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Du X, Jia H, Chang Y, Zhao Y, Song J. Progress of organoid platform in cardiovascular research. Bioact Mater 2024; 40:88-103. [PMID: 38962658 PMCID: PMC11220467 DOI: 10.1016/j.bioactmat.2024.05.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 07/05/2024] Open
Abstract
Cardiovascular disease is a significant cause of death in humans. Various models are necessary for the study of cardiovascular diseases, but once cellular and animal models have some defects, such as insufficient fidelity. As a new technology, organoid has certain advantages and has been used in many applications in the study of cardiovascular diseases. This article aims to summarize the application of organoid platforms in cardiovascular diseases, including organoid construction schemes, modeling, and application of cardiovascular organoids. Advances in cardiovascular organoid research have provided many models for different cardiovascular diseases in a variety of areas, including myocardium, blood vessels, and valves. Physiological and pathological models of different diseases, drug research models, and methods for evaluating and promoting the maturation of different kinds of organ tissues are provided for various cardiovascular diseases, including cardiomyopathy, myocardial infarction, and atherosclerosis. This article provides a comprehensive overview of the latest research progress in cardiovascular organ tissues, including construction protocols for cardiovascular organoid tissues and their evaluation system, different types of disease models, and applications of cardiovascular organoid models in various studies. The problems and possible solutions in organoid development are summarized.
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Affiliation(s)
- Xingchao Du
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Science, PUMC, 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Hao Jia
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Science, PUMC, 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Yuan Chang
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Science, PUMC, 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Yiqi Zhao
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Science, PUMC, 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Jiangping Song
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Science, PUMC, 167 Beilishi Road, Xicheng District, Beijing, 100037, China
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2
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Liu Y, Wai AP, Zolzaya T, Iida Y, Okada S, Iizasa H, Yoshiyama H. Exploring the anti-EBV potential of suberoylanilide hydroxamic acid: Induction of apoptosis in infected cells through suppressing BART gene expression and inducing lytic infection. Virology 2024; 597:110161. [PMID: 38981317 DOI: 10.1016/j.virol.2024.110161] [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: 03/29/2024] [Revised: 06/09/2024] [Accepted: 06/24/2024] [Indexed: 07/11/2024]
Abstract
Epstein-Barr virus (EBV) is linked to lymphoma and epithelioma but lacks drugs specifically targeting EBV-positive tumors. BamHI A Rightward Transcript (BART) miRNAs are expressed in all EBV-positive tumors, suppressing both lytic infection and host cell apoptosis. We identified suberoylanilide hydroxamic acid (SAHA), an inhibitor of histone deacetylase enzymes, as an agent that suppresses BART promoter activity and transcription of BART miRNAs. SAHA treatment demonstrated a more pronounced inhibition of cell proliferation in EBV-positive cells compared to EBV-negative cells, affecting both p53 wild-type and mutant gastric epithelial cells. SAHA treatment enhanced lytic infection in wild-type EBV-infected cells, while also enhancing cell death in BZLF1-deficient EBV-infected cells. It reduced BART gene expression by 85% and increased the expression of proapoptotic factors targeted by BART miRNAs. These findings suggest that SAHA not only induces lytic infection but also leads to cell death by suppressing BART miRNA transcription and promoting the apoptotic program.
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Affiliation(s)
- Yuxin Liu
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Aung Phyo Wai
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Tumurgan Zolzaya
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Yuichi Iida
- Department of Immunology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Shunpei Okada
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Hisashi Iizasa
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Hironori Yoshiyama
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
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3
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Kantor B, O'Donovan B, Rittiner J, Hodgson D, Lindner N, Guerrero S, Dong W, Zhang A, Chiba-Falek O. The therapeutic implications of all-in-one AAV-delivered epigenome-editing platform in neurodegenerative disorders. Nat Commun 2024; 15:7259. [PMID: 39179542 PMCID: PMC11344155 DOI: 10.1038/s41467-024-50515-6] [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: 04/09/2023] [Accepted: 07/12/2024] [Indexed: 08/26/2024] Open
Abstract
Safely and efficiently controlling gene expression is a long-standing goal of biomedical research, and CRISPR/Cas system can be harnessed to create powerful tools for epigenetic editing. Adeno-associated-viruses (AAVs) represent the delivery vehicle of choice for therapeutic platform. However, their small packaging capacity isn't suitable for large constructs including most CRISPR/dCas9-effector vectors. Thus, AAV-based CRISPR/Cas systems have been delivered via two separate viral vectors. Here we develop a compact CRISPR/dCas9-based repressor system packaged in AAV as a single optimized vector. The system comprises the small Staphylococcus aureus (Sa)dCas9 and an engineered repressor molecule, a fusion of MeCP2's transcription repression domain (TRD) and KRAB. The dSaCas9-KRAB-MeCP2(TRD) vector platform repressed robustly and sustainably the expression of multiple genes-of-interest, in vitro and in vivo, including ApoE, the strongest genetic risk factor for late onset Alzheimer's disease (LOAD). Our platform broadens the CRISPR/dCas9 toolset available for transcriptional manipulation of gene expression in research and therapeutic settings.
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Affiliation(s)
- Boris Kantor
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA.
- Viral Vector Core, Duke University School of Medicine, Durham, NC, USA.
- Center for Advanced Genomic Technologies, Duke University School of Medicine, Durham, NC, USA.
| | - Bernadette O'Donovan
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
| | - Joseph Rittiner
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Viral Vector Core, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University School of Medicine, Durham, NC, USA
| | - Dellila Hodgson
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
| | - Nicholas Lindner
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Viral Vector Core, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University School of Medicine, Durham, NC, USA
| | - Sophia Guerrero
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Viral Vector Core, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University School of Medicine, Durham, NC, USA
| | - Wendy Dong
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Viral Vector Core, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University School of Medicine, Durham, NC, USA
| | - Austin Zhang
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Viral Vector Core, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University School of Medicine, Durham, NC, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA.
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4
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Pachter N, Allen K, Hookway TA. Exogenous ECM in an environmentally-mediated in vitro model for cardiac fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.20.608840. [PMID: 39229021 PMCID: PMC11370619 DOI: 10.1101/2024.08.20.608840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Few clinical solutions exist for cardiac fibrosis, creating the need for a tunable in vitro model to better understand fibrotic disease mechanisms and screen potential therapeutic compounds. Here, we combined cardiomyocytes, cardiac fibroblasts, and exogenous extracellular matrix (ECM) proteins to create an environmentally-mediated in vitro cardiac fibrosis model. Cells and ECM were combined into 2 types of cardiac tissues- aggregates and tissue rings. The addition of collagen I had a drastic negative impact on aggregate formation, but ring formation was not as drastically affected. In both tissue types, collagen and other ECM did not severely affect contractile function. Histological analysis showed direct incorporation of collagen into tissues, indicating that we can directly modulate the cells' ECM environment. This modulation affects tissue formation and distribution of cells, indicating that this model provides a useful platform for understanding how cells respond to changes in their extracellular environment and for potential therapeutic screening.
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Affiliation(s)
- Natalie Pachter
- Department of Biomedical Engineering, Binghamton University, the State University of New York, Binghamton, NY 13902, United States
| | - Kristen Allen
- Department of Biomedical Engineering, Binghamton University, the State University of New York, Binghamton, NY 13902, United States
| | - Tracy A Hookway
- Department of Biomedical Engineering, Binghamton University, the State University of New York, Binghamton, NY 13902, United States
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5
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Israr J, Kumar A. Current progress in CRISPR-Cas systems for autoimmune diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 208:231-259. [PMID: 39266185 DOI: 10.1016/bs.pmbts.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2024]
Abstract
A body develops an autoimmune illness when its immune system mistakenly targets healthy cells and organs. Eight million people are affected by more than 80 autoimmune diseases. The public's and individuals' well-being is put at risk. Type 1 diabetes, lupus, rheumatoid arthritis, and multiple sclerosisare autoimmune diseases. Tissue injury, nociceptive responses, and persistent inflammation are the results of these stresses. Concerns about healthcare costs, health, and physical limitations contribute to these issues. Given their prevalence, it is crucial to enhance our knowledge, conduct thorough research, and provide all-encompassing support to women dealing with autoimmune diseases. This will lead to better public health and better patient outcomes. Most bacteria's immune systems employ CRISPR-Cas, a state-of-the-art technique for editing genes. For Cas to break DNA with pinpoint accuracy, a guide RNA employs a predetermined enzymatic pathway. Genetic modifications started. After it was developed, this method was subjected to much research on autoimmune diseases. By modifying immune pathways, CRISPR gene editing can alleviate symptoms, promote immune system tolerance, and decrease autoimmune reactivity. The autoimmune diseases that CRISPR-Cas9 targets now have no treatment or cure. Results from early clinical trials and preclinical studies of autoimmune medicines engineered using CRISPR showed promise. Modern treatments for rheumatoid arthritis,multiple sclerosis, and type 1 diabetes aim to alter specific genetic or immune mechanisms. Accurate CRISPR editing can fix autoimmune genetic disorders. Modifying effector cells with CRISPR can decrease autoimmune reactions. These cells include cytotoxic T and B lymphocytes. Because of improvements in delivery techniques and kits, CRISPR medications are now safer, more effective, and more accurately targeted. It all comes down to intricate immunological reactions and unexpected side consequences. Revolutionary cures for autoimmune problems and highly personalized medical therapies have been made possible by recent advancements in CRISPR.
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Affiliation(s)
- Juveriya Israr
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow, Barabanki, Uttar Pradesh, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Mandhana, Kanpur, Uttar Pradesh, India.
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6
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Matsui S, Shiley JR, Buckley M, Lim HW, Hu YC, Mayhew CN, Iwafuchi M. Protocol for establishing inducible CRISPRd system for blocking transcription factor-binding sites in human pluripotent stem cells. STAR Protoc 2024; 5:103233. [PMID: 39133612 PMCID: PMC11357809 DOI: 10.1016/j.xpro.2024.103233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/29/2024] [Accepted: 07/10/2024] [Indexed: 09/01/2024] Open
Abstract
Transcription factor (TF) gene knockout or knockdown experiments provide comprehensive downstream effects on gene regulation. However, distinguishing primary direct effects from secondary effects remains challenging. To assess the direct effect of TF binding events, we present a protocol for establishing a doxycycline (Dox)-inducible CRISPRd system in human pluripotent stem cells (hPSCs). We describe the steps for establishing CRISPRd host hPSCs, designing and preparing single-guide RNA (sgRNA) expression lentivirus vectors, generating CRISPRd hPSCs transduced with sgRNAs, and analyzing CRISPRd TF-block effects by chromatin immunoprecipitation (ChIP)-qPCR. For complete details on the use and execution of this protocol, please refer to Matsui et al.1.
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Affiliation(s)
- Satoshi Matsui
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA.
| | - Joseph R Shiley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Morgan Buckley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Hee-Woong Lim
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Christopher N Mayhew
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA.
| | - Makiko Iwafuchi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA.
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7
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Qiao A, Wei Y, Liu Y, Kahn-Krell A, Ye L, Nguyen T, Zhang J. Doxycycline-Mediated Control of Cyclin D2 Overexpression in Human-Induced Pluripotent Stem Cells. Int J Mol Sci 2024; 25:8714. [PMID: 39201401 PMCID: PMC11354523 DOI: 10.3390/ijms25168714] [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: 06/08/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 09/02/2024] Open
Abstract
Previous studies have demonstrated that when the cyclin D2 (CCND2), a cell-cycle regulatory protein, is overexpressed in human-induced pluripotent stem cells (hiPSCs), cardiomyocytes (CMs) differentiated from these CCND2-overexpressing hiPSCs can proliferate after transplantation into infarcted hearts, which significantly improves the cells' potency for myocardial regeneration. However, persistent CM proliferation could lead to tumor growth or the development of arrhythmogenic complications; thus, the goal of the current study was to generate a line of hiPSCs in which CCND2 overexpression could be tightly controlled. First, we transfected hiPSCs with vectors coding for a doxycycline-inducible Tet-On transactivator and S. pyogenes dCas9 fused to the VPR activation domain; then, the same hiPSCs were engineered to express guide RNAs targeting the CCND2 promotor. Thus, treatment with doxycycline (dox) activated dCas9-VPR expression, and the guide RNAs directed dCas9-VPR to the CCND2 promoter, which activated CCND2 expression. Subsequent experiments confirmed that CCND2 expression was dox-dependent in this newly engineered line of hiPSCs (doxCCND2-hiPSCs): CCND2 protein was abundantly expressed after 48 h of treatment with dox and declined to near baseline level ~96 h after dox treatment was discontinued.
