. Through the lens of a microscope, tumour pathology optically captures such aberrations projected onto a tissue slide and has categorized human epithelial neoplasms into distinct histological subtypes based on the diverse morphogenetic and molecular programmes that they manifest. Tumour histology often reflects tumour aggressiveness, patient prognosis and therapeutic vulnerability, and thus has been used as a de facto diagnostic tool and for making clinical decisions. However, it remains elusive how the diverse histological subtypes arise and translate into pleiotropic biological phenotypes. Molecular analysis of clinical tumour tissues and their culture, including patient-derived organoids, and add-back genetic reconstruction of tumorigenic pathways using gene engineering in culture models and rodents further elucidated molecular mechanisms that underlie morphological variations. Such mechanisms include genetic mutations and epigenetic alterations in cellular identity codes that erode hard-wired morphological programmes and histologically digress tumours from the native tissues. Interestingly, tumours acquire the ability to grow independently of the niche-driven stem cell ecosystem along with these morphological alterations, providing a biological rationale for histological diversification during tumorigenesis. This Review comprehensively summarizes our current understanding of such plasticity in the histological and lineage commitment fostered cooperatively by molecular alterations and the tumour environment, and describes basic and clinical implications for future cancer therapy.
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Affiliation(s)
- Masayuki Fujii
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan.
| | - Shigeki Sekine
- Division of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Toshiro Sato
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan.
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16
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Xiu Z, Yang Q, Xie F, Han F, He W, Liao W. Revolutionizing digestive system tumor organoids research: Exploring the potential of tumor organoids. J Tissue Eng 2024; 15:20417314241255470. [PMID: 38808253 PMCID: PMC11131411 DOI: 10.1177/20417314241255470] [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] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024] Open
Abstract
Digestive system tumors are the leading cause of cancer-related deaths worldwide. Despite ongoing research, our understanding of their mechanisms and treatment remain inadequate. One promising tool for clinical applications is the use of gastrointestinal tract tumor organoids, which serve as an important in vitro model. Tumor organoids exhibit a genotype similar to the patient's tumor and effectively mimic various biological processes, including tissue renewal, stem cell, and ecological niche functions, and tissue response to drugs, mutations, or injury. As such, they are valuable for drug screening, developing novel drugs, assessing patient outcomes, and supporting immunotherapy. In addition, innovative materials and techniques can be used to optimize tumor organoid culture systems. Several applications of digestive system tumor organoids have been described and have shown promising results in related aspects. In this review, we discuss the current progress, limitations, and prospects of this model for digestive system tumors.
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Affiliation(s)
- Zhian Xiu
- Department of Medical Laboratory, Clinical Medical College, Affiliated Hospital of Jiujiang University, Jiujiang, Jiangxi, China
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, Jiangxi, China
| | - Qian Yang
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fusheng Xie
- Department of Medical Laboratory, Clinical Medical College, Affiliated Hospital of Jiujiang University, Jiujiang, Jiangxi, China
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, Jiangxi, China
| | - Feng Han
- Department of Medical Laboratory, Clinical Medical College, Affiliated Hospital of Jiujiang University, Jiujiang, Jiangxi, China
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, Jiangxi, China
| | - Weiwei He
- Department of Medical Laboratory, Clinical Medical College, Affiliated Hospital of Jiujiang University, Jiujiang, Jiangxi, China
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, Jiangxi, China
| | - Weifang Liao
- Department of Medical Laboratory, Clinical Medical College, Affiliated Hospital of Jiujiang University, Jiujiang, Jiangxi, China
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, Jiangxi, China
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17
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Zhu L, Cheng C, Liu S, Yang L, Han P, Cui T, Zhang Y. Advancements and application prospects of three-dimensional models for primary liver cancer: a comprehensive review. Front Bioeng Biotechnol 2023; 11:1343177. [PMID: 38188493 PMCID: PMC10771299 DOI: 10.3389/fbioe.2023.1343177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024] Open
Abstract
Primary liver cancer (PLC) is one of the most commonly diagnosed cancers worldwide and a leading cause of cancer-related deaths. However, traditional liver cancer models fail to replicate tumor heterogeneity and the tumor microenvironment, limiting the study and personalized treatment of liver cancer. To overcome these limitations, scientists have introduced three-dimensional (3D) culture models as an emerging research tool. These 3D models, utilizing biofabrication technologies such as 3D bioprinting and microfluidics, enable more accurate simulation of the in vivo tumor microenvironment, replicating cell morphology, tissue stiffness, and cell-cell interactions. Compared to traditional two-dimensional (2D) models, 3D culture models better mimic tumor heterogeneity, revealing differential sensitivity of tumor cell subpopulations to targeted therapies or immunotherapies. Additionally, these models can be used to assess the efficacy of potential treatments, providing guidance for personalized therapy. 3D liver cancer models hold significant value in tumor biology, understanding the mechanisms of disease progression, and drug screening. Researchers can gain deeper insights into the impact of the tumor microenvironment on tumor cells and their interactions with the surrounding milieu. Furthermore, these models allow for the evaluation of treatment responses, offering more accurate guidance for clinical interventions. In summary, 3D models provide a realistic and reliable tool for advancing PLC research. By simulating tumor heterogeneity and the microenvironment, these models contribute to a better understanding of the disease mechanisms and offer new strategies for personalized treatment. Therefore, 3D models hold promising prospects for future PLC research.
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Affiliation(s)
- Liuyang Zhu
- First Central Clinical College of Tianjin Medical University, Tianjin, China
| | | | - Sen Liu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
| | - Long Yang
- Department of Hepatobiliary Surgery, Tianjin First Central Hospital, Tianjin, China
| | - Pinsheng Han
- Nankai University of Medicine College, Tianjin, China
| | - Tao Cui
- National Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin Institute of Pharmaceutical Research, Tianjin, China
- Research Unit for Drug Metabolism, Chinese Academy of Medical Sciences, Beijing, China
| | - Yamin Zhang
- Department of Hepatobiliary Surgery, Tianjin First Central Hospital, Tianjin, China
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18
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Neikes HK, Kliza KW, Gräwe C, Wester RA, Jansen PWTC, Lamers LA, Baltissen MP, van Heeringen SJ, Logie C, Teichmann SA, Lindeboom RGH, Vermeulen M. Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq. Nat Biotechnol 2023; 41:1801-1809. [PMID: 36973556 DOI: 10.1038/s41587-023-01715-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 02/16/2023] [Indexed: 03/29/2023]
Abstract
Transcription factor binding across the genome is regulated by DNA sequence and chromatin features. However, it is not yet possible to quantify the impact of chromatin context on transcription factor binding affinities. Here, we report a method called binding affinities to native chromatin by sequencing (BANC-seq) to determine absolute apparent binding affinities of transcription factors to native DNA across the genome. In BANC-seq, a concentration range of a tagged transcription factor is added to isolated nuclei. Concentration-dependent binding is then measured per sample to quantify apparent binding affinities across the genome. BANC-seq adds a quantitative dimension to transcription factor biology, which enables stratification of genomic targets based on transcription factor concentration and prediction of transcription factor binding sites under non-physiological conditions, such as disease-associated overexpression of (onco)genes. Notably, whereas consensus DNA binding motifs for transcription factors are important to establish high-affinity binding sites, these motifs are not always strictly required to generate nanomolar-affinity interactions in the genome.
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Affiliation(s)
- Hannah K Neikes
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Katarzyna W Kliza
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Roelof A Wester
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Lieke A Lamers
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Simon J van Heeringen
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Colin Logie
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | | | - Rik G H Lindeboom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands.
