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Chen HJC, Mazzaferro S, Tian T, Mali I, Merkle FT. Differentiation, Transcriptomic Profiling, and Calcium Imaging of Human Hypothalamic Neurons. Curr Protoc 2023; 3:e786. [PMID: 37272700 PMCID: PMC7614736 DOI: 10.1002/cpz1.786] [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] [Indexed: 06/06/2023]
Abstract
Neurons in the hypothalamus orchestrate homeostatic physiological processes and behaviors essential for life. Human pluripotent stem cells (hPSCs) can be differentiated into many types of hypothalamic neurons, progenitors, and glia. This updated unit includes published studies and protocols with new advances in the differentiation, maturation, and interrogation by transcriptomic profiling and calcium imaging of human hypothalamic cell populations. Specifically, new methods to freeze and thaw hypothalamic progenitors after they have been patterned and before substantial neurogenesis has occurred are provided that will facilitate experimental flexibility and planning. Also included are updated recipes and protocols for neuronal maturation, with details on the equipment and methods for examining their transcriptomic response and cell-autonomous properties in culture in the presence of synaptic blockers. Together, these protocols facilitate the adoption and use of this model system for fundamental biological discovery and therapeutic translation to human diseases such as obesity, diabetes, sleep disorders, infertility, and chronic stress. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: hPSC maintenance Basic Protocol 2: Hypothalamic neuron differentiation Support Protocol 1: Cortical neuron (control) differentiation Basic Protocol 3: Neuronal maturation Support Protocol 2: Cryopreservation and thawing of neuronal progenitors Support Protocol 3: Quality control: Confirmation of hypothalamic patterning and neurogenesis Support Protocol 4: Bulk RNA sequencing of hypothalamic cultures Basic Protocol 4: Calcium imaging of hypothalamic neurons using Fura-2 AM Alternate Protocol: Calcium imaging of green fluorescent hypothalamic neurons using Rhod-3 AM.
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Affiliation(s)
- Hsiao-Jou Cortina Chen
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Wellcome Trust–Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Simone Mazzaferro
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Wellcome Trust–Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Tian Tian
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Wellcome Trust–Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Iman Mali
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
| | - Florian T. Merkle
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Wellcome Trust–Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
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2
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Zhang M, Yi F, Wu J, Tang Y. The efficient generation of knockout microglia cells using a dual-sgRNA strategy by CRISPR/Cas9. Front Mol Neurosci 2022; 15:1008827. [PMID: 36311032 PMCID: PMC9614382 DOI: 10.3389/fnmol.2022.1008827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 11/06/2023] Open
Abstract
Gene deletion in microglia has become an important and exciting approach for studying neuroinflammation, especially after the development of the CRISPR/Cas9 system for genome editing during the last decade. In this study, we described a protocol for the highly efficient generation of knockout microglia cells using a dual-short guide RNA (sgRNA) strategy by CRISPR/Cas9. Leucine-rich repeat kinase 2 (LRRK2), a pathogenic gene of Parkinson's disease (PD), has played versatile roles during the disease development. Despite many key insights into LRRK2 studies, the normal and disease-related functions of LRRK2 in microglia and neuroinflammation remain to be fully investigated. Given the importance of LRRK2 in PD pathogenesis, we designed and applied the protocol to target LRRK2. Specifically, we designed two sgRNAs targeting the N terminus of LRRK2, spanning the 5' untranslated region (UTR) and exon 1, and screened knockout cells by single-cell expansion. In practice, the dual-sgRNA system can facilitate in obtaining knockout cells in a more convenient, rapid, and accurate way. Candidate knockout cells can be easily distinguished by genomic PCR and running on agarose gels, based on the different band sizes. Successful knockouts were further verified by Sanger sequencing and Western blot. Using this protocol, we obtained an LRRK2-deficient microglia cell line, which was characterized by longer cellular processes, enhanced adhesion, and weakened migration capacity. The knockout microglia may further serve as an important cellular tool to reveal conserved and novel aspects of LRRK2 functions in the development and progression of PD. Our protocol using dual-sgRNA targeting guarantees > 60% targeting efficiency and could also be applied to targeting other genes/loci, especially non-coding RNAs and regulatory elements.
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Affiliation(s)
- Mengfei Zhang
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Fang Yi
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Junjiao Wu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, China
| | - Yu Tang
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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3
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Concise Review: Stem Cell Models of SCN1A-Related Encephalopathies—Current Perspective and Future Therapies. Cells 2022; 11:cells11193119. [PMID: 36231081 PMCID: PMC9561991 DOI: 10.3390/cells11193119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Mutations in the SCN1A gene can cause a variety of phenotypes, ranging from mild forms, such as febrile seizures and generalized epilepsy with febrile seizures plus, to severe, such as Dravet and non-Dravet developmental epileptic encephalopathies. Until now, more than two thousand pathogenic variants of the SCN1A gene have been identified and different pathogenic mechanisms (loss vs. gain of function) described, but the precise molecular mechanisms responsible for the deficits exhibited by patients are not fully elucidated. Additionally, the phenotypic variability proves the involvement of other genetic factors in its final expression. This is the reason why animal models and cell line models used to explore the molecular pathology of SCN1A-related disorders are only of limited use. The results of studies based on such models cannot be directly translated to affected individuals because they do not address each patient’s unique genetic background. The generation of functional neurons and glia for patient-derived iPSCs, together with the generation of isogenic controls using CRISPR/Cas technology, and finally, the 3D brain organoid models, seem to be a good way to solve this problem. Here, we review SCN1A-related encephalopathies, as well as the stem cell models used to explore their molecular basis.
