151
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Deng G, Wang R, Sun Y, Huang CP, Yeh S, You B, Feng C, Li G, Ma S, Chang C. Targeting androgen receptor (AR) with antiandrogen Enzalutamide increases prostate cancer cell invasion yet decreases bladder cancer cell invasion via differentially altering the AR/circRNA-ARC1/miR-125b-2-3p or miR-4736/PPARγ/MMP-9 signals. Cell Death Differ 2021; 28:2145-2159. [PMID: 34127806 PMCID: PMC8257744 DOI: 10.1038/s41418-021-00743-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 02/05/2023] Open
Abstract
Androgen-deprivation therapy (ADT) via targeting androgens/androgen receptor (AR) signals may suppress cell proliferation in both prostate cancer (PCa) and bladder cancer (BCa), yet its impact on the cell invasion of these two urological cancers remains unclear. Here we found targeting androgens/AR with either the recently developed antiandrogen Enzalutamide (Enz) or AR-shRNAs led to increase PCa cell invasion, yet decrease BCa cell invasion. Mechanistic dissection revealed that suppressing androgens/AR signals could result in differential alterations of the selective circular RNAs (circRNAs) as a result of differential endogenous AR transcription. A negative autoregulation in PCa, yet a positive autoregulation in BCa, as a result of differential binding of AR to different androgen-response elements (AREs) and a discriminating histone H3K4 methylation, likely contributes to this outcome between these two urological tumors. Further mechanistic studies indicated that AR-encoded circRNA-ARC1 might sponge/alter the availability of the miRNAs miR-125b-2-3p and/or miR-4736, to impact the metastasis-related PPARγ/MMP-9 signals to alter the PCa vs. BCa cell invasion. The preclinical study using the in vivo mouse model confirms in vitro cell lines data, showing that Enz treatment could increase PCa metastasis, which can be suppressed after suppressing circRNA-ARC1 with sh-circRNA-ARC1. Together, these in vitro/in vivo results demonstrate that antiandrogen therapy with Enz via targeting AR may lead to either increase PCa cell invasion or decrease BCa cell invasion. Targeting these newly identified AR/circRNA-ARC1/miR-125b-2-3p and/or miR-4736/PPARγ/MMP-9 signals may help in the development of new therapies to better suppress the Enz-altered PCa vs. BCa metastasis.
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Affiliation(s)
- Gang Deng
- Department of Urology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology, Radiation Oncology and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Ronghao Wang
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology, Radiation Oncology and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Yin Sun
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology, Radiation Oncology and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Chi-Ping Huang
- Department of Urology, China Medical University/Hospital, Taichung, Taiwan
| | - Shuyuan Yeh
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology, Radiation Oncology and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Bosen You
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology, Radiation Oncology and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Changyong Feng
- Department of Biostatistics, University of Rochester Medical Center, Rochester, NY, USA
| | - Gonghui Li
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology, Radiation Oncology and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Shenglin Ma
- Department of Urology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Chawnshang Chang
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology, Radiation Oncology and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA.
- Department of Urology, China Medical University/Hospital, Taichung, Taiwan.
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152
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Gähwiler EKN, Motta SE, Martin M, Nugraha B, Hoerstrup SP, Emmert MY. Human iPSCs and Genome Editing Technologies for Precision Cardiovascular Tissue Engineering. Front Cell Dev Biol 2021; 9:639699. [PMID: 34262897 PMCID: PMC8273765 DOI: 10.3389/fcell.2021.639699] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/31/2021] [Indexed: 12/12/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) originate from the reprogramming of adult somatic cells using four Yamanaka transcription factors. Since their discovery, the stem cell (SC) field achieved significant milestones and opened several gateways in the area of disease modeling, drug discovery, and regenerative medicine. In parallel, the emergence of clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) revolutionized the field of genome engineering, allowing the generation of genetically modified cell lines and achieving a precise genome recombination or random insertions/deletions, usefully translated for wider applications. Cardiovascular diseases represent a constantly increasing societal concern, with limited understanding of the underlying cellular and molecular mechanisms. The ability of iPSCs to differentiate into multiple cell types combined with CRISPR-Cas9 technology could enable the systematic investigation of pathophysiological mechanisms or drug screening for potential therapeutics. Furthermore, these technologies can provide a cellular platform for cardiovascular tissue engineering (TE) approaches by modulating the expression or inhibition of targeted proteins, thereby creating the possibility to engineer new cell lines and/or fine-tune biomimetic scaffolds. This review will focus on the application of iPSCs, CRISPR-Cas9, and a combination thereof to the field of cardiovascular TE. In particular, the clinical translatability of such technologies will be discussed ranging from disease modeling to drug screening and TE applications.