- The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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19
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Salahudeen AA, Seoane JA, Yuki K, Mah AT, Smith AR, Kolahi K, De la O SM, Hart DJ, Ding J, Ma Z, Barkal SA, Shukla ND, Zhang CH, Cantrell MA, Batish A, Usui T, Root DE, Hahn WC, Curtis C, Kuo CJ. Functional screening of amplification outlier oncogenes in organoid models of early tumorigenesis. Cell Rep 2023; 42:113355. [PMID: 37922313 PMCID: PMC10841581 DOI: 10.1016/j.celrep.2023.113355] [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: 11/03/2021] [Revised: 08/30/2023] [Accepted: 10/12/2023] [Indexed: 11/05/2023] Open
Abstract
Somatic copy number gains are pervasive across cancer types, yet their roles in oncogenesis are insufficiently evaluated. This inadequacy is partly due to copy gains spanning large chromosomal regions, obscuring causal loci. Here, we employed organoid modeling to evaluate candidate oncogenic loci identified via integrative computational analysis of extreme copy gains overlapping with extreme expression dysregulation in The Cancer Genome Atlas. Subsets of "outlier" candidates were contextually screened as tissue-specific cDNA lentiviral libraries within cognate esophagus, oral cavity, colon, stomach, pancreas, and lung organoids bearing initial oncogenic mutations. Iterative analysis nominated the kinase DYRK2 at 12q15 as an amplified head and neck squamous carcinoma oncogene in p53-/- oral mucosal organoids. Similarly, FGF3, amplified at 11q13 in 41% of esophageal squamous carcinomas, promoted p53-/- esophageal organoid growth reversible by small molecule and soluble receptor antagonism of FGFRs. Our studies establish organoid-based contextual screening of candidate genomic drivers, enabling functional evaluation during early tumorigenesis.
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Affiliation(s)
- Ameen A Salahudeen
- Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA; University of Illinois at Chicago College of Medicine, Department of Medicine, Division of Hematology and Oncology, Chicago, IL 60612, USA; Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago College of Medicine, Chicago, IL 60612, USA; University of Illinois Cancer Center, Chicago, IL 60612, USA.
| | - Jose A Seoane
- Stanford University School of Medicine, Department of Medicine, Divisions of Oncology, Stanford, CA 94305, USA; Cancer Computational Biology Group, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain.
| | - Kanako Yuki
- Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
| | - Amanda T Mah
- Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
| | - Amber R Smith
- Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
| | - Kevin Kolahi
- Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
| | - Sean M De la O
- Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
| | - Daniel J Hart
- Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
| | - Jie Ding
- Stanford University School of Medicine, Department of Medicine, Divisions of Oncology, Stanford, CA 94305, USA
| | - Zhicheng Ma
- Stanford University School of Medicine, Department of Medicine, Divisions of Oncology, Stanford, CA 94305, USA
| | - Sammy A Barkal
- Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
| | - Navika D Shukla
- Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
| | - Chuck H Zhang
- Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
| | - Michael A Cantrell
- Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
| | - Arpit Batish
- Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
| | - Tatsuya Usui
- Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
| | - David E Root
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - William C Hahn
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Department of Medical Oncology, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Christina Curtis
- Stanford University School of Medicine, Department of Medicine, Divisions of Oncology, Stanford, CA 94305, USA; Stanford University School of Medicine, Department of Medicine, Divisions of Genetics, Stanford, CA 94305, USA
| | - Calvin J Kuo
- Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA.
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20
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Zhang Z, Hui L. Progress in patient-derived liver cancer cell models: a step forward for precision medicine. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1707-1717. [PMID: 37766458 PMCID: PMC10679880 DOI: 10.3724/abbs.2023224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/03/2023] [Indexed: 09/29/2023] Open
Abstract
The development of effective precision treatments for liver cancers has been hindered by the scarcity of preclinical models that accurately reflect the heterogeneity of this disease. Recent progress in developing patient-derived liver cancer cell lines and organoids has paved the way for precision medicine research. These expandable resources of liver cancer cell models enable a full spectrum of pharmacogenomic analysis for liver cancers. Moreover, patient-derived and short-term cultured two-dimensional tumor cells or three-dimensional organoids can serve as patient avatars, allowing for the prediction of patients' response to drugs and facilitating personalized treatment for liver cancer patients. Furthermore, the current novel techniques have expanded the scope of cancer research, including innovative organoid culture, gene editing and bioengineering. In this review, we provide an overview of the progress in patient-derived liver cancer cell models, focusing on their applications in precision and personalized medicine research. We also discuss the challenges and future perspectives in this field.
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Affiliation(s)
- Zhengtao Zhang
- Key Laboratory of Systems Health Science of Zhejiang ProvinceSchool of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310024China
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200031China
| | - Lijian Hui
- Key Laboratory of Systems Health Science of Zhejiang ProvinceSchool of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310024China
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200031China
- School of Life Science and TechnologyShanghaiTech UniversityShanghai200031China
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijing100101China
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21
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Weng G, Tao J, Liu Y, Qiu J, Su D, Wang R, Luo W, Zhang T. Organoid: Bridging the gap between basic research and clinical practice. Cancer Lett 2023; 572:216353. [PMID: 37599000 DOI: 10.1016/j.canlet.2023.216353] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/11/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
Abstract
Nowadays, the diagnosis and treatment system of malignant tumors has increasingly tended to be more precise and personalized while the existing tumor models are still unable to fully meet the needs of clinical practice. Notably, the emerging organoid platform has been proven to have huge potential in the field of basic-translational medicine, which is expected to promote a paradigm shift in personalized medicine. Here, given the unique advantages of organoid platform, we mainly explore the prominent role of organoid models in basic research and clinical practice from perspectives of tumor biology, tumorigenic microbes-host interaction, clinical decision-making, and regenerative strategy. In addition, we also put forward some practical suggestions on how to construct a new generation of organoid platform, which is destined to vigorously promote the reform of basic-translational medicine.
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Affiliation(s)
- Guihu Weng
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Jinxin Tao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Yueze Liu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Jiangdong Qiu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Dan Su
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Ruobing Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Wenhao Luo
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Taiping Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China.
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22
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Rohatgi N, Zou W, Li Y, Cho K, Collins PL, Tycksen E, Pandey G, DeSelm CJ, Patti GJ, Dey A, Teitelbaum SL. BAP1 promotes osteoclast function by metabolic reprogramming. Nat Commun 2023; 14:5923. [PMID: 37740028 PMCID: PMC10516877 DOI: 10.1038/s41467-023-41629-4] [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: 12/03/2021] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
Treatment of osteoporosis commonly diminishes osteoclast number which suppresses bone formation thus compromising fracture prevention. Bone formation is not suppressed, however, when bone degradation is reduced by retarding osteoclast functional resorptive capacity, rather than differentiation. We find deletion of deubiquitinase, BRCA1-associated protein 1 (Bap1), in myeloid cells (Bap1∆LysM), arrests osteoclast function but not formation. Bap1∆LysM osteoclasts fail to organize their cytoskeleton which is essential for bone degradation consequently increasing bone mass in both male and female mice. The deubiquitinase activity of BAP1 modifies osteoclast function by metabolic reprogramming. Bap1 deficient osteoclast upregulate the cystine transporter, Slc7a11, by enhanced H2Aub occupancy of its promoter. SLC7A11 controls cellular reactive oxygen species levels and redirects the mitochondrial metabolites away from the tricarboxylic acid cycle, both being necessary for osteoclast function. Thus, in osteoclasts BAP1 appears to regulate the epigenetic-metabolic axis and is a potential target to reduce bone degradation while maintaining osteogenesis in osteoporotic patients.
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Affiliation(s)
- Nidhi Rohatgi
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Wei Zou
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yongjia Li
- Department of Pharmacology, Jiangsu University School of Medicine, Zhenjiang, Jiangsu Province, 212013, PR China
| | - Kevin Cho
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Patrick L Collins
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, 43210, USA
| | - Eric Tycksen
- Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Gaurav Pandey
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Carl J DeSelm
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Gary J Patti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Steven L Teitelbaum
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
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23
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Tiroille V, Krug A, Bokobza E, Kahi M, Bulcaen M, Ensinck MM, Geurts MH, Hendriks D, Vermeulen F, Larbret F, Gutierrez-Guerrero A, Chen Y, Van Zundert I, Rocha S, Rios AC, Medaer L, Gijsbers R, Mangeot PE, Clevers H, Carlon MS, Bost F, Verhoeyen E. Nanoblades allow high-level genome editing in murine and human organoids. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:57-74. [PMID: 37435135 PMCID: PMC10331042 DOI: 10.1016/j.omtn.2023.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/04/2023] [Indexed: 07/13/2023]
Abstract
Genome engineering has become more accessible thanks to the CRISPR-Cas9 gene-editing system. However, using this technology in synthetic organs called "organoids" is still very inefficient. This is due to the delivery methods for the CRISPR-Cas9 machinery, which include electroporation of CRISPR-Cas9 DNA, mRNA, or ribonucleoproteins containing the Cas9-gRNA complex. However, these procedures are quite toxic for the organoids. Here, we describe the use of the "nanoblade (NB)" technology, which outperformed by far gene-editing levels achieved to date for murine- and human tissue-derived organoids. We reached up to 75% of reporter gene knockout in organoids after treatment with NBs. Indeed, high-level NB-mediated knockout for the androgen receptor encoding gene and the cystic fibrosis transmembrane conductance regulator gene was achieved with single gRNA or dual gRNA containing NBs in murine prostate and colon organoids. Likewise, NBs achieved 20%-50% gene editing in human organoids. Most importantly, in contrast to other gene-editing methods, this was obtained without toxicity for the organoids. Only 4 weeks are required to obtain stable gene knockout in organoids and NBs simplify and allow rapid genome editing in organoids with little to no side effects including unwanted insertion/deletions in off-target sites thanks to transient Cas9/RNP expression.