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Affiliation(s)
- Aijun Qiao
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (A.Q.); (Y.W.); (Y.L.); (A.K.-K.); (L.Y.); (T.N.)
| | - Yuhua Wei
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (A.Q.); (Y.W.); (Y.L.); (A.K.-K.); (L.Y.); (T.N.)
| | - Yanwen Liu
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (A.Q.); (Y.W.); (Y.L.); (A.K.-K.); (L.Y.); (T.N.)
| | - Asher Kahn-Krell
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (A.Q.); (Y.W.); (Y.L.); (A.K.-K.); (L.Y.); (T.N.)
| | - Lei Ye
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (A.Q.); (Y.W.); (Y.L.); (A.K.-K.); (L.Y.); (T.N.)
| | - Thanh Nguyen
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (A.Q.); (Y.W.); (Y.L.); (A.K.-K.); (L.Y.); (T.N.)
| | - Jianyi Zhang
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (A.Q.); (Y.W.); (Y.L.); (A.K.-K.); (L.Y.); (T.N.)
- Department of Medicine/Cardiovascular Diseases, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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8
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Kanbar K, El Darzi R, Jaalouk DE. Precision oncology revolution: CRISPR-Cas9 and PROTAC technologies unleashed. Front Genet 2024; 15:1434002. [PMID: 39144725 PMCID: PMC11321987 DOI: 10.3389/fgene.2024.1434002] [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: 05/16/2024] [Accepted: 07/02/2024] [Indexed: 08/16/2024] Open
Abstract
Cancer continues to present a substantial global health challenge, with its incidence and mortality rates persistently reflecting its significant impact. The emergence of precision oncology has provided a breakthrough in targeting oncogenic drivers previously deemed "undruggable" by conventional therapeutics and by limiting off-target cytotoxicity. Two groundbreaking technologies that have revolutionized the field of precision oncology are primarily CRISPR-Cas9 gene editing and more recently PROTAC (PROteolysis TArgeting Chimeras) targeted protein degradation technology. CRISPR-Cas9, in particular, has gained widespread recognition and acclaim due to its remarkable ability to modify DNA sequences precisely. Rather than editing the genetic code, PROTACs harness the ubiquitin proteasome degradation machinery to degrade proteins of interest selectively. Even though CRISPR-Cas9 and PROTAC technologies operate on different principles, they share a common goal of advancing precision oncology whereby both approaches have demonstrated remarkable potential in preclinical and promising data in clinical trials. CRISPR-Cas9 has demonstrated its clinical potential in this field due to its ability to modify genes directly and indirectly in a precise, efficient, reversible, adaptable, and tissue-specific manner, and its potential as a diagnostic tool. On the other hand, the ability to administer in low doses orally, broad targeting, tissue specificity, and controllability have reinforced the clinical potential of PROTAC. Thus, in the field of precision oncology, gene editing using CRISPR technology has revolutionized targeted interventions, while the emergence of PROTACs has further expanded the therapeutic landscape by enabling selective protein degradation. Rather than viewing them as mutually exclusive or competing methods in the field of precision oncology, their use is context-dependent (i.e., based on the molecular mechanisms of the disease) and they potentially could be used synergistically complementing the strengths of CRISPR and vice versa. Herein, we review the current status of CRISPR and PROTAC designs and their implications in the field of precision oncology in terms of clinical potential, clinical trial data, limitations, and compare their implications in precision clinical oncology.
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Affiliation(s)
- Karim Kanbar
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
| | - Roy El Darzi
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
| | - Diana E. Jaalouk
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
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9
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Matsui S, Shiley JR, Granitto M, Ludwig K, Buckley M, Koigi S, Mirizio G, Hu YC, Mayhew CN, Iwafuchi M. Protocol for establishing inducible CRISPR interference system for multiple-gene silencing in human pluripotent stem cells. STAR Protoc 2024; 5:103221. [PMID: 39083383 PMCID: PMC11342178 DOI: 10.1016/j.xpro.2024.103221] [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: 04/06/2024] [Revised: 05/29/2024] [Accepted: 07/03/2024] [Indexed: 08/02/2024] Open
Abstract
Inducible loss-of-function strategies are crucial for understanding gene function. However, creating inducible, multiple-gene knockout models is challenging and time-consuming. Here, we present a protocol for establishing a doxycycline-inducible CRISPR interference (CRISPRi) system to concurrently silence multiple genes in human induced pluripotent stem cells (hPSCs). We describe the steps for establishing host CRISPRi hPSCs, designing and cloning single-guide RNAs (sgRNAs) into a lentivirus plasmid, and establishing monoclonal CRISPRi hPSC lines transduced with sgRNAs. We also detail the procedures for selecting effective CRISPRi clones. For complete details on the use and execution of this protocol, please refer to Matsui et al.1.
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Affiliation(s)
- Satoshi Matsui
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Joseph R Shiley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Marissa Granitto
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Katie Ludwig
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Morgan Buckley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Sandra Koigi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Gerardo Mirizio
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Christopher N Mayhew
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA.
| | - Makiko Iwafuchi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA.
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10
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Prondzynski M, Berkson P, Trembley MA, Tharani Y, Shani K, Bortolin RH, Sweat ME, Mayourian J, Yucel D, Cordoves AM, Gabbin B, Hou C, Anyanwu NJ, Nawar F, Cotton J, Milosh J, Walker D, Zhang Y, Lu F, Liu X, Parker KK, Bezzerides VJ, Pu WT. Efficient and reproducible generation of human iPSC-derived cardiomyocytes and cardiac organoids in stirred suspension systems. Nat Commun 2024; 15:5929. [PMID: 39009604 PMCID: PMC11251028 DOI: 10.1038/s41467-024-50224-0] [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: 02/13/2023] [Accepted: 07/01/2024] [Indexed: 07/17/2024] Open
Abstract
Human iPSC-derived cardiomyocytes (hiPSC-CMs) have proven invaluable for cardiac disease modeling and regeneration. Challenges with quality, inter-batch consistency, cryopreservation and scale remain, reducing experimental reproducibility and clinical translation. Here, we report a robust stirred suspension cardiac differentiation protocol, and we perform extensive morphological and functional characterization of the resulting bioreactor-differentiated iPSC-CMs (bCMs). Across multiple different iPSC lines, the protocol produces 1.2E6/mL bCMs with ~94% purity. bCMs have high viability after cryo-recovery (>90%) and predominantly ventricular identity. Compared to standard monolayer-differentiated CMs, bCMs are more reproducible across batches and have more mature functional properties. The protocol also works with magnetically stirred spinner flasks, which are more economical and scalable than bioreactors. Minor protocol modifications generate cardiac organoids fully in suspension culture. These reproducible, scalable, and resource-efficient approaches to generate iPSC-CMs and organoids will expand their applications, and our benchmark data will enable comparison to cells produced by other cardiac differentiation protocols.
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Affiliation(s)
| | - Paul Berkson
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Michael A Trembley
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Yashasvi Tharani
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Kevin Shani
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, 02134, USA
| | - Raul H Bortolin
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Mason E Sweat
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Joshua Mayourian
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Dogacan Yucel
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Albert M Cordoves
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, 02134, USA
| | - Beatrice Gabbin
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Cuilan Hou
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Cardiology, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Nnaemeka J Anyanwu
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, 02134, USA
| | - Farina Nawar
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Justin Cotton
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Joseph Milosh
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - David Walker
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Yan Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Fujian Lu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Xujie Liu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Fuwai Hospital, Chinese Academy of Medical Science, Shenzhen, Shenzhen, Guangdong Province, 518057, China
| | - Kevin Kit Parker
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, 02134, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | | | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
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11
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Zhao J, Liang S, Cen HH, Li Y, Baker RK, Ruprai B, Gao G, Zhang C, Ren H, Tang C, Chen L, Liu Y, Lynn FC, Johnson JD, Kieffer TJ. PDX1+ cell budding morphogenesis in a stem cell-derived islet spheroid system. Nat Commun 2024; 15:5894. [PMID: 39003281 PMCID: PMC11246529 DOI: 10.1038/s41467-024-50109-2] [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: 01/06/2024] [Accepted: 07/01/2024] [Indexed: 07/15/2024] Open
Abstract
Remarkable advances in protocol development have been achieved to manufacture insulin-secreting islets from human pluripotent stem cells (hPSCs). Distinct from current approaches, we devised a tunable strategy to generate islet spheroids enriched for major islet cell types by incorporating PDX1+ cell budding morphogenesis into staged differentiation. In this process that appears to mimic normal islet morphogenesis, the differentiating islet spheroids organize with endocrine cells that are intermingled or arranged in a core-mantle architecture, accompanied with functional heterogeneity. Through in vitro modelling of human pancreas development, we illustrate the importance of PDX1 and the requirement for EphB3/4 signaling in eliciting cell budding morphogenesis. Using this new approach, we model Mitchell-Riley syndrome with RFX6 knockout hPSCs illustrating unexpected morphogenesis defects in the differentiation towards islet cells. The tunable differentiation system and stem cell-derived islet models described in this work may facilitate addressing fundamental questions in islet biology and probing human pancreas diseases.
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Affiliation(s)
- Jia Zhao
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada.
| | - Shenghui Liang
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Haoning Howard Cen
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Yanjun Li
- Institute of Molecular Medicine, School of Future Technology, National Biomedical Imaging Center, Peking University, Beijing, China
| | - Robert K Baker
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Balwinder Ruprai
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Guang Gao
- Imaging Core Facility, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Chloe Zhang
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Huixia Ren
- Institute of Molecular Medicine, School of Future Technology, National Biomedical Imaging Center, Peking University, Beijing, China
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Liangyi Chen
- Institute of Molecular Medicine, School of Future Technology, National Biomedical Imaging Center, Peking University, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Yanmei Liu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, South China Normal University, 510631, Guangzhou, China
- Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, 510631, Guangzhou, China
| | - Francis C Lynn
- BC Children's Hospital Research Institute, Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - James D Johnson
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Timothy J Kieffer
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
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12
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Edenhofer FC, Térmeg A, Ohnuki M, Jocher J, Kliesmete Z, Briem E, Hellmann I, Enard W. Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi. iScience 2024; 27:110090. [PMID: 38947524 PMCID: PMC11214527 DOI: 10.1016/j.isci.2024.110090] [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: 09/15/2023] [Revised: 03/28/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Comparisons of molecular phenotypes across primates provide unique information to understand human biology and evolution, and single-cell RNA-seq CRISPR interference (CRISPRi) screens are a powerful approach to analyze them. Here, we generate and validate three human, three gorilla, and two cynomolgus iPS cell lines that carry a dox-inducible KRAB-dCas9 construct at the AAVS1 locus. We show that despite variable expression levels of KRAB-dCas9 among lines, comparable downregulation of target genes and comparable phenotypic effects are observed in a single-cell RNA-seq CRISPRi screen. Hence, we provide valuable resources for performing and further extending CRISPRi in human and non-human primates.
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Affiliation(s)
- Fiona C. Edenhofer
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Anita Térmeg
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Mari Ohnuki
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan
- Hakubi Center, Kyoto University, Kyoto 606-8501, Japan
| | - Jessica Jocher
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Zane Kliesmete
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Eva Briem
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
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13
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Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, da Silva EB, O'Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small molecule in situ resin capture provides a compound first approach to natural product discovery. Nat Commun 2024; 15:5230. [PMID: 38898025 PMCID: PMC11187115 DOI: 10.1038/s41467-024-49367-x] [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: 08/24/2023] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Culture-based microbial natural product discovery strategies fail to realize the extraordinary biosynthetic potential detected across earth's microbiomes. Here we introduce Small Molecule In situ Resin Capture (SMIRC), a culture-independent method to obtain natural products directly from the environments in which they are produced. We use SMIRC to capture numerous compounds including two new carbon skeletons that were characterized using NMR and contain structural features that are, to the best of our knowledge, unprecedented among natural products. Applications across diverse marine habitats reveal biome-specific metabolomic signatures and levels of chemical diversity in concordance with sequence-based predictions. Expanded deployments, in situ cultivation, and metagenomics facilitate compound discovery, enhance yields, and link compounds to candidate producing organisms, although microbial community complexity creates challenges for the later. This compound-first approach to natural product discovery provides access to poorly explored chemical space and has implications for drug discovery and the detection of chemically mediated biotic interactions.
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Affiliation(s)
- Alexander Bogdanov
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Mariam N Salib
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alexander B Chase
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Earth Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Heinz Hammerlindl
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Mitchell N Muskat
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Tadeusz F Molinski
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Paul R Jensen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.
