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Parente IA, Chiara L, Bertoni S. Exploring the potential of human intestinal organoids: Applications, challenges, and future directions. Life Sci 2024; 352:122875. [PMID: 38942359 DOI: 10.1016/j.lfs.2024.122875] [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: 05/01/2024] [Revised: 06/13/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
The complex and dynamic environment of the gastrointestinal tract shapes one of the fastest renewing tissues in the human body, the intestinal epithelium. Considering the lack of human preclinical studies, reliable models that mimic the intestinal environment are increasingly explored. Patient-derived intestinal organoids are powerful tools that recapitulate in vitro many pathophysiological features of the human intestine. In this review, the possible applications of human intestinal organoids in different research fields are highlighted. From physiologically relevant to intestinal disease modeling, regenerative medicine, and toxicology studies, the potential of intestinal organoids will be here presented and discussed. Despite the remarkable opportunities offered, limitations related to ethical concerns, tissue collection, reproducibility, and methodologies may hinder the full exploitation of this cell-based model into high throughput studies and clinical practice. Currently, distinct approaches can be used to overcome the numerous challenges found along the way and to allow the full implementation of this ground-breaking technology.
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Affiliation(s)
- Inês A Parente
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Linda Chiara
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Simona Bertoni
- Department of Food and Drug, University of Parma, Parma, Italy.
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2
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Huang Y, Liu T, Huang Q, Wang Y. From Organ-on-a-Chip to Human-on-a-Chip: A Review of Research Progress and Latest Applications. ACS Sens 2024; 9:3466-3488. [PMID: 38991227 DOI: 10.1021/acssensors.4c00004] [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] [Indexed: 07/13/2024]
Abstract
Organ-on-a-Chip (OOC) technology, which emulates the physiological environment and functionality of human organs on a microfluidic chip, is undergoing significant technological advancements. Despite its rapid evolution, this technology is also facing notable challenges, such as the lack of vascularization, the development of multiorgan-on-a-chip systems, and the replication of the human body on a single chip. The progress of microfluidic technology has played a crucial role in steering OOC toward mimicking the human microenvironment, including vascularization, microenvironment replication, and the development of multiorgan microphysiological systems. Additionally, advancements in detection, analysis, and organoid imaging technologies have enhanced the functionality and efficiency of Organs-on-Chips (OOCs). In particular, the integration of artificial intelligence has revolutionized organoid imaging, significantly enhancing high-throughput drug screening. Consequently, this review covers the research progress of OOC toward Human-on-a-chip, the integration of sensors in OOCs, and the latest applications of organoid imaging technologies in the biomedical field.
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Affiliation(s)
- Yisha Huang
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, Sichuan 610212, China
| | - Tong Liu
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qi Huang
- School of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Yuxi Wang
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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3
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Gopallawa I, Gupta C, Jawa R, Cyril A, Jawa V, Chirmule N, Gujar V. Applications of Organoids in Advancing Drug Discovery and Development. J Pharm Sci 2024:S0022-3549(24)00233-8. [PMID: 39002723 DOI: 10.1016/j.xphs.2024.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/14/2024] [Accepted: 06/14/2024] [Indexed: 07/15/2024]
Abstract
Organoids are small, self-organizing three-dimensional cell cultures that are derived from stem cells or primary organs. These cultures replicate the complexity of an organ, which cannot be achieved by single-cell culture systems. Organoids can be used in testing of new drugs instead of animals. Development and validation of organoids is thus important to reduce the reliance on animals for drug testing. In this review, we have discussed the developmental and regulatory aspects of organoids and highlighted their importance in drug development. We have first summarized different types of culture-based organoid systems such as submerged Matrigel, micro-fluidic 3D cultures, inducible pluripotent stem cells, and air-liquid interface cultures. These systems help us understand the intricate interplay between cells and their surrounding milieu for identifying functions of target receptors, soluble factors, and spatial interactions. Further, we have discussed the advances in humanized severe-combined immunodeficiency mouse models and their applications in the pharmacology of immune-oncology. Since regulatory aspects are important in using organoids for drug development, we have summarized FDA and EMA regulations on organoid research to support pre-clinical studies. Finally, we have included some unique studies highlighting the use of organoids in studying infectious diseases, cancer, and fundamental biology. These studies also exemplify the latest technological advances in organoid development resulting in improved efficiency. Overall, this review comprehensively summarizes the applications of organoids in early drug development during discovery and pre-clinical studies.
