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Khorshid Sokhangouy S, Alizadeh F, Lotfi M, Sharif S, Ashouri A, Yoosefi Y, Bozorg Qomi S, Abbaszadegan MR. Recent advances in CRISPR-Cas systems for colorectal cancer research and therapeutics. Expert Rev Mol Diagn 2024:1-26. [PMID: 39132997 DOI: 10.1080/14737159.2024.2388777] [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: 12/20/2023] [Accepted: 07/28/2024] [Indexed: 08/13/2024]
Abstract
INTRODUCTION Colon cancer, ranked as the fourth leading global cause of cancer death, exhibits a complex progression marked by genetic variations. Over the past decade, the utilization of diverse CRISPR systems has propelled accelerated research into colorectal cancer (CRC) treatment. AREAS COVERED CRISPR/Cas9, a key player in this research, identifies new oncogenes, tumor suppressor genes (TSGs), and drug-resistance genes. Additionally, it facilitates the construction of experimental models, conducts genome-wide library screening, and develops new therapeutic targets, especially for targeted knockout in vivo or molecular targeted drug delivery, contributing to personalized treatments and significantly enhancing the care of colon cancer patients. In this review, we provide insights into the mechanism of the CRISPR/Cas9 system, offering a comprehensive exploration of its applications in CRC, spanning screening, modeling, gene functions, diagnosis, and gene therapy. While acknowledging its transformative potential, the article highlights the challenges and limitations of CRISPR systems. EXPERT OPINION The application of CRISPR/Cas9 in CRC research provides a promising avenue for personalized treatments. Its potential for identifying key genes and enabling experimental models and genome-wide screening enhances patient care. This review underscores the significance of CRISPR-Cas9 gene editing technology across basic research, diagnosis, and the treatment landscape of colon cancer.
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Affiliation(s)
| | - Farzaneh Alizadeh
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Malihe Lotfi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Sharif
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atefeh Ashouri
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yasamin Yoosefi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeed Bozorg Qomi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Abbaszadegan
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Coan M, Haefliger S, Ounzain S, Johnson R. Targeting and engineering long non-coding RNAs for cancer therapy. Nat Rev Genet 2024; 25:578-595. [PMID: 38424237 DOI: 10.1038/s41576-024-00693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
RNA therapeutics (RNATx) aim to treat diseases, including cancer, by targeting or employing RNA molecules for therapeutic purposes. Amongst the most promising targets are long non-coding RNAs (lncRNAs), which regulate oncogenic molecular networks in a cell type-restricted manner. lncRNAs are distinct from protein-coding genes in important ways that increase their therapeutic potential yet also present hurdles to conventional clinical development. Advances in genome editing, oligonucleotide chemistry, multi-omics and RNA engineering are paving the way for efficient and cost-effective lncRNA-focused drug discovery pipelines. In this Review, we present the emerging field of lncRNA therapeutics for oncology, with emphasis on the unique strengths and challenges of lncRNAs within the broader RNATx framework. We outline the necessary steps for lncRNA therapeutics to deliver effective, durable, tolerable and personalized treatments for cancer.
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Affiliation(s)
- Michela Coan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Simon Haefliger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland.
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland.
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3
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van der Graaff D, Seghers S, Vanclooster P, Deben C, Vandamme T, Prenen H. Advancements in Research and Treatment Applications of Patient-Derived Tumor Organoids in Colorectal Cancer. Cancers (Basel) 2024; 16:2671. [PMID: 39123399 PMCID: PMC11311786 DOI: 10.3390/cancers16152671] [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: 07/05/2024] [Revised: 07/20/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Colorectal cancer (CRC) remains a significant health burden globally, being the second leading cause of cancer-related mortality. Despite significant therapeutic advancements, resistance to systemic antineoplastic agents remains an important obstacle, highlighting the need for innovative screening tools to tailor patient-specific treatment. This review explores the application of patient-derived tumor organoids (PDTOs), three-dimensional, self-organizing models derived from patient tumor samples, as screening tools for drug resistance in CRC. PDTOs offer unique advantages over traditional models by recapitulating the tumor architecture, cellular heterogeneity, and genomic landscape and are a valuable ex vivo predictive drug screening tool. This review provides an overview of the current literature surrounding the use of PDTOs as an instrument for predicting therapy responses in CRC. We also explore more complex models, such as co-cultures with important stromal cells, such as cancer-associated fibroblasts, and organ-on-a-chip models. Furthermore, we discuss the use of PDTOs for drug repurposing, offering a new approach to identify the existing drugs effective against drug-resistant CRC. Additionally, we explore how PDTOs serve as models to gain insights into drug resistance mechanisms, using newer techniques, such as single-cell RNA sequencing and CRISPR-Cas9 genome editing. Through this review, we aim to highlight the potential of PDTOs in advancing our understanding of predicting therapy responses, drug resistance, and biomarker identification in CRC management.
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Affiliation(s)
| | - Sofie Seghers
- Department of Medical Oncology, University Hospital Antwerp, 2650 Edegem, Belgium
- Center for Oncological Research (CORE), University of Antwerp, 2610 Wilrijk, Belgium
| | | | - Christophe Deben
- Center for Oncological Research (CORE), University of Antwerp, 2610 Wilrijk, Belgium
| | - Timon Vandamme
- Department of Medical Oncology, University Hospital Antwerp, 2650 Edegem, Belgium
- Center for Oncological Research (CORE), University of Antwerp, 2610 Wilrijk, Belgium
| | - Hans Prenen
- Department of Medical Oncology, University Hospital Antwerp, 2650 Edegem, Belgium
- Center for Oncological Research (CORE), University of Antwerp, 2610 Wilrijk, Belgium
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4
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Wan X, Liu Y, Peng Y, Wang J, Yan SM, Zhang L, Wu W, Zhao L, Chen X, Ren K, Long H, Luo Y, Yan Q, Zhang L, Lei D, Liu P, Li S, Liu L, Guo L, Du J, Zhang M, Dai S, Yang Y, Liu H, Chen N, Bei J, Feng L, Liu Y, Zeng MS, Chen C, Zhong Q. Primary and Orthotopic Murine Models of Nasopharyngeal Carcinoma Reveal Molecular Mechanisms Underlying its Malignant Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403161. [PMID: 39049720 DOI: 10.1002/advs.202403161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/07/2024] [Indexed: 07/27/2024]
Abstract
Nasopharyngeal carcinoma (NPC), a squamous cell carcinoma originating in the nasopharynx, is a leading malignancy in south China and other south and east Asia areas. It is frequently associated with Epstein-Barr virus (EBV) infection, while there are also some NPC patients without EBV infection. Here, it is shown that the EBV+ (EBV positive) and EBV- (EBV negative) NPCs contain both shared and distinct genetic abnormalities, among the latter are increased mutations in TP53. To investigate the functional roles of NPC-associated genetic alterations, primary, orthotopic, and genetically defined NPC models were developed in mice, a key tool missed in the field. These models, initiated with gene-edited organoids of normal nasopharyngeal epithelium, faithfully recapitulated the pathological features of human disease. With these models, it is found that Trp53 and Cdkn2a deficiency are crucial for NPC initiation and progression. And latent membrane protein1 (LMP1), an EBV-coding oncoprotein, significantly promoted the distal metastasis. Further, loss of TGFBR2, which is frequently disrupted both in EBV- and EBV+ NPCs, dramatically accelerated the progression and lung metastasis of NPC probably by altering tumor microenvironment. Taken together, this work establishes a platform to dissect the genetic mechanisms underlying NPC pathogenesis and might be of value for future translational studies.
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Affiliation(s)
- Xudong Wan
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yuantao Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, 510060, China
| | - Yiman Peng
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jian Wang
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Shu-Mei Yan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, 510060, China
| | - Lu Zhang
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Wanchun Wu
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lei Zhao
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xuelan Chen
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kexin Ren
- Department of Otolaryngology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Haicheng Long
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yiling Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, 510060, China
| | - Qin Yan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, 510060, China
| | - Lele Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, 510060, China
| | - Dengzhi Lei
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Pengpeng Liu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Shujun Li
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lihui Liu
- Department of Otolaryngology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Linjie Guo
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jiajia Du
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Mengsha Zhang
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Siqi Dai
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yi Yang
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Hongyu Liu
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nianyong Chen
- Department of Otolaryngology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jinxin Bei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, 510060, China
| | - Lin Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, 510060, China
| | - Yu Liu
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, 510060, China
| | - Chong Chen
- Division of Thoracic Tumor Multimodality Treatment, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, Sichuan, 610212, China
| | - Qian Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, 510060, China
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5
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Kim TW, Koo SY, Riessland M, Chaudhry F, Kolisnyk B, Cho HS, Russo MV, Saurat N, Mehta S, Garippa R, Betel D, Studer L. TNF-NF-κB-p53 axis restricts in vivo survival of hPSC-derived dopamine neurons. Cell 2024; 187:3671-3689.e23. [PMID: 38866017 DOI: 10.1016/j.cell.2024.05.030] [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: 11/20/2022] [Revised: 12/15/2023] [Accepted: 05/16/2024] [Indexed: 06/14/2024]
Abstract
Ongoing, early-stage clinical trials illustrate the translational potential of human pluripotent stem cell (hPSC)-based cell therapies in Parkinson's disease (PD). However, an unresolved challenge is the extensive cell death following transplantation. Here, we performed a pooled CRISPR-Cas9 screen to enhance postmitotic dopamine neuron survival in vivo. We identified p53-mediated apoptotic cell death as a major contributor to dopamine neuron loss and uncovered a causal link of tumor necrosis factor alpha (TNF-α)-nuclear factor κB (NF-κB) signaling in limiting cell survival. As a translationally relevant strategy to purify postmitotic dopamine neurons, we identified cell surface markers that enable purification without the need for genetic reporters. Combining cell sorting and treatment with adalimumab, a clinically approved TNF-α inhibitor, enabled efficient engraftment of postmitotic dopamine neurons with extensive reinnervation and functional recovery in a preclinical PD mouse model. Thus, transient TNF-α inhibition presents a clinically relevant strategy to enhance survival and enable engraftment of postmitotic hPSC-derived dopamine neurons in PD.
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Affiliation(s)
- Tae Wan Kim
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Department of Interdisciplinary Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - So Yeon Koo
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Weill Cornell Neuroscience PhD Program, New York, NY, USA
| | - Markus Riessland
- Department of Neurobiology and Behavior, Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY 11794, USA
| | - Fayzan Chaudhry
- Tri-Institutional PhD program in Computational Biology, New York, NY, USA
| | - Benjamin Kolisnyk
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Hyein S Cho
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Marco Vincenzo Russo
- Gene Editing and Screening Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Nathalie Saurat
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Sanjoy Mehta
- Gene Editing and Screening Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ralph Garippa
- Gene Editing and Screening Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Doron Betel
- Division of Hematology & Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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Dang Q, Zuo L, Hu X, Zhou Z, Chen S, Liu S, Ba Y, Zuo A, Xu H, Weng S, Zhang Y, Luo P, Cheng Q, Liu Z, Han X. Molecular subtypes of colorectal cancer in the era of precision oncotherapy: Current inspirations and future challenges. Cancer Med 2024; 13:e70041. [PMID: 39054866 PMCID: PMC11272957 DOI: 10.1002/cam4.70041] [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: 03/29/2024] [Revised: 07/07/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is among the most hackneyed malignancies. Even patients with identical clinical symptoms and the same TNM stage still exhibit radically different clinical outcomes after receiving equivalent treatment regimens, indicating extensive heterogeneity of CRC. Myriad molecular subtypes of CRC have been exploited for decades, including the most compelling consensus molecular subtype (CMS) classification that has been broadly applied for patient stratification and biomarker-drug combination formulation. Encountering barriers to clinical translation, however, CMS classification fails to fully reflect inter- or intra-tumor heterogeneity of CRC. As a consequence, addressing heterogeneity and precisely managing CRC patients with unique characteristics remain arduous tasks for clinicians. REVIEW In this review, we systematically summarize molecular subtypes of CRC and further elaborate on their clinical applications, limitations, and future orientations. CONCLUSION In recent years, exploration of subtypes through cell lines, animal models, patient-derived xenografts (PDXs), organoids, and clinical trials contributes to refining biological insights and unraveling subtype-specific therapies in CRC. Therapeutic interventions including nanotechnology, clustered regulatory interspaced short palindromic repeat/CRISPR-associated nuclease 9 (CRISPR/Cas9), gut microbiome, and liquid biopsy are powerful tools with the possibility to shift the immunologic landscape and outlook for CRC precise medicine.