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Simkin D, Papakis V, Bustos BI, Ambrosi CM, Ryan SJ, Baru V, Williams LA, Dempsey GT, McManus OB, Landers JE, Lubbe SJ, George AL, Kiskinis E. Homozygous might be hemizygous: CRISPR/Cas9 editing in iPSCs results in detrimental on-target defects that escape standard quality controls. Stem Cell Reports 2022; 17:993-1008. [PMID: 35276091 PMCID: PMC9023783 DOI: 10.1016/j.stemcr.2022.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 12/20/2022] Open
Abstract
The ability to precisely edit the genome of human induced pluripotent stem cell (iPSC) lines using CRISPR/Cas9 has enabled the development of cellular models that can address genotype to phenotype relationships. While genome editing is becoming an essential tool in iPSC-based disease modeling studies, there is no established quality control workflow for edited cells. Moreover, large on-target deletions and insertions that occur through DNA repair mechanisms have recently been uncovered in CRISPR/Cas9-edited loci. Yet the frequency of these events in human iPSCs remains unclear, as they can be difficult to detect. We examined 27 iPSC clones generated after targeting 9 loci and found that 33% had acquired large, on-target genomic defects, including insertions and loss of heterozygosity. Critically, all defects had escaped standard PCR and Sanger sequencing analysis. We describe a cost-efficient quality control strategy that successfully identified all edited clones with detrimental on-target events and could facilitate the integrity of iPSC-based studies.
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Affiliation(s)
- Dina Simkin
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Vasileios Papakis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Bernabe I Bustos
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Center of Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | | | | | | | | | | | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Steven J Lubbe
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Center of Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Alfred L George
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA; Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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5
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Benamozig O, Baudrier L, Billon P. A detection method for the capture of genomic signatures: From disease diagnosis to genome editing. Methods Enzymol 2021; 661:251-282. [PMID: 34776215 DOI: 10.1016/bs.mie.2021.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Variations in the genetic information originate from errors during DNA replication, error-prone repair of DNA damages, or genome editing. The most common approach to detect changes in DNA sequences employs sequencing technologies. However, they remain expensive and time-consuming, limiting their utility for routine laboratory experiments. We recently developed DinucleoTidE Signature CapTure (DTECT). DTECT is a marker-free and versatile detection method that captures targeted dinucleotide signatures resulting from the digestion of genomic amplicons by the type IIS restriction enzyme AcuI. Here, we describe the DTECT protocol to identify mutations introduced by CRISPR-based precision genome editing technologies or resulting from genetic variation. DTECT enables accurate detection of mutations using basic laboratory equipment and off-the-shelf reagents with qualitative or quantitative capture of signatures.
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Affiliation(s)
- Orléna Benamozig
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, Calgary, AB, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Lou Baudrier
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, Calgary, AB, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Pierre Billon
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, Calgary, AB, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada.
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6
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Motosugi N, Okada C, Sugiyama A, Kawasaki T, Kimura M, Shiina T, Umezawa A, Akutsu H, Fukuda A. Deletion of lncRNA XACT does not change expression dosage of X-linked genes, but affects differentiation potential in hPSCs. Cell Rep 2021; 35:109222. [PMID: 34107248 DOI: 10.1016/j.celrep.2021.109222] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/08/2021] [Accepted: 05/14/2021] [Indexed: 12/28/2022] Open
Abstract
Female human pluripotent stem cells (hPSCs) regularly show erosion of X chromosome inactivation featured by the loss of the long non-coding (lnc) RNA XIST and the accumulation of lncXACT. Here, we report that a common mechanism for the initiation of erosion depends on XIST loss but not XACT accumulation on inactive X chromosomes. We further demonstrate that XACT deletion does not affect X-linked gene dosage in eroded hPSCs and that aberrant XIST RNA diffusion induced by the CRISPR activation system is independent of the presence of XACT RNA. In contrast, the deletion of XACT results in the upregulation of neuron-related genes, facilitating neural differentiation in both male and eroded female hPSCs. XACT RNA repression by CRIPSR inhibition results in the same phenotype. Our study finds that XACT is dispensable for maintaining the erosion of X-lined gene repression on inactive X chromosomes but affects neural differentiation in hPSCs.
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Affiliation(s)
- Nami Motosugi
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Chisa Okada
- Support Center for Medical Research and Education, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Akiko Sugiyama
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Tomoyuki Kawasaki
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Minoru Kimura
- The Institute of Medical Sciences, Tokai University, Isehara, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Atsushi Fukuda
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan; The Institute of Medical Sciences, Tokai University, Isehara, Japan; Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, Japan; Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan.