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Affiliation(s)
- Victor Tiroille
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- Equipe labélisée Ligue National Contre le Cancer, Basel, Switzerland
| | - Adrien Krug
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
| | - Emma Bokobza
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- Equipe labélisée Ligue National Contre le Cancer, Basel, Switzerland
| | - Michel Kahi
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- Equipe labélisée Ligue National Contre le Cancer, Basel, Switzerland
| | - Mattijs Bulcaen
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Marjolein M. Ensinck
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Maarten H. Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | | | | | - Alejandra Gutierrez-Guerrero
- CIRI – International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, F-69007 Lyon, France
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Department of Medicine, Memorial Sloan; Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Indra Van Zundert
- Synthetic Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, the Netherlands
| | - Susana Rocha
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Anne C. Rios
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Louise Medaer
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Rik Gijsbers
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Philippe E. Mangeot
- CIRI – International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, F-69007 Lyon, France
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Marianne S. Carlon
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Frédéric Bost
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- Equipe labélisée Ligue National Contre le Cancer, Basel, Switzerland
| | - Els Verhoeyen
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- CIRI – International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, F-69007 Lyon, France
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24
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Lam YK, Yu J, Huang H, Ding X, Wong AM, Leung HH, Chan AW, Ng KK, Xu M, Wang X, Wong N. TP53 R249S mutation in hepatic organoids captures the predisposing cancer risk. Hepatology 2023; 78:727-740. [PMID: 36221953 PMCID: PMC10086078 DOI: 10.1002/hep.32802] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 12/08/2022]
Abstract
BACKGROUND AND AIMS Major genomic drivers of hepatocellular carcinoma (HCC) are nowadays well recognized, although models to establish their roles in human HCC initiation remain scarce. Here, we used human liver organoids in experimental systems to mimic the early stages of human liver carcinogenesis from the genetic lesions of TP53 loss and L3 loop R249S mutation. In addition, chromatin immunoprecipitation sequencing (ChIP-seq) of HCC cell lines shed important functional insights into the initiation of HCC consequential to the loss of tumor-suppressive function from TP53 deficiency and gain-of-function activities from mutant p53. APPROACH AND RESULTS Human liver organoids were generated from surgical nontumor liver tissues. CRISPR knockout of TP53 in liver organoids consistently demonstrated tumor-like morphological changes, increased in stemness and unrestricted in vitro propagation. To recapitulate TP53 status in human HCC, we overexpressed mutant R249S in TP53 knockout organoids. A spontaneous increase in tumorigenic potentials and bona fide HCC histology in xenotransplantations were observed. ChIP-seq analysis of HCC cell lines underscored gain-of-function properties from L3 loop p53 mutants in chromatin remodeling and overcoming extrinsic stress. More importantly, direct transcriptional activation of PSMF1 by mutant R249S could increase organoid resistance to endoplasmic reticulum stress, which was readily abrogated by PSMF1 knockdown in rescue experiments. In a patient cohort of primary HCC tumors and genome-edited liver organoids, quantitative polymerase chain reaction corroborated ChIP-seq findings and verified preferential genes modulated by L3 mutants, especially those enriched by R249S. CONCLUSIONS We showed differential tumorigenic effects from TP53 loss and L3 mutations, which together confer normal hepatocytes with early clonal advantages and prosurvival functions.
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Affiliation(s)
- Yin Kau Lam
- Department of Surgery, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Hong Kong, China
| | - Jianqing Yu
- Department of Surgery, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Hong Kong, China
| | - Hao Huang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Xiaofan Ding
- Department of Surgery, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Hong Kong, China
| | - Alissa M. Wong
- Department of Surgery, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Hong Kong, China
| | - Howard H. Leung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Anthony W. Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kelvin K. Ng
- Department of Surgery, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Hong Kong, China
| | - Mingjing Xu
- Department of Surgery, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Hong Kong, China
| | - Xin Wang
- Department of Surgery, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Hong Kong, China
| | - Nathalie Wong
- Department of Surgery, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Hong Kong, China
- State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
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25
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Geurts MH, Gandhi S, Boretto MG, Akkerman N, Derks LLM, van Son G, Celotti M, Harshuk-Shabso S, Peci F, Begthel H, Hendriks D, Schürmann P, Andersson-Rolf A, Chuva de Sousa Lopes SM, van Es JH, van Boxtel R, Clevers H. One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids. Nat Commun 2023; 14:4998. [PMID: 37591832 PMCID: PMC10435570 DOI: 10.1038/s41467-023-40701-3] [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: 05/17/2022] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
Optimization of CRISPR/Cas9-mediated genome engineering has resulted in base editors that hold promise for mutation repair and disease modeling. Here, we demonstrate the application of base editors for the generation of complex tumor models in human ASC-derived organoids. First we show efficacy of cytosine and adenine base editors in modeling CTNNB1 hot-spot mutations in hepatocyte organoids. Next, we use C > T base editors to insert nonsense mutations in PTEN in endometrial organoids and demonstrate tumorigenicity even in the heterozygous state. Moreover, drug sensitivity assays on organoids harboring either PTEN or PTEN and PIK3CA mutations reveal the mechanism underlying the initial stages of endometrial tumorigenesis. To further increase the scope of base editing we combine SpCas9 and SaCas9 for simultaneous C > T and A > G editing at individual target sites. Finally, we show that base editor multiplexing allow modeling of colorectal tumorigenesis in a single step by simultaneously transfecting sgRNAs targeting five cancer genes.
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Affiliation(s)
- Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands.
- Oncode Institute, 3521AL, Utrecht, the Netherlands.
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands.
| | - Shashank Gandhi
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA, 94720, USA
| | - Matteo G Boretto
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Ninouk Akkerman
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Lucca L M Derks
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Gijs van Son
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Martina Celotti
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Sarina Harshuk-Shabso
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Flavia Peci
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Paul Schürmann
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Amanda Andersson-Rolf
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | | | - Johan H van Es
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Ruben van Boxtel
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands.
- Oncode Institute, 3521AL, Utrecht, the Netherlands.
- Pharma Research Early Development, Basel, Switzerland.
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26
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Zhou B, Feng Z, Xu J, Xie J. Organoids: approaches and utility in cancer research. Chin Med J (Engl) 2023; 136:1783-1793. [PMID: 37365679 PMCID: PMC10406116 DOI: 10.1097/cm9.0000000000002477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Indexed: 06/28/2023] Open
Abstract
ABSTRACT Organoids are three-dimensional cellular structures with self-organizing and self-differentiation capacities. They faithfully recapitulate structures and functions of in vivo organs as represented by functionality and microstructural definitions. Heterogeneity in in vitro disease modeling is one of the main reasons for anti-cancer therapy failures. Establishing a powerful model to represent tumor heterogeneity is crucial for elucidating tumor biology and developing effective therapeutic strategies. Tumor organoids can retain the original tumor heterogeneity and are commonly used to mimic the cancer microenvironment when co-cultured with fibroblasts and immune cells; therefore, considerable effort has been made recently to promote the use of this new technology from basic research to clinical studies in tumors. In combination with gene editing technology and microfluidic chip systems, engineered tumor organoids show promising abilities to recapitulate tumorigenesis and metastasis. In many studies, the responses of tumor organoids to various drugs have shown a positive correlation with patient responses. Owing to these consistent responses and personalized characteristics with patient data, tumor organoids show excellent potential for preclinical research. Here, we summarize the properties of different tumor models and review their current state and progress in tumor organoids. We further discuss the substantial challenges and prospects in the rapidly developing tumor organoid field.