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Affiliation(s)
- Qin Dang
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
- Department of Colorectal SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Lulu Zuo
- Center for Reproductive MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Xinru Hu
- Department of Cardiology, West China HospitalSichuan UniversityChengduSichuanChina
| | - Zhaokai Zhou
- Department of UrologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Shuang Chen
- Center for Reproductive MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Shutong Liu
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Yuhao Ba
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Anning Zuo
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Hui Xu
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Siyuan Weng
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Yuyuan Zhang
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Peng Luo
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Quan Cheng
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Zaoqu Liu
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
- Interventional Treatment and Clinical Research Center of Henan ProvinceZhengzhouHenanChina
- Interventional Institute of Zhengzhou UniversityZhengzhouHenanChina
- Institute of Basic Medical SciencesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xinwei Han
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
- Interventional Treatment and Clinical Research Center of Henan ProvinceZhengzhouHenanChina
- Interventional Institute of Zhengzhou UniversityZhengzhouHenanChina
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7
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Xiao QX, Geng MJ, Sun YF, Pi Y, Xiong LL. Stem Cell Therapy in Neonatal Hypoxic-Ischemic Encephalopathy and Cerebral Palsy: a Bibliometric Analysis and New Strategy. Mol Neurobiol 2024; 61:4538-4564. [PMID: 38102517 DOI: 10.1007/s12035-023-03848-0] [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: 08/07/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
The aim of this study was to identify related scientific outputs and emerging topics of stem cells in neonatal hypoxic-ischemic encephalopathy (NHIE) and cerebral palsy (CP) through bibliometrics and literature review. All relevant publications on stem cell therapy for NHIE and CP were screened from websites and analyzed research trends. VOSviewer and CiteSpace were applied to visualize and quantitatively analyze the published literature to provide objective presentation and prediction. In addition, the clinical trials, published articles, and projects of the National Natural Science Foundation of China associated with stem cell therapy for NHIE and CP were summarized. A total of 294 publications were associated with stem cell therapy for NHIE and CP. Most publications and citations came from the USA and China. Monash University and University Medical Center Utrecht produced the most publications. Pediatric research published the most studies on stem cell therapy for NHIE and CP. Heijnen C and Kavelaars A published the most articles. Cluster analyses show that current research trend is more inclined toward the repair mechanism and clinical translation of stem cell therapy for NHIE and CP. By summarizing various studies of stem cells in NHIE and CP, it is indicated that this research direction is a hot topic at present. Furthermore, organoid transplantation, as an emerging and new therapeutic approach, brings new hope for the treatment of NHIE and CP. This study comprehensively summarized and analyzed the research trend of global stem cell therapy for NHIE and CP. It has shown a marked increase in stem cell therapy for NHIE and CP research. In the future, more efforts will be made on exploring stem cell or organoid therapy for NHIE and CP and more valuable related mechanisms of action to achieve clinical translation as soon as possible.
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Affiliation(s)
- Qiu-Xia Xiao
- Department of Anesthesiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Min-Jian Geng
- Department of Anesthesiology, Nanchong Central Hospital, Nanchong, 637000, Sichuan, China
| | - Yi-Fei Sun
- Institute of Neurological Disease, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yu Pi
- Department of Anesthesiology, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Liu-Lin Xiong
- Department of Anesthesiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China.
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Tardito S, Matis S, Zocchi MR, Benelli R, Poggi A. Epidermal Growth Factor Receptor Targeting in Colorectal Carcinoma: Antibodies and Patient-Derived Organoids as a Smart Model to Study Therapy Resistance. Int J Mol Sci 2024; 25:7131. [PMID: 39000238 PMCID: PMC11241078 DOI: 10.3390/ijms25137131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer-related death worldwide. Therefore, the need for new therapeutic strategies is still a challenge. Surgery and chemotherapy represent the first-line interventions; nevertheless, the prognosis for metastatic CRC (mCRC) patients remains unacceptable. An important step towards targeted therapy came from the inhibition of the epidermal growth factor receptor (EGFR) pathway, by the anti-EGFR antibody, Cetuximab, or by specific tyrosine kinase inhibitors (TKI). Cetuximab, a mouse-human chimeric monoclonal antibody (mAb), binds to the extracellular domain of EGFR thus impairing EGFR-mediated signaling and reducing cell proliferation. TKI can affect the EGFR biochemical pathway at different steps along the signaling cascade. Apart from Cetuximab, other anti-EGFR mAbs have been developed, such as Panitumumab. Both antibodies have been approved for the treatment of KRAS-NRAS wild type mCRC, alone or in combination with chemotherapy. These antibodies display strong differences in activating the host immune system against CRC, due to their different immunoglobulin isotypes. Although anti-EGFR antibodies are efficient, drug resistance occurs with high frequency. Resistant tumor cell populations can either already be present before therapy or develop later by biochemical adaptations or new genomic mutations in the EGFR pathway. Numerous efforts have been made to improve the efficacy of the anti-EGFR mAbs or to find new agents that are able to block downstream EGFR signaling cascade molecules. Indeed, we examined the importance of analyzing the anti-EGFR antibody-drug conjugates (ADC) developed to overcome resistance and/or stimulate the tumor host's immunity against CRC growth. Also, patient-derived CRC organoid cultures represent a useful and feasible in vitro model to study tumor behavior and therapy response. Organoids can reflect tumor genetic heterogeneity found in the tissue of origin, representing a unique tool for personalized medicine. Thus, CRC-derived organoid cultures are a smart model for studying the tumor microenvironment and for the preclinical assay of anti-EGFR drugs.
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Affiliation(s)
- Samuele Tardito
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC 20010, USA;
| | - Serena Matis
- Molecular Oncology and Angiogenesis Unit, IRRCS Ospedale Policlinico San Martino, 16132 Genoa, Italy;
| | - Maria Raffaella Zocchi
- Department of Immunology, Transplant and Infectious Diseases, IRCCS Scientific Institute San Raffaele, 20132 Milan, Italy;
| | - Roberto Benelli
- Molecular Oncology and Angiogenesis Unit, IRRCS Ospedale Policlinico San Martino, 16132 Genoa, Italy;
| | - Alessandro Poggi
- Molecular Oncology and Angiogenesis Unit, IRRCS Ospedale Policlinico San Martino, 16132 Genoa, Italy;
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9
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S. V. S, Augustine D, Mushtaq S, Baeshen HA, Ashi H, Hassan RN, Alshahrani M, Patil S. Revitalizing oral cancer research: Crispr-Cas9 technology the promise of genetic editing. Front Oncol 2024; 14:1383062. [PMID: 38915370 PMCID: PMC11194394 DOI: 10.3389/fonc.2024.1383062] [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: 02/06/2024] [Accepted: 05/08/2024] [Indexed: 06/26/2024] Open
Abstract
This review presents an in-depth analysis of the immense potential of CRISPR-Cas9 technology in revolutionizing oral cancer research. It underscores the inherent limitations of conventional treatments while emphasizing the pressing need for groundbreaking approaches. The unparalleled capability of CRISPR-Cas9 to precisely target and modify specific genes involved in cancer progression heralds a new era in therapeutic intervention. Employing genome-wide CRISPR screens, vulnerabilities in oral cancer cells can be identified, thereby unravelling promising targets for therapeutic interventions. In the realm of oral cancer, the disruptive power of CRISPR-Cas9 manifests through its capacity to perturb genes that are intricately associated with drug resistance, consequently augmenting the efficacy of chemotherapy. To address the challenges that arise, this review diligently examines pertinent issues such as off-target effects, efficient delivery mechanisms, and the ethical considerations surrounding germline editing. Through precise gene editing, facilitated by CRISPR/Cas9, it becomes possible to overcome drug resistance by rectifying mutations, thereby enhancing the efficacy of personalized treatment strategies. This review delves into the prospects of CRISPR-Cas9, illuminating its potential applications in the domains of medicine, agriculture, and biotechnology. It is paramount to emphasize the necessity of ongoing research endeavors and the imperative to develop targeted therapies tailored specifically for oral cancer. By embracing this comprehensive overview, we can pave the way for ground-breaking treatments that instill renewed hope for enhanced outcomes in individuals afflicted by oral cancer.
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Affiliation(s)
- Sowmya S. V.
- Department of Oral Pathology and Microbiology, Faculty of Dental Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Dominic Augustine
- Department of Oral Pathology and Microbiology, Faculty of Dental Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Shazia Mushtaq
- College of Applied Medical Sciences, Dental Health Department, King Saud University, Riyadh, Saudi Arabia
| | - Hosam Ali Baeshen
- Department of Orthodontics, Faculty of Dentistry, King Abdulziz University, Jeddah, Saudi Arabia
| | - Heba Ashi
- Department of Dental Public Health, Faculty of Dentistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem Nabil Hassan
- Biological Sciences Department (Genome), Faculty of Sciences, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Mohammed Alshahrani
- Endodontic Department, Faculty of Dentistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UT, United States
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10
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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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11
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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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12
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Tang Q, Ratnayake R, Seabra G, Jiang Z, Fang R, Cui L, Ding Y, Kahveci T, Bian J, Li C, Luesch H, Li Y. Morphological profiling for drug discovery in the era of deep learning. Brief Bioinform 2024; 25:bbae284. [PMID: 38886164 PMCID: PMC11182685 DOI: 10.1093/bib/bbae284] [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: 03/09/2024] [Revised: 05/13/2024] [Accepted: 06/03/2024] [Indexed: 06/20/2024] Open
Abstract
Morphological profiling is a valuable tool in phenotypic drug discovery. The advent of high-throughput automated imaging has enabled the capturing of a wide range of morphological features of cells or organisms in response to perturbations at the single-cell resolution. Concurrently, significant advances in machine learning and deep learning, especially in computer vision, have led to substantial improvements in analyzing large-scale high-content images at high throughput. These efforts have facilitated understanding of compound mechanism of action, drug repurposing, characterization of cell morphodynamics under perturbation, and ultimately contributing to the development of novel therapeutics. In this review, we provide a comprehensive overview of the recent advances in the field of morphological profiling. We summarize the image profiling analysis workflow, survey a broad spectrum of analysis strategies encompassing feature engineering- and deep learning-based approaches, and introduce publicly available benchmark datasets. We place a particular emphasis on the application of deep learning in this pipeline, covering cell segmentation, image representation learning, and multimodal learning. Additionally, we illuminate the application of morphological profiling in phenotypic drug discovery and highlight potential challenges and opportunities in this field.