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7
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Hocker JD, Poirion OB, Zhu F, Buchanan J, Zhang K, Chiou J, Wang TM, Zhang Q, Hou X, Li YE, Zhang Y, Farah EN, Wang A, McCulloch AD, Gaulton KJ, Ren B, Chi NC, Preissl S. Cardiac cell type-specific gene regulatory programs and disease risk association. SCIENCE ADVANCES 2021; 7:eabf1444. [PMID: 33990324 PMCID: PMC8121433 DOI: 10.1126/sciadv.abf1444] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/25/2021] [Indexed: 05/07/2023]
Abstract
Misregulated gene expression in human hearts can result in cardiovascular diseases that are leading causes of mortality worldwide. However, the limited information on the genomic location of candidate cis-regulatory elements (cCREs) such as enhancers and promoters in distinct cardiac cell types has restricted the understanding of these diseases. Here, we defined >287,000 cCREs in the four chambers of the human heart at single-cell resolution, which revealed cCREs and candidate transcription factors associated with cardiac cell types in a region-dependent manner and during heart failure. We further found cardiovascular disease-associated genetic variants enriched within these cCREs including 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Additional functional studies revealed that two of these variants affect a cCRE controlling KCNH2/HERG expression and action potential repolarization. Overall, this atlas of human cardiac cCREs provides the foundation for illuminating cell type-specific gene regulation in human hearts during health and disease.
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Affiliation(s)
- James D Hocker
- Medical Scientist Training Program, University of California, San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Olivier B Poirion
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Fugui Zhu
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Justin Buchanan
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Kai Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Joshua Chiou
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA
| | - Tsui-Min Wang
- Departments of Bioengineering and Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qingquan Zhang
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiaomeng Hou
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Yang E Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Elie N Farah
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Allen Wang
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Andrew D McCulloch
- Departments of Bioengineering and Medicine, University of California, San Diego, La Jolla, CA, USA
- Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kyle J Gaulton
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Neil C Chi
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
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Bayarsaikhan D, Bayarsaikhan G, Lee B. Recent advances in stem cells and gene editing: Drug discovery and therapeutics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:231-269. [PMID: 34127195 DOI: 10.1016/bs.pmbts.2021.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The recently introduced genome editing technology has had a remarkable impact on genetic medicine. Zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas nucleases are the three major platforms used for priming of stem cells or correction of mutated genes. Among these nucleases, CRISPR/Cas is the most easily applicable. Various CRISPR/Cas variants such as base editors, prime editors, mad7 nucleases, RESCUE, REPAIR, digenome sequencing, and SHERLOCK are being developed and considered as a promising tool for gene therapy and drug discovery. These advances in the CRISPR/Cas platform have enabled the correction of gene mutations from DNA to RNA level and validation of the safety of genome editing performance at a very precise level by allowing the detection of one base-pair mismatch. These promising alternatives of the CRISPR/Cas system can benefit millions of patients with intractable diseases. Although the therapeutic effects of stem cells have been confirmed in a wide range of disease models, their safety still remains an issue. Hence, scientists are concentrating on generating functionally improved stem cells by using programmable nucleases such as CRISPR. Therefore, in this chapter, we have summarized the applicable options of the CRISPR/Cas platforms by weighing their advantages and limitations in drug discovery and gene therapy.
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Affiliation(s)
- Delger Bayarsaikhan
- Lee Gil Ya Cancer and Diabetes Institute, School of Medicine, Gachon University, Incheon City, Republic of Korea
| | - Govigerel Bayarsaikhan
- Lee Gil Ya Cancer and Diabetes Institute, School of Medicine, Gachon University, Incheon City, Republic of Korea
| | - Bonghee Lee
- Lee Gil Ya Cancer and Diabetes Institute, School of Medicine, Gachon University, Incheon City, Republic of Korea.
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9
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Christidi E, Huang H, Shafaattalab S, Maillet A, Lin E, Huang K, Laksman Z, Davis MK, Tibbits GF, Brunham LR. Variation in RARG increases susceptibility to doxorubicin-induced cardiotoxicity in patient specific induced pluripotent stem cell-derived cardiomyocytes. Sci Rep 2020; 10:10363. [PMID: 32587261 PMCID: PMC7316788 DOI: 10.1038/s41598-020-65979-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 05/11/2020] [Indexed: 01/04/2023] Open
Abstract
Doxorubicin is a potent anticancer drug used to treat a variety of cancer types. However, its use is limited by doxorubicin-induced cardiotoxicity (DIC). A missense variant in the RARG gene (S427L; rs2229774) has been implicated in susceptibility to DIC in a genome wide association study. The goal of this study was to investigate the functional role of this RARG variant in DIC. We used induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs) from patients treated with doxorubicin. iPSC-CMs from individuals who experienced DIC (cases) showed significantly greater sensitivity to doxorubicin compared to iPSC-CMs from doxorubicin-treated individuals who did not develop DIC (controls) in cell viability and optical mapping experiments. Using CRISPR/Cas9, we generated isogenic cell lines that differed only at the RARG locus. Genetic correction of RARG-S427L to wild type resulted in reduced doxorubicin-induced double stranded DNA breaks, reactive oxygen species production, and cell death. Conversely, introduction of RARG-S427L increased susceptibility to doxorubicin. Finally, genetic disruption of the RARG gene resulted in protection from cell death due to doxorubicin treatment. Our findings suggest that the presence of RARG-S427L increases sensitivity to DIC, establishing a direct, causal role for this variant in DIC.