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Affiliation(s)
- Eric K. N. Gähwiler
- Institute for Regenerative Medicine (IREM), University of Zurich, Zurich, Switzerland
| | - Sarah E. Motta
- Institute for Regenerative Medicine (IREM), University of Zurich, Zurich, Switzerland
- Wyss Zurich, University and ETH Zurich, Zurich, Switzerland
| | - Marcy Martin
- Division of Pediatric Cardiology, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, United States
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford School of Medicine, Stanford, CA, United States
- Stanford Cardiovascular Institute, Stanford School of Medicine, Stanford, CA, United States
| | - Bramasta Nugraha
- Molecular Parasitology Lab, Institute of Parasitology, University of Zurich, Zurich, Switzerland
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - Simon P. Hoerstrup
- Institute for Regenerative Medicine (IREM), University of Zurich, Zurich, Switzerland
- Wyss Zurich, University and ETH Zurich, Zurich, Switzerland
| | - Maximilian Y. Emmert
- Institute for Regenerative Medicine (IREM), University of Zurich, Zurich, Switzerland
- Wyss Zurich, University and ETH Zurich, Zurich, Switzerland
- Department of Cardiovascular Surgery, Charité Universitätsmedizin Berlin, Berlin, Germany
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, Berlin, Germany
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153
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Libby ARG, Joy DA, Elder NH, Bulger EA, Krakora MZ, Gaylord EA, Mendoza-Camacho F, Butts JC, McDevitt TC. Axial elongation of caudalized human organoids mimics aspects of neural tube development. Development 2021; 148:269182. [PMID: 34142711 DOI: 10.1242/dev.198275] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/07/2021] [Indexed: 12/12/2022]
Abstract
Axial elongation of the neural tube is crucial during mammalian embryogenesis for anterior-posterior body axis establishment and subsequent spinal cord development, but these processes cannot be interrogated directly in humans as they occur post-implantation. Here, we report an organoid model of neural tube extension derived from human pluripotent stem cell (hPSC) aggregates that have been caudalized with Wnt agonism, enabling them to recapitulate aspects of the morphological and temporal gene expression patterns of neural tube development. Elongating organoids consist largely of neuroepithelial compartments and contain TBXT+SOX2+ neuro-mesodermal progenitors in addition to PAX6+NES+ neural progenitors. A critical threshold of Wnt agonism stimulated singular axial extensions while maintaining multiple cell lineages, such that organoids displayed regionalized anterior-to-posterior HOX gene expression with hindbrain (HOXB1) regions spatially distinct from brachial (HOXC6) and thoracic (HOXB9) regions. CRISPR interference-mediated silencing of TBXT, a Wnt pathway target, increased neuroepithelial compartmentalization, abrogated HOX expression and disrupted uniaxial elongation. Together, these results demonstrate the potent capacity of caudalized hPSC organoids to undergo axial elongation in a manner that can be used to dissect the cellular organization and patterning decisions that dictate early human nervous system development.
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Affiliation(s)
- Ashley R G Libby
- Developmental and Stem Cell Biology PhD Program, University of California, San Francisco, CA 94143, USA.,Gladstone Institutes, San Francisco, CA 94158, USA
| | - David A Joy
- Gladstone Institutes, San Francisco, CA 94158, USA.,UC Berkeley-UC San Francisco Graduate Program in Bioengineering, San Francisco, CA 94158, USA
| | - Nicholas H Elder
- Developmental and Stem Cell Biology PhD Program, University of California, San Francisco, CA 94143, USA.,Gladstone Institutes, San Francisco, CA 94158, USA
| | - Emily A Bulger
- Developmental and Stem Cell Biology PhD Program, University of California, San Francisco, CA 94143, USA.,Gladstone Institutes, San Francisco, CA 94158, USA
| | | | - Eliza A Gaylord
- Developmental and Stem Cell Biology PhD Program, University of California, San Francisco, CA 94143, USA
| | - Frederico Mendoza-Camacho
- Developmental and Stem Cell Biology PhD Program, University of California, San Francisco, CA 94143, USA
| | | | - Todd C McDevitt
- Gladstone Institutes, San Francisco, CA 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
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154
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Damiati LA, El-Messeiry S. An Overview of RNA-Based Scaffolds for Osteogenesis. Front Mol Biosci 2021; 8:682581. [PMID: 34169095 PMCID: PMC8217814 DOI: 10.3389/fmolb.2021.682581] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/06/2021] [Indexed: 12/20/2022] Open
Abstract
Tissue engineering provides new hope for the combination of cells, scaffolds, and bifactors for bone osteogenesis. This is achieved by mimicking the bone's natural behavior in recruiting the cell's molecular machinery for our use. Many researchers have focused on developing an ideal scaffold with specific features, such as good cellular adhesion, cell proliferation, differentiation, host integration, and load bearing. Various types of coating materials (organic and non-organic) have been used to enhance bone osteogenesis. In the last few years, RNA-mediated gene therapy has captured attention as a new tool for bone regeneration. In this review, we discuss the use of RNA molecules in coating and delivery, including messenger RNA (mRNA), RNA interference (RNAi), and long non-coding RNA (lncRNA) on different types of scaffolds (such as polymers, ceramics, and metals) in osteogenesis research. In addition, the effect of using gene-editing tools-particularly CRISPR systems-to guide RNA scaffolds in bone regeneration is also discussed. Given existing knowledge about various RNAs coating/expression may help to understand the process of bone formation on the scaffolds during osseointegration.