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Affiliation(s)
- Qiaosi Tang
- Calico Life Sciences, South San Francisco, CA 94080, United States
| | - Ranjala Ratnayake
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, United States
| | - Gustavo Seabra
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, United States
| | - Zhe Jiang
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, United States
| | - Ruogu Fang
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, United States
- J. Crayton Pruitt Family Department of Biomedical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL 32611, United States
| | - Lina Cui
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, United States
| | - Tamer Kahveci
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, United States
| | - Jiang Bian
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32611, United States
| | - Chenglong Li
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, United States
| | - Hendrik Luesch
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, United States
| | - Yanjun Li
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, United States
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, United States
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13
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Ciucci G, Braga L, Zacchigna S. Discovery platforms for RNA therapeutics. Br J Pharmacol 2024. [PMID: 38760893 DOI: 10.1111/bph.16424] [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: 11/29/2023] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 05/20/2024] Open
Abstract
RNA therapeutics are emerging as a unique opportunity to drug currently "undruggable" molecules and diseases. While their advantages over conventional, small molecule drugs, their therapeutic implications and the tools for their effective in vivo delivery have been extensively reviewed, little attention has been so far paid to the technological platforms exploited for the discovery of RNA therapeutics. Here, we provide an overview of the existing platforms and ex vivo assays for RNA discovery, their advantages and disadvantages, as well as their main fields of application, with specific focus on RNA therapies that have reached either phase 3 or market approval.
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Affiliation(s)
- Giulio Ciucci
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Luca Braga
- Functional Cell Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Serena Zacchigna
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
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14
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Osonoi S, Takebe T. Organoid-guided precision hepatology for metabolic liver disease. J Hepatol 2024; 80:805-821. [PMID: 38237864 DOI: 10.1016/j.jhep.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 03/09/2024]
Abstract
Metabolic dysfunction-associated steatotic liver disease affects millions of people worldwide. Progress towards a definitive cure has been incremental and treatment is currently limited to lifestyle modification. Hepatocyte-specific lipid accumulation is the main trigger of lipotoxic events, driving inflammation and fibrosis. The underlying pathology is extraordinarily heterogenous, and the manifestations of steatohepatitis are markedly influenced by metabolic communications across non-hepatic organs. Synthetic human tissue models have emerged as powerful platforms to better capture the mechanistic diversity in disease progression, while preserving person-specific genetic traits. In this review, we will outline current research efforts focused on integrating multiple synthetic tissue models of key metabolic organs, with an emphasis on organoid-based systems. By combining functional genomics and population-scale en masse profiling methodologies, human tissues derived from patients can provide insights into personalised genetic, transcriptional, biochemical, and metabolic states. These collective efforts will advance our understanding of steatohepatitis and guide the development of rational solutions for mechanism-directed diagnostic and therapeutic investigation.
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Affiliation(s)
- Sho Osonoi
- Center for Stem Cell and Organoid Medicine (CuSTOM), Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Endocrinology and Metabolism, Hirosaki University Graduate School of Medicine, Hirosaki, 036-8562, Japan
| | - Takanori Takebe
- Center for Stem Cell and Organoid Medicine (CuSTOM), Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; WPI Premium Institute for Human Metaverse Medicine (WPI-PRIMe) and Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan; Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; Communication Design Center, Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan.
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15
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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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16
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Martin D, Rödel F, Hehlgans S, Looso M, Ziegler PK, Fleischmann M, Diefenhardt M, Fries L, Kalinauskaite G, Tinhofer I, Zips D, Gani C, Rödel C, Fokas E. Inflammatory pathways confer resistance to chemoradiotherapy in anal squamous cell carcinoma. NPJ Precis Oncol 2024; 8:93. [PMID: 38653773 DOI: 10.1038/s41698-024-00585-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
Anal squamous cell carcinoma (ASCC) is associated with immunosuppression and infection with human papillomavirus (HPV). Response to standard chemoradiotherapy (CRT) varies considerably. A comprehensive molecular characterization of CRT resistance is lacking, and little is known about the interplay between tumor immune contexture, host immunity, and immunosuppressive and/or immune activating effects of CRT. Patients with localized ASCC, treated with CRT at three different sites of the German Cancer Consortium (DKTK) were included. Patient cohorts for molecular analysis included baseline formalin fixed paraffin embedded biopsies for immunohistochemistry (n = 130), baseline RNA sequencing (n = 98), peripheral blood immune profiling (n = 47), and serum cytokine measurement (n = 35). Gene set enrichment analysis showed that pathways for IFNγ, IFNα, inflammatory response, TNFα signaling via NF-κB, and EMT were significantly enriched in poor responders (all p < 0.001). Expression of interferon-induced transmembrane protein 1 (IFITM1), both on mRNA and protein levels, was associated with reduced Freedom from locoregional failure (FFLF, p = 0.037) and freedom from distant metastasis (FFDM, p = 0.014). An increase of PD-L1 expression on CD4+ T-cells (p < 0.001) and an increase in HLA-DR expression on T-cells (p < 0.001) was observed in the peripheral blood after CRT. Elevated levels of regulatory T-cells and CXCL2 were associated with reduced FFLF (p = 0.0044 and p = 0.004, respectively). Inflammatory pathways in tissue in line with elevated levels of regulatory T-cells and CXCL2 in peripheral blood are associated with resistance to CRT. To counteract this resistance mechanism, the RADIANCE randomized phase-2 trial currently tests the addition of the immune checkpoint inhibitor durvalumab to standard CRT in locally advanced ASCC.
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Affiliation(s)
- D Martin
- Department of Radiotherapy and Oncology, Goethe University Frankfurt, University Hospital, Frankfurt, Germany.
- German Cancer Consortium (DKTK), Partner Site Frankfurt, A Partnership between DKFZ and University Hospital Frankfurt, Frankfurt, Germany.
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, Germany.
| | - F Rödel
- Department of Radiotherapy and Oncology, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, A Partnership between DKFZ and University Hospital Frankfurt, Frankfurt, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, Germany
| | - S Hehlgans
- Department of Radiotherapy and Oncology, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - M Looso
- Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit, Bad Nauheim, Germany
| | - P K Ziegler
- German Cancer Consortium (DKTK), Partner Site Frankfurt, A Partnership between DKFZ and University Hospital Frankfurt, Frankfurt, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, Germany
- Dr. Senckenberg Institute of Pathology, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - M Fleischmann
- Department of Radiotherapy and Oncology, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, A Partnership between DKFZ and University Hospital Frankfurt, Frankfurt, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, Germany
| | - M Diefenhardt
- Department of Radiotherapy and Oncology, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, A Partnership between DKFZ and University Hospital Frankfurt, Frankfurt, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, Germany
| | - L Fries
- Department of Radiotherapy and Oncology, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - G Kalinauskaite
- Department of Radiooncology and Radiotherapy, Charité University Hospital Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, A Partnership between DKFZ and Charité University Hospital Berlin, Berlin, Germany
| | - I Tinhofer
- Department of Radiooncology and Radiotherapy, Charité University Hospital Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, A Partnership between DKFZ and Charité University Hospital Berlin, Berlin, Germany
| | - D Zips
- Department of Radiooncology and Radiotherapy, Charité University Hospital Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, A Partnership between DKFZ and Charité University Hospital Berlin, Berlin, Germany
| | - C Gani
- Eberhard Karls University, Tübingen, University Hospital Tübingen, Department of Radiation Oncology, Tübingen, Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen, A Partnership between DKFZ and University Hospital Tübingen, Tübingen, Germany
| | - C Rödel
- Department of Radiotherapy and Oncology, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, A Partnership between DKFZ and University Hospital Frankfurt, Frankfurt, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, Germany
| | - E Fokas
- Department of Radiotherapy and Oncology, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, A Partnership between DKFZ and University Hospital Frankfurt, Frankfurt, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, Germany
- Department of Radiation Oncology, Cyberknife and Radiotherapy, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
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17
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Chen X, Zhong S, Zhan Y, Zhang X. CRISPR-Cas9 applications in T cells and adoptive T cell therapies. Cell Mol Biol Lett 2024; 29:52. [PMID: 38609863 PMCID: PMC11010303 DOI: 10.1186/s11658-024-00561-1] [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: 12/04/2023] [Accepted: 03/15/2024] [Indexed: 04/14/2024] Open
Abstract
T cell immunity is central to contemporary cancer and autoimmune therapies, encompassing immune checkpoint blockade and adoptive T cell therapies. Their diverse characteristics can be reprogrammed by different immune challenges dependent on antigen stimulation levels, metabolic conditions, and the degree of inflammation. T cell-based therapeutic strategies are gaining widespread adoption in oncology and treating inflammatory conditions. Emerging researches reveal that clustered regularly interspaced palindromic repeats-associated protein 9 (CRISPR-Cas9) genome editing has enabled T cells to be more adaptable to specific microenvironments, opening the door to advanced T cell therapies in preclinical and clinical trials. CRISPR-Cas9 can edit both primary T cells and engineered T cells, including CAR-T and TCR-T, in vivo and in vitro to regulate T cell differentiation and activation states. This review first provides a comprehensive summary of the role of CRISPR-Cas9 in T cells and its applications in preclinical and clinical studies for T cell-based therapies. We also explore the application of CRISPR screen high-throughput technology in editing T cells and anticipate the current limitations of CRISPR-Cas9, including off-target effects and delivery challenges, and envisioned improvements in related technologies for disease screening, diagnosis, and treatment.
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Affiliation(s)
- Xiaoying Chen
- Department of Cardiology, Cardiovascular Institute of Zhengzhou University, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450003, China
| | - Shuhan Zhong
- Department of Hematology, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, 310003, China
| | - Yonghao Zhan
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450003, China.
| | - Xuepei Zhang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450003, China.
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18
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Zhang E, Sun Q, Zhang C, Ma H, Zhang J, Ding Y, Wang G, Jin C, Jin C, Fu Y, Yan C, Zhu M, Wang C, Dai J, Jin G, Hu Z, Shen H, Ma H. Comprehensive functional interrogation of susceptibility loci in GWASs identified KIAA0391 as a novel oncogenic driver via regulating pyroptosis in NSCLC. Cancer Lett 2024; 585:216646. [PMID: 38262497 DOI: 10.1016/j.canlet.2024.216646] [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: 09/13/2023] [Revised: 11/23/2023] [Accepted: 01/05/2024] [Indexed: 01/25/2024]
Abstract
Approximately 51 non-small-cell lung cancer (NSCLC) risk loci have been identified by genome-wide association studies (GWASs). We conducted a high throughput RNA-interference (RNAi) screening to identify the candidate causal genes in NSCLC risk loci. KIAA0391 at 14q13.1 had the highest score and could promote proliferation and metastasis of NSCLC in vitro and in vivo. We next prioritized rs3783313 as a causal variant at 14q13.1, by integrating a large-scale population study consisting of 27,120 lung cancer cases and 27,355 controls, functional annotation, and expression quantitative trait locus (eQTL) analysis. Then we found that rs3783313 could facilitate a promoter-enhancer interaction to upregulate KIAA0391 expression by affecting the affinity of transcription factor NFYA. Mechanistically, KIAA0391 knockdown dramatically influenced pyroptosis-related pathways and increased the expression of CASP1. And KIAA0391 transcriptionally repressed CASP1 by binding to SMAD2 and induced an anti-pyroptosis phenotype, promoting tumorigenesis of NSCLC, which provides new insights and potential target for NSCLC.
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Affiliation(s)
- Erbao Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Qi Sun
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Chang Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou Second People's Hospital, Changzhou Medical Center, Nanjing Medical University, Nanjing 211166, China
| | - Huimin Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Jing Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Yue Ding
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Guoqing Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Chen Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Chenying Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Yating Fu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Caiwang Yan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Cheng Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; Research Unit of Prospective Cohort of Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing 100142, China.