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Affiliation(s)
- Effimia Christidi
- Centre for Heart Lung Innovation, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Haojun Huang
- Centre for Heart Lung Innovation, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Sanam Shafaattalab
- Molecular Cardiac Physiology Group, Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
- Department of Cardiovascular Science, British Columbia Children's Hospital, Vancouver, Canada
| | | | - Eric Lin
- Molecular Cardiac Physiology Group, Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
| | - Kate Huang
- Centre for Heart Lung Innovation, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Zachary Laksman
- Heart Rhythm Services, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Margot K Davis
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Glen F Tibbits
- Molecular Cardiac Physiology Group, Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
- Department of Cardiovascular Science, British Columbia Children's Hospital, Vancouver, Canada
| | - Liam R Brunham
- Centre for Heart Lung Innovation, Department of Medicine, University of British Columbia, Vancouver, Canada.
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
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10
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Lara CO, Burgos CF, Moraga-Cid G, Carrasco MA, Yévenes GE. Pentameric Ligand-Gated Ion Channels as Pharmacological Targets Against Chronic Pain. Front Pharmacol 2020; 11:167. [PMID: 32218730 PMCID: PMC7079299 DOI: 10.3389/fphar.2020.00167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 02/07/2020] [Indexed: 12/31/2022] Open
Abstract
Chronic pain is a common detrimental condition that affects around 20% of the world population. The current drugs to treat chronic pain states, especially neuropathic pain, have a limited clinical efficiency and present significant adverse effects that complicates their regular use. Recent studies have proposed new therapeutic strategies focused on the pharmacological modulation of G-protein-coupled receptors, transporters, enzymes, and ion channels expressed on the nociceptive pathways. The present work intends to summarize recent advances on the pharmacological modulation of pentameric ligand-gated ion channels, which plays a key role in pain processing. Experimental data have shown that novel allosteric modulators targeting the excitatory nicotinic acetylcholine receptor, as well as the inhibitory GABAA and glycine receptors, reverse chronic pain-related behaviors in preclinical assays. Collectively, these evidences strongly suggest the pharmacological modulation of pentameric ligand-gated ion channels is a promising strategy towards the development of novel therapeutics to treat chronic pain states in humans.
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Affiliation(s)
- César O Lara
- Department of Physiology, Faculty of Biological Sciences, University of Concepcion, Concepcion, Chile
| | - Carlos F Burgos
- Department of Physiology, Faculty of Biological Sciences, University of Concepcion, Concepcion, Chile
| | - Gustavo Moraga-Cid
- Department of Physiology, Faculty of Biological Sciences, University of Concepcion, Concepcion, Chile
| | - Mónica A Carrasco
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Talca, Talca, Chile
| | - Gonzalo E Yévenes
- Department of Physiology, Faculty of Biological Sciences, University of Concepcion, Concepcion, Chile
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11
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van den Brink L, Grandela C, Mummery CL, Davis RP. Inherited cardiac diseases, pluripotent stem cells, and genome editing combined-the past, present, and future. Stem Cells 2020; 38:174-186. [PMID: 31664757 PMCID: PMC7027796 DOI: 10.1002/stem.3110] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/09/2019] [Indexed: 12/15/2022]
Abstract
Research on mechanisms underlying monogenic cardiac diseases such as primary arrhythmias and cardiomyopathies has until recently been hampered by inherent limitations of heterologous cell systems, where mutant genes are expressed in noncardiac cells, and physiological differences between humans and experimental animals. Human-induced pluripotent stem cells (hiPSCs) have proven to be a game changer by providing new opportunities for studying the disease in the specific cell type affected, namely the cardiomyocyte. hiPSCs are particularly valuable because not only can they be differentiated into unlimited numbers of these cells, but they also genetically match the individual from whom they were derived. The decade following their discovery showed the potential of hiPSCs for advancing our understanding of cardiovascular diseases, with key pathophysiological features of the patient being reflected in their corresponding hiPSC-derived cardiomyocytes (the past). Now, recent advances in genome editing for repairing or introducing genetic mutations efficiently have enabled the disease etiology and pathogenesis of a particular genotype to be investigated (the present). Finally, we are beginning to witness the promise of hiPSC in personalized therapies for individual patients, as well as their application in identifying genetic variants responsible for or modifying the disease phenotype (the future). In this review, we discuss how hiPSCs could contribute to improving the diagnosis, prognosis, and treatment of an individual with a suspected genetic cardiac disease, thereby developing better risk stratification and clinical management strategies for these potentially lethal but treatable disorders.