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Affiliation(s)
- Indiwari Gopallawa
- Clinical Pharmacology & Safety Sciences, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, USA
| | | | - Rayan Jawa
- University of Pennsylvania, Philadelphia, PA, USA
| | - Arya Cyril
- Department of Psychology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Vibha Jawa
- Bristol Myers Squibb, Lawrenceville, NY, USA.
| | | | - Vikramsingh Gujar
- Anatomy and Cell Biology, Oklahoma State University Center for Health Sciences, Tulsa, OK, USA
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4
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Cutrona MB, Wu J, Yang K, Peng J, Chen T. Pancreatic cancer organoid-screening captures personalized sensitivity and chemoresistance suppression upon cytochrome P450 3A5-targeted inhibition. iScience 2024; 27:110289. [PMID: 39055940 PMCID: PMC11269815 DOI: 10.1016/j.isci.2024.110289] [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: 11/27/2023] [Revised: 04/12/2024] [Accepted: 06/13/2024] [Indexed: 07/28/2024] Open
Abstract
Cytochrome P450 3A5 (CYP3A5) has been proposed as a predictor of therapy response in subtypes of pancreatic ductal adenocarcinoma cancer (PDAC). To validate CYP3A5 as a therapeutic target, we developed a high-content image organoid-based screen to quantify the phenotypic responses to the selective inhibition of CYP3A5 enzymatic activity by clobetasol propionate (CBZ), using a cohort of PDAC-derived organoids (PDACOs). The chemoresistance of PDACOs to a panel of standard-of-care drugs, alone or in combination with CBZ, was investigated. PDACO pharmaco-profiling revealed CBZ to have anti-cancer activity that was dependent on the CYP3A5 level. In addition, CBZ restored chemo-vulnerability to cisplatin in a subset of PDACOs. A correlative proteomic analysis established that CBZ caused the suppression of multiple cancer pathways sustained by or associated with a mutant form of p53. Limiting the active pool of CYP3A5 enables targeted and personalized therapy to suppress pro-oncogenic mechanisms that fuel chemoresistance in some PDAC tumors.
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Affiliation(s)
- Meritxell B. Cutrona
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA
| | - Ka Yang
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA
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5
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Mao Y, Hu H. Establishment of advanced tumor organoids with emerging innovative technologies. Cancer Lett 2024; 598:217122. [PMID: 39029781 DOI: 10.1016/j.canlet.2024.217122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/21/2024] [Accepted: 07/12/2024] [Indexed: 07/21/2024]
Abstract
Tumor organoids have emerged as a crucial preclinical model for multiple cancer research. Their high establishment rates, stability, and ability to replicate key biological features of original tumor cells in vivo render them invaluable for exploring tumor molecular mechanisms, discovering potential anti-tumor drugs, and predicting clinical drug efficacy. Here, we review the establishment of tumor organoid models and provide an extensive overview of organoid culturing strategies. We also emphasize the significance of integrating cellular components of the tumor microenvironment and physicochemical factors in the organoid culturing system, highlighting the importance of artificial intelligence technology in advancing organoid construction. Moreover, we summarize recent advancements in utilizing organoid systems for novel anti-cancer drug screening and discuss promising trends for enhancing advanced organoids in next-generation disease modeling.
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Affiliation(s)
- Yunuo Mao
- The Key Laboratory of Experimental Teratology, Ministry of Education, Department of Systems Biomedicine, School of Basic Medical Sciences, Shandong University, Jinan, 250012, PR China
| | - Huili Hu
- The Key Laboratory of Experimental Teratology, Ministry of Education, Department of Systems Biomedicine, School of Basic Medical Sciences, Shandong University, Jinan, 250012, PR China.
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6
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Wang Z, Hulikova A, Swietach P. Innovating cancer drug discovery with refined phenotypic screens. Trends Pharmacol Sci 2024:S0165-6147(24)00120-2. [PMID: 39013672 DOI: 10.1016/j.tips.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/10/2024] [Accepted: 06/17/2024] [Indexed: 07/18/2024]
Abstract
Before molecular pathways in cancer were known to a depth that could predict targets, drug development relied on phenotypic screening, where the effectiveness of candidate chemicals is judged from functional readouts without considering the mechanisms of action. The unraveling of tumor-specific pathways has brought targets for molecularly driven drug discovery, but precedents in the field have shown that awareness of pathways does not necessarily predict therapeutic efficacy, and many cancers still lack druggable targets. Phenotypic screening therefore retains a niche in drug development where a targeted approach is not informative. We analyze the unique advantages of phenotypic screens, and how technological advances have improved their discovery power. Notable advances include the use of larger biological panels and refined protocols that address the disease-relevance and increase data content with imaging and omic approaches.
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Affiliation(s)
- Zhenyi Wang
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK
| | - Alzbeta Hulikova
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK
| | - Pawel Swietach
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK.
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Vitale S, Calapà F, Colonna F, Luongo F, Biffoni M, De Maria R, Fiori ME. Advancements in 3D In Vitro Models for Colorectal Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405084. [PMID: 38962943 DOI: 10.1002/advs.202405084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Indexed: 07/05/2024]
Abstract
The process of drug discovery and pre-clinical testing is currently inefficient, expensive, and time-consuming. Most importantly, the success rate is unsatisfactory, as only a small percentage of tested drugs are made available to oncological patients. This is largely due to the lack of reliable models that accurately predict drug efficacy and safety. Even animal models often fail to replicate human-specific pathologies and human body's complexity. These factors, along with ethical concerns regarding animal use, urge the development of suitable human-relevant, translational in vitro models.