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; Research Unit of Prospective Cohort of Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing 100142, China.
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19
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Wilson EL, Yu Y, Leal NS, Woodward JA, Patikas N, Morris JL, Field SF, Plumbly W, Paupe V, Chowdhury SR, Antrobus R, Lindop GE, Adia YM, Loh SHY, Prudent J, Martins LM, Metzakopian E. Genome-wide CRISPR/Cas9 screen shows that loss of GET4 increases mitochondria-endoplasmic reticulum contact sites and is neuroprotective. Cell Death Dis 2024; 15:203. [PMID: 38467609 PMCID: PMC10928201 DOI: 10.1038/s41419-024-06568-y] [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: 06/26/2023] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024]
Abstract
Organelles form membrane contact sites between each other, allowing for the transfer of molecules and signals. Mitochondria-endoplasmic reticulum (ER) contact sites (MERCS) are cellular subdomains characterized by close apposition of mitochondria and ER membranes. They have been implicated in many diseases, including neurodegenerative, metabolic, and cardiac diseases. Although MERCS have been extensively studied, much remains to be explored. To uncover novel regulators of MERCS, we conducted a genome-wide, flow cytometry-based screen using an engineered MERCS reporter cell line. We found 410 genes whose downregulation promotes MERCS and 230 genes whose downregulation decreases MERCS. From these, 29 genes were selected from each population for arrayed screening and 25 were validated from the high population and 13 from the low population. GET4 and BAG6 were highlighted as the top 2 genes that upon suppression increased MERCS from both the pooled and arrayed screens, and these were subjected to further investigation. Multiple microscopy analyses confirmed that loss of GET4 or BAG6 increased MERCS. GET4 and BAG6 were also observed to interact with the known MERCS proteins, inositol 1,4,5-trisphosphate receptors (IP3R) and glucose-regulated protein 75 (GRP75). In addition, we found that loss of GET4 increased mitochondrial calcium uptake upon ER-Ca2+ release and mitochondrial respiration. Finally, we show that loss of GET4 rescues motor ability, improves lifespan and prevents neurodegeneration in a Drosophila model of Alzheimer's disease (Aβ42Arc). Together, these results suggest that GET4 is involved in decreasing MERCS and that its loss is neuroprotective.
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Affiliation(s)
- Emma L Wilson
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Yizhou Yu
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Nuno S Leal
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - James A Woodward
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Nikolaos Patikas
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK
| | - Jordan L Morris
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Sarah F Field
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK
| | - William Plumbly
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK
| | - Vincent Paupe
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Suvagata R Chowdhury
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Rd, Cambridge, CB2 0XY, UK
| | - Georgina E Lindop
- Cambridge Advanced Imaging Centre, University of Cambridge, Anatomy Building, Downing Site, Cambridge, CB2 3DY, UK
| | - Yusuf M Adia
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Samantha H Y Loh
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Julien Prudent
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK.
| | - L Miguel Martins
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK.
| | - Emmanouil Metzakopian
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK.
- bit bio, The Dorothy Hodgkin Building, Babraham Research Campus, Cambridge, CB22 3FH, UK.
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20
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Jose A, Kulkarni P, Thilakan J, Munisamy M, Malhotra AG, Singh J, Kumar A, Rangnekar VM, Arya N, Rao M. Integration of pan-omics technologies and three-dimensional in vitro tumor models: an approach toward drug discovery and precision medicine. Mol Cancer 2024; 23:50. [PMID: 38461268 PMCID: PMC10924370 DOI: 10.1186/s12943-023-01916-6] [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: 08/05/2023] [Accepted: 12/15/2023] [Indexed: 03/11/2024] Open
Abstract
Despite advancements in treatment protocols, cancer is one of the leading cause of deaths worldwide. Therefore, there is a need to identify newer and personalized therapeutic targets along with screening technologies to combat cancer. With the advent of pan-omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, and lipidomics, the scientific community has witnessed an improved molecular and metabolomic understanding of various diseases, including cancer. In addition, three-dimensional (3-D) disease models have been efficiently utilized for understanding disease pathophysiology and as screening tools in drug discovery. An integrated approach utilizing pan-omics technologies and 3-D in vitro tumor models has led to improved understanding of the intricate network encompassing various signalling pathways and molecular cross-talk in solid tumors. In the present review, we underscore the current trends in omics technologies and highlight their role in understanding genotypic-phenotypic co-relation in cancer with respect to 3-D in vitro tumor models. We further discuss the challenges associated with omics technologies and provide our outlook on the future applications of these technologies in drug discovery and precision medicine for improved management of cancer.
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Affiliation(s)
- Anmi Jose
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Pallavi Kulkarni
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Jaya Thilakan
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Murali Munisamy
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Anvita Gupta Malhotra
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Jitendra Singh
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Ashok Kumar
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Vivek M Rangnekar
- Markey Cancer Center and Department of Radiation Medicine, University of Kentucky, Lexington, KY, 40536, USA
| | - Neha Arya
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India.
| | - Mahadev Rao
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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21
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Qu S, Xu R, Yi G, Li Z, Zhang H, Qi S, Huang G. Patient-derived organoids in human cancer: a platform for fundamental research and precision medicine. MOLECULAR BIOMEDICINE 2024; 5:6. [PMID: 38342791 PMCID: PMC10859360 DOI: 10.1186/s43556-023-00165-9] [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: 05/13/2023] [Accepted: 12/08/2023] [Indexed: 02/13/2024] Open
Abstract
Cancer is associated with a high degree of heterogeneity, encompassing both inter- and intra-tumor heterogeneity, along with considerable variability in clinical response to common treatments across patients. Conventional models for tumor research, such as in vitro cell cultures and in vivo animal models, demonstrate significant limitations that fall short of satisfying the research requisites. Patient-derived tumor organoids, which recapitulate the structures, specific functions, molecular characteristics, genomics alterations and expression profiles of primary tumors. They have been efficaciously implemented in illness portrayal, mechanism exploration, high-throughput drug screening and assessment, discovery of innovative therapeutic targets and potential compounds, and customized treatment regimen for cancer patients. In contrast to conventional models, tumor organoids offer an intuitive, dependable, and efficient in vitro research model by conserving the phenotypic, genetic diversity, and mutational attributes of the originating tumor. Nevertheless, the organoid technology also confronts the bottlenecks and challenges, such as how to comprehensively reflect intra-tumor heterogeneity, tumor microenvironment, tumor angiogenesis, reduce research costs, and establish standardized construction processes while retaining reliability. This review extensively examines the use of tumor organoid techniques in fundamental research and precision medicine. It emphasizes the importance of patient-derived tumor organoid biobanks for drug development, screening, safety evaluation, and personalized medicine. Additionally, it evaluates the application of organoid technology as an experimental tumor model to better understand the molecular mechanisms of tumor. The intent of this review is to explicate the significance of tumor organoids in cancer research and to present new avenues for the future of tumor research.
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Affiliation(s)
- Shanqiang Qu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838, Guangzhou, 510515, Guangdong, China
- The Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
- Nanfang Glioma Center, Guangzhou, 510515, Guangdong, China
- Institute of Brain disease, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838, Guangzhou, 510515, Guangdong, China
| | - Rongyang Xu
- The Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
- The First Clinical Medical College of Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Guozhong Yi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838, Guangzhou, 510515, Guangdong, China
- Nanfang Glioma Center, Guangzhou, 510515, Guangdong, China
- Institute of Brain disease, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838, Guangzhou, 510515, Guangdong, China
| | - Zhiyong Li
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838, Guangzhou, 510515, Guangdong, China
- Nanfang Glioma Center, Guangzhou, 510515, Guangdong, China
- Institute of Brain disease, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838, Guangzhou, 510515, Guangdong, China
| | - Huayang Zhang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838, Guangzhou, 510515, Guangdong, China
- The Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Songtao Qi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838, Guangzhou, 510515, Guangdong, China.
- The Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China.
- Nanfang Glioma Center, Guangzhou, 510515, Guangdong, China.
- Institute of Brain disease, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838, Guangzhou, 510515, Guangdong, China.
| | - Guanglong Huang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838, Guangzhou, 510515, Guangdong, China.
- The Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China.
- Nanfang Glioma Center, Guangzhou, 510515, Guangdong, China.
- Institute of Brain disease, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838, Guangzhou, 510515, Guangdong, China.
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22
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Cameron O, Neves JF, Gentleman E. Listen to Your Gut: Key Concepts for Bioengineering Advanced Models of the Intestine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2302165. [PMID: 38009508 PMCID: PMC10837392 DOI: 10.1002/advs.202302165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 10/12/2023] [Indexed: 11/29/2023]
Abstract
The intestine performs functions central to human health by breaking down food and absorbing nutrients while maintaining a selective barrier against the intestinal microbiome. Key to this barrier function are the combined efforts of lumen-lining specialized intestinal epithelial cells, and the supportive underlying immune cell-rich stromal tissue. The discovery that the intestinal epithelium can be reproduced in vitro as intestinal organoids introduced a new way to understand intestinal development, homeostasis, and disease. However, organoids reflect the intestinal epithelium in isolation whereas the underlying tissue also contains myriad cell types and impressive chemical and structural complexity. This review dissects the cellular and matrix components of the intestine and discusses strategies to replicate them in vitro using principles drawing from bottom-up biological self-organization and top-down bioengineering. It also covers the cellular, biochemical and biophysical features of the intestinal microenvironment and how these can be replicated in vitro by combining strategies from organoid biology with materials science. Particularly accessible chemistries that mimic the native extracellular matrix are discussed, and bioengineering approaches that aim to overcome limitations in modelling the intestine are critically evaluated. Finally, the review considers how further advances may extend the applications of intestinal models and their suitability for clinical therapies.
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Affiliation(s)
- Oliver Cameron
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonSE1 9RTUK
| | - Joana F. Neves
- Centre for Host‐Microbiome InteractionsKing's College LondonLondonSE1 9RTUK
| | - Eileen Gentleman
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonSE1 9RTUK
- Department of Biomedical SciencesUniversity of LausanneLausanne1005Switzerland
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23
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Gong X, Du J, Peng RW, Chen C, Yang Z. CRISPRing KRAS: A Winding Road with a Bright Future in Basic and Translational Cancer Research. Cancers (Basel) 2024; 16:460. [PMID: 38275900 PMCID: PMC10814442 DOI: 10.3390/cancers16020460] [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: 01/02/2024] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Once considered "undruggable" due to the strong affinity of RAS proteins for GTP and the structural lack of a hydrophobic "pocket" for drug binding, the development of proprietary therapies for KRAS-mutant tumors has long been a challenging area of research. CRISPR technology, the most successful gene-editing tool to date, is increasingly being utilized in cancer research. Here, we provide a comprehensive review of the application of the CRISPR system in basic and translational research in KRAS-mutant cancer, summarizing recent advances in the mechanistic understanding of KRAS biology and the underlying principles of drug resistance, anti-tumor immunity, epigenetic regulatory networks, and synthetic lethality co-opted by mutant KRAS.
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Affiliation(s)
- Xian Gong
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou 350001, China; (X.G.); (J.D.)
- Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical University, Fuzhou 350001, China
| | - Jianting Du
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou 350001, China; (X.G.); (J.D.)
- Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical University, Fuzhou 350001, China
| | - Ren-Wang Peng
- Division of General Thoracic Surgery, Department of BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, Murtenstrasse 28, 3008 Bern, Switzerland;
| | - Chun Chen
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou 350001, China; (X.G.); (J.D.)
- Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical University, Fuzhou 350001, China
| | - Zhang Yang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou 350001, China; (X.G.); (J.D.)
- Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical University, Fuzhou 350001, China
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24
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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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25
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Mao Q, Ye Q, Xu Y, Jiang J, Fan Y, Zhuang L, Liu G, Wang T, Zhang Z, Feng T, Kong S, Lu J, Zhang H, Wang H, Lin CP. Murine trophoblast organoids as a model for trophoblast development and CRISPR-Cas9 screening. Dev Cell 2023; 58:2992-3008.e7. [PMID: 38056451 DOI: 10.1016/j.devcel.2023.11.007] [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: 03/06/2023] [Revised: 07/27/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023]
Abstract
The placenta becomes one of the most diversified organs during placental mammal radiation. The main in vitro model for studying mouse trophoblast development is the 2D differentiation model of trophoblast stem cells, which is highly skewed to certain lineages and thus hampers systematic screens. Here, we established culture conditions for the establishment, maintenance, and differentiation of murine trophoblast organoids. Murine trophoblast organoids under the maintenance condition contain stem cell-like populations, whereas differentiated organoids possess various trophoblasts resembling placental ones in vivo. Ablation of Nubpl or Gcm1 in trophoblast organoids recapitulated their deficiency phenotypes in vivo, suggesting that those organoids are valid in vitro models for trophoblast development. Importantly, we performed an efficient CRISPR-Cas9 screening in mouse trophoblast organoids using a focused sgRNA (single guide RNA) library targeting G protein-coupled receptors. Together, our results establish an organoid model to investigate mouse trophoblast development and a practicable approach to performing forward screening in trophoblast lineages.
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Affiliation(s)
- Qian Mao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qinying Ye
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yiwen Xu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jingwei Jiang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yunhao Fan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lili Zhuang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Guohui Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tengfei Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhenwu Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Teng Feng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shuangbo Kong
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Jinhua Lu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Hui Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Haopeng Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Chao-Po Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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26
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Hu Y, Liu L, Jiang Q, Fang W, Chen Y, Hong Y, Zhai X. CRISPR/Cas9: a powerful tool in colorectal cancer research. J Exp Clin Cancer Res 2023; 42:308. [PMID: 37993945 PMCID: PMC10664500 DOI: 10.1186/s13046-023-02901-z] [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: 09/14/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant cancers worldwide and seriously threatens human health. The clustered regulatory interspaced short palindromic repeat/CRISPR-associate nuclease 9 (CRISPR/Cas9) system is an adaptive immune system of bacteria or archaea. Since its introduction, research into various aspects of treatment approaches for CRC has been accelerated, including investigation of the oncogenes, tumor suppressor genes (TSGs), drug resistance genes, target genes, mouse model construction, and especially in genome-wide library screening. Furthermore, the CRISPR/Cas9 system can be utilized for gene therapy for CRC, specifically involving in the molecular targeted drug delivery or targeted knockout in vivo. In this review, we elucidate the mechanism of the CRISPR/Cas9 system and its comprehensive applications in CRC. Additionally, we discussed the issue of off-target effects associated with CRISPR/Cas9, which serves to restrict its practical application. Future research on CRC should in-depth and systematically utilize the CRISPR/Cas9 system thereby achieving clinical practice.
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Affiliation(s)
- Yang Hu
- Department of Gastroenterology, The First People's Hospital of Jiande, Hangzhou, 311600, China
| | - Liang Liu
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Qi Jiang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Weiping Fang
- Department of Gastroenterology, The First People's Hospital of Jiande, Hangzhou, 311600, China
| | - Yazhu Chen
- West China Hospital of Sichuan University, Chengdu, 610044, China.
| | - Yuntian Hong
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Xiang Zhai
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
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27
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Li H, Zhu Y, Wang X, Feng Y, Qian Y, Ma Q, Li X, Chen Y, Chen K. Joining Forces: The Combined Application of Therapeutic Viruses and Nanomaterials in Cancer Therapy. Molecules 2023; 28:7679. [PMID: 38005401 PMCID: PMC10674375 DOI: 10.3390/molecules28227679] [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: 09/29/2023] [Revised: 11/10/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Cancer, on a global scale, presents a monumental challenge to our healthcare systems, posing a significant threat to human health. Despite the considerable progress we have made in the diagnosis and treatment of cancer, realizing precision cancer therapy, reducing side effects, and enhancing efficacy remain daunting tasks. Fortunately, the emergence of therapeutic viruses and nanomaterials provides new possibilities for tackling these issues. Therapeutic viruses possess the ability to accurately locate and attack tumor cells, while nanomaterials serve as efficient drug carriers, delivering medication precisely to tumor tissues. The synergy of these two elements has led to a novel approach to cancer treatment-the combination of therapeutic viruses and nanomaterials. This advantageous combination has overcome the limitations associated with the side effects of oncolytic viruses and the insufficient tumoricidal capacity of nanomedicines, enabling the oncolytic viruses to more effectively breach the tumor's immune barrier. It focuses on the lesion site and even allows for real-time monitoring of the distribution of therapeutic viruses and drug release, achieving a synergistic effect. This article comprehensively explores the application of therapeutic viruses and nanomaterials in tumor treatment, dissecting their working mechanisms, and integrating the latest scientific advancements to predict future development trends. This approach, which combines viral therapy with the application of nanomaterials, represents an innovative and more effective treatment strategy, offering new perspectives in the field of tumor therapy.
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Affiliation(s)
- Hongyu Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
- Ocean College, Beibu Gulf University, Qinzhou 535011, China
| | - Yunhuan Zhu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
| | - Xin Wang
- Center of Infectious Disease Research, School of Life Science, Westlake University, Hangzhou 310024, China;
| | - Yilu Feng
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
| | - Yuncheng Qian
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
| | - Qiman Ma
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
| | - Xinyuan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
| | - Yihan Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
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28
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Liang J, Wei J, Cao J, Qian J, Gao R, Li X, Wang D, Gu Y, Dong L, Yu J, Zhao B, Wang X. In-organoid single-cell CRISPR screening reveals determinants of hepatocyte differentiation and maturation. Genome Biol 2023; 24:251. [PMID: 37907970 PMCID: PMC10617096 DOI: 10.1186/s13059-023-03084-8] [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: 05/19/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023] Open
Abstract
BACKGROUND Harnessing hepatocytes for basic research and regenerative medicine demands a complete understanding of the genetic determinants underlying hepatocyte differentiation and maturation. Single-cell CRISPR screens in organoids could link genetic perturbations with parallel transcriptomic readout in single cells, providing a powerful method to delineate roles of cell fate regulators. However, a big challenge for identifying key regulators during data analysis is the low expression levels of transcription factors (TFs), which are difficult to accurately estimate due to noise and dropouts in single-cell sequencing. Also, it is often the changes in TF activities in the transcriptional cascade rather than the expression levels of TFs that are relevant to the cell fate transition. RESULTS Here, we develop Organoid-based Single-cell CRISPR screening Analyzed with Regulons (OSCAR), a framework using regulon activities as readouts to dissect gene knockout effects in organoids. In adult-stem-cell-derived liver organoids, we map transcriptomes in 80,576 cells upon 246 perturbations associated with transcriptional regulation of hepatocyte formation. Using OSCAR, we identify known and novel positive and negative regulators, among which Fos and Ubr5 are the top-ranked ones. Further single-gene loss-of-function assays demonstrate that Fos depletion in mouse and human liver organoids promote hepatocyte differentiation by specific upregulation of liver metabolic genes and pathways, and conditional knockout of Ubr5 in mouse liver delays hepatocyte maturation. CONCLUSIONS Altogether, we provide a framework to explore lineage specifiers in a rapid and systematic manner, and identify hepatocyte determinators with potential clinical applications.
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Affiliation(s)
- Junbo Liang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking, Union Medical College, Beijing, 100005, China
| | - Jinsong Wei
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jun Cao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking, Union Medical College, Beijing, 100005, China
- Institute of Clinical Medicine, Peking Union Medical College and Chinese Academy of Medical Sciences, Translational Medicine Center, Peking Union Medical College Hospital, Beijing, 100730, China
| | - Jun Qian
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking, Union Medical College, Beijing, 100005, China
| | - Ran Gao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking, Union Medical College, Beijing, 100005, China
| | - Xiaoyu Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Dingding Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking, Union Medical College, Beijing, 100005, China
| | - Yani Gu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking, Union Medical College, Beijing, 100005, China
| | - Lei Dong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovative Center, Nanjing University, Nanjing, 210023, China
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking, Union Medical College, Beijing, 100005, China
| | - Bing Zhao
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China.
- Institute of Respiratory Disease, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
- Institute of Organoid Technology, Kunming Medical University, Kunming, 650500, China.
| | - Xiaoyue Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking, Union Medical College, Beijing, 100005, China.
- Institute of Clinical Medicine, Peking Union Medical College and Chinese Academy of Medical Sciences, Translational Medicine Center, Peking Union Medical College Hospital, Beijing, 100730, China.
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29
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Ravichandran M, Maddalo D. Applications of CRISPR-Cas9 for advancing precision medicine in oncology: from target discovery to disease modeling. Front Genet 2023; 14:1273994. [PMID: 37908590 PMCID: PMC10613999 DOI: 10.3389/fgene.2023.1273994] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/27/2023] [Indexed: 11/02/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9) system is a powerful tool that enables precise and efficient gene manipulation. In a relatively short time, CRISPR has risen to become the preferred gene-editing system due to its high efficiency, simplicity, and programmability at low costs. Furthermore, in the recent years, the CRISPR toolkit has been rapidly expanding, and the emerging advancements have shown tremendous potential in uncovering molecular mechanisms and new therapeutic strategies for human diseases. In this review, we provide our perspectives on the recent advancements in CRISPR technology and its impact on precision medicine, ranging from target identification, disease modeling, and diagnostics. We also discuss the impact of novel approaches such as epigenome, base, and prime editing on preclinical cancer drug discovery.
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Affiliation(s)
- Mirunalini Ravichandran
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, United States
| | - Danilo Maddalo
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, United States
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30
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Wang C, Huang M, Lin Y, Zhang Y, Pan J, Jiang C, Cheng M, Li S, He W, Li Z, Tu Z, Fan J, Zeng H, Lin J, Wang Y, Yao N, Liu T, Qi Q, Liu X, Zhang Z, Chen M, Xia L, Zhang D, Ye W. ENO2-derived phosphoenolpyruvate functions as an endogenous inhibitor of HDAC1 and confers resistance to antiangiogenic therapy. Nat Metab 2023; 5:1765-1786. [PMID: 37667133 DOI: 10.1038/s42255-023-00883-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/31/2023] [Indexed: 09/06/2023]
Abstract
Metabolic reprogramming is associated with resistance to antiangiogenic therapy in cancer. However, its molecular mechanisms have not been clearly elucidated. Here, we identify the glycolytic enzyme enolase 2 (ENO2) as a driver of resistance to antiangiogenic therapy in colorectal cancer (CRC) mouse models and human participants. ENO2 overexpression induces neuroendocrine differentiation, promotes malignant behaviour in CRC and desensitizes CRC to antiangiogenic drugs. Mechanistically, the ENO2-derived metabolite phosphoenolpyruvate (PEP) selectively inhibits histone deacetylase 1 (HDAC1) activity, which increases the acetylation of β-catenin and activates the β-catenin pathway in CRC. Inhibition of ENO2 with enolase inhibitors AP-III-a4 or POMHEX synergizes the efficacy of antiangiogenic drugs in vitro and in mice bearing drug-resistant CRC xenograft tumours. Together, our findings reveal that ENO2 constitutes a useful predictive biomarker and therapeutic target for resistance to antiangiogenic therapy in CRC, and uncover a previously undefined and metabolism-independent role of PEP in regulating resistance to antiangiogenic therapy by functioning as an endogenous HDAC1 inhibitor.