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Affiliation(s)
- Lettine van den Brink
- Department of Anatomy and EmbryologyLeiden University Medical CenterRC LeidenThe Netherlands
| | - Catarina Grandela
- Department of Anatomy and EmbryologyLeiden University Medical CenterRC LeidenThe Netherlands
| | - Christine L. Mummery
- Department of Anatomy and EmbryologyLeiden University Medical CenterRC LeidenThe Netherlands
| | - Richard P. Davis
- Department of Anatomy and EmbryologyLeiden University Medical CenterRC LeidenThe Netherlands
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12
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Liu W, Deng C, Godoy-Parejo C, Zhang Y, Chen G. Developments in cell culture systems for human pluripotent stem cells. World J Stem Cells 2019; 11:968-981. [PMID: 31768223 PMCID: PMC6851012 DOI: 10.4252/wjsc.v11.i11.968] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/21/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) are important resources for cell-based therapies and pharmaceutical applications. In order to realize the potential of hPSCs, it is critical to develop suitable technologies required for specific applications. Most hPSC technologies depend on cell culture, and are critically influenced by culture medium composition, extracellular matrices, handling methods, and culture platforms. This review summarizes the major technological advances in hPSC culture, and highlights the opportunities and challenges in future therapeutic applications.
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Affiliation(s)
- Weiwei Liu
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau 999078, China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
- Bioimaging and Stem Cell Core Facility, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Chunhao Deng
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau 999078, China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Carlos Godoy-Parejo
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau 999078, China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Yumeng Zhang
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau 999078, China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Guokai Chen
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau 999078, China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China.
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13
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Zhang Y, Li T, Preissl S, Amaral ML, Grinstein JD, Farah EN, Destici E, Qiu Y, Hu R, Lee AY, Chee S, Ma K, Ye Z, Zhu Q, Huang H, Fang R, Yu L, Izpisua Belmonte JC, Wu J, Evans SM, Chi NC, Ren B. Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Nat Genet 2019; 51:1380-1388. [PMID: 31427791 PMCID: PMC6722002 DOI: 10.1038/s41588-019-0479-7] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/09/2019] [Indexed: 12/24/2022]
Abstract
Chromatin architecture has been implicated in cell type-specific gene regulatory programs, yet how chromatin remodels during development remains to be fully elucidated. Here, by interrogating chromatin reorganization during human pluripotent stem cell (hPSC) differentiation, we discover a role for the primate-specific endogenous retrotransposon human endogenous retrovirus subfamily H (HERV-H) in creating topologically associating domains (TADs) in hPSCs. Deleting these HERV-H elements eliminates their corresponding TAD boundaries and reduces the transcription of upstream genes, while de novo insertion of HERV-H elements can introduce new TAD boundaries. The ability of HERV-H to create TAD boundaries depends on high transcription, as transcriptional repression of HERV-H elements prevents the formation of boundaries. This ability is not limited to hPSCs, as these actively transcribed HERV-H elements and their corresponding TAD boundaries also appear in pluripotent stem cells from other hominids but not in more distantly related species lacking HERV-H elements. Overall, our results provide direct evidence for retrotransposons in actively shaping cell type- and species-specific chromatin architecture.
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Affiliation(s)
- Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Ting Li
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Sebastian Preissl
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Jonathan D Grinstein
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Elie N Farah
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, 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
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Sora Chee
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Kaiyue Ma
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Zhen Ye
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Quan Zhu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Hui Huang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Leqian Yu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sylvia M Evans
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, 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.
- Institute of Genomic Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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14
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Niu W, Parent JM. Modeling genetic epilepsies in a dish. Dev Dyn 2019; 249:56-75. [DOI: 10.1002/dvdy.79] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/21/2019] [Accepted: 06/21/2019] [Indexed: 02/07/2023] Open
Affiliation(s)
- Wei Niu
- Department of Neurology and Neuroscience Graduate ProgramUniversity of Michigan Medical Center and VA Ann Arbor Healthcare System Ann Arbor Michigan
| | - Jack M. Parent
- Department of Neurology and Neuroscience Graduate ProgramUniversity of Michigan Medical Center and VA Ann Arbor Healthcare System Ann Arbor Michigan
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15
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lncRNA PSORS1C3 is regulated by glucocorticoids and fine-tunes OCT4 expression in non-pluripotent cells. Sci Rep 2019; 9:8370. [PMID: 31182783 PMCID: PMC6557835 DOI: 10.1038/s41598-019-44827-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 05/20/2019] [Indexed: 11/29/2022] Open
Abstract
OCT4 is a transcription factor known for its regulatory roles in stemness, tumorigenesis and stress response. Considering its versatile functions, expression of OCT4 is regulated at different levels. PSORS1C3, a long non-coding RNA overlapped with OCT4, has a putative association with immune mediated diseases; however, its exact functions remained to be elucidated. Here, we demonstrated that PSORS1C3 is regulated by glucocorticoids (GC), has two endogenously active promoters, promoter 0 and 1, and two sets of transcripts, short and long variants. According to our findings, PSORS1C3 promoters behaved differently during neural differentiation of NT2 cells and glucocorticoid receptor (GR) activation. In both processes the expression pattern of short variants differed from that of long variants and was similar to OCT4 expression. Furthermore, our data revealed that PSORS1C3’s promoter 0 could act as an enhancer for OCT4 in non-pluripotent cells, where its deletion caused a significant decrease in OCT4 expression. Meanwhile, during GR activation promoter 0 functioned as a negative regulator and alleviated transcription induction of OCT4 after GC treatment. Altogether, our work clarified the structure and regulation of PSORS1C3, explained its relation to immune-related disease through GR signaling and introduced it as a novel fine-tuner of OCT4 expression in non-pluripotent cells.