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Affiliation(s)
- Sara Vitale
- Department of Oncology and Molecular Medicine (OMM), Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, 00161, Italy
| | - Federica Calapà
- Dipartimento di Medicina e Chirurgia traslazionale, Università Cattolica del Sacro Cuore, Largo F. Vito 1, Rome, Italy
| | - Francesca Colonna
- Department of Oncology and Molecular Medicine (OMM), Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, 00161, Italy
| | - Francesca Luongo
- Dipartimento di Medicina e Chirurgia traslazionale, Università Cattolica del Sacro Cuore, Largo F. Vito 1, Rome, Italy
| | - Mauro Biffoni
- Department of Oncology and Molecular Medicine (OMM), Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, 00161, Italy
| | - Ruggero De Maria
- Dipartimento di Medicina e Chirurgia traslazionale, Università Cattolica del Sacro Cuore, Largo F. Vito 1, Rome, Italy
- Fondazione Policlinico Universitario "A. Gemelli" - IRCCS, Largo F. Vito 1, Rome, Italy
| | - Micol E Fiori
- Department of Oncology and Molecular Medicine (OMM), Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, 00161, Italy
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Coronel R, García-Moreno E, Siendones E, Barrero MJ, Martínez-Delgado B, Santos-Ocaña C, Liste I, Cascajo-Almenara MV. Brain organoid as a model to study the role of mitochondria in neurodevelopmental disorders: achievements and weaknesses. Front Cell Neurosci 2024; 18:1403734. [PMID: 38978706 PMCID: PMC11228165 DOI: 10.3389/fncel.2024.1403734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/13/2024] [Indexed: 07/10/2024] Open
Abstract
Mitochondrial diseases are a group of severe pathologies that cause complex neurodegenerative disorders for which, in most cases, no therapy or treatment is available. These organelles are critical regulators of both neurogenesis and homeostasis of the neurological system. Consequently, mitochondrial damage or dysfunction can occur as a cause or consequence of neurodevelopmental or neurodegenerative diseases. As genetic knowledge of neurodevelopmental disorders advances, associations have been identified between genes that encode mitochondrial proteins and neurological symptoms, such as neuropathy, encephalomyopathy, ataxia, seizures, and developmental delays, among others. Understanding how mitochondrial dysfunction can alter these processes is essential in researching rare diseases. Three-dimensional (3D) cell cultures, which self-assemble to form specialized structures composed of different cell types, represent an accessible manner to model organogenesis and neurodevelopmental disorders. In particular, brain organoids are revolutionizing the study of mitochondrial-based neurological diseases since they are organ-specific and model-generated from a patient's cell, thereby overcoming some of the limitations of traditional animal and cell models. In this review, we have collected which neurological structures and functions recapitulate in the different types of reported brain organoids, focusing on those generated as models of mitochondrial diseases. In addition to advancements in the generation of brain organoids, techniques, and approaches for studying neuronal structures and physiology, drug screening and drug repositioning studies performed in brain organoids with mitochondrial damage and neurodevelopmental disorders have also been reviewed. This scope review will summarize the evidence on limitations in studying the function and dynamics of mitochondria in brain organoids.
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Affiliation(s)
- Raquel Coronel
- Neural Regeneration Unit, Functional Unit for Research on Chronic Diseases (UFIEC), National Institute of Health Carlos III (ISCIII), Madrid, Spain
- Department of Systems Biology, Faculty of Medicine and Health Sciences, University of Alcalá (UAH), Alcalá de Henares, Spain
| | - Enrique García-Moreno
- Andalusian Centre for Developmental Biology, CIBERER, National Institute of Health Carlos III (ISCIII), Pablo de Olavide University-CSIC-JA, Seville, Spain
| | - Emilio Siendones
- Andalusian Centre for Developmental Biology, CIBERER, National Institute of Health Carlos III (ISCIII), Pablo de Olavide University-CSIC-JA, Seville, Spain
| | - Maria J. Barrero
- Models and Mechanisms Unit, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Beatriz Martínez-Delgado
- Molecular Genetics Unit, Institute of Rare Diseases Research (IIER), CIBER of Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Carlos Santos-Ocaña
- Andalusian Centre for Developmental Biology, CIBERER, National Institute of Health Carlos III (ISCIII), Pablo de Olavide University-CSIC-JA, Seville, Spain
| | - Isabel Liste
- Neural Regeneration Unit, Functional Unit for Research on Chronic Diseases (UFIEC), National Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - M. V. Cascajo-Almenara
- Andalusian Centre for Developmental Biology, CIBERER, National Institute of Health Carlos III (ISCIII), Pablo de Olavide University-CSIC-JA, Seville, Spain
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9
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Song Y, Chen M, Wei Y, Ma X, Shi H. Signaling pathways in colorectal cancer implications for the target therapies. MOLECULAR BIOMEDICINE 2024; 5:21. [PMID: 38844562 PMCID: PMC11156834 DOI: 10.1186/s43556-024-00178-y] [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: 07/10/2023] [Accepted: 02/29/2024] [Indexed: 06/09/2024] Open
Abstract
Colorectal carcinoma (CRC) stands as a pressing global health issue, marked by the unbridled proliferation of immature cells influenced by multifaceted internal and external factors. Numerous studies have explored the intricate mechanisms of tumorigenesis in CRC, with a primary emphasis on signaling pathways, particularly those associated with growth factors and chemokines. However, the sheer diversity of molecular targets introduces complexity into the selection of targeted therapies, posing a significant challenge in achieving treatment precision. The quest for an effective CRC treatment is further complicated by the absence of pathological insights into the mutations or alterations occurring in tumor cells. This study reveals the transfer of signaling from the cell membrane to the nucleus, unveiling recent advancements in this crucial cellular process. By shedding light on this novel dimension, the research enhances our understanding of the molecular intricacies underlying CRC, providing a potential avenue for breakthroughs in targeted therapeutic strategies. In addition, the study comprehensively outlines the potential immune responses incited by the aberrant activation of signaling pathways, with a specific focus on immune cells, cytokines, and their collective impact on the dynamic landscape of drug development. This research not only contributes significantly to advancing CRC treatment and molecular medicine but also lays the groundwork for future breakthroughs and clinical trials, fostering optimism for improved outcomes and refined approaches in combating colorectal carcinoma.