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Affiliation(s)
- Chenran Wang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
- The First Affiliated Hospital of Jinan University, Guangzhou, China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Maohua Huang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Yuning Lin
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Yiming Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Jinghua Pan
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Chang Jiang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Minjing Cheng
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Shenrong Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Wenzhuo He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zhengqiu Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Zhengchao Tu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Jun Fan
- School of Medicine, Jinan University, Guangzhou, China
| | - Huhu Zeng
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Jiahui Lin
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Yongjin Wang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Nan Yao
- School of Medicine, Jinan University, Guangzhou, China
| | - Tongzheng Liu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Qi Qi
- School of Medicine, Jinan University, Guangzhou, China
| | - Xiangning Liu
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Zhimin Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Minfeng Chen
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China.
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China.
| | - Liangping Xia
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
| | - Dongmei Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China.
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China.
| | - Wencai Ye
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China.
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China.
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31
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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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32
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Sockell A, Wong W, Longwell S, Vu T, Karlsson K, Mokhtari D, Schaepe J, Lo YH, Cornelius V, Kuo C, Van Valen D, Curtis C, Fordyce PM. A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids. Cell Syst 2023; 14:764-776.e6. [PMID: 37734323 DOI: 10.1016/j.cels.2023.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 02/24/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023]
Abstract
Organoids are powerful experimental models for studying the ontogeny and progression of various diseases including cancer. Organoids are conventionally cultured in bulk using an extracellular matrix mimic. However, bulk-cultured organoids physically overlap, making it impossible to track the growth of individual organoids over time in high throughput. Moreover, local spatial variations in bulk matrix properties make it difficult to assess whether observed phenotypic heterogeneity between organoids results from intrinsic cell differences or differences in the microenvironment. Here, we developed a microwell-based method that enables high-throughput quantification of image-based parameters for organoids grown from single cells, which can further be retrieved from their microwells for molecular profiling. Coupled with a deep learning image-processing pipeline, we characterized phenotypic traits including growth rates, cellular movement, and apical-basal polarity in two CRISPR-engineered human gastric organoid models, identifying genomic changes associated with increased growth rate and changes in accessibility and expression correlated with apical-basal polarity. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Alexandra Sockell
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Wing Wong
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Scott Longwell
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Thy Vu
- Department of Biochemistry, UT Austin, Austin, TX 78712, USA
| | - Kasper Karlsson
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Julia Schaepe
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yuan-Hung Lo
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Vincent Cornelius
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Calvin Kuo
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - David Van Valen
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christina Curtis
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94110, USA.
| | - Polly M Fordyce
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94110, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
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33
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Li C, Fleck JS, Martins-Costa C, Burkard TR, Themann J, Stuempflen M, Peer AM, Vertesy Á, Littleboy JB, Esk C, Elling U, Kasprian G, Corsini NS, Treutlein B, Knoblich JA. Single-cell brain organoid screening identifies developmental defects in autism. Nature 2023; 621:373-380. [PMID: 37704762 PMCID: PMC10499611 DOI: 10.1038/s41586-023-06473-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/21/2023] [Indexed: 09/15/2023]
Abstract
The development of the human brain involves unique processes (not observed in many other species) that can contribute to neurodevelopmental disorders1-4. Cerebral organoids enable the study of neurodevelopmental disorders in a human context. We have developed the CRISPR-human organoids-single-cell RNA sequencing (CHOOSE) system, which uses verified pairs of guide RNAs, inducible CRISPR-Cas9-based genetic disruption and single-cell transcriptomics for pooled loss-of-function screening in mosaic organoids. Here we show that perturbation of 36 high-risk autism spectrum disorder genes related to transcriptional regulation uncovers their effects on cell fate determination. We find that dorsal intermediate progenitors, ventral progenitors and upper-layer excitatory neurons are among the most vulnerable cell types. We construct a developmental gene regulatory network of cerebral organoids from single-cell transcriptomes and chromatin modalities and identify autism spectrum disorder-associated and perturbation-enriched regulatory modules. Perturbing members of the BRG1/BRM-associated factor (BAF) chromatin remodelling complex leads to enrichment of ventral telencephalon progenitors. Specifically, mutating the BAF subunit ARID1B affects the fate transition of progenitors to oligodendrocyte and interneuron precursor cells, a phenotype that we confirmed in patient-specific induced pluripotent stem cell-derived organoids. Our study paves the way for high-throughput phenotypic characterization of disease susceptibility genes in organoid models with cell state, molecular pathway and gene regulatory network readouts.
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Affiliation(s)
- Chong Li
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria.
| | - Jonas Simon Fleck
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Catarina Martins-Costa
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Jan Themann
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Marlene Stuempflen
- Department of Radiodiagnostics, Medical University of Vienna, Vienna, Austria
| | - Angela Maria Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Ábel Vertesy
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Jamie B Littleboy
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Christopher Esk
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Gregor Kasprian
- Department of Radiodiagnostics, Medical University of Vienna, Vienna, Austria
| | - Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria.
- Department of Neurology, Medical University of Vienna, Vienna, Austria.
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34
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Yang Q, Li M, Yang X, Xiao Z, Tong X, Tuerdi A, Li S, Lei L. Flourishing tumor organoids: History, emerging technology, and application. Bioeng Transl Med 2023; 8:e10559. [PMID: 37693042 PMCID: PMC10487342 DOI: 10.1002/btm2.10559] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/16/2023] [Accepted: 05/25/2023] [Indexed: 09/12/2023] Open
Abstract
Malignant tumors are one of the leading causes of death which impose an increasingly heavy burden on all countries. Therefore, the establishment of research models that closely resemble original tumor characteristics is crucial to further understanding the mechanisms of malignant tumor development, developing safer and more effective drugs, and formulating personalized treatment plans. Recently, organoids have been widely used in tumor research owing to their advantages including preserving the structure, heterogeneity, and cellular functions of the original tumor, together with the ease of manipulation. This review describes the history and characteristics of tumor organoids and the synergistic combination of three-dimensional (3D) culture approaches for tumor organoids with emerging technologies, including tissue-engineered cell scaffolds, microfluidic devices, 3D bioprinting, rotating wall vessels, and clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9). Additionally, the progress in research and the applications in basic and clinical research of tumor organoid models are summarized. This includes studies of the mechanism of tumor development, drug development and screening, precision medicine, immunotherapy, and simulation of the tumor microenvironment. Finally, the existing shortcomings of tumor organoids and possible future directions are discussed.
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Affiliation(s)
- Qian Yang
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Mengmeng Li
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xinming Yang
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Zian Xiao
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xinying Tong
- Department of Hemodialysis, the Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Ayinuer Tuerdi
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Shisheng Li
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Lanjie Lei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
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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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36
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Zhang Z, Bao X, Lin CP. Progress and Prospects of Gene Editing in Pluripotent Stem Cells. Biomedicines 2023; 11:2168. [PMID: 37626665 PMCID: PMC10452926 DOI: 10.3390/biomedicines11082168] [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: 06/30/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 08/27/2023] Open
Abstract
Applying programmable nucleases in gene editing has greatly shaped current research in basic biology and clinical translation. Gene editing in human pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), is highly relevant to clinical cell therapy and thus should be examined with particular caution. First, since all mutations in PSCs will be carried to all their progenies, off-target edits of editors will be amplified. Second, due to the hypersensitivity of PSCs to DNA damage, double-strand breaks (DSBs) made by gene editing could lead to low editing efficiency and the enrichment of cell populations with defective genomic safeguards. In this regard, DSB-independent gene editing tools, such as base editors and prime editors, are favored due to their nature to avoid these consequences. With more understanding of the microbial world, new systems, such as Cas-related nucleases, transposons, and recombinases, are also expanding the toolbox for gene editing. In this review, we discuss current applications of programmable nucleases in PSCs for gene editing, the efforts researchers have made to optimize these systems, as well as new tools that can be potentially employed for differentiation modeling and therapeutic applications.
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Affiliation(s)
| | | | - Chao-Po Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (Z.Z.); (X.B.)
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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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38
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Jiang X, Oyang L, Peng Q, Liu Q, Xu X, Wu N, Tan S, Yang W, Han Y, Lin J, Xia L, Peng M, Tang Y, Luo X, Su M, Shi Y, Zhou Y, Liao Q. Organoids: opportunities and challenges of cancer therapy. Front Cell Dev Biol 2023; 11:1232528. [PMID: 37576596 PMCID: PMC10413981 DOI: 10.3389/fcell.2023.1232528] [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: 05/31/2023] [Accepted: 07/18/2023] [Indexed: 08/15/2023] Open
Abstract
Organoids are a class of multicellular structures with the capability of self-organizing and the characteristic of original tissues, they are generated from stem cells in 3D culture in vitro. Organoids can mimic the occurrence and progression of original tissues and widely used in disease models in recent years. The ability of tumor organoids to retain characteristic of original tumors make them unique for tumorigenesis and cancer therapy. However, the history of organoid development and the application of organoid technology in cancer therapy are not well understood. In this paper, we reviewed the history of organoids development, the culture methods of tumor organoids establishing and the applications of organoids in cancer research for better understanding the process of tumor development and providing better strategies for cancer therapy. The standardization of organoids cultivation facilitated the large-scale production of tumor organoids. Moreover, it was found that combination of tumor organoids and other cells such as immune cells, fibroblasts and nervous cells would better mimic the microenvironment of tumor progression. This might be important developing directions for tumor organoids in the future.
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Affiliation(s)
- Xianjie Jiang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha, Hunan, China
| | - Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha, Hunan, China
| | - Qiang Liu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha, Hunan, China
| | - Xuemeng Xu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha, Hunan, China
| | - Shiming Tan
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Wenjuan Yang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yaqian Han
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha, Hunan, China
| | - Jinguan Lin
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Longzheng Xia
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Mingjing Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha, Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha, Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha, Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha, Hunan, China
| | - Yingrui Shi
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha, Hunan, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha, Hunan, China
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha, Hunan, China
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Tian CM, Yang MF, Xu HM, Zhu MZ, Yue NN, Zhang Y, Shi RY, Yao J, Wang LS, Liang YJ, Li DF. Stem cell-derived intestinal organoids: a novel modality for IBD. Cell Death Discov 2023; 9:255. [PMID: 37479716 PMCID: PMC10362068 DOI: 10.1038/s41420-023-01556-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023] Open
Abstract
The organoids represent one of the greatest revolutions in the biomedical field in the past decade. This three-dimensional (3D) micro-organ cultured in vitro has a structure highly similar to that of the tissue and organ. Using the regeneration ability of stem cells, a 3D organ-like structure called intestinal organoids is established, which can mimic the characteristics of real intestinal organs, including morphology, function, and personalized response to specific stimuli. Here, we discuss current stem cell-based organ-like 3D intestinal models, including understanding the molecular pathophysiology, high-throughput screening drugs, drug efficacy testing, toxicological evaluation, and organ-based regeneration of inflammatory bowel disease (IBD). We summarize the advances and limitations of the state-of-the-art reconstruction platforms for intestinal organoids. The challenges, advantages, and prospects of intestinal organs as an in vitro model system for precision medicine are also discussed. Key applications of stem cell-derived intestinal organoids. Intestinal organoids can be used to model infectious diseases, develop new treatments, drug screens, precision medicine, and regenerative medicine.