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Affiliation(s)
- Laila A. Damiati
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Sarah El-Messeiry
- Department of Genetics, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
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155
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Sato K, Parag-Sharma K, Terajima M, Musicant AM, Murphy RM, Ramsey MR, Hibi H, Yamauchi M, Amelio AL. Lysyl hydroxylase 2-induced collagen cross-link switching promotes metastasis in head and neck squamous cell carcinomas. Neoplasia 2021; 23:594-606. [PMID: 34107376 PMCID: PMC8192727 DOI: 10.1016/j.neo.2021.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 12/24/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the 6th most common cancer worldwide and incidence rates are continuing to rise globally. HNSCC patient prognosis is closely related to the occurrence of tumor metastases, and collagen within the tumor microenvironment (TME) plays a key role in this process. Lysyl hydroxylase 2 (LH2), encoded by the Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 2 (PLOD2) gene, catalyzes hydroxylation of telopeptidyl lysine (Lys) residues of fibrillar collagens which then undergo subsequent modifications to form stable intermolecular cross-links that change the biomechanical properties (i.e. quality) of the TME. While LH2-catalyzed collagen modification has been implicated in driving tumor progression and metastasis in diverse cancers, little is known about its role in HNSCC progression. Thus, using gain- and loss-of-function studies, we examined the effects of LH2 expression levels on collagen cross-linking and cell behavior in vitro and in vivo using a tractable bioluminescent imaging-based orthotopic xenograft model. We found that LH2 overexpression dramatically increases HNSCC cell migratory and invasive abilities in vitro and that LH2-driven changes in collagen cross-linking robustly induces metastasis in vivo. Specifically, the amount of LH2-mediated collagen cross-links increased significantly with PLOD2 overexpression, without affecting the total quantity of collagen cross-links. Conversely, LH2 knockdown significantly blunted HNSCC cells invasive capacity in vitro and metastatic potential in vivo. Thus, regardless of the total "quantity" of collagen crosslinks, it is the "quality" of these cross-links that is the key driver of HNSCC tumor metastatic dissemination. These data implicate LH2 as a key regulator of HNSCC tumor invasion and metastasis by modulating collagen cross-link quality and suggest that therapeutic strategies targeting LH2-mediated collagen cross-linking in the TME may be effective in controlling tumor progression and improving disease outcomes.