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14
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Shi S, Hamann CA, Lee JC, Brunger JM. Use of CRISPRoff and synthetic Notch to modulate and relay endogenous gene expression programs in engineered cells. Front Bioeng Biotechnol 2024; 12:1346810. [PMID: 38957576 PMCID: PMC11218679 DOI: 10.3389/fbioe.2024.1346810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
Uncovering the stimulus-response histories that give rise to cell fates and behaviors is an area of great interest in developmental biology, tissue engineering, and regenerative medicine. A comprehensive accounting of cell experiences that lead to the development of organs and tissues can help us to understand developmental anomalies that may underly disease. Perhaps more provocatively, such a record can also reveal clues as to how to drive cell collective decision-making processes, which may yield predictable cell-based therapies or facilitate production of tissue substitutes for transplantation or in vitro screening of prospective therapies to mitigate disease. Toward this end, various methods have been applied to molecularly trace developmental trajectories and record interaction histories of cells. Typical methods involve artificial gene circuits based on recombinases that activate a suite of fluorescent reporters or CRISPR-Cas9 genome writing technologies whose nucleic acid-based record keeping serves to chronicle cell-cell interactions or past exposure to stimuli of interests. Exciting expansions of the synthetic biology toolkit with artificial receptors that permit establishment of defined input-to-output linkages of cell decision-making processes opens the door to not only record cell-cell interactions, but to also potentiate directed manipulation of the outcomes of such interactions via regulation of carefully selected transgenes. Here, we combine CRISPR-based strategies to genetically and epigenetically manipulate cells to express components of the synthetic Notch receptor platform, a widely used artificial cell signaling module. Our approach gives rise to the ability to conditionally record interactions between human cells, where the record of engagement depends on expression of a state-specific marker of a subset of cells in a population. Further, such signal-competent interactions can be used to direct differentiation of human embryonic stem cells toward pre-selected fates based on assigned synNotch outputs. We also implemented CRISPR-based manipulation of native gene expression profiles to bias outcomes of cell engagement histories in a targeted manner. Thus, we present a useful strategy that gives rise to both state-specific recording of cell-cell interactions as well as methods to intentionally influence products of such cell-cell exchanges.
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Affiliation(s)
- Shuqun Shi
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States
| | - Catherine A. Hamann
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States
| | - Joanne C. Lee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States
| | - Jonathan M. Brunger
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, United States
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15
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Qin M, Deng C, Wen L, Luo G, Meng Y. CRISPR-Cas and CRISPR-based screening system for precise gene editing and targeted cancer therapy. J Transl Med 2024; 22:516. [PMID: 38816739 PMCID: PMC11138051 DOI: 10.1186/s12967-024-05235-2] [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: 01/03/2024] [Accepted: 04/24/2024] [Indexed: 06/01/2024] Open
Abstract
Target cancer therapy has been developed for clinical cancer treatment based on the discovery of CRISPR (clustered regularly interspaced short palindromic repeat) -Cas system. This forefront and cutting-edge scientific technique improves the cancer research into molecular level and is currently widely utilized in genetic investigation and clinical precision cancer therapy. In this review, we summarized the genetic modification by CRISPR/Cas and CRISPR screening system, discussed key components for successful CRISPR screening, including Cas enzymes, guide RNA (gRNA) libraries, target cells or organs. Furthermore, we focused on the application for CAR-T cell therapy, drug target, drug screening, or drug selection in both ex vivo and in vivo with CRISPR screening system. In addition, we elucidated the advantages and potential obstacles of CRISPR system in precision clinical medicine and described the prospects for future genetic therapy.In summary, we provide a comprehensive and practical perspective on the development of CRISPR/Cas and CRISPR screening system for the treatment of cancer defects, aiming to further improve the precision and accuracy for clinical treatment and individualized gene therapy.
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Affiliation(s)
- Mingming Qin
- Reproductive Medical Center, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University (Foshan Women and Children Hospital), Foshan, Guangdong, 528000, China
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Chunhao Deng
- Chinese Medicine and Translational Medicine R&D center, Zhuhai UM Science & Technology Research Institute, Zhuhai, Guangdong, 519031, China
| | - Liewei Wen
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, Zhuhai Clinical Medical College of Jinan University, Zhuhai, Guangdong, 519000, China
| | - Guoqun Luo
- Reproductive Medical Center, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University (Foshan Women and Children Hospital), Foshan, Guangdong, 528000, China.
| | - Ya Meng
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, Zhuhai Clinical Medical College of Jinan University, Zhuhai, Guangdong, 519000, China.
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16
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Kantor B, Odonovan B, Rittiner J, Hodgson D, Lindner N, Guerrero S, Dong W, Zhang A, Chiba-Falek O. All-in-one AAV-delivered epigenome-editing platform: proof-of-concept and therapeutic implications for neurodegenerative disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.14.536951. [PMID: 38798630 PMCID: PMC11118458 DOI: 10.1101/2023.04.14.536951] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Safely and efficiently controlling gene expression is a long-standing goal of biomedical research, and the recently discovered bacterial CRISPR/Cas system can be harnessed to create powerful tools for epigenetic editing. Current state-of-the-art systems consist of a deactivated-Cas9 nuclease (dCas9) fused to one of several epigenetic effector motifs/domains, along with a guide RNA (gRNA) which defines the genomic target. Such systems have been used to safely and effectively silence or activate a specific gene target under a variety of circumstances. Adeno-associated vectors (AAVs) are the therapeutic platform of choice for the delivery of genetic cargo; however, their small packaging capacity is not suitable for delivery of large constructs, which includes most CRISPR/dCas9-effector systems. To circumvent this, many AAV-based CRISPR/Cas tools are delivered in two pieces, from two separate viral cassettes. However, this approach requires higher viral payloads and usually is less efficient. Here we develop a compact dCas9-based repressor system packaged within a single, optimized AAV vector. The system uses a smaller dCas9 variant derived from Staphylococcus aureus ( Sa ). A novel repressor was engineered by fusing the small transcription repression domain (TRD) from MeCP2 with the KRAB repression domain. The final d Sa Cas9-KRAB-MeCP2(TRD) construct can be efficiently packaged, along with its associated gRNA, into AAV particles. Using reporter assays, we demonstrate that the platform is capable of robustly and sustainably repressing the expression of multiple genes-of-interest, both in vitro and in vivo . Moreover, we successfully reduced the expression of ApoE, the stronger genetic risk factor for late onset Alzheimer's disease (LOAD). This new platform will broaden the CRISPR/dCas9 toolset available for transcriptional manipulation of gene expression in research and therapeutic settings.
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17
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Franks SN, Heon-Roberts R, Ryan BJ. CRISPRi: a way to integrate iPSC-derived neuronal models. Biochem Soc Trans 2024; 52:539-551. [PMID: 38526223 PMCID: PMC11088925 DOI: 10.1042/bst20230190] [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: 09/07/2023] [Revised: 02/28/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024]
Abstract
The genetic landscape of neurodegenerative diseases encompasses genes affecting multiple cellular pathways which exert effects in an array of neuronal and glial cell-types. Deconvolution of the roles of genes implicated in disease and the effects of disease-associated variants remains a vital step in the understanding of neurodegeneration and the development of therapeutics. Disease modelling using patient induced pluripotent stem cells (iPSCs) has enabled the generation of key cell-types associated with disease whilst maintaining the genomic variants that predispose to neurodegeneration. The use of CRISPR interference (CRISPRi), alongside other CRISPR-perturbations, allows the modelling of the effects of these disease-associated variants or identifying genes which modify disease phenotypes. This review summarises the current applications of CRISPRi in iPSC-derived neuronal models, such as fluorescence-activated cell sorting (FACS)-based screens, and discusses the future opportunities for disease modelling, identification of disease risk modifiers and target/drug discovery in neurodegeneration.
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Affiliation(s)
- Sarah N.J. Franks
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Rachel Heon-Roberts
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Brent J. Ryan
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
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18
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Chatterjee S, Leach-Mehrwald M, Huang CK, Xiao K, Fuchs M, Otto M, Lu D, Dang V, Winkler T, Dunbar CE, Thum T, Bär C. Telomerase is essential for cardiac differentiation and sustained metabolism of human cardiomyocytes. Cell Mol Life Sci 2024; 81:196. [PMID: 38658440 PMCID: PMC11043037 DOI: 10.1007/s00018-024-05239-7] [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: 10/24/2023] [Revised: 03/29/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024]
Abstract
Telomeres as the protective ends of linear chromosomes, are synthesized by the enzyme telomerase (TERT). Critically short telomeres essentially contribute to aging-related diseases and are associated with a broad spectrum of disorders known as telomeropathies. In cardiomyocytes, telomere length is strongly correlated with cardiomyopathies but it remains ambiguous whether short telomeres are the cause or the result of the disease. In this study, we employed an inducible CRISPRi human induced pluripotent stem cell (hiPSC) line to silence TERT expression enabling the generation of hiPSCs and hiPSC-derived cardiomyocytes with long and short telomeres. Reduced telomerase activity and shorter telomere lengths of hiPSCs induced global transcriptomic changes associated with cardiac developmental pathways. Consequently, the differentiation potential towards cardiomyocytes was strongly impaired and single cell RNA sequencing revealed a shift towards a more smooth muscle cell like identity in the cells with the shortest telomeres. Poor cardiomyocyte function and increased sensitivity to stress directly correlated with the extent of telomere shortening. Collectively our data demonstrates a TERT dependent cardiomyogenic differentiation defect, highlighting the CRISPRi TERT hiPSCs model as a powerful platform to study the mechanisms and consequences of short telomeres in the heart and also in the context of telomeropathies.
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Affiliation(s)
- Shambhabi Chatterjee
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
- Center of Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Megan Leach-Mehrwald
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Cheng-Kai Huang
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Ke Xiao
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Maximilian Fuchs
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Mandy Otto
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Dongchao Lu
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
- Center of Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Vinh Dang
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Winkler
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia E Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
- Center of Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Christian Bär
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany.
- Center of Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany.
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany.
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19
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Pandey GK, Vadlamudi S, Currin KW, Moxley AH, Nicholas JC, McAfee JC, Broadaway KA, Mohlke KL. Liver regulatory mechanisms of noncoding variants at lipid and metabolic trait loci. HGG ADVANCES 2024; 5:100275. [PMID: 38297830 PMCID: PMC10881423 DOI: 10.1016/j.xhgg.2024.100275] [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: 10/01/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
Genome-wide association studies (GWASs) have identified hundreds of risk loci for liver disease and lipid-related metabolic traits, although identifying their target genes and molecular mechanisms remains challenging. We predicted target genes at GWAS signals by integrating them with molecular quantitative trait loci for liver gene expression (eQTL) and liver chromatin accessibility QTL (caQTL). We predicted specific regulatory caQTL variants at four GWAS signals located near EFHD1, LITAF, ZNF329, and GPR180. Using transcriptional reporter assays, we determined that caQTL variants rs13395911, rs11644920, rs34003091, and rs9556404 exhibit allelic differences in regulatory activity. We also performed a protein binding assay for rs13395911 and found that FOXA2 differentially interacts with the alleles of rs13395911. For variants rs13395911 and rs11644920 in putative enhancer regulatory elements, we used CRISPRi to demonstrate that repression of the enhancers altered the expression of the predicted target and/or nearby genes. Repression of the element at rs13395911 reduced the expression of EFHD1, and repression of the element at rs11644920 reduced the expression of LITAF, SNN, and TXNDC11. Finally, we showed that EFHD1 is a metabolically active gene in HepG2 cells. Together, these results provide key steps to connect genetic variants with cellular mechanisms and help elucidate the causes of liver disease.
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Affiliation(s)
- Gautam K Pandey
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Kevin W Currin
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anne H Moxley
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jayna C Nicholas
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jessica C McAfee
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - K Alaine Broadaway
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
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20
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Wu Z, Shen S, Mizikovsky D, Cao Y, Naval-Sanchez M, Tan SZ, Alvarez YD, Sun Y, Chen X, Zhao Q, Kim D, Yang P, Hill TA, Jones A, Fairlie DP, Pébay A, Hewitt AW, Tam PPL, White MD, Nefzger CM, Palpant NJ. Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm. Dev Cell 2024; 59:705-722.e8. [PMID: 38354738 DOI: 10.1016/j.devcel.2024.01.019] [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: 03/08/2023] [Revised: 10/27/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024]
Abstract
Wnt signaling is a critical determinant of cell lineage development. This study used Wnt dose-dependent induction programs to gain insights into molecular regulation of stem cell differentiation. We performed single-cell RNA sequencing of hiPSCs responding to a dose escalation protocol with Wnt agonist CHIR-99021 during the exit from pluripotency to identify cell types and genetic activity driven by Wnt stimulation. Results of activated gene sets and cell types were used to build a multiple regression model that predicts the efficiency of cardiomyocyte differentiation. Cross-referencing Wnt-associated gene expression profiles to the Connectivity Map database, we identified the small-molecule drug, tranilast. We found that tranilast synergistically activates Wnt signaling to promote cardiac lineage differentiation, which we validate by in vitro analysis of hiPSC differentiation and in vivo analysis of developing quail embryos. Our study provides an integrated workflow that links experimental datasets, prediction models, and small-molecule databases to identify drug-like compounds that control cell differentiation.