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Affiliation(s)
- Cheng-Mei Tian
- Department of Gastroenterology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China
- Department of Emergency, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China
| | - Mei-Feng Yang
- Department of Hematology, Yantian District People's Hospital, Shenzhen, 518020, Guangdong, China
| | - Hao-Ming Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 51000, China
| | - Min-Zheng Zhu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 51000, China
| | - Ning-Ning Yue
- Department of Gastroenterology, Shenzhen People's Hospital The Second Clinical Medical College, Jinan University, Shenzhen, 518020, Guangdong, China
| | - Yuan Zhang
- Department of Medical Administration, Huizhou Institute of Occupational Diseases Control and Prevention, Huizhou, 516000, Guangdong, China
| | - Rui-Yue Shi
- Department of Gastroenterology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China.
| | - Jun Yao
- Department of Gastroenterology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China.
| | - Li-Sheng Wang
- Department of Gastroenterology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China.
| | - Yu-Jie Liang
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen, 518020, Guangdong, China.
| | - De-Feng Li
- Department of Gastroenterology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China.
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40
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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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41
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Wang Y, Zhang X, Wang Z. Cellular barcoding: From developmental tracing to anti-tumor drug discovery. Cancer Lett 2023:216281. [PMID: 37336285 DOI: 10.1016/j.canlet.2023.216281] [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: 03/22/2023] [Revised: 05/31/2023] [Accepted: 06/10/2023] [Indexed: 06/21/2023]
Abstract
Clonal evolution has gained immense attention in explaining cancer cell status, history, and fate during cancer progression. Current single-cell or spatial transcriptome technologies have broadened our understanding of various mechanisms underlying cancer initiation, relapse, and drug resistance. However, technical challenges still hinder a better understanding of the dynamics of distinctive phenotypic states and abnormal trajectories from normal physiological transition to malignant stages. Cellular barcoding enabled lineage tracing on parallelly massive cells at single-cell resolution through different mechanisms lately, enabling new insights into exploring developmental trajectories, cancer progression, and targeted therapies. This review summarizes the latest noteworthy and robust strategies for different types of cellular barcodes. To introduce the major characteristics, advantages and limitations of these different strategies, this review will further guide in choosing or improving cellular barcoding technologies and their applications in cancer research.
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Affiliation(s)
- Yuqing Wang
- Medical Center of Hematology, The Second Affiliated Hospital, Army Medical University, Chongqing, 40037, China; State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 40037, China
| | - Xi Zhang
- Medical Center of Hematology, The Second Affiliated Hospital, Army Medical University, Chongqing, 40037, China; State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 40037, China; Jinfeng Laboratory, Chongqing, 401329, China.
| | - Zheng Wang
- Medical Center of Hematology, The Second Affiliated Hospital, Army Medical University, Chongqing, 40037, China; State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 40037, China; Bio-Med Informatics Research Center & Clinical Research Center, The Second Affiliated Hospital, Army Medical University, Chongqing, 400037, China; Jinfeng Laboratory, Chongqing, 401329, China.
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42
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Mircetic J, Camgöz A, Abohawya M, Ding L, Dietzel J, Tobar SG, Paszkowski-Rogacz M, Seidlitz T, Schmäche T, Mehnert MC, Sidorova O, Weitz J, Buchholz F, Stange DE. CRISPR/Cas9 Screen in Gastric Cancer Patient-Derived Organoids Reveals KDM1A-NDRG1 Axis as a Targetable Vulnerability. SMALL METHODS 2023; 7:e2201605. [PMID: 36908010 DOI: 10.1002/smtd.202201605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/01/2023] [Indexed: 06/09/2023]
Abstract
Viability CRISPR screens have proven indispensable in parsing genome function. However, their application in new, more physiologically relevant culturing systems like patient-derived organoids (PDOs) has been much slower. To probe epigenetic contribution to gastric cancer (GC), the third leading cause of cancer-related deaths worldwide, the first negative selection CRISPR screen in GC PDOs that faithfully preserve primary tumor characteristics is performed. Extensive quality control measurements showing feasibility of CRISPR screens in primary organoid culture are provided. The screen reveals the histone lysine demethylase-1A (KDM1A) to constitute a GC vulnerability. Both genetic and pharmacological inhibition of KDM1A cause organoid growth retardation. Further, it is shown that most of KDM1A cancer-supporting functions center on repression of N-myc downstream regulates gene-1 (NDRG1). De-repression of NDRG1 by KDM1A inhibitors (KDM1Ai) causes inhibition of Wnt signaling and a strong G1 cell cycle arrest. Finally, by profiling 20 GC PDOs, it is shown that NDRG1 upregulation predicts KDM1Ai response with 100% sensitivity and 82% specificity in the tested cohort. Thus, this work pioneers the use of negative selection CRISPR screens in patient-derived organoids, identifies a marker of KDM1Ai response, and accordingly a cohort of patients who may benefit from such therapy.
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Affiliation(s)
- Jovan Mircetic
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), 01309, Dresden, Germany
- Mildred Scheel Early Career Center (MSNZ) P2, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Aylin Camgöz
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
| | - Moustafa Abohawya
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), 01309, Dresden, Germany
| | - Li Ding
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Julia Dietzel
- Mildred Scheel Early Career Center (MSNZ) P2, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Sebastián García Tobar
- Mildred Scheel Early Career Center (MSNZ) P2, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Therese Seidlitz
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Tim Schmäche
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Marie-Christin Mehnert
- Mildred Scheel Early Career Center (MSNZ) P2, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Olga Sidorova
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Experimental and Clinical Research Center (ECRC) of the Max Delbrück Center (MDC) and Charité Berlin, 10117, Berlin, Germany
| | - Jürgen Weitz
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Frank Buchholz
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Daniel E Stange
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), 01309, Dresden, Germany
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
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43
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Yin G, Huang J, Petela J, Jiang H, Zhang Y, Gong S, Wu J, Liu B, Shi J, Gao Y. Targeting small GTPases: emerging grasps on previously untamable targets, pioneered by KRAS. Signal Transduct Target Ther 2023; 8:212. [PMID: 37221195 DOI: 10.1038/s41392-023-01441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/28/2023] [Accepted: 04/14/2023] [Indexed: 05/25/2023] Open
Abstract
Small GTPases including Ras, Rho, Rab, Arf, and Ran are omnipresent molecular switches in regulating key cellular functions. Their dysregulation is a therapeutic target for tumors, neurodegeneration, cardiomyopathies, and infection. However, small GTPases have been historically recognized as "undruggable". Targeting KRAS, one of the most frequently mutated oncogenes, has only come into reality in the last decade due to the development of breakthrough strategies such as fragment-based screening, covalent ligands, macromolecule inhibitors, and PROTACs. Two KRASG12C covalent inhibitors have obtained accelerated approval for treating KRASG12C mutant lung cancer, and allele-specific hotspot mutations on G12D/S/R have been demonstrated as viable targets. New methods of targeting KRAS are quickly evolving, including transcription, immunogenic neoepitopes, and combinatory targeting with immunotherapy. Nevertheless, the vast majority of small GTPases and hotspot mutations remain elusive, and clinical resistance to G12C inhibitors poses new challenges. In this article, we summarize diversified biological functions, shared structural properties, and complex regulatory mechanisms of small GTPases and their relationships with human diseases. Furthermore, we review the status of drug discovery for targeting small GTPases and the most recent strategic progress focused on targeting KRAS. The discovery of new regulatory mechanisms and development of targeting approaches will together promote drug discovery for small GTPases.
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Affiliation(s)
- Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China.
| | - Jing Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Johnny Petela
- Wake Forest University School of Medicine, Winston-Salem, NC, 27101, USA
| | - Hongmei Jiang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Yuetong Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Siqi Gong
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Jiaxin Wu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Bei Liu
- National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, 100871, China
| | - Jianyou Shi
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology, Chengdu, 610072, China.
| | - Yijun Gao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
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44
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Betge J, Jackstadt R. From organoids to bedside: Advances in modeling, decoding and targeting of colorectal cancer. Int J Cancer 2023; 152:1304-1313. [PMID: 36121667 DOI: 10.1002/ijc.34297] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/25/2022] [Accepted: 09/13/2022] [Indexed: 02/03/2023]
Abstract
Patient derived organoids closely resemble the biology of tissues and tumors. They are enabling ex vivo modeling of human diseases and dissecting key features of tumor biology like anatomical diversity or inter- and intra-tumoral heterogeneity. In the last years, organoids were established as models for drug discovery and explored to guide clinical decision making. In this review, we discuss the recent developments in organoid based research, elaborating on the developments in colorectal cancer as a prime example. We focus our review on the role of organoids to decode cancer cell dynamics and tumor microenvironmental complexity with the underlying bi-directional crosstalk. Additionally, advancements in the development of living biobanks, screening approaches, organoid based precision medicine and challenges of co-clinical trials are highlighted. We discuss ongoing efforts to overcome challenges that the field faces and indicate potential future directions.
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Affiliation(s)
- Johannes Betge
- Junior Clinical Cooperation Unit Translational Gastrointestinal Oncology and Preclinical Models, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,DKFZ-Hector Cancer Institute at University Medical Center Mannheim, Mannheim, Germany
| | - Rene Jackstadt
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
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45
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Kim TW, Koo SY, Riessland M, Cho H, Chaudhry F, Kolisnyk B, Russo MV, Saurat N, Mehta S, Garippa R, Betel D, Studer L. TNF-NFkB-p53 axis restricts in vivo survival of hPSC-derived dopamine neuron. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534819. [PMID: 37034664 PMCID: PMC10081262 DOI: 10.1101/2023.03.29.534819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Ongoing, first-in-human clinical trials illustrate the feasibility and translational potential of human pluripotent stem cell (hPSC)-based cell therapies in Parkinson's disease (PD). However, a major unresolved challenge in the field is the extensive cell death following transplantation with <10% of grafted dopamine neurons surviving. Here, we performed a pooled CRISPR/Cas9 screen to enhance survival of postmitotic dopamine neurons in vivo . We identified p53-mediated apoptotic cell death as major contributor to dopamine neuron loss and uncovered a causal link of TNFa-NFκB signaling in limiting cell survival. As a translationally applicable strategy to purify postmitotic dopamine neurons, we performed a cell surface marker screen that enabled purification without the need for genetic reporters. Combining cell sorting with adalimumab pretreatment, a clinically approved and widely used TNFa inhibitor, enabled efficient engraftment of postmitotic dopamine neurons leading to extensive re-innervation and functional recovery in a preclinical PD mouse model. Thus, transient TNFa inhibition presents a clinically relevant strategy to enhance survival and enable engraftment of postmitotic human PSC-derived dopamine neurons in PD. Highlights In vivo CRISPR-Cas9 screen identifies p53 limiting survival of grafted human dopamine neurons. TNFα-NFκB pathway mediates p53-dependent human dopamine neuron deathCell surface marker screen to enrich human dopamine neurons for translational use. FDA approved TNF-alpha inhibitor rescues in vivo dopamine neuron survival with in vivo function.