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16
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Rahman S, Datta M, Kim J, Jan AT. CRISPR/Cas: An intriguing genomic editing tool with prospects in treating neurodegenerative diseases. Semin Cell Dev Biol 2019; 96:22-31. [PMID: 31102655 DOI: 10.1016/j.semcdb.2019.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 01/04/2023]
Abstract
The CRISPR/Cas genome editing tool has led to a revolution in biological research. Its ability to target multiple genomic loci simultaneously allows its application in gene function and genomic manipulation studies. Its involvement in the sequence specific gene editing in different backgrounds has changed the scenario of treating genetic diseases. By unravelling the mysteries behind complex neuronal circuits, it not only paved way in understanding the pathogenesis of the disease but helped in the development of large animal models of different neuronal diseases; thereby opened the gateways of successfully treating different neuronal diseases. This review explored the possibility of using of CRISPR/Cas in engineering DNA at the embryonic stage, as well as during the functioning of different cell types in the brain, to delineate implications related to the use of this super-specialized genome editing tool to overcome various neurodegenerative diseases that arise as a result of genetic mutations.
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Affiliation(s)
- Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Manali Datta
- Amity Institute of Biotechnology, Amity University Rajasthan, 303007, India
| | - Jihoe Kim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea.
| | - Arif Tasleem Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India.
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17
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Quarta C, Fisette A, Xu Y, Colldén G, Legutko B, Tseng YT, Reim A, Wierer M, De Rosa MC, Klaus V, Rausch R, Thaker VV, Graf E, Strom TM, Poher AL, Gruber T, Le Thuc O, Cebrian-Serrano A, Kabra D, Bellocchio L, Woods SC, Pflugfelder GO, Nogueiras R, Zeltser L, Grunwald Kadow IC, Moon A, García-Cáceres C, Mann M, Treier M, Doege CA, Tschöp MH. Functional identity of hypothalamic melanocortin neurons depends on Tbx3. Nat Metab 2019; 1:222-235. [PMID: 32694784 PMCID: PMC8291379 DOI: 10.1038/s42255-018-0028-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/13/2018] [Indexed: 02/07/2023]
Abstract
Heterogeneous populations of hypothalamic neurons orchestrate energy balance via the release of specific signatures of neuropeptides. However, how specific intracellular machinery controls peptidergic identities and function of individual hypothalamic neurons remains largely unknown. The transcription factor T-box 3 (Tbx3) is expressed in hypothalamic neurons sensing and governing energy status, whereas human TBX3 haploinsufficiency has been linked with obesity. Here, we demonstrate that loss of Tbx3 function in hypothalamic neurons causes weight gain and other metabolic disturbances by disrupting both the peptidergic identity and plasticity of Pomc/Cart and Agrp/Npy neurons. These alterations are observed after loss of Tbx3 in both immature hypothalamic neurons and terminally differentiated mouse neurons. We further establish the importance of Tbx3 for body weight regulation in Drosophila melanogaster and show that TBX3 is implicated in the differentiation of human embryonic stem cells into hypothalamic Pomc neurons. Our data indicate that Tbx3 directs the terminal specification of neurons as functional components of the melanocortin system and is required for maintaining their peptidergic identity. In summary, we report the discovery of a key mechanistic process underlying the functional heterogeneity of hypothalamic neurons governing body weight and systemic metabolism.
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Affiliation(s)
- Carmelo Quarta
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- INSERM, Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U1215, Bordeaux, France
- University of Bordeaux, Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, Bordeaux, France
| | - Alexandre Fisette
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Yanjun Xu
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Division of Metabolic Diseases, Technische Universität München, Munich, Germany
| | - Gustav Colldén
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Beata Legutko
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Yu-Ting Tseng
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Alexander Reim
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Maria Caterina De Rosa
- Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Valentina Klaus
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Division of Metabolic Diseases, Technische Universität München, Munich, Germany
| | - Rick Rausch
- Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Vidhu V Thaker
- Naomi Berrie Diabetes Center, Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Anne-Laure Poher
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Tim Gruber
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Ophélia Le Thuc
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Alberto Cebrian-Serrano
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Dhiraj Kabra
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Luigi Bellocchio
- INSERM U1215, NeuroCentre Magendie, Bordeaux, France
- Université de Bordeaux, NeuroCentre Magendie, Bordeaux, France
| | - Stephen C Woods
- University of Cincinnati College of Medicine, Department of Psychiatry and Behavioral Neuroscience, Metabolic Diseases Institute, Cincinnati, OH, USA
| | - Gert O Pflugfelder
- Institute of Developmental and Neurobiology. Johannes Gutenberg-University, Mainz, Germany
| | - Rubén Nogueiras
- Department of Physiology, CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria, Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Lori Zeltser
- Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Ilona C Grunwald Kadow
- Technical University of Munich, School of Life Sciences, ZIEL - Institute for Food and Health, Freising, Germany
| | - Anne Moon
- Department of Molecular and Functional Genomics, Geisinger Clinic, Danville PA, USA
- Departments of Pediatrics and Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Cristina García-Cáceres
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Mathias Treier
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia A Doege
- Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Matthias H Tschöp
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
- Division of Metabolic Diseases, Technische Universität München, Munich, Germany.