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Affiliation(s)
- Zhixuan Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sophie Shen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Dalia Mizikovsky
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuanzhao Cao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Marina Naval-Sanchez
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Siew Zhuan Tan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yanina D Alvarez
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuliangzi Sun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Xiaoli Chen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Qiongyi Zhao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Daniel Kim
- Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Pengyi Yang
- Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Timothy A Hill
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alun Jones
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P Fairlie
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Patrick P L Tam
- Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Melanie D White
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Christian M Nefzger
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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21
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Xiao F, Zhang X, Morton SU, Kim SW, Fan Y, Gorham JM, Zhang H, Berkson PJ, Mazumdar N, Cao Y, Chen J, Hagen J, Liu X, Zhou P, Richter F, Shen Y, Ward T, Gelb BD, Seidman JG, Seidman CE, Pu WT. Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease. Nat Genet 2024; 56:420-430. [PMID: 38378865 PMCID: PMC11218660 DOI: 10.1038/s41588-024-01669-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/23/2024] [Indexed: 02/22/2024]
Abstract
Rare coding mutations cause ∼45% of congenital heart disease (CHD). Noncoding mutations that perturb cis-regulatory elements (CREs) likely contribute to the remaining cases, but their identification has been problematic. Using a lentiviral massively parallel reporter assay (lentiMPRA) in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), we functionally evaluated 6,590 noncoding de novo variants (ncDNVs) prioritized from the whole-genome sequencing of 750 CHD trios. A total of 403 ncDNVs substantially affected cardiac CRE activity. A majority increased enhancer activity, often at regions with undetectable reference sequence activity. Of ten DNVs tested by introduction into their native genomic context, four altered the expression of neighboring genes and iPSC-CM transcriptional state. To prioritize future DNVs for functional testing, we used the MPRA data to develop a regression model, EpiCard. Analysis of an independent CHD cohort by EpiCard found enrichment of DNVs. Together, we developed a scalable system to measure the effect of ncDNVs on CRE activity and deployed it to systematically assess the contribution of ncDNVs to CHD.
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Affiliation(s)
- Feng Xiao
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Xiaoran Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Sarah U Morton
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Seong Won Kim
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Youfei Fan
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Huan Zhang
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul J Berkson
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Neil Mazumdar
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Yangpo Cao
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jian Chen
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Jacob Hagen
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Xujie Liu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Pingzhu Zhou
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Felix Richter
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York City, NY, USA
| | - Tarsha Ward
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Division of Cardiology, Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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22
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Farah EN, Hu RK, Kern C, Zhang Q, Lu TY, Ma Q, Tran S, Zhang B, Carlin D, Monell A, Blair AP, Wang Z, Eschbach J, Li B, Destici E, Ren B, Evans SM, Chen S, Zhu Q, Chi NC. Spatially organized cellular communities form the developing human heart. Nature 2024; 627:854-864. [PMID: 38480880 PMCID: PMC10972757 DOI: 10.1038/s41586-024-07171-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/07/2024] [Indexed: 03/18/2024]
Abstract
The heart, which is the first organ to develop, is highly dependent on its form to function1,2. However, how diverse cardiac cell types spatially coordinate to create the complex morphological structures that are crucial for heart function remains unclear. Here we integrated single-cell RNA-sequencing with high-resolution multiplexed error-robust fluorescence in situ hybridization to resolve the identity of the cardiac cell types that develop the human heart. This approach also provided a spatial mapping of individual cells that enables illumination of their organization into cellular communities that form distinct cardiac structures. We discovered that many of these cardiac cell types further specified into subpopulations exclusive to specific communities, which support their specialization according to the cellular ecosystem and anatomical region. In particular, ventricular cardiomyocyte subpopulations displayed an unexpected complex laminar organization across the ventricular wall and formed, with other cell subpopulations, several cellular communities. Interrogating cell-cell interactions within these communities using in vivo conditional genetic mouse models and in vitro human pluripotent stem cell systems revealed multicellular signalling pathways that orchestrate the spatial organization of cardiac cell subpopulations during ventricular wall morphogenesis. These detailed findings into the cellular social interactions and specialization of cardiac cell types constructing and remodelling the human heart offer new insights into structural heart diseases and the engineering of complex multicellular tissues for human heart repair.
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Affiliation(s)
- Elie N Farah
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Robert K Hu
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Colin Kern
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qingquan Zhang
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Ting-Yu Lu
- Materials Science and Engineering Program, University of California San Diego, La Jolla, CA, USA
| | - Qixuan Ma
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Shaina Tran
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Bo Zhang
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Daniel Carlin
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Alexander Monell
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Andrew P Blair
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Zilu Wang
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Jacqueline Eschbach
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Bin Li
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Eugin Destici
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Bing Ren
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sylvia M Evans
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Shaochen Chen
- Materials Science and Engineering Program, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Quan Zhu
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Neil C Chi
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA.
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23
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Prondzynski M, Bortolin RH, Berkson P, Trembley MA, Shani K, Sweat ME, Mayourian J, Cordoves AM, Anyanwu NJ, Tharani Y, Cotton J, Milosh JB, Walker D, Zhang Y, Liu F, Liu X, Parker KK, Bezzerides VJ, Pu WT. Efficient and reproducible generation of human iPSC-derived cardiomyocytes using a stirred bioreactor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581789. [PMID: 38464269 PMCID: PMC10925150 DOI: 10.1101/2024.02.24.581789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
In the last decade human iPSC-derived cardiomyocytes (hiPSC-CMs) proved to be valuable for cardiac disease modeling and cardiac regeneration, yet challenges with scale, quality, inter-batch consistency, and cryopreservation remain, reducing experimental reproducibility and limiting clinical translation. Here, we report a robust cardiac differentiation protocol that uses Wnt modulation and a stirred suspension bioreactor to produce on average 124 million hiPSC-CMs with >90% purity using a variety of hiPSC lines (19 differentiations; 10 iPSC lines). After controlled freeze and thaw, bioreactor-derived CMs (bCMs) showed high viability (>90%), interbatch reproducibility in cellular morphology, function, drug response and ventricular identity, which was further supported by single cell transcriptomes. bCMs on microcontact printed substrates revealed a higher degree of sarcomere maturation and viability during long-term culture compared to monolayer-derived CMs (mCMs). Moreover, functional investigation of bCMs in 3D engineered heart tissues showed earlier and stronger force production during long-term culture, and robust pacing capture up to 4 Hz when compared to mCMs. bCMs derived from this differentiation protocol will expand the applications of hiPSC-CMs by providing a reproducible, scalable, and resource efficient method to generate cardiac cells with well-characterized structural and functional properties superior to standard mCMs.
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Affiliation(s)
| | - Raul H Bortolin
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Paul Berkson
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Michael A Trembley
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kevin Shani
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences
| | - Mason E Sweat
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Joshua Mayourian
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Albert M Cordoves
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences
| | - Nnaemeka J Anyanwu
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences
| | - Yashasvi Tharani
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Justin Cotton
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Joseph B Milosh
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - David Walker
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Yan Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Fujian Liu
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Xujie Liu
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Fuwai Hospital, Chinese Academy of Medical Science, Shenzhen. Shenzhen, Guangdong Province, 518057, China
| | - Kevin K Parker
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences
- Harvard Stem Cell Institute, Cambridge, USA
| | | | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, USA
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24
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Karbassi E, Padgett R, Bertero A, Reinecke H, Klaiman JM, Yang X, Hauschka SD, Murry CE. Targeted CRISPR activation is functional in engineered human pluripotent stem cells but undergoes silencing after differentiation into cardiomyocytes and endothelium. Cell Mol Life Sci 2024; 81:95. [PMID: 38372898 PMCID: PMC10876724 DOI: 10.1007/s00018-023-05101-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 02/20/2024]
Abstract
Human induced pluripotent stem cells (hiPSCs) offer opportunities to study human biology where primary cell types are limited. CRISPR technology allows forward genetic screens using engineered Cas9-expressing cells. Here, we sought to generate a CRISPR activation (CRISPRa) hiPSC line to activate endogenous genes during pluripotency and differentiation. We first targeted catalytically inactive Cas9 fused to VP64, p65 and Rta activators (dCas9-VPR) regulated by the constitutive CAG promoter to the AAVS1 safe harbor site. These CRISPRa hiPSC lines effectively activate target genes in pluripotency, however the dCas9-VPR transgene expression is silenced after differentiation into cardiomyocytes and endothelial cells. To understand this silencing, we systematically tested different safe harbor sites and different promoters. Targeting to safe harbor sites hROSA26 and CLYBL loci also yielded hiPSCs that expressed dCas9-VPR in pluripotency but silenced during differentiation. Muscle-specific regulatory cassettes, derived from cardiac troponin T or muscle creatine kinase promoters, were also silent after differentiation when dCas9-VPR was introduced. In contrast, in cell lines where the dCas9-VPR sequence was replaced with cDNAs encoding fluorescent proteins, expression persisted during differentiation in all loci and with all promoters. Promoter DNA was hypermethylated in CRISPRa-engineered lines, and demethylation with 5-azacytidine enhanced dCas9-VPR gene expression. In summary, the dCas9-VPR cDNA is readily expressed from multiple loci during pluripotency but induces silencing in a locus- and promoter-independent manner during differentiation to mesoderm derivatives. Researchers intending to use this CRISPRa strategy during stem cell differentiation should pilot their system to ensure it remains active in their population of interest.
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Affiliation(s)
- Elaheh Karbassi
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Ruby Padgett
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alessandro Bertero
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Molecular Biotechnology Center "Guido Tarone", Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy
| | - Hans Reinecke
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Jordan M Klaiman
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Xiulan Yang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Stephen D Hauschka
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Translational Muscle Research, University of Washington, Seattle, WA, 98109, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98109, USA
| | - Charles E Murry
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA.
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA.
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, 98195, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
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25
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Carreras Mascaro A, Grochowska MM, Boumeester V, Dits NFJ, Bilgiҫ EN, Breedveld GJ, Vergouw L, de Jong FJ, van Royen ME, Bonifati V, Mandemakers W. LRP10 and α-synuclein transmission in Lewy body diseases. Cell Mol Life Sci 2024; 81:75. [PMID: 38315424 PMCID: PMC10844361 DOI: 10.1007/s00018-024-05135-0] [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: 06/27/2023] [Revised: 01/13/2024] [Accepted: 01/21/2024] [Indexed: 02/07/2024]
Abstract
Autosomal dominant variants in LRP10 have been identified in patients with Lewy body diseases (LBDs), including Parkinson's disease (PD), Parkinson's disease-dementia (PDD), and dementia with Lewy bodies (DLB). Nevertheless, there is little mechanistic insight into the role of LRP10 in disease pathogenesis. In the brains of control individuals, LRP10 is typically expressed in non-neuronal cells like astrocytes and neurovasculature, but in idiopathic and genetic cases of PD, PDD, and DLB, it is also present in α-synuclein-positive neuronal Lewy bodies. These observations raise the questions of what leads to the accumulation of LRP10 in Lewy bodies and whether a possible interaction between LRP10 and α-synuclein plays a role in disease pathogenesis. Here, we demonstrate that wild-type LRP10 is secreted via extracellular vesicles (EVs) and can be internalised via clathrin-dependent endocytosis. Additionally, we show that LRP10 secretion is highly sensitive to autophagy inhibition, which induces the formation of atypical LRP10 vesicular structures in neurons in human-induced pluripotent stem cells (iPSC)-derived brain organoids. Furthermore, we show that LRP10 overexpression leads to a strong induction of monomeric α-synuclein secretion, together with time-dependent, stress-sensitive changes in intracellular α-synuclein levels. Interestingly, patient-derived astrocytes carrying the c.1424 + 5G > A LRP10 variant secrete aberrant high-molecular-weight species of LRP10 in EV-free media fractions. Finally, we show that this truncated patient-derived LRP10 protein species (LRP10splice) binds to wild-type LRP10, reduces LRP10 wild-type levels, and antagonises the effect of LRP10 on α-synuclein levels and distribution. Together, this work provides initial evidence for a possible functional role of LRP10 in LBDs by modulating intra- and extracellular α-synuclein levels, and pathogenic mechanisms linked to the disease-associated c.1424 + 5G > A LRP10 variant, pointing towards potentially important disease mechanisms in LBDs.
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Affiliation(s)
- Ana Carreras Mascaro
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Martyna M Grochowska
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Valerie Boumeester
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Natasja F J Dits
- Department of Urology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ece Naz Bilgiҫ
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Guido J Breedveld
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Leonie Vergouw
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Frank Jan de Jong
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Martin E van Royen
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Vincenzo Bonifati
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wim Mandemakers
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.