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Affiliation(s)
- Kotaro Sato
- Department of Oral and Maxillofacial Surgery, Graduate School of Medicine, Nagoya University, Nagoya, Japan
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, The University of North Carolina at Chapel Hill, NC, USA
- Division of Oral and Craniofacial health Sciences, Adams School of Dentistry, The University of North Carolina at Chapel Hill, NC, USA
| | - Kshitij Parag-Sharma
- Graduate Curriculum in Cell Biology & Physiology, Biological & Biomedical Sciences Program, UNC School of Medicine, The University of North Carolina at Chapel Hill, NC, USA
| | - Masahiko Terajima
- Division of Oral and Craniofacial health Sciences, Adams School of Dentistry, The University of North Carolina at Chapel Hill, NC, USA
| | - Adele M. Musicant
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, The University of North Carolina at Chapel Hill, NC, USA
- Division of Oral and Craniofacial health Sciences, Adams School of Dentistry, The University of North Carolina at Chapel Hill, NC, USA
| | - Ryan M. Murphy
- Graduate Curriculum in Pharmacology, Biological & Biomedical Sciences Program, UNC School of Medicine, The University of North Carolina at Chapel Hill, NC, USA
| | - Matthew R. Ramsey
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hideharu Hibi
- Department of Oral and Maxillofacial Surgery, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Mitsuo Yamauchi
- Division of Oral and Craniofacial health Sciences, Adams School of Dentistry, The University of North Carolina at Chapel Hill, NC, USA
| | - Antonio L. Amelio
- Division of Oral and Craniofacial health Sciences, Adams School of Dentistry, The University of North Carolina at Chapel Hill, NC, USA
- Department of Cell Biology and Physiology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Biomedical Research Imaging Center, UNC School of Medicine, The University of North Carolina at Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, Cancer Cell Biology Program, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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156
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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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157
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The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotency. PLoS Genet 2021; 17:e1009587. [PMID: 34033652 PMCID: PMC8184003 DOI: 10.1371/journal.pgen.1009587] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 06/07/2021] [Accepted: 05/06/2021] [Indexed: 12/29/2022] Open
Abstract
Human pluripotent stem cells (PSCs) express human endogenous retrovirus type-H (HERV-H), which exists as more than a thousand copies on the human genome and frequently produces chimeric transcripts as long-non-coding RNAs (lncRNAs) fused with downstream neighbor genes. Previous studies showed that HERV-H expression is required for the maintenance of PSC identity, and aberrant HERV-H expression attenuates neural differentiation potentials, however, little is known about the actual of function of HERV-H. In this study, we focused on ESRG, which is known as a PSC-related HERV-H-driven lncRNA. The global transcriptome data of various tissues and cell lines and quantitative expression analysis of PSCs showed that ESRG expression is much higher than other HERV-Hs and tightly silenced after differentiation. However, the loss of function by the complete excision of the entire ESRG gene body using a CRISPR/Cas9 platform revealed that ESRG is dispensable for the maintenance of the primed and naïve pluripotent states. The loss of ESRG hardly affected the global gene expression of PSCs or the differentiation potential toward trilineage. Differentiated cells derived from ESRG-deficient PSCs retained the potential to be reprogrammed into induced PSCs (iPSCs) by the forced expression of OCT3/4, SOX2, and KLF4. In conclusion, ESRG is dispensable for the maintenance and recapturing of human pluripotency. We have been interested in the role of human endogenous retrovirus (HERVs) in human pluripotent stem cells (PSCs). Although we and others have demonstrated that HERV expression is crucial for somatic cell reprogramming to a pluripotent state and the characteristics of PSCs. Little is known which one of more than 1,000 copies of HERVs is important. Thus, in this study, we focused on a HERV-related gene, ESRG which is expressed strongly and specifically in human PSCs but not in differentiated cells. Using a CRISPR/Cas9 platform, we generated complete knockout cell lines by deleting the entire gene body of ESRG. Our results demonstrate that ESRG is dispensable for the PSC characters such as gene expression, self-renewing capacity, and differentiation potential. In addition, ESRG does not contribute to the reprogramming of differentiated cells to a pluripotent state. Altogether, we concluded that ESRG is an excellent marker of pluripotency but dispensable for the PSC identity.
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158
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Dewell TE, Gjoni K, Liu AZ, Libby ARG, Moore AT, So PL, Conklin BR. Transcription factor overexpression drives reliable differentiation of retinal pigment epithelium from human induced pluripotent stem cells. Stem Cell Res 2021; 53:102368. [PMID: 34087997 DOI: 10.1016/j.scr.2021.102368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/10/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022] Open
Abstract
Age-related macular degeneration and genetic forms of blindness such as Best Disease and Retinitis Pigmentosa can be caused by degeneration of the Retinal Pigment Epithelium (RPE). RPE generated from patient-derived induced pluripotent stem cells (iPSCs) is valuable for both the study of disease mechanisms and development of therapeutic strategies. However, protocols to produce iPSC-derived RPE in vitro are often inefficient, labor-intensive, low-throughput, and highly variable between cell lines and within batches. Here, we report a robust, scalable method to generate iPSC-RPE using doxycycline-inducible expression of eye field transcription factors OTX2, PAX6 and MITF paired with RPE-permissive culture media. Doxycycline addition induces exogenous expression of these transcription factors in Best Disease patient- and wildtype iPSCs to efficiently produce monolayers of RPE with characteristic morphology and gene expression. Further, these RPE monolayers display functionality features including light absorption via pigmentation, polarity-driven fluid transport, and phagocytosis. With this method, we achieve a highly efficient and easily scalable differentiation without the need for mechanical isolation or enrichment methods, generating RPE cultures applicable for in vitro studies.