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Affiliation(s)
- Yanlin Song
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, People's Republic of China
| | - Ming Chen
- West China School of Medicine, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, People's Republic of China
| | - Yuhao Wei
- West China School of Medicine, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, People's Republic of China
| | - Xuelei Ma
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, People's Republic of China.
| | - Huashan Shi
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, People's Republic of China.
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Banerjee J, Tiwari AK, Banerjee S. Drug repurposing for cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 207:123-150. [PMID: 38942535 DOI: 10.1016/bs.pmbts.2024.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
In the dynamic landscape of cancer therapeutics, the innovative strategy of drug repurposing emerges as a transformative paradigm, heralding a new era in the fight against malignancies. This book chapter aims to embark on the comprehension of the strategic deployment of approved drugs for repurposing and the meticulous journey of drug repurposing from earlier times to the current era. Moreover, the chapter underscores the multifaceted and complex nature of cancer biology, and the evolving field of cancer drug therapeutics while emphasizing the mandate of drug repurposing to advance cancer therapeutics. Importantly, the narrative explores the latest tools, technologies, and cutting-edge methodologies including high-throughput screening, omics technologies, and artificial intelligence-driven approaches, for shaping and accelerating the pace of drug repurposing to uncover novel cancer therapeutic avenues. The chapter critically assesses the breakthroughs, expanding the repertoire of repurposing drug candidates in cancer, and their major categories. Another focal point of this book chapter is that it addresses the emergence of combination therapies involving repurposed drugs, reflecting a shift towards personalized and synergistic treatment approaches. The expert analysis delves into the intricacies of combinatorial regimens, elucidating their potential to target heterogeneous cancer populations and overcome resistance mechanisms, thereby enhancing treatment efficacy. Therefore, this chapter provides in-depth insights into the potential of repurposing towards bringing the much-needed big leap in the field of cancer therapeutics.
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Affiliation(s)
- Juni Banerjee
- Department of Biotechnology and Bioengineering, Institute of Advanced Research (IAR), Gandhinagar, Gujarat, India
| | - Anand Krishna Tiwari
- Department of Biotechnology and Bioengineering, Institute of Advanced Research (IAR), Gandhinagar, Gujarat, India
| | - Shuvomoy Banerjee
- Department of Biotechnology and Bioengineering, Institute of Advanced Research (IAR), Gandhinagar, Gujarat, India.
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Yan S, He Y, Zhu Y, Ye W, Chen Y, Zhu C, Zhan F, Ma Z. Human patient derived organoids: an emerging precision medicine model for gastrointestinal cancer research. Front Cell Dev Biol 2024; 12:1384450. [PMID: 38638528 PMCID: PMC11024315 DOI: 10.3389/fcell.2024.1384450] [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: 02/09/2024] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
Gastrointestinal cancers account for approximately one-third of the total global cancer incidence and mortality with a poor prognosis. It is one of the leading causes of cancer-related deaths worldwide. Most of these diseases lack effective treatment, occurring as a result of inappropriate models to develop safe and potent therapies. As a novel preclinical model, tumor patient-derived organoids (PDOs), can be established from patients' tumor tissue and cultured in the laboratory in 3D architectures. This 3D model can not only highly simulate and preserve key biological characteristics of the source tumor tissue in vitro but also reproduce the in vivo tumor microenvironment through co-culture. Our review provided an overview of the different in vitro models in current tumor research, the derivation of cells in PDO models, and the application of PDO model technology in gastrointestinal cancers, particularly the applications in combination with CRISPR/Cas9 gene editing technology, tumor microenvironment simulation, drug screening, drug development, and personalized medicine. It also elucidates the ethical status quo of organoid research and the current challenges encountered in clinical research, and offers a forward-looking assessment of the potential paths for clinical organoid research advancement.