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Affiliation(s)
- Bingrui Zhou
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Zhiwei Feng
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Jun Xu
- Department of Hepatobiliary and Pancreatic Surgery and Liver Transplant Center, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, Shanxi 030001, China
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27
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Fang Z, Li P, Du F, Shang L, Li L. The role of organoids in cancer research. Exp Hematol Oncol 2023; 12:69. [PMID: 37537666 PMCID: PMC10401879 DOI: 10.1186/s40164-023-00433-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/30/2023] [Indexed: 08/05/2023] Open
Abstract
Organoids are established through in vitro 3D culture, and they can mimic the structure and physiological functions of organs or tissues in vivo. Organoids have attracted much attention in recent years. They can provide a reliable technology platform for cancer research and treatment and are a valuable preclinical model for academic research and personalized medicine. A number of studies have confirmed that organoids have great application prospects in new drug development, drug screening, tumour mechanism research, and precision medicine. In this review, we mainly focus on recent advances in the application of organoids in cancer research. We also discussed the opportunities and challenges facing organoids, hoping to indicate directions for the development of organoids in the future.
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Affiliation(s)
- Zhen Fang
- Department of Gastroenterological Surgery, Shandong Provincial Hospital of Shandong First Medical University, Jingwuweiqi street, 324, Jinan, 250021, Shandong, China
- Department of Digestive Tumour Translational Medicine, Engineering Laboratory of Shandong Province, Shandong Provincial Hospital, Jinan, 250021, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, 250021, Shandong, China
| | - Peijuan Li
- Emergency Department, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Fengying Du
- Department of Gastroenterological Surgery, Shandong Provincial Hospital of Shandong First Medical University, Jingwuweiqi street, 324, Jinan, 250021, Shandong, China
- Department of Digestive Tumour Translational Medicine, Engineering Laboratory of Shandong Province, Shandong Provincial Hospital, Jinan, 250021, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, 250021, Shandong, China
| | - Liang Shang
- Department of Gastroenterological Surgery, Shandong Provincial Hospital of Shandong First Medical University, Jingwuweiqi street, 324, Jinan, 250021, Shandong, China.
- Department of Digestive Tumour Translational Medicine, Engineering Laboratory of Shandong Province, Shandong Provincial Hospital, Jinan, 250021, Shandong, China.
- Medical Science and Technology Innovation Center, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, 250021, Shandong, China.
| | - Leping Li
- Department of Gastroenterological Surgery, Shandong Provincial Hospital of Shandong First Medical University, Jingwuweiqi street, 324, Jinan, 250021, Shandong, China.
- Department of Digestive Tumour Translational Medicine, Engineering Laboratory of Shandong Province, Shandong Provincial Hospital, Jinan, 250021, Shandong, China.
- Medical Science and Technology Innovation Center, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, 250021, Shandong, China.
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28
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Li C, Holman JB, Shi Z, Qiu B, Ding W. On-chip modeling of tumor evolution: Advances, challenges and opportunities. Mater Today Bio 2023; 21:100724. [PMID: 37483380 PMCID: PMC10359640 DOI: 10.1016/j.mtbio.2023.100724] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/16/2023] [Accepted: 07/06/2023] [Indexed: 07/25/2023] Open
Abstract
Tumor evolution is the accumulation of various tumor cell behaviors from tumorigenesis to tumor metastasis and is regulated by the tumor microenvironment (TME). However, the mechanism of solid tumor progression has not been completely elucidated, and thus, the development of tumor therapy is still limited. Recently, Tumor chips constructed by culturing tumor cells and stromal cells on microfluidic chips have demonstrated great potential in modeling solid tumors and visualizing tumor cell behaviors to exploit tumor progression. Herein, we review the methods of developing engineered solid tumors on microfluidic chips in terms of tumor types, cell resources and patterns, the extracellular matrix and the components of the TME, and summarize the recent advances of microfluidic chips in demonstrating tumor cell behaviors, including proliferation, epithelial-to-mesenchymal transition, migration, intravasation, extravasation and immune escape of tumor cells. We also outline the combination of tumor organoids and microfluidic chips to elaborate tumor organoid-on-a-chip platforms, as well as the practical limitations that must be overcome.
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Affiliation(s)
- Chengpan Li
- Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei, Anhui, 230027, China
- Center for Biomedical Imaging, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Joseph Benjamin Holman
- Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Zhengdi Shi
- Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Bensheng Qiu
- Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei, Anhui, 230027, China
- Center for Biomedical Imaging, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Weiping Ding
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
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29
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Szabó L, Seubert AC, Kretzschmar K. Modelling adult stem cells and their niche in health and disease with epithelial organoids. Semin Cell Dev Biol 2023; 144:20-30. [PMID: 36127261 DOI: 10.1016/j.semcdb.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 10/14/2022]
Abstract
Adult stem cells are responsible for homoeostasis and regeneration of epithelial tissues. Stem cell function is regulated by both cell autonomous mechanisms as well as the niche. Deregulated stem cell function contributes to diseases such as cancer. Epithelial organoid cultures generated from tissue-resident adult stem cells have allowed unprecedented insights into the biology of epithelial tissues. The subsequent adaptation of organoid technology enabled the modelling of the communication of stem cells with their cellular and non-cellular niche as well as diseases. Starting from its first model described in 2009, the murine small intestinal organoid, we discuss here how epithelial organoid cultures have been become a prime in vitro research tool for cell and developmental biology, bioengineering, and biomedicine in the last decade.
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Affiliation(s)
- Lili Szabó
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, IZKF/MSNZ, Würzburg, Germany
| | - Anna C Seubert
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, IZKF/MSNZ, Würzburg, Germany
| | - Kai Kretzschmar
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, IZKF/MSNZ, Würzburg, Germany.
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30
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Yan HHN, Chan AS, Lai FPL, Leung SY. Organoid cultures for cancer modeling. Cell Stem Cell 2023; 30:917-937. [PMID: 37315564 DOI: 10.1016/j.stem.2023.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/20/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023]
Abstract
Organoids derived from adult stem cells (ASCs) and pluripotent stem cells (PSCs) are important preclinical models for studying cancer and developing therapies. Here, we review primary tissue-derived and PSC-derived cancer organoid models and detail how they have the potential to inform personalized medical approaches in different organ contexts and contribute to the understanding of early carcinogenic steps, cancer genomes, and biology. We also compare the differences between ASC- and PSC-based cancer organoid systems, discuss their limitations, and highlight recent improvements to organoid culture approaches that have helped to make them an even better representation of human tumors.
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Affiliation(s)
- Helen H N Yan
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China.
| | - April S Chan
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Frank Pui-Ling Lai
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Suet Yi Leung
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China; Jockey Club Centre for Clinical Innovation and Discovery, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong SAR, China; Centre for PanorOmic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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31
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Chen Y, Liu Y, Chen S, Zhang L, Rao J, Lu X, Ma Y. Liver organoids: a promising three-dimensional model for insights and innovations in tumor progression and precision medicine of liver cancer. Front Immunol 2023; 14:1180184. [PMID: 37334366 PMCID: PMC10272526 DOI: 10.3389/fimmu.2023.1180184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023] Open
Abstract
Primary liver cancer (PLC) is one type of cancer with high incidence rate and high mortality rate in the worldwide. Systemic therapy is the major treatment for PLC, including surgical resection, immunotherapy and targeted therapy. However, mainly due to the heterogeneity of tumors, responses to the above drug therapy differ from person to person, indicating the urgent needs for personalized treatment for PLC. Organoids are 3D models derived from adult liver tissues or pluripotent stem cells. Based on the ability to recapitulate the genetic and functional features of in vivo tissues, organoids have assisted biomedical research to make tremendous progress in understanding disease origin, progression and treatment strategies since their invention and application. In liver cancer research, liver organoids contribute greatly to reflecting the heterogeneity of liver cancer and restoring tumor microenvironment (TME) by co-organizing tumor vasculature and stromal components in vitro. Therefore, they provide a promising platform for further investigation into the biology of liver cancer, drug screening and precision medicine for PLC. In this review, we discuss the recent advances of liver organoids in liver cancer, in terms of generation methods, application in precision medicine and TME modeling.