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46
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Silva-Pedrosa R, Salgado AJ, Ferreira PE. Revolutionizing Disease Modeling: The Emergence of Organoids in Cellular Systems. Cells 2023; 12:cells12060930. [PMID: 36980271 PMCID: PMC10047824 DOI: 10.3390/cells12060930] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/03/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Cellular models have created opportunities to explore the characteristics of human diseases through well-established protocols, while avoiding the ethical restrictions associated with post-mortem studies and the costs associated with researching animal models. The capability of cell reprogramming, such as induced pluripotent stem cells (iPSCs) technology, solved the complications associated with human embryonic stem cells (hESC) usage. Moreover, iPSCs made significant contributions for human medicine, such as in diagnosis, therapeutic and regenerative medicine. The two-dimensional (2D) models allowed for monolayer cellular culture in vitro; however, they were surpassed by the three-dimensional (3D) cell culture system. The 3D cell culture provides higher cell-cell contact and a multi-layered cell culture, which more closely respects cellular morphology and polarity. It is more tightly able to resemble conditions in vivo and a closer approach to the architecture of human tissues, such as human organoids. Organoids are 3D cellular structures that mimic the architecture and function of native tissues. They are generated in vitro from stem cells or differentiated cells, such as epithelial or neural cells, and are used to study organ development, disease modeling, and drug discovery. Organoids have become a powerful tool for understanding the cellular and molecular mechanisms underlying human physiology, providing new insights into the pathogenesis of cancer, metabolic diseases, and brain disorders. Although organoid technology is up-and-coming, it also has some limitations that require improvements.
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Affiliation(s)
- Rita Silva-Pedrosa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057 Braga, Portugal
- Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - António José Salgado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Pedro Eduardo Ferreira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057 Braga, Portugal
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47
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Meng X, Wu TG, Lou QY, Niu KY, Jiang L, Xiao QZ, Xu T, Zhang L. Optimization of CRISPR-Cas system for clinical cancer therapy. Bioeng Transl Med 2023; 8:e10474. [PMID: 36925702 PMCID: PMC10013785 DOI: 10.1002/btm2.10474] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/24/2022] [Accepted: 12/07/2022] [Indexed: 12/25/2022] Open
Abstract
Cancer is a genetic disease caused by alterations in genome and epigenome and is one of the leading causes for death worldwide. The exploration of disease development and therapeutic strategies at the genetic level have become the key to the treatment of cancer and other genetic diseases. The functional analysis of genes and mutations has been slow and laborious. Therefore, there is an urgent need for alternative approaches to improve the current status of cancer research. Gene editing technologies provide technical support for efficient gene disruption and modification in vivo and in vitro, in particular the use of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems. Currently, the applications of CRISPR-Cas systems in cancer rely on different Cas effector proteins and the design of guide RNAs. Furthermore, effective vector delivery must be met for the CRISPR-Cas systems to enter human clinical trials. In this review article, we describe the mechanism of the CRISPR-Cas systems and highlight the applications of class II Cas effector proteins. We also propose a synthetic biology approach to modify the CRISPR-Cas systems, and summarize various delivery approaches facilitating the clinical application of the CRISPR-Cas systems. By modifying the CRISPR-Cas system and optimizing its in vivo delivery, promising and effective treatments for cancers using the CRISPR-Cas system are emerging.
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Affiliation(s)
- Xiang Meng
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China
| | - Tian-Gang Wu
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China
| | - Qiu-Yue Lou
- Anhui Provincial Center for Disease Control and Prevention Hefei People's Republic of China
| | - Kai-Yuan Niu
- Clinical Pharmacology, William Harvey Research Institute (WHRI), Barts and The London School of Medicine and Dentistry Queen Mary University of London (QMUL) Heart Centre (G23) London UK.,Department of Otolaryngology The Third Affiliated Hospital of Anhui Medical University Hefei China
| | - Lei Jiang
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China
| | - Qing-Zhong Xiao
- Clinical Pharmacology, William Harvey Research Institute (WHRI), Barts and The London School of Medicine and Dentistry Queen Mary University of London (QMUL) Heart Centre (G23) London UK
| | - Tao Xu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products Anhui Medical University Hefei China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province Hefei China
| | - Lei Zhang
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China.,Department of Periodontology Anhui Stomatology Hospital Affiliated to Anhui Medical University Hefei China
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48
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Ahmed A, Reinhold C, Breunig E, Phan TS, Dietrich L, Kostadinova F, Urwyler C, Merk VM, Noti M, Toja da Silva I, Bode K, Nahle F, Plazzo AP, Koerner J, Stuber R, Menche C, Karamitopoulou E, Farin HF, Gollob KJ, Brunner T. Immune escape of colorectal tumours via local LRH-1/Cyp11b1-mediated synthesis of immunosuppressive glucocorticoids. Mol Oncol 2023. [PMID: 36861295 PMCID: PMC10399709 DOI: 10.1002/1878-0261.13414] [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: 12/08/2022] [Accepted: 02/28/2023] [Indexed: 03/03/2023] Open
Abstract
Control of tumour development and growth by the immune system critically defines patient fate and survival. What regulates the escape of colorectal tumours from destruction by the immune system remains currently unclear. Here, we investigated the role of intestinal synthesis of glucocorticoids in the tumour development during an inflammation-induced mouse model of colorectal cancer. We demonstrate that the local synthesis of immunoregulatory glucocorticoids has dual roles in the regulation of intestinal inflammation and tumour development. In the inflammation phase, LRH-1/Nr5A2-regulated and Cyp11b1-mediated intestinal glucocorticoid synthesis prevents tumour development and growth. In established tumours, however, tumour-autonomous Cyp11b1-mediated glucocorticoid synthesis suppresses anti-tumour immune responses and promotes immune escape. Transplantation of glucocorticoid synthesis-proficient colorectal tumour organoids into immunocompetent recipient mice resulted in rapid tumour growth, whereas transplantation of Cyp11b1-deleted and glucocorticoid synthesis-deficient tumour organoids was characterized by reduced tumour growth and increased immune cell infiltration. In human colorectal tumours, high expression of steroidogenic enzymes correlated with the expression of other immune checkpoints and suppressive cytokines, and negatively correlated with overall patients' survival. Thus, LRH-1-regulated tumour-specific glucocorticoid synthesis contributes to tumour immune escape and represents a novel potential therapeutic target.
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Affiliation(s)
- Asma Ahmed
- Division of Biochemical Pharmacology, Department of Biology, University of Konstanz, Germany.,Department of Pharmacology, Faculty of Medicine, University of Khartoum, Sudan
| | - Cindy Reinhold
- Division of Biochemical Pharmacology, Department of Biology, University of Konstanz, Germany
| | - Eileen Breunig
- Division of Biochemical Pharmacology, Department of Biology, University of Konstanz, Germany
| | - Truong San Phan
- Division of Biochemical Pharmacology, Department of Biology, University of Konstanz, Germany
| | - Lea Dietrich
- Division of Biochemical Pharmacology, Department of Biology, University of Konstanz, Germany
| | - Feodora Kostadinova
- Division of Biochemical Pharmacology, Department of Biology, University of Konstanz, Germany
| | - Corinne Urwyler
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland
| | - Verena M Merk
- Division of Biochemical Pharmacology, Department of Biology, University of Konstanz, Germany
| | - Mario Noti
- Institute of Pathology, University of Bern, Switzerland
| | - Israel Toja da Silva
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil.,National Institute for Science and Technology - Oncogenomics and Therapeutic Innovation (INCT-INOTE), São Paulo, Brazil
| | - Konstantin Bode
- Division of Biochemical Pharmacology, Department of Biology, University of Konstanz, Germany
| | - Fatima Nahle
- Division of Biochemical Pharmacology, Department of Biology, University of Konstanz, Germany
| | - Anna Pia Plazzo
- Division of Biochemical Pharmacology, Department of Biology, University of Konstanz, Germany
| | - Julia Koerner
- Division of Immunology, Department of Biology, University of Konstanz, Germany
| | - Regula Stuber
- Institute of Pathology, University of Bern, Switzerland
| | - Constantin Menche
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany.,Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | | | - Henner F Farin
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany.,Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Kenneth J Gollob
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil.,National Institute for Science and Technology - Oncogenomics and Therapeutic Innovation (INCT-INOTE), São Paulo, Brazil.,Albert Einstein Israelite Hospital, São Paulo, Brazil
| | - Thomas Brunner
- Division of Biochemical Pharmacology, Department of Biology, University of Konstanz, Germany
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49
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Zhen S, Chen H, Lu J, Yang X, Tuo X, Chang S, Tian Y, Li X. Intravaginal delivery for CRISPR-Cas9 technology: For example, the treatment of HPV infection. J Med Virol 2023; 95:e28552. [PMID: 36734062 DOI: 10.1002/jmv.28552] [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: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/04/2023]
Abstract
The increasing incidence of sexually transmitted diseases in women, including human papillomavirus (HPV) infection, has led to the need to develop user-friendly potential prevention methods. At present, although there are several therapeutic parts, none of them has a preventive effect, but they are only limited to providing patients with symptom relief. Researchers have now recognized the need to find effective local preventive agents. One of the potential undiscovered local fungicides is the vaginal delivery of CRISPR/Cas9. CRISPR/Cas9 delivery involves silencing gene expression in a sequence-specific manner in the pathogenic agent, thus showing microbicidal activity. However, vaginal mucosal barrier and physiological changes (such as pH value and variable epithelial thickness in the menstrual cycle) are the main obstacles to effective delivery and cell uptake of CRISPR/Cas9. To enhance the vaginal delivery of CRISPR/Cas9, so far, nano-carrier systems such as lipid delivery systems, macromolecular systems, polymer nanoparticles, aptamers, and cell-penetrating peptides have been extensively studied. In this paper, various nano-carriers and their prospects in the preclinical stage are described, as well as the future significance of CRISPR/Cas9 vaginal delivery based on nano-carriers.
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Affiliation(s)
- Shuai Zhen
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Genetic Disease Diagnosis Center of Shaanxi Province, Xi'an, Shaanxi, China
- Medical Genetics Centre, Northwest Women's and Children's Hospital, Xi'an, China
| | - Hong Chen
- Department of Pharmacy, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jiaojiao Lu
- Department of Radiology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiling Yang
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaoqian Tuo
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shixue Chang
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yuhan Tian
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xu Li
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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50
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Maity S, Mukherjee R, Banerjee S. Recent Advances and Therapeutic Strategies Using CRISPR Genome Editing Technique for the Treatment of Cancer. Mol Biotechnol 2023; 65:206-226. [PMID: 35999480 DOI: 10.1007/s12033-022-00550-9] [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: 12/13/2021] [Accepted: 08/10/2022] [Indexed: 01/18/2023]
Abstract
CRISPR genome editing technique has the potential to target cancer cells in a precise manner. The latest advancements have helped to address one of the prominent concerns about this strategy which is the off-target integrations observed with dsDNA and have resulted in more studies being carried out for potentially safer and more targeted gene therapy, so as to make it available for the clinical trials in order to effectively treat cancer. CRISPR screens offer great potential for the high throughput investigation of the gene functionality in various tumors. It extends its capability to identify the tumor growth essential genes, therapeutic resistant genes, and immunotherapeutic responses. CRISPR screens are mostly performed in in vitro models, but latest advancements focus on developing in vivo models to view cancer progression in animal models. It also allows the detection of factors responsible for tumorigenesis. In CRISPR screens key parameters are optimized in order to meet proficient gene targeting efficiencies. It also detects various molecular effectors required for gene regulation in different cancers, essential pathways which modulate cytotoxicity to immunotherapy in cancer cells, important genes which contribute to cancer cell survival in hypoxic states and modulate cancer long non-coding RNAs. The current review focuses on the recent developments in the therapeutic application of CRISPR technology for cancer therapy. Furthermore, the associated challenges and safety concerns along with the various strategies that can be implemented to overcome these drawbacks has been discussed.
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Affiliation(s)
- Shreyasi Maity
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore, 632 014, Tamil Nadu, India
| | - Rishyani Mukherjee
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore, 632 014, Tamil Nadu, India
| | - Satarupa Banerjee
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore, 632 014, Tamil Nadu, India.
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