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Affiliation(s)
- Sicheng Yan
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, China
- School of Basic Medicine College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuxuan He
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, China
- School of Basic Medicine College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuehong Zhu
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, China
- School of Basic Medicine College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Wangfang Ye
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, China
- School of Basic Medicine College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yan Chen
- Department of Colorectal Surgery, Huzhou Central Hospital, The Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, Huzhou, China
| | - Cong Zhu
- Department of Colorectal Surgery, Huzhou Central Hospital, The Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, Huzhou, China
| | - Fuyuan Zhan
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, China
- School of Basic Medicine College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhihong Ma
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, China
- School of Basic Medicine College, Zhejiang Chinese Medical University, Hangzhou, China
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12
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Spisak S, Chen D, Likasitwatanakul P, Doan P, Li Z, Bala P, Vizkeleti L, Tisza V, De Silva P, Giannakis M, Wolpin B, Qi J, Sethi NS. Identifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system. Nat Commun 2024; 15:2230. [PMID: 38472198 PMCID: PMC10933491 DOI: 10.1038/s41467-024-46285-w] [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: 02/02/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators of these key cellular programs, we engineer a dual endogenous reporter system by genome-editing the SOX9 and KRT20 loci of human CRC cell lines to express fluorescent reporters, broadcasting aberrant stem cell-like and differentiation activity, respectively. By applying a CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs to this platform, we identify factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominate SMARCB1 of the BAF complex (also known as SWI/SNF) as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency and required for in vivo growth of human CRC models. These studies highlight the utility of biologically designed endogenous reporter platforms to uncover regulators with therapeutic potential.
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Affiliation(s)
- Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - David Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Pornlada Likasitwatanakul
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Paul Doan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Zhixin Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Pratyusha Bala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Laura Vizkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094, Budapest, Hungary
| | - Viktoria Tisza
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Pushpamali De Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nilay S Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA.
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA.
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13
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Smabers LP, Wensink E, Verissimo CS, Koedoot E, Pitsa KC, Huismans MA, Higuera Barón C, Doorn M, Valkenburg-van Iersel LB, Cirkel GA, Brousali A, Overmeer R, Koopman M, Braat MN, Penning de Vries B, Elias SG, Vries RG, Kranenburg O, Boj SF, Roodhart JM. Organoids as a biomarker for personalized treatment in metastatic colorectal cancer: drug screen optimization and correlation with patient response. J Exp Clin Cancer Res 2024; 43:61. [PMID: 38414064 PMCID: PMC10898042 DOI: 10.1186/s13046-024-02980-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/09/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND The inability to predict treatment response of colorectal cancer patients results in unnecessary toxicity, decreased efficacy and survival. Response testing on patient-derived organoids (PDOs) is a promising biomarker for treatment efficacy. The aim of this study is to optimize PDO drug screening methods for correlation with patient response and explore the potential to predict responses to standard chemotherapies. METHODS We optimized drug screen methods on 5-11 PDOs per condition of the complete set of 23 PDOs from patients treated for metastatic colorectal cancer (mCRC). PDOs were exposed to 5-fluorouracil (5-FU), irinotecan- and oxaliplatin-based chemotherapy. We compared medium with and without N-acetylcysteine (NAC), different readouts and different combination treatment set-ups to capture the strongest association with patient response. We expanded the screens using the optimized methods for all PDOs. Organoid sensitivity was correlated to the patient's response, determined by % change in the size of target lesions. We assessed organoid sensitivity in relation to prior exposure to chemotherapy, mutational status and sidedness. RESULTS Drug screen optimization involved excluding N-acetylcysteine from the medium and biphasic curve fitting for 5-FU & oxaliplatin combination screens. CellTiter-Glo measurements were comparable with CyQUANT and did not affect the correlation with patient response. Furthermore, the correlation improved with application of growth rate metrics, when 5-FU & oxaliplatin was screened in a ratio, and 5-FU & SN-38 using a fixed dose of SN-38. Area under the curve was the most robust drug response curve metric. After optimization, organoid and patient response showed a correlation coefficient of 0.58 for 5-FU (n = 6, 95% CI -0.44,0.95), 0.61 for irinotecan- (n = 10, 95% CI -0.03,0.90) and 0.60 for oxaliplatin-based chemotherapy (n = 11, 95% CI -0.01,0.88). Median progression-free survival of patients with resistant PDOs to oxaliplatin-based chemotherapy was significantly shorter than sensitive PDOs (3.3 vs 10.9 months, p = 0.007). Increased resistance to 5-FU in patients with prior exposure to 5-FU/capecitabine was adequately reflected in PDOs (p = 0.003). CONCLUSIONS Our study emphasizes the critical impact of the screening methods for determining correlation between PDO drug screens and mCRC patient outcomes. Our 5-step optimization strategy provides a basis for future research on the clinical utility of PDO screens.