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Affiliation(s)
- Yukun Chen
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yujun Liu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shimin Chen
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Long Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jiawei Rao
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xinjun Lu
- Department of Biliary-Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yi Ma
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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32
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Rüland L, Andreatta F, Massalini S, Chuva de Sousa Lopes S, Clevers H, Hendriks D, Artegiani B. Organoid models of fibrolamellar carcinoma mutations reveal hepatocyte transdifferentiation through cooperative BAP1 and PRKAR2A loss. Nat Commun 2023; 14:2377. [PMID: 37137901 PMCID: PMC10156813 DOI: 10.1038/s41467-023-37951-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 04/06/2023] [Indexed: 05/05/2023] Open
Abstract
Fibrolamellar carcinoma (FLC) is a lethal primary liver cancer, affecting young patients in absence of chronic liver disease. Molecular understanding of FLC tumorigenesis is limited, partly due to the scarcity of experimental models. Here, we CRISPR-engineer human hepatocyte organoids to recreate different FLC backgrounds, including the predominant genetic alteration, the DNAJB1-PRKACA fusion, as well as a recently reported background of FLC-like tumors, encompassing inactivating mutations of BAP1 and PRKAR2A. Phenotypic characterizations and comparisons with primary FLC tumor samples revealed mutant organoid-tumor similarities. All FLC mutations caused hepatocyte dedifferentiation, yet only combined loss of BAP1 and PRKAR2A resulted in hepatocyte transdifferentiation into liver ductal/progenitor-like cells that could exclusively grow in a ductal cell environment. BAP1-mutant hepatocytes represent primed cells attempting to proliferate in this cAMP-stimulating environment, but require concomitant PRKAR2A loss to overcome cell cycle arrest. In all analyses, DNAJB1-PRKACAfus organoids presented with milder phenotypes, suggesting differences between FLC genetic backgrounds, or for example the need for additional mutations, interactions with niche cells, or a different cell-of-origin. These engineered human organoid models facilitate the study of FLC.
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Affiliation(s)
- Laura Rüland
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Simone Massalini
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Hans Clevers
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
- Pharma, Research and Early Development (pRED) of F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Benedetta Artegiani
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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33
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Sun XC, Kong DF, Zhao J, Faber KN, Xia Q, He K. Liver organoids: established tools for disease modeling and drug development. Hepatol Commun 2023; 7:02009842-202304010-00019. [PMID: 36972388 PMCID: PMC10043560 DOI: 10.1097/hc9.0000000000000105] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/17/2023] [Indexed: 03/29/2023] Open
Abstract
In the past decade, liver organoids have evolved rapidly as valuable research tools, providing novel insights into almost all types of liver diseases, including monogenic liver diseases, alcohol-associated liver disease, metabolic-associated fatty liver disease, various types of (viral) hepatitis, and liver cancers. Liver organoids in part mimic the microphysiology of the human liver and fill a gap in high-fidelity liver disease models to a certain extent. They hold great promise to elucidate the pathogenic mechanism of a diversity of liver diseases and play a crucial role in drug development. Moreover, it is challenging but opportunistic to apply liver organoids for tailored therapies of various liver diseases. The establishment, applications, and challenges of different types of liver organoids, for example, derived from embryonic, adult, or induced pluripotent stem cells, to model different liver diseases, are presented in this review.
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Affiliation(s)
- Xi-Cheng Sun
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China
- Shanghai Institute of Transplantation, Shanghai, China
| | - De-Fu Kong
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jie Zhao
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China
- Shanghai Institute of Transplantation, Shanghai, China
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China
- Shanghai Institute of Transplantation, Shanghai, China
| | - Kang He
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China
- Shanghai Institute of Transplantation, Shanghai, China
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34
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El Harane S, Zidi B, El Harane N, Krause KH, Matthes T, Preynat-Seauve O. Cancer Spheroids and Organoids as Novel Tools for Research and Therapy: State of the Art and Challenges to Guide Precision Medicine. Cells 2023; 12:cells12071001. [PMID: 37048073 PMCID: PMC10093533 DOI: 10.3390/cells12071001] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Spheroids and organoids are important novel players in medical and life science research. They are gradually replacing two-dimensional (2D) cell cultures. Indeed, three-dimensional (3D) cultures are closer to the in vivo reality and open promising perspectives for academic research, drug screening, and personalized medicine. A large variety of cells and tissues, including tumor cells, can be the starting material for the generation of 3D cultures, including primary tissues, stem cells, or cell lines. A panoply of methods has been developed to generate 3D structures, including spontaneous or forced cell aggregation, air-liquid interface conditions, low cell attachment supports, magnetic levitation, and scaffold-based technologies. The choice of the most appropriate method depends on (i) the origin of the tissue, (ii) the presence or absence of a disease, and (iii) the intended application. This review summarizes methods and approaches for the generation of cancer spheroids and organoids, including their advantages and limitations. We also highlight some of the challenges and unresolved issues in the field of cancer spheroids and organoids, and discuss possible therapeutic applications.
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Affiliation(s)
- Sanae El Harane
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Bochra Zidi
- Department of Medicine, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Nadia El Harane
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Thomas Matthes
- Department of Medicine, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Olivier Preynat-Seauve
- Department of Medicine, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
- Laboratory of Experimental Cell Therapy, Department of Diagnostics, Geneva University Hospitals, 1206 Geneva, Switzerland
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35
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Huber A, Dijkstra C, Ernst M, Eissmann MF. Generation of gene-of-interest knockouts in murine organoids using CRISPR-Cas9. STAR Protoc 2023; 4:102076. [PMID: 36853714 PMCID: PMC9918790 DOI: 10.1016/j.xpro.2023.102076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/11/2022] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
Gene-of-interest knockout organoids present a powerful and versatile research tool to study a gene's effects on many biological and pathological processes. Here, we present a straightforward and broadly applicable protocol to generate gene knockouts in mouse organoids using CRISPR-Cas9 technology. We describe the processes of transient transfecting organoids with pre-assembled CRISPR-Cas9 ribonucleoprotein complexes, organoid cell sorting, and establishing clonal organoid culture pairs. We then detail how to confirm the knockout via Western blot analysis.
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Affiliation(s)
- Anne Huber
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia.
| | - Christine Dijkstra
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia
| | - Moritz F Eissmann
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia.
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36
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van Tienderen GS, Rosmark O, Lieshout R, Willemse J, de Weijer F, Elowsson Rendin L, Westergren-Thorsson G, Doukas M, Groot Koerkamp B, van Royen ME, van der Laan LJ, Verstegen MM. Extracellular matrix drives tumor organoids toward desmoplastic matrix deposition and mesenchymal transition. Acta Biomater 2023; 158:115-131. [PMID: 36427688 DOI: 10.1016/j.actbio.2022.11.038] [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] [Received: 07/08/2022] [Revised: 10/31/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022]
Abstract
Patient-derived tumor organoids have been established as promising tools for in vitro modelling of multiple tumors, including cholangiocarcinoma (CCA). However, organoids are commonly cultured in basement membrane extract (BME) which does not recapitulate the intricacies of the extracellular matrix (ECM). We combined CCA organoids (CCAOs) with native tumor and liver scaffolds, obtained by decellularization, to effectuate a model to study the interaction between epithelial tumor cells and their surrounding ECM. Decellularization resulted in removal of cells while preserving ECM structure and retaining important characteristics of the tissue origin, including stiffness and presence of desmoplasia. The transcriptome of CCAOs in a tumor scaffold much more resembled that of patient-paired CCA tissue in vivo compared to CCAOs cultured in BME or liver scaffolds. This was accompanied by an increase in chemoresistance to clinically-relevant chemotherapeutics. CCAOs in decellularized scaffolds revealed environment-dependent proliferation dynamics, driven by the occurrence of epithelial-mesenchymal transition. Furthermore, CCAOs initiated an environment-specific desmoplastic reaction by increasing production of multiple collagen types. In conclusion, convergence of organoid-based models with native ECM scaffolds will lead to better understanding of the in vivo tumor environment. STATEMENT OF SIGNIFICANCE: The extracellular matrix (ECM) influences various facets of tumor behavior. Understanding the exact role of the ECM in controlling tumor cell fate is pertinent to understand tumor progression and develop novel therapeutics. This is particularly the case for cholangiocarcinoma (CCA), whereby the ECM displays a distinct tumor environment, characterized by desmoplasia. However, current models to study the interaction between epithelial tumor cells and the environment are lacking. We have developed a fully patient-derived model encompassing CCA organoids (CCAOs) and human decellularized tumor and tumor-free liver ECM. The tumor ECM induced recapitulation of various aspects of CCA, including migration dynamics, transcriptome and proteome profiles, and chemoresistance. Lastly, we uncover that epithelial tumor cells contribute to matrix deposition, and that this phenomenon is dependent on the level of desmoplasia already present.