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26
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Matsui S, Granitto M, Buckley M, Ludwig K, Koigi S, Shiley J, Zacharias WJ, Mayhew CN, Lim HW, Iwafuchi M. Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate. Mol Cell 2024; 84:476-489.e10. [PMID: 38211589 PMCID: PMC10872272 DOI: 10.1016/j.molcel.2023.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/30/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024]
Abstract
Pioneer transcription factors (TFs) regulate cell fate by establishing transcriptionally primed and active states. However, cell fate control requires the coordination of both lineage-specific gene activation and repression of alternative-lineage programs, a process that is poorly understood. Here, we demonstrate that the pioneer TF FOXA coordinates with PRDM1 TF to recruit nucleosome remodeling and deacetylation (NuRD) complexes and Polycomb repressive complexes (PRCs), which establish highly occupied, accessible nucleosome conformation with bivalent epigenetic states, thereby preventing precocious and alternative-lineage gene expression during human endoderm differentiation. Similarly, the pioneer TF OCT4 coordinates with PRDM14 to form bivalent enhancers and repress cell differentiation programs in human pluripotent stem cells, suggesting that this may be a common and critical function of pioneer TFs. We propose that pioneer and PRDM TFs coordinate to safeguard cell fate through epigenetic repression mechanisms.
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Affiliation(s)
- Satoshi Matsui
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Marissa Granitto
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Morgan Buckley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Katie Ludwig
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Sandra Koigi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Joseph Shiley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - William J Zacharias
- Division of Pulmonary Biology and Pulmonary and Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Christopher N Mayhew
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
| | - Makiko Iwafuchi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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27
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Friedman CE, Cheetham SW, Negi S, Mills RJ, Ogawa M, Redd MA, Chiu HS, Shen S, Sun Y, Mizikovsky D, Bouveret R, Chen X, Voges HK, Paterson S, De Angelis JE, Andersen SB, Cao Y, Wu Y, Jafrani YMA, Yoon S, Faulkner GJ, Smith KA, Porrello E, Harvey RP, Hogan BM, Nguyen Q, Zeng J, Kikuchi K, Hudson JE, Palpant NJ. HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function. Dev Cell 2024; 59:91-107.e6. [PMID: 38091997 DOI: 10.1016/j.devcel.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 05/09/2023] [Accepted: 11/13/2023] [Indexed: 01/11/2024]
Abstract
Genomic regulation of cardiomyocyte differentiation is central to heart development and function. This study uses genetic loss-of-function human-induced pluripotent stem cell-derived cardiomyocytes to evaluate the genomic regulatory basis of the non-DNA-binding homeodomain protein HOPX. We show that HOPX interacts with and controls cardiac genes and enhancer networks associated with diverse aspects of heart development. Using perturbation studies in vitro, we define how upstream cell growth and proliferation control HOPX transcription to regulate cardiac gene programs. We then use cell, organoid, and zebrafish regeneration models to demonstrate that HOPX-regulated gene programs control cardiomyocyte function in development and disease. Collectively, this study mechanistically links cell signaling pathways as upstream regulators of HOPX transcription to control gene programs underpinning cardiomyocyte identity and function.
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Affiliation(s)
- Clayton E Friedman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Seth W Cheetham
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sumedha Negi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Richard J Mills
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia; Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia; School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Masahito Ogawa
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - Meredith A Redd
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Han Sheng Chiu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sophie Shen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuliangzi Sun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Dalia Mizikovsky
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Romaric Bouveret
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - Xiaoli Chen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Holly K Voges
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Scott Paterson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jessica E De Angelis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Stacey B Andersen
- Genome Innovation Hub, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuanzhao Cao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yohaann M A Jafrani
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sohye Yoon
- Genome Innovation Hub, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Geoffrey J Faulkner
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia; Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Kelly A Smith
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Enzo Porrello
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne, VIC 3052, Australia; Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - Benjamin M Hogan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kazu Kikuchi
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - James E Hudson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia; School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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28
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Yang C, Lei Y, Ren T, Yao M. The Current Situation and Development Prospect of Whole-Genome Screening. Int J Mol Sci 2024; 25:658. [PMID: 38203828 PMCID: PMC10779205 DOI: 10.3390/ijms25010658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
High-throughput genetic screening is useful for discovering critical genes or gene sequences that trigger specific cell functions and/or phenotypes. Loss-of-function genetic screening is mainly achieved through RNA interference (RNAi), CRISPR knock-out (CRISPRko), and CRISPR interference (CRISPRi) technologies. Gain-of-function genetic screening mainly depends on the overexpression of a cDNA library and CRISPR activation (CRISPRa). Base editing can perform both gain- and loss-of-function genetic screening. This review discusses genetic screening techniques based on Cas9 nuclease, including Cas9-mediated genome knock-out and dCas9-based gene activation and interference. We compare these methods with previous genetic screening techniques based on RNAi and cDNA library overexpression and propose future prospects and applications for CRISPR screening.
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Affiliation(s)
| | | | | | - Mingze Yao
- Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education and Institute of Biomedical Sciences, Shanxi University, Taiyuan 030006, China; (C.Y.); (Y.L.); (T.R.)
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29
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Gao L, Behrens A, Rodschinka G, Forcelloni S, Wani S, Strasser K, Nedialkova DD. Selective gene expression maintains human tRNA anticodon pools during differentiation. Nat Cell Biol 2024; 26:100-112. [PMID: 38191669 PMCID: PMC10791582 DOI: 10.1038/s41556-023-01317-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/16/2023] [Indexed: 01/10/2024]
Abstract
Transfer RNAs are essential for translating genetic information into proteins. The human genome contains hundreds of predicted tRNA genes, many in multiple copies. How their expression is regulated to control tRNA repertoires is unknown. Here we combined quantitative tRNA profiling and chromatin immunoprecipitation with sequencing to measure tRNA expression following the differentiation of human induced pluripotent stem cells into neuronal and cardiac cells. We find that tRNA transcript levels vary substantially, whereas tRNA anticodon pools, which govern decoding rates, are more stable among cell types. Mechanistically, RNA polymerase III transcribes a wide range of tRNA genes in human induced pluripotent stem cells but on differentiation becomes constrained to a subset we define as housekeeping tRNAs. This shift is mediated by decreased mTORC1 signalling, which activates the RNA polymerase III repressor MAF1. Our data explain how tRNA anticodon pools are buffered to maintain decoding speed across cell types and reveal that mTORC1 drives selective tRNA expression during differentiation.
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Affiliation(s)
- Lexi Gao
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andrew Behrens
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Geraldine Rodschinka
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sergio Forcelloni
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sascha Wani
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Katrin Strasser
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Danny D Nedialkova
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany.
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30
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Mohassel P, Abdullah M, Eichler FS, Dunn TM. Serine Palmitoyltransferase (SPT)-related Neurodegenerative and Neurodevelopmental Disorders. J Neuromuscul Dis 2024; 11:735-747. [PMID: 38788085 PMCID: PMC11307022 DOI: 10.3233/jnd-240014] [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] [Accepted: 04/22/2024] [Indexed: 05/26/2024]
Abstract
Motor neuron diseases and peripheral neuropathies are heterogeneous groups of neurodegenerative disorders that manifest with distinct symptoms due to progressive dysfunction or loss of specific neuronal subpopulations during different stages of development. A few monogenic, neurodegenerative diseases associated with primary metabolic disruptions of sphingolipid biosynthesis have been recently discovered. Sphingolipids are a subclass of lipids that form critical building blocks of all cellular and subcellular organelle membranes including the membrane components of the nervous system cells. They are especially abundant within the lipid portion of myelin. In this review, we will focus on our current understanding of disease phenotypes in three monogenic, neuromuscular diseases associated with pathogenic variants in components of serine palmitoyltransferase, the first step in sphingolipid biosynthesis. These include hereditary sensory and autonomic neuropathy type 1 (HSAN1), a sensory predominant peripheral neuropathy, and two neurodegenerative disorders: juvenile amyotrophic lateral sclerosis affecting the upper and lower motor neurons with sparing of sensory neurons, and a complicated form of hereditary spastic paraplegia with selective involvement of the upper motor neurons and more broad CNS neurodegeneration. We will also review our current understanding of disease pathomechanisms, therapeutic approaches, and the unanswered questions to explore in future studies.
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Affiliation(s)
- Payam Mohassel
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Meher Abdullah
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Florian S. Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Teresa M. Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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31
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Punetha M, Saini S, Chaudhary S, Yadav PS, Whitworth K, Green J, Kumar D, Kues WA. Induced Pluripotent Stem Cells in the Era of Precise Genome Editing. Curr Stem Cell Res Ther 2024; 19:307-315. [PMID: 36880183 DOI: 10.2174/1574888x18666230307115326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/22/2022] [Accepted: 12/06/2022] [Indexed: 03/08/2023]
Abstract
Genome editing has enhanced our ability to understand the role of genetics in a number of diseases by facilitating the development of more precise cellular and animal models to study pathophysiological processes. These advances have shown extraordinary promise in a multitude of areas, from basic research to applied bioengineering and biomedical research. Induced pluripotent stem cells (iPSCs) are known for their high replicative capacity and are excellent targets for genetic manipulation as they can be clonally expanded from a single cell without compromising their pluripotency. Clustered, regularly interspaced short palindromic repeats (CRISPR) and CRISPR/Cas RNA-guided nucleases have rapidly become the method of choice for gene editing due to their high specificity, simplicity, low cost, and versatility. Coupling the cellular versatility of iPSCs differentiation with CRISPR/Cas9-mediated genome editing technology can be an effective experimental technique for providing new insights into the therapeutic use of this technology. However, before using these techniques for gene therapy, their therapeutic safety and efficacy following models need to be assessed. In this review, we cover the remarkable progress that has been made in the use of genome editing tools in iPSCs, their applications in disease research and gene therapy as well as the hurdles that remain in the actual implementation of CRISPR/Cas systems.
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Affiliation(s)
- Meeti Punetha
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, 125001, Haryana, India
| | - Sheetal Saini
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, 125001, Haryana, India
| | - Suman Chaudhary
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, 125001, Haryana, India
| | - Prem Singh Yadav
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, 125001, Haryana, India
| | - Kristin Whitworth
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jonathan Green
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Dharmendra Kumar
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, 125001, Haryana, India
| | - Wilfried A Kues
- Department of Biotechnology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Höltystr 10, 31535, Neustadt, Germany
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32
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Ren X, Yang H, Nierenberg JL, Sun Y, Chen J, Beaman C, Pham T, Nobuhara M, Takagi MA, Narayan V, Li Y, Ziv E, Shen Y. High-throughput PRIME-editing screens identify functional DNA variants in the human genome. Mol Cell 2023; 83:4633-4645.e9. [PMID: 38134886 PMCID: PMC10766087 DOI: 10.1016/j.molcel.2023.11.021] [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: 05/12/2023] [Revised: 10/07/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023]
Abstract
Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and single-base resolution manner remains challenging. Here, we develop a pooled prime-editing screen method, PRIME, that can be applied to characterize thousands of coding and non-coding variants in a single experiment with high reproducibility. To showcase its applications, we first identified essential nucleotides for a 716 bp MYC enhancer via PRIME-mediated single-base resolution analysis. Next, we applied PRIME to functionally characterize 1,304 genome-wide association study (GWAS)-identified non-coding variants associated with breast cancer and 3,699 variants from ClinVar. We discovered that 103 non-coding variants and 156 variants of uncertain significance are functional via affecting cell fitness. Collectively, we demonstrate that PRIME is capable of characterizing genetic variants at single-base resolution and scale, advancing accurate genome annotation for disease risk prediction, diagnosis, and therapeutic target identification.