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18
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Snijders KE, Cooper JD, Vallier L, Bertero A. Conditional Gene Knockout in Human Cells with Inducible CRISPR/Cas9. Methods Mol Biol 2019; 1961:185-209. [PMID: 30912047 DOI: 10.1007/978-1-4939-9170-9_12] [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] [Indexed: 01/05/2024]
Abstract
The advent of the easily programmable and efficient CRISPR/Cas9 nuclease system has revolutionized genetic engineering. While conventional gene knockout experiments using CRISPR/Cas9 are very valuable, these are not well suited to study stage-specific gene function in dynamic situations such as development or disease. Here we describe a CRISPR/Cas9-based OPTimized inducible gene KnockOut method (OPTiKO) for conditional loss-of-function studies in human cells. This approach relies on an improved tetracycline-inducible system for conditional expression of single guide RNAs (sgRNAs) that drive Cas9 activity. In order to ensure homogeneous and stable expression, the necessary transgenes are expressed following rapid and efficient single-step genetic engineering of the AAVS1 genomic safe harbor. When implemented in human pluripotent stem cells (hPSCs), the approach can be then efficiently applied to virtually any hPSC-derived human cell type at various stages of development or disease.
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Affiliation(s)
- Kirsten E Snijders
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - James D Cooper
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Ludovic Vallier
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.
- Department of Surgery, University of Cambridge, Cambridge, UK.
- Wellcome Trust Sanger Institute, Hinxton, UK.
| | - Alessandro Bertero
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK.
- Department of Surgery, University of Cambridge, Cambridge, UK.
- Department of Pathology, University of Washington, Seattle, WA, USA.
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19
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Chen YH, Pruett-Miller SM. Improving single-cell cloning workflow for gene editing in human pluripotent stem cells. Stem Cell Res 2018; 31:186-192. [PMID: 30099335 DOI: 10.1016/j.scr.2018.08.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/27/2018] [Accepted: 08/02/2018] [Indexed: 01/01/2023] Open
Abstract
The availability of human pluripotent stem cells (hPSCs) and progress in genome engineering technology have altered the way we approach scientific research and drug development screens. Unfortunately, the procedures for genome editing of hPSCs often subject cells to harsh conditions that compromise viability: a major problem that is compounded by the innate challenge of single-cell culture. Here we describe a generally applicable workflow that supports single-cell cloning and expansion of hPSCs after genome editing and single-cell sorting. Stem-Flex and RevitaCell supplement, in combination with Geltrex or Vitronectin (VN), promote reliable single-cell growth in a feeder-free and defined environment. Characterization of final genome-edited clones reveals that pluripotency and normal karyotype are retained following this single-cell culture protocol. This time-efficient and simplified culture method paves the way for high-throughput hPSC culture and will be valuable for both basic research and clinical applications.
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Affiliation(s)
- Yi-Hsien Chen
- Washington University School of Medicine, Department of Genetics, St. Louis 63110, USA; Genome Engineering and iPSC Center, USA.
| | - Shondra M Pruett-Miller
- St. Jude Children's Research Hospital, Department of Cell & Molecular Biology, Memphis 38105, USA; Center for Advanced Genome Engineering, USA.
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20
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Abstract
In the current review, we discuss the process of modeling pediatric epileptic encephalopathies with a focus on in vitro iPSC-based technologies. We highlight the potential benefits as well as the challenges of these approaches and propose appropriate standards for the field.
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21
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Hazelbaker DZ, Beccard A, Bara AM, Dabkowski N, Messana A, Mazzucato P, Lam D, Manning D, Eggan K, Barrett LE. A Scaled Framework for CRISPR Editing of Human Pluripotent Stem Cells to Study Psychiatric Disease. Stem Cell Reports 2018; 9:1315-1327. [PMID: 29020615 PMCID: PMC5639480 DOI: 10.1016/j.stemcr.2017.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 12/22/2022] Open
Abstract
Scaling of CRISPR-Cas9 technology in human pluripotent stem cells (hPSCs) represents an important step for modeling complex disease and developing drug screens in human cells. However, variables affecting the scaling efficiency of gene editing in hPSCs remain poorly understood. Here, we report a standardized CRISPR-Cas9 approach, with robust benchmarking at each step, to successfully target and genotype a set of psychiatric disease-implicated genes in hPSCs and provide a resource of edited hPSC lines for six of these genes. We found that transcriptional state and nucleosome positioning around targeted loci was not correlated with editing efficiency. However, editing frequencies varied between different hPSC lines and correlated with genomic stability, underscoring the need for careful cell line selection and unbiased assessments of genomic integrity. Together, our step-by-step quantification and in-depth analyses provide an experimental roadmap for scaling Cas9-mediated editing in hPSCs to study psychiatric disease, with broader applicability for other polygenic diseases.