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Affiliation(s)
- Tessa E Dewell
- Gladstone Institutes, 1650 Owens Street, San Francisco, CA 94158, USA
| | - Ketrin Gjoni
- Gladstone Institutes, 1650 Owens Street, San Francisco, CA 94158, USA
| | - Angela Z Liu
- Gladstone Institutes, 1650 Owens Street, San Francisco, CA 94158, USA
| | - Ashley R G Libby
- Gladstone Institutes, 1650 Owens Street, San Francisco, CA 94158, USA; Developmental and Stem Cell Biology Program, University of California, 1675 Owens St, San Francisco, CA 94158, USA
| | - Anthony T Moore
- UCSF Department of Ophthalmology, 10 Koret Way, San Francisco, CA 94143-0730, USA
| | - Po-Lin So
- Gladstone Institutes, 1650 Owens Street, San Francisco, CA 94158, USA; Innovative Genomics Institute, 2151 Berkeley Way, Berkeley, CA 94720, USA; Gladstone Institutes Stem Cell Core, 1650 Owens Street, San Francisco, CA 94158, USA
| | - Bruce R Conklin
- Gladstone Institutes, 1650 Owens Street, San Francisco, CA 94158, USA; UCSF Department of Ophthalmology, 10 Koret Way, San Francisco, CA 94143-0730, USA; Innovative Genomics Institute, 2151 Berkeley Way, Berkeley, CA 94720, USA; UCSF Department of Medicine, 535 Mission Bay Blvd South, San Francisco, CA 94158, USA.
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159
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Hoang P, Kowalczewski A, Sun S, Winston TS, Archilla AM, Lemus SM, Ercan-Sencicek AG, Gupta AR, Liu W, Kontaridis MI, Amack JD, Ma Z. Engineering spatial-organized cardiac organoids for developmental toxicity testing. Stem Cell Reports 2021; 16:1228-1244. [PMID: 33891865 PMCID: PMC8185451 DOI: 10.1016/j.stemcr.2021.03.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 12/16/2022] Open
Abstract
Emerging technologies in stem cell engineering have produced sophisticated organoid platforms by controlling stem cell fate via biomaterial instructive cues. By micropatterning and differentiating human induced pluripotent stem cells (hiPSCs), we have engineered spatially organized cardiac organoids with contracting cardiomyocytes in the center surrounded by stromal cells distributed along the pattern perimeter. We investigated how geometric confinement directed the structural morphology and contractile functions of the cardiac organoids and tailored the pattern geometry to optimize organoid production. Using modern data-mining techniques, we found that pattern sizes significantly affected contraction functions, particularly in the parameters related to contraction duration and diastolic functions. We applied cardiac organoids generated from 600 μm diameter circles as a developmental toxicity screening assay and quantified the embryotoxic potential of nine pharmaceutical compounds. These cardiac organoids have potential use as an in vitro platform for studying organoid structure-function relationships, developmental processes, and drug-induced cardiac developmental toxicity. Micropattern-based geometric confinement directs cardiac organoid development Cardiac organoid structure-function relationships are guided by organoid size Cardiac organoids can be used as an in vitro embryotoxicity assessment tool
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Affiliation(s)
- Plansky Hoang
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA; BioInspired Syracuse Institute for Material and Living Systems, Syracuse, NY, USA
| | - Andrew Kowalczewski
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA; BioInspired Syracuse Institute for Material and Living Systems, Syracuse, NY, USA
| | - Shiyang Sun
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA; BioInspired Syracuse Institute for Material and Living Systems, Syracuse, NY, USA
| | - Tackla S Winston
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA; BioInspired Syracuse Institute for Material and Living Systems, Syracuse, NY, USA
| | - Adriana M Archilla
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA; BioInspired Syracuse Institute for Material and Living Systems, Syracuse, NY, USA
| | - Stephanie M Lemus
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA; BioInspired Syracuse Institute for Material and Living Systems, Syracuse, NY, USA
| | | | - Abha R Gupta
- Department of Pediatrics, Child Study Center, Yale School of Medicine, New Haven, CT, USA
| | - Wenzhong Liu
- Department of Pediatrics, Child Study Center, Yale School of Medicine, New Haven, CT, USA
| | | | - Jeffrey D Amack
- BioInspired Syracuse Institute for Material and Living Systems, Syracuse, NY, USA; Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Zhen Ma
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA; BioInspired Syracuse Institute for Material and Living Systems, Syracuse, NY, USA.