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Affiliation(s)
- Lidwien P Smabers
- Department of Medical Oncology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Emerens Wensink
- Department of Medical Oncology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | | | | | | | - Maarten A Huismans
- Molecular Cancer Research, Center for Molecular Medicine, UMCU, Utrecht, The Netherlands
| | | | | | | | - Geert A Cirkel
- Department of Medical Oncology, Meander Medical Center, Amersfoort, The Netherlands
| | - Anneta Brousali
- Utrecht Platform for Organoid Technology (UPORT), UMCU, Utrecht, The Netherlands
| | | | - Miriam Koopman
- Department of Medical Oncology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Manon N Braat
- Department of Radiology, UMCU, Utrecht, The Netherlands
| | - Bas Penning de Vries
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, UMCU, Utrecht, The Netherlands
| | - Sjoerd G Elias
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, UMCU, Utrecht, The Netherlands
| | | | - Onno Kranenburg
- Utrecht Platform for Organoid Technology (UPORT), UMCU, Utrecht, The Netherlands
- Laboratory of Translational Oncology, Division of Imaging and Cancer, UMCU, Utrecht, The Netherlands
| | | | - Jeanine M Roodhart
- Department of Medical Oncology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands.
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14
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Di Maggio F, Boccia G, Nunziato M, Filotico M, Montesarchio V, D'Armiento M, Corcione F, Salvatore F. A Novel DNA Variant in SMARCA4 Gene Found in a Patient Affected by Early Onset Colon Cancer. Int J Mol Sci 2024; 25:2716. [PMID: 38473962 DOI: 10.3390/ijms25052716] [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: 02/12/2024] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
Colorectal cancer is the third leading cause of death from neoplasia worldwide. Thanks to new screening programs, we are now seeing an increase in Early Onset of ColoRectal Cancer (EOCRC) in patients below the age of 50. Herein, we report a clinical case of a woman affected by EOCRC. This case illustrates the importance of genetic predisposition testing also in tumor patients. Indeed, for our patient, we used a combined approach of multiple molecular and cellular biology technologies that revealed the presence of an interesting novel variant in the SMARCA4 gene. The latter gene is implicated in damage repair processes and related, if mutated, to the onset of various tumor types. In addition, we stabilized Patient-Derived Organoids from the tumor tissue of the same patient and the result confirmed the presence of this novel pathogenic variant that has never been found before even in early onset cancer. In conclusion, with this clinical case, we want to underscore the importance of including patients even those below the age of 50 years in appropriate screening programs which should also include genetic tests for predisposition to early onset cancers.
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Affiliation(s)
- Federica Di Maggio
- CEINGE-Biotecnologie Avanzate Franco Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131 Naples, Italy
| | - Giuseppe Boccia
- Department of Public Health, University of Naples "Federico II", 80131 Naples, Italy
| | - Marcella Nunziato
- CEINGE-Biotecnologie Avanzate Franco Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131 Naples, Italy
| | - Marcello Filotico
- Department of Public Health, University of Naples "Federico II", 80131 Naples, Italy
| | | | - Maria D'Armiento
- Pathology Unit, Department of Public Health, University of Naples "Federico II", 80131 Naples, Italy
| | - Francesco Corcione
- Department of Public Health, University of Naples "Federico II", 80131 Naples, Italy
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate Franco Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131 Naples, Italy
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15
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Khorsandi D, Yang JW, Foster S, Khosravi S, Hosseinzadeh Kouchehbaghi N, Zarei F, Lee YB, Runa F, Gangrade A, Voskanian L, Adnan D, Zhu Y, Wang Z, Jucaud V, Dokmeci MR, Shen X, Bishehsari F, Kelber JA, Khademhosseini A, de Barros NR. Patient-Derived Organoids as Therapy Screening Platforms in Cancer Patients. Adv Healthc Mater 2024:e2302331. [PMID: 38359321 DOI: 10.1002/adhm.202302331] [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: 07/21/2023] [Revised: 11/28/2023] [Indexed: 02/17/2024]
Abstract
Patient-derived organoids (PDOs) developed ex vivo and in vitro are increasingly used for therapeutic screening. They provide a more physiologically relevant model for drug discovery and development compared to traditional cell lines. However, several challenges remain to be addressed to fully realize the potential of PDOs in therapeutic screening. This paper summarizes recent advancements in PDO development and the enhancement of PDO culture models. This is achieved by leveraging materials engineering and microfabrication technologies, including organs-on-a-chip and droplet microfluidics. Additionally, this work discusses the application of PDOs in therapy screening to meet diverse requirements and overcome bottlenecks in cancer treatment. Furthermore, this work introduces tools for data processing and analysis of organoids, along with their microenvironment. These tools aim to achieve enhanced readouts. Finally, this work explores the challenges and future perspectives of using PDOs in drug development and personalized screening for cancer patients.