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Affiliation(s)
- Gilles S van Tienderen
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Oskar Rosmark
- Lung Biology, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Ruby Lieshout
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Jorke Willemse
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Floor de Weijer
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Linda Elowsson Rendin
- Lung Biology, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | | | - Michail Doukas
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Bas Groot Koerkamp
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Martin E van Royen
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Luc Jw van der Laan
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Monique Ma Verstegen
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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37
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Chen L, Wei X, Gu D, Xu Y, Zhou H. Human liver cancer organoids: Biological applications, current challenges, and prospects in hepatoma therapy. Cancer Lett 2023; 555:216048. [PMID: 36603689 DOI: 10.1016/j.canlet.2022.216048] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023]
Abstract
Liver cancer and disease are among the most socially challenging global health concerns. Although organ transplantation, surgical resection and anticancer drugs are the main methods for the treatment of liver cancer, there are still no proven cures owing to the lack of donor livers and tumor heterogeneity. Recently, advances in tumor organoid technology have attracted considerable attention as they can simulate the spatial constructs and pathophysiological characteristics of tumorigenesis and metastasis in a more realistic manner. Organoids may further contribute to the development of tailored therapies. Combining organoids with other emerging techniques, such as CRISPR-HOT, organ-on-a-chip, and 3D bioprinting, may further develop organoids and address their bottlenecks to create more practical models that generalize different tissue or organ interactions in tumor progression. In this review, we summarize the various methods in which liver organoids may be generated and describe their biological and clinical applications, present challenges, and prospects for their integration with emerging technologies. These rapidly developing liver organoids may become the focus of in vitro clinical model development and therapeutic research for liver diseases in the near future.
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Affiliation(s)
- Lichan Chen
- Department of Laboratory Medicine, Inst Translat Med, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Xiafei Wei
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China.
| | - Dayong Gu
- Department of Laboratory Medicine, Inst Translat Med, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Yong Xu
- Department of Laboratory Medicine, Inst Translat Med, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Hongzhong Zhou
- Department of Laboratory Medicine, Inst Translat Med, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Guangzhou Medical University, Guangzhou, China.
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38
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Liver Organoids as an In Vitro Model to Study Primary Liver Cancer. Int J Mol Sci 2023; 24:ijms24054529. [PMID: 36901961 PMCID: PMC10003131 DOI: 10.3390/ijms24054529] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Primary liver cancers (PLC), including hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), are among the leading causes of cancer-related mortality worldwide. Bi-dimensional in vitro models are unable to recapitulate the key features of PLC; consequently, recent advancements in three-dimensional in vitro systems, such as organoids, opened up new avenues for the development of innovative models for studying tumour's pathological mechanisms. Liver organoids show self-assembly and self-renewal capabilities, retaining essential aspects of their respective in vivo tissue and allowing modelling diseases and personalized treatment development. In this review, we will discuss the current advances in the field of liver organoids focusing on existing development protocols and possible applications in regenerative medicine and drug discovery.
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39
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Calvisi DF, Boulter L, Vaquero J, Saborowski A, Fabris L, Rodrigues PM, Coulouarn C, Castro RE, Segatto O, Raggi C, van der Laan LJW, Carpino G, Goeppert B, Roessler S, Kendall TJ, Evert M, Gonzalez-Sanchez E, Valle JW, Vogel A, Bridgewater J, Borad MJ, Gores GJ, Roberts LR, Marin JJG, Andersen JB, Alvaro D, Forner A, Banales JM, Cardinale V, Macias RIR, Vicent S, Chen X, Braconi C, Verstegen MMA, Fouassier L. Criteria for preclinical models of cholangiocarcinoma: scientific and medical relevance. Nat Rev Gastroenterol Hepatol 2023:10.1038/s41575-022-00739-y. [PMID: 36755084 DOI: 10.1038/s41575-022-00739-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/20/2022] [Indexed: 02/10/2023]
Abstract
Cholangiocarcinoma (CCA) is a rare malignancy that develops at any point along the biliary tree. CCA has a poor prognosis, its clinical management remains challenging, and effective treatments are lacking. Therefore, preclinical research is of pivotal importance and necessary to acquire a deeper understanding of CCA and improve therapeutic outcomes. Preclinical research involves developing and managing complementary experimental models, from in vitro assays using primary cells or cell lines cultured in 2D or 3D to in vivo models with engrafted material, chemically induced CCA or genetically engineered models. All are valuable tools with well-defined advantages and limitations. The choice of a preclinical model is guided by the question(s) to be addressed; ideally, results should be recapitulated in independent approaches. In this Consensus Statement, a task force of 45 experts in CCA molecular and cellular biology and clinicians, including pathologists, from ten countries provides recommendations on the minimal criteria for preclinical models to provide a uniform approach. These recommendations are based on two rounds of questionnaires completed by 35 (first round) and 45 (second round) experts to reach a consensus with 13 statements. An agreement was defined when at least 90% of the participants voting anonymously agreed with a statement. The ultimate goal was to transfer basic laboratory research to the clinics through increased disease understanding and to develop clinical biomarkers and innovative therapies for patients with CCA.
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Affiliation(s)
- Diego F Calvisi
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Luke Boulter
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.,Cancer Research UK Scottish Centre, Institute of Genetics and Cancer, Edinburgh, UK
| | - Javier Vaquero
- TGF-β and Cancer Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,National Biomedical Research Institute on Liver and Gastrointestinal Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain
| | - Anna Saborowski
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Luca Fabris
- Department of Molecular Medicine, University of Padua School of Medicine, Padua, Italy.,Digestive Disease Section, Yale University School of Medicine, New Haven, CT, USA
| | - Pedro M Rodrigues
- National Biomedical Research Institute on Liver and Gastrointestinal Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Cédric Coulouarn
- Inserm, Univ Rennes 1, OSS (Oncogenesis Stress Signalling), UMR_S 1242, Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
| | - Rui E Castro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Oreste Segatto
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Chiara Raggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC Transplantation Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Guido Carpino
- Department of Movement, Human and Health Sciences, Division of Health Sciences, University of Rome "Foro Italico", Rome, Italy
| | - Benjamin Goeppert
- Institute of Pathology and Neuropathology, Ludwigsburg, Germany.,Institute of Pathology, Kantonsspital Baselland, Liestal, Switzerland
| | - Stephanie Roessler
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Timothy J Kendall
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Matthias Evert
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Ester Gonzalez-Sanchez
- TGF-β and Cancer Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,National Biomedical Research Institute on Liver and Gastrointestinal Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Juan W Valle
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK.,Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - John Bridgewater
- Department of Medical Oncology, UCL Cancer Institute, London, UK
| | - Mitesh J Borad
- Mayo Clinic Cancer Center, Mayo Clinic, Phoenix, AZ, USA
| | - Gregory J Gores
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Jose J G Marin
- National Biomedical Research Institute on Liver and Gastrointestinal Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Experimental Hepatology and Drug Targeting (HEVEPHARM), IBSAL, University of Salamanca, Salamanca, Spain
| | - Jesper B Andersen
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Domenico Alvaro
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Alejandro Forner
- National Biomedical Research Institute on Liver and Gastrointestinal Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Liver Unit, Barcelona Clinic Liver Cancer (BCLC) Group, Hospital Clinic Barcelona, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Jesus M Banales
- National Biomedical Research Institute on Liver and Gastrointestinal Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.,Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - Vincenzo Cardinale
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy
| | - Rocio I R Macias
- National Biomedical Research Institute on Liver and Gastrointestinal Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Experimental Hepatology and Drug Targeting (HEVEPHARM), IBSAL, University of Salamanca, Salamanca, Spain
| | - Silve Vicent
- University of Navarra, Centre for Applied Medical Research, Program in Solid Tumours, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC, Instituto de Salud Carlos III), Madrid, Spain
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, CA, USA
| | - Chiara Braconi
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Monique M A Verstegen
- Department of Surgery, Erasmus MC Transplantation Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Laura Fouassier
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine (CRSA), Paris, France.