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160
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Matsuo S, Nishinaka-Arai Y, Kazuki Y, Oshimura M, Nakahata T, Niwa A, Saito MK. Pluripotent stem cell model of early hematopoiesis in Down syndrome reveals quantitative effects of short-form GATA1 protein on lineage specification. PLoS One 2021; 16:e0247595. [PMID: 33780474 PMCID: PMC8007000 DOI: 10.1371/journal.pone.0247595] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Children with Down syndrome (DS) are susceptible to two blood disorders, transient abnormal myelopoiesis (TAM) and Down syndrome-associated acute megakaryocytic leukemia (DS-AMKL). Mutations in GATA binding protein 1 (GATA1) have been identified as the cause of these diseases, and the expression levels of the resulting protein, short-form GATA1 (GATA1s), are known to correlate with the severity of TAM. On the other hand, despite the presence of GATA1 mutations in almost all cases of DS-AMKL, the incidence of DS-AMKL in TAM patients is inversely correlated with the expression of GATA1s. This discovery has required the need to clarify the role of GATA1s in generating the cells of origin linked to the risk of both diseases. Focusing on this point, we examined the characteristics of GATA1 mutant trisomy-21 pluripotent stem cells transfected with a doxycycline (Dox)-inducible GATA1s expression cassette in a stepwise hematopoietic differentiation protocol. We found that higher GATA1s expression significantly reduced commitment into the megakaryocytic lineage at the early hematopoietic progenitor cell (HPC) stage, but once committed, the effect was reversed in progenitor cells and acted to maintain the progenitors. These differentiation stage-dependent reversal effects were in contrast to the results of myeloid lineage, where GATA1s simply sustained and increased the number of immature myeloid cells. These results suggest that although GATA1 mutant cells cause the increase in myeloid and megakaryocytic progenitors regardless of the intensity of GATA1s expression, the pathways vary with the expression level. This study provides experimental support for the paradoxical clinical features of GATA1 mutations in the two diseases.
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Affiliation(s)
- Shiori Matsuo
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yoko Nishinaka-Arai
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- * E-mail: (YNA); (AN); (MKS)
| | - Yasuhiro Kazuki
- Chromosome Engineering Research Center, Tottori University, Tottori, Japan
- Division of Genome and Cellular Functions, Department of Molecular and Cellular Biology, School of Life Science, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Mitsuo Oshimura
- Chromosome Engineering Research Center, Tottori University, Tottori, Japan
| | - Tatsutoshi Nakahata
- Drug Discovery Technology Development Office, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Akira Niwa
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- * E-mail: (YNA); (AN); (MKS)
| | - Megumu K. Saito
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- * E-mail: (YNA); (AN); (MKS)
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161
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Liu T, Zhang S, Huang C, Ma S, Bai R, Li Y, Chang Y, Hang C, Saleem A, Dong T, Guo T, Jiang Y, Lu W, Zhang L, Jianwen L, Jiang H, Lan F. Microscale grooves regulate maturation development of hPSC-CMs by the transient receptor potential channels (TRP channels). J Cell Mol Med 2021; 25:3469-3483. [PMID: 33689230 PMCID: PMC8034460 DOI: 10.1111/jcmm.16429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/11/2022] Open
Abstract
The use of human pluripotent stem cell‐derived cardiomyocytes (hPSC‐CMs) is limited in drug discovery and cardiac disease mechanism studies due to cell immaturity. Micro‐scaled grooves can promote the maturation of cardiomyocytes by aligning them in order, but the mechanism of cardiomyocytes alignment has not been studied. From the level of calcium activity, gene expression and cell morphology, we verified that the W20H5 grooves can effectively promote the maturation of cardiomyocytes. The transient receptor potential channels (TRP channels) also play an important role in the maturation and development of cardiomyocytes. These findings support the engineered hPSC‐CMs as a powerful model to study cardiac disease mechanism and partly mimic the myocardial morphological development. The important role of the TRP channels in the maturation and development of myocardium is first revealed.