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Affiliation(s)
- Danial Khorsandi
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
| | - Jia-Wei Yang
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
| | - Samuel Foster
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
| | - Safoora Khosravi
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
- Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Negar Hosseinzadeh Kouchehbaghi
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
- Department of Textile Engineering, Amirkabir University of Technology (Tehran Polytechnic), Hafez Avenue, Tehran, 1591634311, Iran
| | - Fahimeh Zarei
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
| | - Yun Bin Lee
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
| | - Farhana Runa
- Department of Biology, California State University Northridge, 18111 Nordhoff Street, Northridge, California, 91330, USA
| | - Ankit Gangrade
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
| | - Leon Voskanian
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
| | - Darbaz Adnan
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Yangzhi Zhu
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
| | - Zhaohui Wang
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Vadim Jucaud
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
| | - Mehmet Remzi Dokmeci
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
| | - Xiling Shen
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
| | - Faraz Bishehsari
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, 60612, USA
- Division of Digestive Diseases, Rush Center for Integrated Microbiome & Chronobiology Research, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Jonathan A Kelber
- Department of Biology, California State University Northridge, 18111 Nordhoff Street, Northridge, California, 91330, USA
- Department of Biology, Baylor University, 101 Bagby Ave, Waco, Texas, 76706, USA
| | - Ali Khademhosseini
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
| | - Natan Roberto de Barros
- Department of Bioengineering, Terasaki Institute for Biomedical Innovation (TIBI), 1018 Westwood Blvd, Los Angeles, California, 91367, USA
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16
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Flood P, Hanrahan N, Nally K, Melgar S. Human intestinal organoids: Modeling gastrointestinal physiology and immunopathology - current applications and limitations. Eur J Immunol 2024; 54:e2250248. [PMID: 37957831 DOI: 10.1002/eji.202250248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/15/2023]
Abstract
Human intestinal organoids are an ideal model system for studying gastrointestinal physiology and immunopathology. Altered physiology and mucosal immune response are hallmarks of numerous intestinal functional and inflammatory diseases, including inflammatory bowel disease (IBD), coeliac disease, irritable bowel syndrome (IBS), and obesity. These conditions impact the normal epithelial functions of the intestine, such as absorption, barrier function, secretion, and host-microbiome communication. They are accompanied by characteristic intestinal symptoms and have significant societal, economic, and healthcare burdens. To develop new treatment options, cutting-edge research is required to investigate their etiology and pathology. Human intestinal organoids derived from patient tissue recapitulate the key physiological and immunopathological aspects of these conditions, providing a promising platform for elucidating disease mechanisms. This review will summarize recent reports on patient-derived human small intestinal and colonic organoids and highlight how these models have been used to study intestinal epithelial functions in the context of inflammation, altered physiology, and immune response. Furthermore, it will elaborate on the various organoid systems in use and the techniques/assays currently available to study epithelial functions. Finally, it will conclude by discussing the limitations and future perspectives of organoid technology.
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Affiliation(s)
- Peter Flood
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Naomi Hanrahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Medicine, School of Medicine, University College Cork, Cork, Ireland
- Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ken Nally
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Silvia Melgar
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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17
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Sturchio A, Rocha EM, Kauffman MA, Marsili L, Mahajan A, Saraf AA, Vizcarra JA, Guo Z, Espay AJ. Recalibrating the Why and Whom of Animal Models in Parkinson Disease: A Clinician's Perspective. Brain Sci 2024; 14:151. [PMID: 38391726 PMCID: PMC10887152 DOI: 10.3390/brainsci14020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/15/2024] [Accepted: 01/20/2024] [Indexed: 02/24/2024] Open
Abstract
Animal models have been used to gain pathophysiologic insights into Parkinson's disease (PD) and aid in the translational efforts of interventions with therapeutic potential in human clinical trials. However, no disease-modifying therapy for PD has successfully emerged from model predictions. These translational disappointments warrant a reappraisal of the types of preclinical questions asked of animal models. Besides the limitations of experimental designs, the one-size convergence and oversimplification yielded by a model cannot recapitulate the molecular diversity within and between PD patients. Here, we compare the strengths and pitfalls of different models, review the discrepancies between animal and human data on similar pathologic and molecular mechanisms, assess the potential of organoids as novel modeling tools, and evaluate the types of questions for which models can guide and misguide. We propose that animal models may be of greatest utility in the evaluation of molecular mechanisms, neural pathways, drug toxicity, and safety but can be unreliable or misleading when used to generate pathophysiologic hypotheses or predict therapeutic efficacy for compounds with potential neuroprotective effects in humans. To enhance the translational disease-modification potential, the modeling must reflect the biology not of a diseased population but of subtypes of diseased humans to distinguish What data are relevant and to Whom.
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Affiliation(s)
- Andrea Sturchio
- James J. and Joan A. Gardner Family Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH 45219, USA
| | - Emily M Rocha
- Pittsburgh Institute for Neurodegenerative Diseases, Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Marcelo A Kauffman
- Consultorio y Laboratorio de Neurogenética, Centro Universitario de Neurología José María Ramos Mejía, Buenos Aires C1221ADC, Argentina
| | - Luca Marsili
- James J. and Joan A. Gardner Family Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH 45219, USA
| | - Abhimanyu Mahajan
- James J. and Joan A. Gardner Family Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH 45219, USA
| | - Ameya A Saraf
- James J. and Joan A. Gardner Family Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH 45219, USA
| | - Joaquin A Vizcarra
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 15213, USA
| | - Ziyuan Guo
- Center for Stem Cell and Organoid Medicine (CuSTOM), Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Alberto J Espay
- James J. and Joan A. Gardner Family Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH 45219, USA
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18
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Spisak S, Chen D, Likasitwatanakul P, Doan P, Li Z, Bala P, Vizkeleti L, Tisza V, De Silva P, Giannakis M, Wolpin B, Qi J, Sethi NS. Utilizing a dual endogenous reporter system to identify functional regulators of aberrant stem cell and differentiation activity in colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.21.545895. [PMID: 38293113 PMCID: PMC10827082 DOI: 10.1101/2023.06.21.545895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators that regulate these key cellular programs in CRC, we developed an endogenous reporter system by genome-editing human CRC cell lines with knock-in fluorescent reporters at the SOX9 and KRT20 locus to report aberrant stem cell-like activity and differentiation, respectively, and then performed pooled genetic perturbation screens. Constructing a dual reporter system that simultaneously monitored aberrant stem cell-like and differentiation activity in the same CRC cell line improved our signal to noise discrimination. Using a focused-library CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs, we identified factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominated SMARCB1 of the BAF complex (also known as SWI/SNF) as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency in CRC and required for in vivo growth of human CRC models. These studies highlight the utility of a biologically designed endogenous reporter system to uncover novel therapeutic targets for drug development.