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Ha D, Kong J, Kim D, Lee K, Lee J, Park M, Ahn H, Oh Y, Kim S. Development of bioinformatics and multi-omics analyses in organoids. BMB Rep 2023; 56:43-48. [PMID: 36284440 PMCID: PMC9887100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 01/28/2023] Open
Abstract
Pre-clinical models are critical in gaining mechanistic and biological insights into disease progression. Recently, patient-derived organoid models have been developed to facilitate our understanding of disease development and to improve the discovery of therapeutic options by faithfully recapitulating in vivo tissues or organs. As technological developments of organoid models are rapidly growing, computational methods are gaining attention in organoid researchers to improve the ability to systematically analyze experimental results. In this review, we summarize the recent advances in organoid models to recapitulate human diseases and computational advancements to analyze experimental results from organoids. [BMB Reports 2023; 56(1): 43-48].
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Affiliation(s)
- Doyeon Ha
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - JungHo Kong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Donghyo Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Kwanghwan Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Juhun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Minhyuk Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Hyunsoo Ahn
- Graduate School of Artificial Intelligence, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Youngchul Oh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea,Graduate School of Artificial Intelligence, Pohang University of Science and Technology, Pohang 37673, Korea,Corresponding author. Tel: +82-54-279-2348; Fax: +82-54-279-2199; E-mail:
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41
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Integrative analysis of multiple genomic data from intrahepatic cholangiocarcinoma organoids enables tumor subtyping. Nat Commun 2023; 14:237. [PMID: 36646721 PMCID: PMC9842736 DOI: 10.1038/s41467-023-35896-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
As genomic analysis technology has advanced, it has become possible to sub-classify intrahepatic cholangiocarcinoma (ICC) at the histological or molecular level. Here, we verify the recently suggested two subgroups of ICC in the organoids model, compare the characteristics between types. ICC patients are subclassified into small-duct (SD) and large-duct (LD) subtype according to histological characteristics. ICC organoids are established, and unsupervised principal component analysis clustering separates each type of ICC. Differential gene expression reveals enrichment on KRAS, TGFβ and ERBB2 signaling pathways in LD-type compared with SD-type (P < 0.05). Gene set enrichment analysis demonstrates that the cholangiocarcinoma class 2 signature, defined by Andersen et al., is enriched in the LD-type (enrichment Score = 2.19, P < 0.001). A protein-protein interaction network analysis identifies ZNF217 as a significant hub protein (odds ratio = 4.96, P = 0.0105). We perform prospective modeling of histological subtype using patient-derived organoids. Moreover, gene expression profiling of ICC organoids enables identification of type-specific targetable pathways.
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Xie C, Gu A, Khan M, Yao X, Chen L, He J, Yuan F, Wang P, Yang Y, Wei Y, Tang F, Su H, Chen J, Li J, Cen B, Xu Z. Opportunities and challenges of hepatocellular carcinoma organoids for targeted drugs sensitivity screening. Front Oncol 2023; 12:1105454. [PMID: 36686807 PMCID: PMC9853547 DOI: 10.3389/fonc.2022.1105454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/16/2022] [Indexed: 01/07/2023] Open
Abstract
Hepatocellular carcinoma is one of the malignancies worldwide with a high mortality rate and an increasing incidence. Molecular Targeted agents are its common first-line treatment. Organoid technology, as a cutting-edge technology, is gradually being applied in the development of therapeutic oncology. Organoid models can be used to perform sensitivity screening of targeted drugs to facilitate the development of innovative therapeutic agents for the treatment of hepatocellular carcinoma. The purpose of this review is to provide an overview of the opportunities and challenges of hepatocellular carcinoma organoids in targeted drug sensitivity testing as well as a future outlook.
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Affiliation(s)
- Cuiying Xie
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Ancheng Gu
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Muhammad Khan
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiangcao Yao
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Leping Chen
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Jiali He
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Fumiao Yuan
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Ping Wang
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Yufan Yang
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Yerong Wei
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Fang Tang
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Hualong Su
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Jiamin Chen
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Jinxia Li
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Bohong Cen
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China,Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong, China,*Correspondence: Bohong Cen, ; Zhongyuan Xu,
| | - Zhongyuan Xu
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China,*Correspondence: Bohong Cen, ; Zhongyuan Xu,
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43
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Rathje F, Klingler S, Aberger F. Organoids for Modeling (Colorectal) Cancer in a Dish. Cancers (Basel) 2022; 14:cancers14215416. [PMID: 36358834 PMCID: PMC9655999 DOI: 10.3390/cancers14215416] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Simple Summary Despite remarkable progress in the treatment of cancer patients, the medical need for drugs with better efficacy is still unmet and high. In addition to accurate prediction of drug efficacy for individual patients, pathophysiologically relevant preclinical model systems with increased predictive power are urgently needed to reduce the high rate of clinical trial failure in oncology. Organoids grown from patient material represent exceptionally valuable model systems to mimic and study human diseased tissues such as tumors. Here, we elaborate an overview of innovative and advanced organoid model systems and highlight the exciting opportunities of organoids for personalized precision medicine and the field of immuno-oncology drug development. Abstract Functional studies of primary cancer have been limited to animal models for a long time making it difficult to study aspects specific to human cancer biology. The development of organoid technology enabled us to culture human healthy and tumor cells as three-dimensional self-organizing structures in vitro for a prolonged time. Organoid cultures conserve the heterogeneity of the originating epithelium regarding cell types and tumor clonality. Therefore, organoids are considered an invaluable tool to study and genetically dissect various aspects of human cancer biology. In this review, we describe the applications, advantages, and limitations of organoids as human cancer models with the main emphasis on colorectal cancer.
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Wang SX, Yan JS, Chan YS. Advancements in MAFLD Modeling with Human Cell and Organoid Models. Int J Mol Sci 2022; 23:11850. [PMID: 36233151 PMCID: PMC9569457 DOI: 10.3390/ijms231911850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Metabolic (dysfunction) associated fatty liver disease (MAFLD) is one of the most prevalent liver diseases and has no approved therapeutics. The high failure rates witnessed in late-phase MAFLD drug trials reflect the complexity of the disease, and how the disease develops and progresses remains to be fully understood. In vitro, human disease models play a pivotal role in mechanistic studies to unravel novel disease drivers and in drug testing studies to evaluate human-specific responses. This review focuses on MAFLD disease modeling using human cell and organoid models. The spectrum of patient-derived primary cells and immortalized cell lines employed to model various liver parenchymal and non-parenchymal cell types essential for MAFLD development and progression is discussed. Diverse forms of cell culture platforms utilized to recapitulate tissue-level pathophysiology in different stages of the disease are also reviewed.