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Affiliation(s)
- Taoyan Liu
- Beijing Lab for Cardiovascular Precision Medicine, Anzhen Hospital, Capital Medical University, Beijing, China.,State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Siyao Zhang
- Beijing Lab for Cardiovascular Precision Medicine, Anzhen Hospital, Capital Medical University, Beijing, China
| | - Chenwu Huang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Shuhong Ma
- Beijing Lab for Cardiovascular Precision Medicine, Anzhen Hospital, Capital Medical University, Beijing, China
| | - Rui Bai
- Beijing Lab for Cardiovascular Precision Medicine, Anzhen Hospital, Capital Medical University, Beijing, China
| | - Yanan Li
- Beijing Lab for Cardiovascular Precision Medicine, Anzhen Hospital, Capital Medical University, Beijing, China
| | - Yun Chang
- Beijing Lab for Cardiovascular Precision Medicine, Anzhen Hospital, Capital Medical University, Beijing, China
| | - Chenwen Hang
- Department of Cardiology, Peking University Third Hospital, Beijing, China
| | - Amina Saleem
- Beijing Lab for Cardiovascular Precision Medicine, Anzhen Hospital, Capital Medical University, Beijing, China
| | - Tao Dong
- Beijing Lab for Cardiovascular Precision Medicine, Anzhen Hospital, Capital Medical University, Beijing, China
| | - Tianwei Guo
- Beijing Lab for Cardiovascular Precision Medicine, Anzhen Hospital, Capital Medical University, Beijing, China
| | - Youxu Jiang
- Beijing Lab for Cardiovascular Precision Medicine, Anzhen Hospital, Capital Medical University, Beijing, China
| | - Wenjing Lu
- Beijing Lab for Cardiovascular Precision Medicine, Anzhen Hospital, Capital Medical University, Beijing, China
| | - Lina Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Luo Jianwen
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Hongfeng Jiang
- Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Feng Lan
- Beijing Lab for Cardiovascular Precision Medicine, Anzhen Hospital, Capital Medical University, Beijing, China
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162
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Watters KE, Kirkpatrick J, Palmer MJ, Koblentz GD. The CRISPR revolution and its potential impact on global health security. Pathog Glob Health 2021; 115:80-92. [PMID: 33590814 PMCID: PMC8550201 DOI: 10.1080/20477724.2021.1880202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Global health security is constantly under threat from infectious diseases. Despite advances in biotechnology that have improved diagnosis and treatment of such diseases, delays in detecting outbreaks and the lack of countermeasures for some biological agents continue to pose severe challenges to global health security. In this review, we describe some of the challenges facing global health security and how genome editing technologies can help overcome them. We provide specific examples of how the genome-editing tool CRISPR is being used to develop new tools to characterize pathogenic agents, diagnose infectious disease, and develop vaccines and therapeutics to mitigate the effects of an outbreak. The article also discusses some of the challenges associated with genome-editing technologies and the efforts that scientists are undertaking to mitigate them. Overall, CRISPR and genome-editing technologies are poised to have a significant positive influence on global health security over the years to come.
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Affiliation(s)
- Kyle E Watters
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jesse Kirkpatrick
- Institute for Philosophy and Public Policy, George Mason University, Fairfax, VA, USA
| | - Megan J Palmer
- Department of Bioengineering, Stanford University, Stanford, CA, USAs
| | - Gregory D Koblentz
- Schar School of Policy and Government, George Mason University, Fairfax, VA, USA
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163
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Chen PC, Hsueh YW, Lee YH, Tsai HW, Tsai KJ, Chiang PM. FGF primes angioblast formation by inducing ETV2 and LMO2 via FGFR1/BRAF/MEK/ERK. Cell Mol Life Sci 2021; 78:2199-2212. [PMID: 32910224 PMCID: PMC11073248 DOI: 10.1007/s00018-020-03630-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/28/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023]
Abstract
It is critical to specify a signal that directly drives the transition that occurs between cell states. However, such inferences are often confounded by indirect intercellular communications or secondary transcriptomic changes due to primary transcription factors. Although FGF is known for its importance during mesoderm-to-endothelium differentiation, its specific role and signaling mechanisms are still unclear due to the confounding factors referenced above. Here, we attempted to minimize the secondary artifacts by manipulating FGF and its downstream mediators with a short incubation time before sampling and protein-synthesis blockage in a low-density angioblastic/endothelial differentiation system. In less than 8 h, FGF started the conversion of KDRlow/PDGFRAlow nascent mesoderm into KDRhigh/PDGFRAlow angioblasts, and the priming by FGF was necessary to endow endothelial formation 72 h later. Further, the angioblastic conversion was mediated by the FGFR1/BRAF/MEK/ERK pathway in mesodermal cells. Finally, two transcription factors, ETV2 and LMO2, were the early direct functional responders downstream of the FGF pathway, and ETV2 alone was enough to complement the absence of FGF. FGF's selective role in mediating the first-step, angioblastic conversion from mesoderm-to-endothelium thus allows for refined control over acquiring and manipulating angioblasts. The noise-minimized differentiation/analysis platform presented here is well-suited for studies on the signaling switches of other mesodermal-lineage fates as well.