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Affiliation(s)
- Dane Z Hazelbaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amanda Beccard
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anne M Bara
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicole Dabkowski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Angelica Messana
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Patrizia Mazzucato
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daisy Lam
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Danielle Manning
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Lindy E Barrett
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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22
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Gupta N, Susa K, Yoda Y, Bonventre JV, Valerius MT, Morizane R. CRISPR/Cas9-based Targeted Genome Editing for the Development of Monogenic Diseases Models with Human Pluripotent Stem Cells. CURRENT PROTOCOLS IN STEM CELL BIOLOGY 2018; 45:e50. [PMID: 30040245 PMCID: PMC6060633 DOI: 10.1002/cpsc.50] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human pluripotent stem cells (hPSCs) represent a formidable tool for disease modeling, drug discovery, and regenerative medicine using human cells and tissues in vitro. Evolving techniques of targeted genome editing, specifically the CRISPR/Cas9 system, allow for the generation of cell lines bearing gene-specific knock-outs, knock-in reporters, and precise mutations. However, there are increasing concerns related to the transfection efficiency, cell viability, and maintenance of pluripotency provided by genome-editing techniques. The procedure presented here employs transient antibiotic selection that overcomes reduced transfection efficiency, avoids cytotoxic flow sorting for increased viability, and generates multiple genome-edited pluripotent hPSC lines expanded from a single parent cell. Avoidance of xenogeneic contamination from feeder cells and reduced operator workload, owing to single-cell passaging rather than clump passaging, are additional benefits. The outlined methods may enable researchers with limited means and technical experience to create human stem cell lines containing desired gene-specific mutations. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Navin Gupta
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Koichiro Susa
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Yoko Yoda
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Joseph V Bonventre
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - M Todd Valerius
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Ryuji Morizane
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
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23
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Adil MM, Schaffer DV. hPSC‐derived Midbrain Dopaminergic Neurons Generated in a Scalable 3‐D Biomaterial. ACTA ACUST UNITED AC 2018; 44:2D.21.1-2D.21.17. [DOI: 10.1002/cpsc.47] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Maroof M. Adil
- Departments of Chemical and Biomolecular Engineering, Molecular and Cell Biology, Bioengineering, and Helen Wills Neuroscience Institute, University of California Berkeley California
| | - David V. Schaffer
- Departments of Chemical and Biomolecular Engineering, Molecular and Cell Biology, Bioengineering, and Helen Wills Neuroscience Institute, University of California Berkeley California
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24
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Kirwan P, Jura M, Merkle FT. Generation and Characterization of Functional Human Hypothalamic Neurons. ACTA ACUST UNITED AC 2017; 81:3.33.1-3.33.24. [PMID: 29064566 DOI: 10.1002/cpns.40] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Neurons in the hypothalamus orchestrate homeostatic physiological processes and behaviors essential for life. Defects in the function of hypothalamic neurons cause a spectrum of human diseases, including obesity, infertility, growth defects, sleep disorders, social disorders, and stress disorders. These diseases have been studied in animal models such as mice, but the rarity and relative inaccessibility of mouse hypothalamic neurons and species-specific differences between mice and humans highlight the need for human cellular models of hypothalamic diseases. We and others have developed methods to differentiate human pluripotent stem cells (hPSCs) into hypothalamic neurons and related cell types, such as astrocytes. This protocol builds on published studies by providing detailed step-by-step instructions for neuronal differentiation, quality control, long-term neuronal maintenance, and the functional interrogation of hypothalamic cells by calcium imaging. Together, these protocols should enable any group with appropriate facilities to generate and study human hypothalamic cells. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Peter Kirwan
- Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom.,The Anne McLaren Laboratory, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Magdalena Jura
- Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom.,The Anne McLaren Laboratory, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Florian T Merkle
- Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom.,The Anne McLaren Laboratory, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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25
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Bassett AR. Editing the genome of hiPSC with CRISPR/Cas9: disease models. Mamm Genome 2017; 28:348-364. [PMID: 28303292 PMCID: PMC5569153 DOI: 10.1007/s00335-017-9684-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/06/2017] [Indexed: 12/20/2022]
Abstract
The advent of human-induced pluripotent stem cell (hiPSC) technology has provided a unique opportunity to establish cellular models of disease from individual patients, and to study the effects of the underlying genetic aberrations upon multiple different cell types, many of which would not normally be accessible. Combining this with recent advances in genome editing techniques such as the clustered regularly interspaced short palindromic repeat (CRISPR) system has provided an ability to repair putative causative alleles in patient lines, or introduce disease alleles into a healthy “WT” cell line. This has enabled analysis of isogenic cell pairs that differ in a single genetic change, which allows a thorough assessment of the molecular and cellular phenotypes that result from this abnormality. Importantly, this establishes the true causative lesion, which is often impossible to ascertain from human genetic studies alone. These isogenic cell lines can be used not only to understand the cellular consequences of disease mutations, but also to perform high throughput genetic and pharmacological screens to both understand the underlying pathological mechanisms and to develop novel therapeutic agents to prevent or treat such diseases. In the future, optimising and developing such genetic manipulation technologies may facilitate the provision of cellular or molecular gene therapies, to intervene and ultimately cure many debilitating genetic disorders.
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Affiliation(s)
- Andrew R Bassett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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