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Affiliation(s)
- Xingjie Ren
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Han Yang
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Jovia L Nierenberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Yifan Sun
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cooper Beaman
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Thu Pham
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Mai Nobuhara
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Maya Asami Takagi
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Vivek Narayan
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC, USA; Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Elad Ziv
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Division of General Internal Medicine, Department of Medicine, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
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33
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Nandy K, Babu D, Rani S, Joshi G, Ijee S, George A, Palani D, Premkumar C, Rajesh P, Vijayanand S, David E, Murugesan M, Velayudhan SR. Efficient gene editing in induced pluripotent stem cells enabled by an inducible adenine base editor with tunable expression. Sci Rep 2023; 13:21953. [PMID: 38081875 PMCID: PMC10713686 DOI: 10.1038/s41598-023-42174-2] [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: 04/22/2023] [Accepted: 09/06/2023] [Indexed: 12/18/2023] Open
Abstract
The preferred method for disease modeling using induced pluripotent stem cells (iPSCs) is to generate isogenic cell lines by correcting or introducing pathogenic mutations. Base editing enables the precise installation of point mutations at specific genomic locations without the need for deleterious double-strand breaks used in the CRISPR-Cas9 gene editing methods. We created a bulk population of iPSCs that homogeneously express ABE8e adenine base editor enzyme under a doxycycline-inducible expression system at the AAVS1 safe harbor locus. These cells enabled fast, efficient and inducible gene editing at targeted genomic regions, eliminating the need for single-cell cloning and screening to identify those with homozygous mutations. We could achieve multiplex genomic editing by creating homozygous mutations in very high efficiencies at four independent genomic loci simultaneously in AAVS1-iABE8e iPSCs, which is highly challenging with previously described methods. The inducible ABE8e expression system allows editing of the genes of interest within a specific time window, enabling temporal control of gene editing to study the cell or lineage-specific functions of genes and their molecular pathways. In summary, the inducible ABE8e system provides a fast, efficient and versatile gene-editing tool for disease modeling and functional genomic studies.
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Affiliation(s)
- Krittika Nandy
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Dinesh Babu
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Sonam Rani
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Gaurav Joshi
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Smitha Ijee
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Anila George
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Dhavapriya Palani
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Chitra Premkumar
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Praveena Rajesh
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - S Vijayanand
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Ernest David
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Mohankumar Murugesan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Shaji R Velayudhan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India.
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India.
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34
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Han JL, Heinson YW, Chua CJ, Liu W, Entcheva E. CRISPRi gene modulation and all-optical electrophysiology in post-differentiated human iPSC-cardiomyocytes. Commun Biol 2023; 6:1236. [PMID: 38062109 PMCID: PMC10703822 DOI: 10.1038/s42003-023-05627-y] [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: 05/22/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Uncovering gene-phenotype relationships can be enabled by precise gene modulation in human induced pluripotent stem-cell-derived cardiomyocytes (iPSC-CMs) and follow up phenotyping using scalable all-optical electrophysiology platforms. Such efforts towards human functional genomics can be aided by recent CRISPR-derived technologies for reversible gene inhibition or activation (CRISPRi/a). We set out to characterize the performance of CRISPRi in post-differentiated iPSC-CMs, targeting key cardiac ion channel genes, KCNH2, KCNJ2, and GJA1, and providing a multiparametric quantification of the effects on cardiac repolarization, stability of the resting membrane potential and conduction properties using all-optical tools. More potent CRISPRi effectors, e.g., Zim3, and optimized viral delivery led to improved performance on par with the use of CRISPRi iPSC lines. Confirmed mild yet specific phenotype changes when CRISPRi is deployed in non-dividing differentiated heart cells is an important step towards more holistic pre-clinical cardiotoxicity testing and for future therapeutic use in vivo.
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Affiliation(s)
- Julie L Han
- Department of Biomedical Engineering, The George Washington University, Washington, DC, 20052, USA
| | - Yuli W Heinson
- Department of Biomedical Engineering, The George Washington University, Washington, DC, 20052, USA
| | - Christianne J Chua
- Department of Biomedical Engineering, The George Washington University, Washington, DC, 20052, USA
| | - Wei Liu
- Department of Biomedical Engineering, The George Washington University, Washington, DC, 20052, USA
| | - Emilia Entcheva
- Department of Biomedical Engineering, The George Washington University, Washington, DC, 20052, USA.
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35
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Liu F, Liu Z, Cheng W, Zhao Q, Zhang X, Zhang H, Yu M, Xu H, Gao Y, Jiang Q, Shi G, Wang L, Gu S, Wang J, Cao N, Chen Z. The PERK Branch of the Unfolded Protein Response Safeguards Protein Homeostasis and Mesendoderm Specification of Human Pluripotent Stem Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303799. [PMID: 37890465 PMCID: PMC10724406 DOI: 10.1002/advs.202303799] [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: 06/12/2023] [Revised: 08/14/2023] [Indexed: 10/29/2023]
Abstract
Cardiac development involves large-scale rearrangements of the proteome. How the developing cardiac cells maintain the integrity of the proteome during the rapid lineage transition remains unclear. Here it is shown that proteotoxic stress visualized by the misfolded and/or aggregated proteins appears during early cardiac differentiation of human pluripotent stem cells and is resolved by activation of the PERK branch of unfolded protein response (UPR). PERK depletion increases misfolded and/or aggregated protein accumulation, leading to pluripotency exit defect and impaired mesendoderm specification of human pluripotent stem cells. Mechanistically, it is found that PERK safeguards mesendoderm specification through its conserved downstream effector ATF4, which subsequently activates a novel transcriptional target WARS1, to cope with the differentiation-induced proteotoxic stress. The results indicate that protein quality control represents a previously unrecognized core component of the cardiogenic regulatory network. Broadly, these findings provide a framework for understanding how UPR is integrated into the developmental program by activating the PERK-ATF4-WARS1 axis.
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Affiliation(s)
- Fang Liu
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
- Department of Clinical LaboratoryThe First Affiliated Hospital of Anhui Medical UniversityHefei230022P. R. China
| | - Zhun Liu
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Weisheng Cheng
- Prenatal Diagnosis CenterDepartment of Obstetrics and GynecologyThe First Affiliated Hospital of Anhui Medical UniversityHefei230022P. R. China
- Department of Medical InformaticsZhongshan School of MedicineSun Yat‐Sen UniversityGuangzhou510080P. R. China
| | - Qingquan Zhao
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Xinyu Zhang
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - He Zhang
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Miao Yu
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - He Xu
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Yichen Gao
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Qianrui Jiang
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Guojun Shi
- Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity ResearchGuangdong Provincial Key Laboratory of DiabetologyThe Third Affiliated Hospital of Sun Yat‐Sen UniversityGuangdong510080P. R. China
| | - Likun Wang
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101P. R. China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049P. R. China
| | - Shanshan Gu
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Jia Wang
- School of Health and Life SciencesUniversity of Health and Rehabilitation SciencesShandong266071China
| | - Nan Cao
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Zhongyan Chen
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
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van Hugte EJH, Lewerissa EI, Wu KM, Scheefhals N, Parodi G, van Voorst TW, Puvogel S, Kogo N, Keller JM, Frega M, Schubert D, Schelhaas HJ, Verhoeven J, Majoie M, van Bokhoven H, Nadif Kasri N. SCN1A-deficient excitatory neuronal networks display mutation-specific phenotypes. Brain 2023; 146:5153-5167. [PMID: 37467479 PMCID: PMC10689919 DOI: 10.1093/brain/awad245] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/21/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
Dravet syndrome is a severe epileptic encephalopathy, characterized by (febrile) seizures, behavioural problems and developmental delay. Eighty per cent of patients with Dravet syndrome have a mutation in SCN1A, encoding Nav1.1. Milder clinical phenotypes, such as GEFS+ (generalized epilepsy with febrile seizures plus), can also arise from SCN1A mutations. Predicting the clinical phenotypic outcome based on the type of mutation remains challenging, even when the same mutation is inherited within one family. This clinical and genetic heterogeneity adds to the difficulties of predicting disease progression and tailoring the prescription of anti-seizure medication. Understanding the neuropathology of different SCN1A mutations may help to predict the expected clinical phenotypes and inform the selection of best-fit treatments. Initially, the loss of Na+-current in inhibitory neurons was recognized specifically to result in disinhibition and consequently seizure generation. However, the extent to which excitatory neurons contribute to the pathophysiology is currently debated and might depend on the patient clinical phenotype or the specific SCN1A mutation. To examine the genotype-phenotype correlations of SCN1A mutations in relation to excitatory neurons, we investigated a panel of patient-derived excitatory neuronal networks differentiated on multi-electrode arrays. We included patients with different clinical phenotypes, harbouring various SCN1A mutations, along with a family in which the same mutation led to febrile seizures, GEFS+ or Dravet syndrome. We hitherto describe a previously unidentified functional excitatory neuronal network phenotype in the context of epilepsy, which corresponds to seizurogenic network prediction patterns elicited by proconvulsive compounds. We found that excitatory neuronal networks were affected differently, depending on the type of SCN1A mutation, but did not segregate according to clinical severity. Specifically, loss-of-function mutations could be distinguished from missense mutations, and mutations in the pore domain could be distinguished from mutations in the voltage sensing domain. Furthermore, all patients showed aggravated neuronal network responses at febrile temperatures compared with controls. Finally, retrospective drug screening revealed that anti-seizure medication affected GEFS+ patient- but not Dravet patient-derived neuronal networks in a patient-specific and clinically relevant manner. In conclusion, our results indicate a mutation-specific excitatory neuronal network phenotype, which recapitulates the foremost clinically relevant features, providing future opportunities for precision therapies.
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Affiliation(s)
- Eline J H van Hugte
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, 6500 HB Nijmegen, The Netherlands
- Department of Epileptology, ACE Kempenhaeghe, 5591 VE Heeze, The Netherlands
| | - Elly I Lewerissa
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, 6500 HB Nijmegen, The Netherlands
| | - Ka Man Wu
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, The Netherlands
| | - Nicky Scheefhals
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, The Netherlands
| | - Giulia Parodi
- Department of Informatics, Bioengineering, Robotics, and Systems Engineering (DIBRIS), University of Genova, 16145 GE Genova, Italy
| | - Torben W van Voorst
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, 6500 HB Nijmegen, The Netherlands
| | - Sofia Puvogel
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, The Netherlands
| | - Naoki Kogo
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, 6500 HB Nijmegen, The Netherlands
| | - Jason M Keller
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, 6500 HB Nijmegen, The Netherlands
| | - Monica Frega
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, The Netherlands
- Department of Clinical Neurophysiology, University of Twente, 7522 NB Enschede, The Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, 6500 HB Nijmegen, The Netherlands
| | - Helenius J Schelhaas
- Department of Neurology, Stichting Epilepsie Instellingen Nederland (SEIN), 2103 SW Heemstede, The Netherlands
| | - Judith Verhoeven
- Department of Epileptology, ACE Kempenhaeghe, 5591 VE Heeze, The Netherlands
| | - Marian Majoie
- Department of Epileptology, ACE Kempenhaeghe, 5591 VE Heeze, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, 6500 HB Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, 6500 HB Nijmegen, The Netherlands
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Heinson YW, Han JL, Entcheva E. OptoDyCE-plate as an affordable high throughput imager for all optical cardiac electrophysiology. JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY PLUS 2023; 6:100054. [PMID: 38130942 PMCID: PMC10735237 DOI: 10.1016/j.jmccpl.2023.100054] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
We present a simple low-cost system for comprehensive functional characterization of cardiac function under spontaneous and paced conditions, in standard 96 and 384-well plates. This full-plate actuator/imager, OptoDyCE-plate, uses optogenetic stimulation and optical readouts of voltage and calcium (parallel recordings from up to 100 wells in 384-well plates are demonstrated). The system is validated with syncytia of human induced pluripotent stem cell derived cardiomyocytes, iPSC-CMs, grown as monolayers, or in quasi-3D isotropic and anisotropic constructs using electrospun matrices, in 96 and 384-well format. Genetic modifications, e.g. interference CRISPR (CRISPRi), and nine compounds of acute and chronic action were tested, including five histone deacetylase inhibitors (HDACis). Their effects on voltage and calcium were compared across growth conditions and pacing rates. We also demonstrated optogenetic point pacing via cell spheroids to study conduction in 96-well format, as well as temporal multiplexing to register voltage and calcium simultaneously on a single camera. Opto-DyCE-plate showed excellent performance even in the small samples in 384-well plates. Anisotropic structured constructs may provide some benefits in drug testing, although drug responses were consistent across tested configurations. Differential voltage vs. calcium responses were seen for some drugs, especially for non-traditional modulators of cardiac function, e.g. HDACi, and pacing rate was a powerful modulator of drug response, highlighting the need for comprehensive multiparametric assessment, as offered by OptoDyCE-plate. Increasing throughput and speed and reducing cost of screening can help stratify potential compounds early in the drug development process and accelerate the development of safer drugs.
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Affiliation(s)
| | | | - Emilia Entcheva
- Department of Biomedical Engineering, The George Washington University, Washington, DC 20052, United States of America
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38
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Schraivogel D, Steinmetz LM, Parts L. Pooled Genome-Scale CRISPR Screens in Single Cells. Annu Rev Genet 2023; 57:223-244. [PMID: 37562410 DOI: 10.1146/annurev-genet-072920-013842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Assigning functions to genes and learning how to control their expression are part of the foundation of cell biology and therapeutic development. An efficient and unbiased method to accomplish this is genetic screening, which historically required laborious clone generation and phenotyping and is still limited by scale today. The rapid technological progress on modulating gene function with CRISPR-Cas and measuring it in individual cells has now relaxed the major experimental constraints and enabled pooled screening with complex readouts from single cells. Here, we review the principles and practical considerations for pooled single-cell CRISPR screening. We discuss perturbation strategies, experimental model systems, matching the perturbation to the individual cells, reading out cell phenotypes, and data analysis. Our focus is on single-cell RNA sequencing and cell sorting-based readouts, including image-enabled cell sorting. We expect this transformative approach to fuel biomedical research for the next several decades.