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Affiliation(s)
- Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - David Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Pornlada Likasitwatanakul
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Bangkok, Thailand
| | - Paul Doan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Zhixin Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Pratyusha Bala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Laura Vizkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary
| | - Viktoria Tisza
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Pushpamail De Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nilay S. Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
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19
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Chai B, Efstathiou C, Yue H, Draviam VM. Opportunities and challenges for deep learning in cell dynamics research. Trends Cell Biol 2023:S0962-8924(23)00228-3. [PMID: 38030542 DOI: 10.1016/j.tcb.2023.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
The growth of artificial intelligence (AI) has led to an increase in the adoption of computer vision and deep learning (DL) techniques for the evaluation of microscopy images and movies. This adoption has not only addressed hurdles in quantitative analysis of dynamic cell biological processes but has also started to support advances in drug development, precision medicine, and genome-phenome mapping. We survey existing AI-based techniques and tools, as well as open-source datasets, with a specific focus on the computational tasks of segmentation, classification, and tracking of cellular and subcellular structures and dynamics. We summarise long-standing challenges in microscopy video analysis from a computational perspective and review emerging research frontiers and innovative applications for DL-guided automation in cell dynamics research.
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Affiliation(s)
- Binghao Chai
- School of Biological and Behavioural Sciences, Queen Mary University of London (QMUL), London E1 4NS, UK
| | - Christoforos Efstathiou
- School of Biological and Behavioural Sciences, Queen Mary University of London (QMUL), London E1 4NS, UK
| | - Haoran Yue
- School of Biological and Behavioural Sciences, Queen Mary University of London (QMUL), London E1 4NS, UK
| | - Viji M Draviam
- School of Biological and Behavioural Sciences, Queen Mary University of London (QMUL), London E1 4NS, UK; The Alan Turing Institute, London NW1 2DB, UK.
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20
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Bteich F, Mohammadi M, Li T, Bhat MA, Sofianidi A, Wei N, Kuang C. Targeting KRAS in Colorectal Cancer: A Bench to Bedside Review. Int J Mol Sci 2023; 24:12030. [PMID: 37569406 PMCID: PMC10418782 DOI: 10.3390/ijms241512030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/13/2023] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease with a myriad of alterations at the cellular and molecular levels. Kristen rat sarcoma (KRAS) mutations occur in up to 40% of CRCs and serve as both a prognostic and predictive biomarker. Oncogenic mutations in the KRAS protein affect cellular proliferation and survival, leading to tumorigenesis through RAS/MAPK pathways. Until recently, only indirect targeting of the pathway had been investigated. There are now several KRAS allele-specific inhibitors in late-phase clinical trials, and many newer agents and targeting strategies undergoing preclinical and early-phase clinical testing. The adequate treatment of KRAS-mutated CRC will inevitably involve combination therapies due to the existence of robust adaptive resistance mechanisms in these tumors. In this article, we review the most recent understanding and findings related to targeting KRAS mutations in CRC, mechanisms of resistance to KRAS inhibitors, as well as evolving treatment strategies for KRAS-mutated CRC patients.
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Affiliation(s)
- Fernand Bteich
- Department of Medical Oncology, Montefiore Medical Center, Bronx, NY 10467, USA;
- Department of Medical Oncology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (M.M.); (T.L.); (M.A.B.); (N.W.)
| | - Mahshid Mohammadi
- Department of Medical Oncology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (M.M.); (T.L.); (M.A.B.); (N.W.)
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Terence Li
- Department of Medical Oncology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (M.M.); (T.L.); (M.A.B.); (N.W.)
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Muzaffer Ahmed Bhat
- Department of Medical Oncology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (M.M.); (T.L.); (M.A.B.); (N.W.)
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Amalia Sofianidi
- Oncology Unit, Third Department of Internal Medicine, Sotiria General Hospital for Chest Diseases, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Ning Wei
- Department of Medical Oncology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (M.M.); (T.L.); (M.A.B.); (N.W.)
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Chaoyuan Kuang
- Department of Medical Oncology, Montefiore Medical Center, Bronx, NY 10467, USA;
- Department of Medical Oncology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (M.M.); (T.L.); (M.A.B.); (N.W.)
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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