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Affiliation(s)
- Shi-Xiang Wang
- Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Ji-Song Yan
- Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Yun-Shen Chan
- Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China
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45
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Lu Z, Zhong A, Liu H, Zhang M, Chen X, Pan X, Wang M, Deng X, Gao L, Zhao L, Wang J, Yang Y, Zhang Q, Wu B, Zheng J, Wang Y, Song X, Liu K, Zhang W, Chen X, Yang K, Chen X, Zhao Y, Zhao C, Wang Y, Chen L, Zhou Z, Hu J, Liu Y, Chen C. Dissecting the genetic and microenvironmental factors of gastric tumorigenesis in mice. Cell Rep 2022; 41:111482. [DOI: 10.1016/j.celrep.2022.111482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/21/2022] [Accepted: 09/19/2022] [Indexed: 11/03/2022] Open
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46
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Wang Q, Guo F, Jin Y, Ma Y. Applications of human organoids in the personalized treatment for digestive diseases. Signal Transduct Target Ther 2022; 7:336. [PMID: 36167824 PMCID: PMC9513303 DOI: 10.1038/s41392-022-01194-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/09/2022] [Accepted: 09/13/2022] [Indexed: 11/15/2022] Open
Abstract
Digestive system diseases arise primarily through the interplay of genetic and environmental influences; there is an urgent need in elucidating the pathogenic mechanisms of these diseases and deploy personalized treatments. Traditional and long-established model systems rarely reproduce either tissue complexity or human physiology faithfully; these shortcomings underscore the need for better models. Organoids represent a promising research model, helping us gain a more profound understanding of the digestive organs; this model can also be used to provide patients with precise and individualized treatment and to build rapid in vitro test models for drug screening or gene/cell therapy, linking basic research with clinical treatment. Over the past few decades, the use of organoids has led to an advanced understanding of the composition of each digestive organ and has facilitated disease modeling, chemotherapy dose prediction, CRISPR-Cas9 genetic intervention, high-throughput drug screening, and identification of SARS-CoV-2 targets, pathogenic infection. However, the existing organoids of the digestive system mainly include the epithelial system. In order to reveal the pathogenic mechanism of digestive diseases, it is necessary to establish a completer and more physiological organoid model. Combining organoids and advanced techniques to test individualized treatments of different formulations is a promising approach that requires further exploration. This review highlights the advancements in the field of organoid technology from the perspectives of disease modeling and personalized therapy.
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Affiliation(s)
- Qinying Wang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fanying Guo
- School of Clinical Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yutao Jin
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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47
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Khurana A, Sayed N, Singh V, Khurana I, Allawadhi P, Rawat PS, Navik U, Pasumarthi SK, Bharani KK, Weiskirchen R. A comprehensive overview of CRISPR/Cas 9 technology and application thereof in drug discovery. J Cell Biochem 2022; 123:1674-1698. [PMID: 36128934 DOI: 10.1002/jcb.30329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/13/2022] [Accepted: 09/01/2022] [Indexed: 11/07/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas technology possesses revolutionary potential to positively affect various domains of drug discovery. It has initiated a rise in the area of genetic engineering and its advantages range from classical science to translational medicine. These genome editing systems have given a new dimension to our capabilities to alter, detect and annotate specified gene sequences. Moreover, the ease, robustness and adaptability of the CRISPR/Cas9 technology have led to its extensive utilization in research areas in such a short period of time. The applications include the development of model cell lines, understanding disease mechanisms, discovering disease targets, developing transgenic animals and plants, and transcriptional modulation. Further, the technology is rapidly growing; hence, an overlook of progressive success is crucial. This review presents the current status of the CRISPR-Cas technology in a tailor-made format from its discovery to several advancements for drug discovery alongwith future trends associated with possibilities and hurdles including ethical concerns.
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Affiliation(s)
- Amit Khurana
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, Aachen, Germany
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Hyderabad, Telangana, India
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Mamnoor, Warangal, Telangana, India
| | - Nilofer Sayed
- Department of Pharmacy, Pravara Rural Education Society's (P.R.E.S.'s) College of Pharmacy, Shreemati Nathibai Damodar Thackersey (SNDT) Women's University, Nashik, Maharashtra, India
| | - Vishakha Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Isha Khurana
- Department of Pharmaceutical Chemistry, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh, India
| | - Prince Allawadhi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Pushkar Singh Rawat
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, Punjab, India
| | - Umashanker Navik
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, Punjab, India
| | | | - Kala Kumar Bharani
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Mamnoor, Warangal, Telangana, India
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, Aachen, Germany
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48
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Therapeutic targets and biomarkers of tumor immunotherapy: response versus non-response. Signal Transduct Target Ther 2022; 7:331. [PMID: 36123348 PMCID: PMC9485144 DOI: 10.1038/s41392-022-01136-2] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/25/2022] [Accepted: 07/25/2022] [Indexed: 02/05/2023] Open
Abstract
Cancers are highly complex diseases that are characterized by not only the overgrowth of malignant cells but also an altered immune response. The inhibition and reprogramming of the immune system play critical roles in tumor initiation and progression. Immunotherapy aims to reactivate antitumor immune cells and overcome the immune escape mechanisms of tumors. Represented by immune checkpoint blockade and adoptive cell transfer, tumor immunotherapy has seen tremendous success in the clinic, with the capability to induce long-term regression of some tumors that are refractory to all other treatments. Among them, immune checkpoint blocking therapy, represented by PD-1/PD-L1 inhibitors (nivolumab) and CTLA-4 inhibitors (ipilimumab), has shown encouraging therapeutic effects in the treatment of various malignant tumors, such as non-small cell lung cancer (NSCLC) and melanoma. In addition, with the advent of CAR-T, CAR-M and other novel immunotherapy methods, immunotherapy has entered a new era. At present, evidence indicates that the combination of multiple immunotherapy methods may be one way to improve the therapeutic effect. However, the overall clinical response rate of tumor immunotherapy still needs improvement, which warrants the development of novel therapeutic designs as well as the discovery of biomarkers that can guide the prescription of these agents. Learning from the past success and failure of both clinical and basic research is critical for the rational design of studies in the future. In this article, we describe the efforts to manipulate the immune system against cancer and discuss different targets and cell types that can be exploited to promote the antitumor immune response.
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49
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Dong R, Zhang B, Zhang X. Liver organoids: an in vitro 3D model for liver cancer study. Cell Biosci 2022; 12:152. [PMID: 36085085 PMCID: PMC9463833 DOI: 10.1186/s13578-022-00890-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/28/2022] [Indexed: 11/21/2022] Open
Abstract
Primary liver cancer (PLC) is the second leading cause of cancer mortality worldwide, and its morbidity unceasingly increases these years. Hepatitis B virus (HBV) infection accounted for approximately 50% of hepatocellular carcinoma (HCC) cases globally in 2015. Due to the lack of an effective model to study HBV-associated liver carcinogenesis, research has made slow progress. Organoid, an in vitro 3D model which maintains self-organization, has recently emerged as a powerful tool to investigate human diseases. In this review, we first summarize the categories and development of liver organoids. Then, we mainly focus on the functions of culture medium components and applications of organoids for HBV infection and HBV-associated liver cancer studies. Finally, we provide insights into a potential patient-derived organoid model from those infected with HBV based on our study, as well as the limitations and future applications of organoids in liver cancer research.
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50
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Høgdall D, O'Rourke CJ, Andersen JB. Molecular therapeutic targets for cholangiocarcinoma: Present challenges and future possibilities. Adv Cancer Res 2022; 156:343-366. [PMID: 35961705 DOI: 10.1016/bs.acr.2022.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A diagnosis of cholangiocarcinoma (CCA) is implicit with poor prognosis and limited treatment options, underscoring the near equivalence of incidence and mortality rates in this disease. In less than 9years from genomic identification to FDA-approval of the corresponding inhibitors, fibroblast growth factor receptor 2 (FGFR2) rearrangements and isocitrate dehydrogenase 1 (IDH1) mutations became exemplary successes of precision oncology in subsets of patients with CCA. However, clinical trial results from multikinase inhibitors in unselected populations have been less successful, while the impact of immunotherapies are only beginning to impact this setting. Development of future therapeutics is incumbent with new challenges. Many driver alterations occur in tumor suppressor-like genes which are not directly druggable. Therapeutically, this will require identification of ensuant "non-oncogene addiction" involving genes which are not themselves oncogenes but become tumor survival dependencies when a specific driver alteration occurs. The low recurrence frequency of genomic alterations between CCA patients will require careful evaluation of targeted agents in biomarker-enrolled trials, including basket trial settings. Systematic expansion of candidate drug targets must integrate genes affected by non-genetic alterations which incorporates the fundamental contribution of the microenvironment and immune system to treatment response, disease facets which have been traditionally overlooked by DNA-centric analyses. As treatment resistance is an inevitability in advanced disease, resistance mechanisms require characterization to guide the development of combination therapies to increase the duration of clinical benefit. Patient-focused clinical, technological and analytical synergy is needed to deliver future solutions to these present therapeutic challenges.
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Affiliation(s)
- Dan Høgdall
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Oncology, Herlev and Gentofte Hospital, Herlev, Copenhagen University Hospital, Copenhagen, Denmark
| | - Colm J O'Rourke
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesper B Andersen
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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