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Affiliation(s)
- Daniel Schraivogel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany;
| | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany;
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA;
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, California, USA
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39
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Tyumentseva M, Tyumentsev A, Akimkin V. CRISPR/Cas9 Landscape: Current State and Future Perspectives. Int J Mol Sci 2023; 24:16077. [PMID: 38003266 PMCID: PMC10671331 DOI: 10.3390/ijms242216077] [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: 10/18/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 is a unique genome editing tool that can be easily used in a wide range of applications, including functional genomics, transcriptomics, epigenetics, biotechnology, plant engineering, livestock breeding, gene therapy, diagnostics, and so on. This review is focused on the current CRISPR/Cas9 landscape, e.g., on Cas9 variants with improved properties, on Cas9-derived and fusion proteins, on Cas9 delivery methods, on pre-existing immunity against CRISPR/Cas9 proteins, anti-CRISPR proteins, and their possible roles in CRISPR/Cas9 function improvement. Moreover, this review presents a detailed outline of CRISPR/Cas9-based diagnostics and therapeutic approaches. Finally, the review addresses the future expansion of genome editors' toolbox with Cas9 orthologs and other CRISPR/Cas proteins.
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Affiliation(s)
- Marina Tyumentseva
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (A.T.); (V.A.)
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40
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Lotfi M, Morshedi Rad D, Mashhadi SS, Ashouri A, Mojarrad M, Mozaffari-Jovin S, Farrokhi S, Hashemi M, Lotfi M, Ebrahimi Warkiani M, Abbaszadegan MR. Recent Advances in CRISPR/Cas9 Delivery Approaches for Therapeutic Gene Editing of Stem Cells. Stem Cell Rev Rep 2023; 19:2576-2596. [PMID: 37723364 PMCID: PMC10661828 DOI: 10.1007/s12015-023-10585-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 09/20/2023]
Abstract
Rapid advancement in genome editing technologies has provided new promises for treating neoplasia, cardiovascular, neurodegenerative, and monogenic disorders. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has emerged as a powerful gene editing tool offering advantages, including high editing efficiency and low cost over the conventional approaches. Human pluripotent stem cells (hPSCs), with their great proliferation and differentiation potential into different cell types, have been exploited in stem cell-based therapy. The potential of hPSCs and the capabilities of CRISPR/Cas9 genome editing has been paradigm-shifting in medical genetics for over two decades. Since hPSCs are categorized as hard-to-transfect cells, there is a critical demand to develop an appropriate and effective approach for CRISPR/Cas9 delivery into these cells. This review focuses on various strategies for CRISPR/Cas9 delivery in stem cells.
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Affiliation(s)
- Malihe Lotfi
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Dorsa Morshedi Rad
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Samaneh Sharif Mashhadi
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atefeh Ashouri
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Mojarrad
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shima Farrokhi
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Hashemi
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Marzieh Lotfi
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia.
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, Australia.
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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41
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Gelebart P, Eriksen Gjerstad M, Benjaminsen S, Han J, Karlsen I, Safont MM, Leitch C, Fandalyuk Z, Popa M, Helgeland L, Papp B, Baran-Marszak F, McCormack E. Inhibition of a new AXL isoform, AXL3, induces apoptosis of mantle cell lymphoma cells. Blood 2023; 142:1478-1493. [PMID: 37339584 DOI: 10.1182/blood.2022015581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/08/2023] [Accepted: 06/04/2023] [Indexed: 06/22/2023] Open
Abstract
Mantle cell lymphoma (MCL) is an aggressive B-cell non-Hodgkin lymphoma having a poor overall survival that is in need for the development of new therapeutics. In this study, we report the identification and expression of a new isoform splice variant of the tyrosine kinase receptor AXL in MCL cells. This new AXL isoform, called AXL3, lacks the ligand-binding domain of the commonly described AXL splice variants and is constitutively activated in MCL cells. Interestingly, functional characterization of AXL3, using CRISPR inhibition, revealed that only the knock down of this isoform leads to apoptosis of MCL cells. Importantly, pharmacological inhibition of AXL activity resulted in a significant decrease in the activation of well-known proproliferative and survival pathways activated in MCL cells (ie, β-catenin, Ak strain transforming, and NF-κB). Therapeutically, preclinical studies using a xenograft mouse model of MCL indicated that bemcentinib is more effective than ibrutinib in reducing the tumor burden and to increase the overall survival. Our study highlights the importance of a previously unidentified AXL splice variant in cancer and the potential of bemcentinib as a targeted therapy for MCL.
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Affiliation(s)
- Pascal Gelebart
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Hematology, Haukeland University Hospital, Bergen, Norway
| | | | | | - Jianhua Han
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ida Karlsen
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | - Calum Leitch
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | - Mihaela Popa
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Lars Helgeland
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Bela Papp
- INSERM, UMR U976, Institut Saint-Louis, Paris, France
- Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Paris, France
| | | | - Emmet McCormack
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Hematology, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Center for Pharmacy, University of Bergen, Bergen, Norway
- Department of Clinical Science, Center for Cancer Biomarkers, University of Bergen, Bergen, Norway
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42
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Tavakol DN, Nash TR, Kim Y, He S, Fleischer S, Graney PL, Brown JA, Liberman M, Tamargo M, Harken A, Ferrando AA, Amundson S, Garty G, Azizi E, Leong KW, Brenner DJ, Vunjak-Novakovic G. Modeling and countering the effects of cosmic radiation using bioengineered human tissues. Biomaterials 2023; 301:122267. [PMID: 37633022 PMCID: PMC10528250 DOI: 10.1016/j.biomaterials.2023.122267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023]
Abstract
Cosmic radiation is the most serious risk that will be encountered during the planned missions to the Moon and Mars. There is a compelling need to understand the effects, safety thresholds, and mechanisms of radiation damage in human tissues, in order to develop measures for radiation protection during extended space travel. As animal models fail to recapitulate the molecular changes in astronauts, engineered human tissues and "organs-on-chips" are valuable tools for studying effects of radiation in vitro. We have developed a bioengineered tissue platform for studying radiation damage in individualized settings. To demonstrate its utility, we determined the effects of radiation using engineered models of two human tissues known to be radiosensitive: engineered cardiac tissues (eCT, a target of chronic radiation damage) and engineered bone marrow (eBM, a target of acute radiation damage). We report the effects of high-dose neutrons, a proxy for simulated galactic cosmic rays, on the expression of key genes implicated in tissue responses to ionizing radiation, phenotypic and functional changes in both tissues, and proof-of-principle application of radioprotective agents. We further determined the extent of inflammatory, oxidative stress, and matrix remodeling gene expression changes, and found that these changes were associated with an early hypertrophic phenotype in eCT and myeloid skewing in eBM. We propose that individualized models of human tissues have potential to provide insights into the effects and mechanisms of radiation during deep-space missions and allow testing of radioprotective measures.
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Affiliation(s)
| | - Trevor R Nash
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Youngbin Kim
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Siyu He
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Sharon Fleischer
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Pamela L Graney
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Jessie A Brown
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Martin Liberman
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Manuel Tamargo
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Andrew Harken
- Center for Radiological Research, Columbia University, New York, NY 10032, USA
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Sally Amundson
- Center for Radiological Research, Columbia University, New York, NY 10032, USA
| | - Guy Garty
- Center for Radiological Research, Columbia University, New York, NY 10032, USA
| | - Elham Azizi
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - David J Brenner
- Center for Radiological Research, Columbia University, New York, NY 10032, USA
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA; Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA.
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43
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Militi S, Nibhani R, Jalali M, Pauklin S. RBL2-E2F-GCN5 guide cell fate decisions during tissue specification by regulating cell-cycle-dependent fluctuations of non-cell-autonomous signaling. Cell Rep 2023; 42:113146. [PMID: 37725511 DOI: 10.1016/j.celrep.2023.113146] [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: 01/15/2023] [Revised: 05/30/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023] Open
Abstract
The retinoblastoma family proteins (RBs) and E2F transcription factors are cell-autonomous regulators of cell-cycle progression, but they also impact fate choice in addition to tumor suppression. The range of mechanisms involved remains to be uncovered. Here, we show that RBs, particularly RBL2/p130, repress WNT ligands such as WNT4 and WNT8A, thereby directing ectoderm specification between neural crest to neuroepithelium. RBL2 achieves this function through cell-cycle-dependent cooperation with E2Fs and GCN5 on the regulatory regions of WNT loci, which direct neuroepithelial versus neural crest specification by temporal fluctuations of WNT/β-catenin and DLL/NOTCH signaling activity. Thus, the RB-E2F bona fide cell-autonomous axis controls cell fate decisions, and RBL2 regulates field effects via WNT ligands. This reveals a non-cell-autonomous function of RBL2-E2F in stem cell and tissue progenitor differentiation that has broader implications for cell-cycle-dependent cell fate specification in organogenesis, adult stem cells, tissue homeostasis, and tumorigenesis.
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Affiliation(s)
- Stefania Militi
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford OX3 7LD, UK
| | - Reshma Nibhani
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford OX3 7LD, UK
| | - Morteza Jalali
- Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford OX3 7LD, UK.
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44
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Balmas E, Sozza F, Bottini S, Ratto ML, Savorè G, Becca S, Snijders KE, Bertero A. Manipulating and studying gene function in human pluripotent stem cell models. FEBS Lett 2023; 597:2250-2287. [PMID: 37519013 DOI: 10.1002/1873-3468.14709] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are uniquely suited to study human development and disease and promise to revolutionize regenerative medicine. These applications rely on robust methods to manipulate gene function in hPSC models. This comprehensive review aims to both empower scientists approaching the field and update experienced stem cell biologists. We begin by highlighting challenges with manipulating gene expression in hPSCs and their differentiated derivatives, and relevant solutions (transfection, transduction, transposition, and genomic safe harbor editing). We then outline how to perform robust constitutive or inducible loss-, gain-, and change-of-function experiments in hPSCs models, both using historical methods (RNA interference, transgenesis, and homologous recombination) and modern programmable nucleases (particularly CRISPR/Cas9 and its derivatives, i.e., CRISPR interference, activation, base editing, and prime editing). We further describe extension of these approaches for arrayed or pooled functional studies, including emerging single-cell genomic methods, and the related design and analytical bioinformatic tools. Finally, we suggest some directions for future advancements in all of these areas. Mastering the combination of these transformative technologies will empower unprecedented advances in human biology and medicine.
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Affiliation(s)
- Elisa Balmas
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Federica Sozza
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Sveva Bottini
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Maria Luisa Ratto
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Giulia Savorè
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Silvia Becca
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Kirsten Esmee Snijders
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Alessandro Bertero
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
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Priesmeier L, Schoger E, Cyganek L, Cecilia Zelarayán L. Combining a tetracycline (Tet)-inducible gRNA system and CRISPRa for titratable and timely controlled enhancement of endogenous SHISA3 activation in human induced pluripotent stem cells (hiPSC). Stem Cell Res 2023; 71:103163. [PMID: 37433260 DOI: 10.1016/j.scr.2023.103163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/01/2023] [Indexed: 07/13/2023] Open
Abstract
Towards increasing the possibility for temporal control of gene expression using CRISPR activation (a) systems, we generated homozygous human induced pluripotent stem cell (hiPSC) lines carrying a doxycycline (dox)-inducible guide(g)-RNA construct targeting the SHISA3 transciptional start site, as proof-of-principle, or a non targeting gRNA as a control. The dox-inducible gRNA cassette was inserted into the human ROSA26 locus in a line with dCas9VPR integrated at the AAVS1 locus (CRISPRa/Tet-iSHISA3). Pluripotency, genomic integrity and differentiation potential into all three germ layers were maintained. Dox-dependent gene induction was validated in hiPSCs as well as derived fibroblasts. These lines provide an attractive tool for cellular reprogramming in hiPSC-derived cells in a timely controlled manner.
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Affiliation(s)
- Laura Priesmeier
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen (UMG), 37075 Göttingen, Göttingen, Germany; German Center for Cardiovascular Research (DZHK) Partner Site, Goettingen, Germany
| | - Eric Schoger
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen (UMG), 37075 Göttingen, Göttingen, Germany; German Center for Cardiovascular Research (DZHK) Partner Site, Goettingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
| | - Lukas Cyganek
- German Center for Cardiovascular Research (DZHK) Partner Site, Goettingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany; Clinic for Cardiology and Pneumology, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany
| | - Laura Cecilia Zelarayán
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen (UMG), 37075 Göttingen, Göttingen, Germany; German Center for Cardiovascular Research (DZHK) Partner Site, Goettingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany.
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46
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Heinson YW, Han JL, Entcheva E. OptoDyCE-plate as an affordable high throughput imager for all optical cardiac electrophysiology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555447. [PMID: 37693544 PMCID: PMC10491208 DOI: 10.1101/2023.08.29.555447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
We present a simple low-cost system for comprehensive functional characterization of cardiac function under spontaneous and paced conditions, in standard 96 and 384-well plates. This full-plate actuator/imager, OptoDyCE-plate, uses optogenetic stimulation and optical readouts of voltage and calcium from all wells in parallel. The system is validated with syncytia of human induced pluripotent stem cell derived cardiomyocytes, iPSC-CMs, grown as monolayers, or in quasi-3D isotropic and anisotropic constructs using electrospun matrices, in 96 and 394-well format. Genetic modifications, e.g. interference CRISPR (CRISPRi), and nine compounds of acute and chronic action were tested, including five histone deacetylase inhibitors (HDACis). Their effects on voltage and calcium were compared across growth conditions and pacing rates. We also demonstrated deployment of optogenetic cell spheroids for point pacing to study conduction in 96-well format, and the use of temporal multiplexing to register voltage and calcium simultaneously on a single camera in this stand-alone platform. Opto-DyCE-plate showed excellent performance even in the small samples in 384-well plates, in the various configurations. Anisotropic structured constructs may provide some benefits in drug testing, although drug responses were consistent across tested configurations. Differential voltage vs. calcium responses were seen for some drugs, especially for non-traditional modulators of cardiac function, e.g. HDACi, and pacing rate was a powerful modulator of drug response, highlighting the need for comprehensive multiparametric assessment, as offered by OptoDyCE-plate. Increasing throughput and speed and reducing cost of screening can help stratify potential compounds early in the drug development process and accelerate the development of safer drugs.
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Affiliation(s)
| | | | - Emilia Entcheva
- Department of Biomedical Engineering, The George Washington University, Washington, DC 20037
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47
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Vasic I, Libby ARG, Maslan A, Bulger EA, Zalazar D, Krakora Compagno MZ, Streets A, Tomoda K, Yamanaka S, McDevitt TC. Loss of TJP1 disrupts gastrulation patterning and increases differentiation toward the germ cell lineage in human pluripotent stem cells. Dev Cell 2023; 58:1477-1488.e5. [PMID: 37354899 PMCID: PMC10529434 DOI: 10.1016/j.devcel.2023.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/17/2023] [Accepted: 05/26/2023] [Indexed: 06/26/2023]
Abstract
Biological patterning events that occur early in development establish proper tissue morphogenesis. Identifying the mechanisms that guide these patterning events is necessary in order to understand the molecular drivers of development and disease and to build tissues in vitro. In this study, we use an in vitro model of gastrulation to study the role of tight junctions and apical/basolateral polarity in modulating bone morphogenic protein-4 (BMP4) signaling and gastrulation-associated patterning in colonies of human pluripotent stem cells (hPSCs). Disrupting tight junctions via knockdown (KD) of the scaffolding tight junction protein-1 (TJP1, also known as ZO1) allows BMP4 to robustly and ubiquitously activate pSMAD1/5 signaling over time, resulting in loss of the patterning phenotype and marked differentiation bias of pluripotent stem cells to primordial germ cell-like cells (PGCLCs). These findings give important insights into how signaling events are regulated and lead to spatial emergence of diverse cell types in vitro.
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Affiliation(s)
- Ivana Vasic
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA 94158
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA 94158
| | - Ashley RG Libby
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA 94158
- Developmental and Stem Cell Biology Ph.D. Program, University of California, San Francisco, San Francisco, CA, USA 94158
| | - Annie Maslan
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA 94158
- Department of Bioengineering, University of California, Berkeley, CA, USA 94720
- Center for Computational Biology, University of California, Berkeley, CA, USA 94720
| | - Emily A Bulger
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA 94158
- Developmental and Stem Cell Biology Ph.D. Program, University of California, San Francisco, San Francisco, CA, USA 94158
| | - David Zalazar
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA 94158
| | | | - Aaron Streets
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA 94158
- Department of Bioengineering, University of California, Berkeley, CA, USA 94720
- Center for Computational Biology, University of California, Berkeley, CA, USA 94720
- Chan Zuckerberg Biohub, San Francisco, CA, USA 94158
| | - Kiichiro Tomoda
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA 94158
- Center for iPS Cell Research and Application, Kyoto, Japan 606-8397
| | - Shinya Yamanaka
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA 94158
- Center for iPS Cell Research and Application, Kyoto, Japan 606-8397
| | - Todd C McDevitt
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA 94158
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA 94158
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48
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Laster DJ, Akel NS, Hendrixson JA, James A, Crawford JA, Fu Q, Berryhill SB, Thostenson JD, Nookaew I, O’Brien CA, Onal M. CRISPR interference provides increased cell type-specificity compared to the Cre-loxP system. iScience 2023; 26:107428. [PMID: 37575184 PMCID: PMC10415806 DOI: 10.1016/j.isci.2023.107428] [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: 12/16/2022] [Revised: 06/12/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
Cre-mediated recombination is frequently used for cell type-specific loss of function (LOF) studies. A major limitation of this system is recombination in unwanted cell types. CRISPR interference (CRISPRi) has been used effectively for global LOF in mice. However, cell type-specific CRISPRi, independent of recombination-based systems, has not been reported. To test the feasibility of cell type-specific CRISPRi, we produced two novel knock-in mouse models that achieve gene suppression when used together: one expressing dCas9::KRAB under the control of a cell type-specific promoter and the other expressing a single guide RNA from a safe harbor locus. We then compared the phenotypes of mice in which the same gene was targeted by either CRISPRi or the Cre-loxP system, with cell specificity conferred by Dmp1 regulatory elements in both cases. We demonstrate that CRISPRi is effective for cell type-specific LOF and that it provides improved cell type-specificity compared to the Cre-loxP system.
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Affiliation(s)
- Dominique J. Laster
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Nisreen S. Akel
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - James A. Hendrixson
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alicen James
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Julie A. Crawford
- Center for Musculoskeletal Disease Research (CMDR), University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Division of Endocrinology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Qiang Fu
- Center for Musculoskeletal Disease Research (CMDR), University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Division of Endocrinology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Stuart B. Berryhill
- Center for Musculoskeletal Disease Research (CMDR), University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Division of Endocrinology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jeff D. Thostenson
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Intawat Nookaew
- Center for Musculoskeletal Disease Research (CMDR), University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Charles A. O’Brien
- Center for Musculoskeletal Disease Research (CMDR), University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Division of Endocrinology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Melda Onal
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Center for Musculoskeletal Disease Research (CMDR), University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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49
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Doorn N, van Hugte EJH, Ciptasari U, Mordelt A, Meijer HGE, Schubert D, Frega M, Nadif Kasri N, van Putten MJAM. An in silico and in vitro human neuronal network model reveals cellular mechanisms beyond Na V1.1 underlying Dravet syndrome. Stem Cell Reports 2023; 18:1686-1700. [PMID: 37419110 PMCID: PMC10444571 DOI: 10.1016/j.stemcr.2023.06.003] [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: 01/10/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 07/09/2023] Open
Abstract
Human induced pluripotent stem cell (hiPSC)-derived neuronal networks on multi-electrode arrays (MEAs) provide a unique phenotyping tool to study neurological disorders. However, it is difficult to infer cellular mechanisms underlying these phenotypes. Computational modeling can utilize the rich dataset generated by MEAs, and advance understanding of disease mechanisms. However, existing models lack biophysical detail, or validation and calibration to relevant experimental data. We developed a biophysical in silico model that accurately simulates healthy neuronal networks on MEAs. To demonstrate the potential of our model, we studied neuronal networks derived from a Dravet syndrome (DS) patient with a missense mutation in SCN1A, encoding sodium channel NaV1.1. Our in silico model revealed that sodium channel dysfunctions were insufficient to replicate the in vitro DS phenotype, and predicted decreased slow afterhyperpolarization and synaptic strengths. We verified these changes in DS patient-derived neurons, demonstrating the utility of our in silico model to predict disease mechanisms.
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Affiliation(s)
- Nina Doorn
- Department of Clinical Neurophysiology, University of Twente, 7522 NB Enschede, the Netherlands.
| | - Eline J H van Hugte
- Department of Neurology, Academic Center for Epileptology Kempenhaeghe, 5591 VE Heeze, the Netherlands; Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neurosciences, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6525 HR Nijmegen, the Netherlands
| | - Ummi Ciptasari
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neurosciences, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6525 HR Nijmegen, the Netherlands
| | - Annika Mordelt
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neurosciences, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6525 HR Nijmegen, the Netherlands
| | - Hil G E Meijer
- Department of Applied Mathematics, University of Twente, 7522 NB Enschede, the Netherlands
| | - Dirk Schubert
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neurosciences, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6525 HR Nijmegen, the Netherlands
| | - Monica Frega
- Department of Clinical Neurophysiology, University of Twente, 7522 NB Enschede, the Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neurosciences, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6525 HR Nijmegen, the Netherlands
| | - Michel J A M van Putten
- Department of Clinical Neurophysiology, University of Twente, 7522 NB Enschede, the Netherlands; Department of Neurology and Clinical Neurophysiology, Medisch Spectrum Twente, 7512 KZ Enschede, the Netherlands
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50
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Hanson-Drury S, Patni AP, Lee DL, Alghadeer A, Zhao YT, Ehnes DD, Vo VN, Kim SY, Jithendra D, Phal A, Edman NI, Schlichthaerle T, Baker D, Young JE, Mathieu J, Ruohola-Baker H. Single Cell RNA Sequencing Reveals Human Tooth Type Identity and Guides In Vitro hiPSC Derived Odontoblast Differentiation (iOB). FRONTIERS IN DENTAL MEDICINE 2023; 4:10.3389/fdmed.2023.1209503. [PMID: 38259324 PMCID: PMC10802932 DOI: 10.3389/fdmed.2023.1209503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Over 90% of the U.S. adult population suffers from tooth structure loss due to caries. Most of the mineralized tooth structure is composed of dentin, a material produced and mineralized by ectomesenchyme derived cells known as odontoblasts. Clinicians, scientists, and the general public share the desire to regenerate this missing tooth structure. To bioengineer missing dentin, increased understanding of human tooth development is required. Here we interrogate at the single cell level the signaling interactions that guide human odontoblast and ameloblast development and which determine incisor or molar tooth germ type identity. During human odontoblast development, computational analysis predicts that early FGF and BMP activation followed by later HH signaling is crucial. Application of this sci-RNA-seq analysis generates a differentiation protocol to produce mature hiPSC derived odontoblasts in vitro (iOB). Further, we elucidate the critical role of FGF signaling in odontoblast maturation and its biomineralization capacity using the de novo designed FGFR1/2c isoform specific minibinder scaffolded as a C6 oligomer that acts as a pathway agonist. We find that FGFR1c is upregulated in functional odontoblasts and specifically plays a crucial role in driving odontoblast maturity. Using computational tools, we show on a molecular level how human molar development is delayed compared to incisors. We reveal that enamel knot development is guided by FGF and WNT in incisors and BMP and ROBO in the molars, and that incisor and molar ameloblast development is guided by FGF, EGF and BMP signaling, with tooth type specific intensity of signaling interactions. Dental ectomesenchyme derived cells are the primary source of signaling ligands responsible for both enamel knot and ameloblast development.
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Affiliation(s)
- Sesha Hanson-Drury
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, United States
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Anjali P. Patni
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, United States
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Genetic Engineering, SRM Institute of Science and Technology, Chennai, India
| | - Deborah L. Lee
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, United States
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Ammar Alghadeer
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, United States
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Biomedical Dental Sciences, College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Yan Ting Zhao
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, United States
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Devon Duron Ehnes
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, United States
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Vivian N. Vo
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Sydney Y. Kim
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Druthi Jithendra
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Biotechnology, SRM Institute of Science and Technology, Chennai, India
| | - Ashish Phal
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Bioengineering, University of Washington, Seattle, WA, United States
| | - Natasha I. Edman
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington,Seattle, WA 98195, USA
| | - Thomas Schlichthaerle
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - David Baker
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Jessica E. Young
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Comparative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Hannele Ruohola-Baker
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, United States
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Biology, University of Washington, Seattle, WA, United States
- Department of Bioengineering, University of Washington, Seattle, WA, United States
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