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Affiliation(s)
- Peng-Chieh Chen
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiaodong Rd., Tainan, 70457, Taiwan
- Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Wen Hsueh
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiaodong Rd., Tainan, 70457, Taiwan
- Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Hsuan Lee
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Hung-Wen Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuen-Jer Tsai
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiaodong Rd., Tainan, 70457, Taiwan
- Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Min Chiang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiaodong Rd., Tainan, 70457, Taiwan.
- Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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164
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Kyriakopoulos G, Katopodi V, Skeparnias I, Kaliatsi EG, Grafanaki K, Stathopoulos C. KRAS G12C Can Either Promote or Impair Cap-Dependent Translation in Two Different Lung Adenocarcinoma Cell Lines. Int J Mol Sci 2021; 22:ijms22042222. [PMID: 33672357 PMCID: PMC7926983 DOI: 10.3390/ijms22042222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/14/2022] Open
Abstract
KRASG12C is among the most common oncogenic mutations in lung adenocarcinoma and a promising target for treatment by small-molecule inhibitors. KRAS oncogenic signaling is responsible for modulation of tumor microenvironment, with translation factors being among the most prominent deregulated targets. In the present study, we used TALENs to edit EGFRWT CL1-5 and A549 cells for integration of a Tet-inducible KRASG12C expression system. Subsequent analysis of both cell lines showed that cap-dependent translation was impaired in CL1-5 cells via involvement of mTORC2 and NF-κB. In contrast, in A549 cells, which additionally harbor the KRASG12S mutation, cap-dependent translation was favored via recruitment of mTORC1, c-MYC and the positive regulation of eIF4F complex. Downregulation of eIF1, eIF5 and eIF5B in the same cell line suggested a stringency loss of start codon selection during scanning of mRNAs. Puromycin staining and polysome profile analysis validated the enhanced translation rates in A549 cells and the impaired cap-dependent translation in CL1-5 cells. Interestingly, elevated translation rates were restored in CL1-5 cells after prolonged induction of KRASG12C through an mTORC1/p70S6K-independent way. Collectively, our results suggest that KRASG12C signaling differentially affects the regulation of the translational machinery. These differences could provide additional insights and facilitate current efforts to effectively target KRAS.
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Affiliation(s)
- George Kyriakopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
| | - Vicky Katopodi
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
- Laboratory for RNA Cancer Biology, Department of Oncology, KU Leuven, 3001 Leuven, Belgium
| | - Ilias Skeparnias
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
| | - Eleni G Kaliatsi
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
| | - Katerina Grafanaki
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
- Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
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165
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Musicant AM, Parag-Sharma K, Gong W, Sengupta M, Chatterjee A, Henry EC, Tsai YH, Hayward MC, Sheth S, Betancourt R, Hackman TG, Padilla RJ, Parker JS, Giudice J, Flaveny CA, Hayes DN, Amelio AL. CRTC1/MAML2 directs a PGC-1α-IGF-1 circuit that confers vulnerability to PPARγ inhibition. Cell Rep 2021; 34:108768. [PMID: 33626346 PMCID: PMC7955229 DOI: 10.1016/j.celrep.2021.108768] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/22/2020] [Accepted: 01/27/2021] [Indexed: 01/03/2023] Open
Abstract
Mucoepidermoid carcinoma (MEC) is a life-threatening salivary gland cancer that is driven primarily by a transcriptional coactivator fusion composed of cyclic AMP-regulated transcriptional coactivator 1 (CRTC1) and mastermind-like 2 (MAML2). The mechanisms by which the chimeric CRTC1/MAML2 (C1/M2) oncoprotein rewires gene expression programs that promote tumorigenesis remain poorly understood. Here, we show that C1/M2 induces transcriptional activation of the non-canonical peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) splice variant PGC-1α4, which regulates peroxisome proliferator-activated receptor gamma (PPARγ)-mediated insulin-like growth factor 1 (IGF-1) expression. This mitogenic transcriptional circuitry is consistent across cell lines and primary tumors. C1/M2-positive tumors exhibit IGF-1 pathway activation, and small-molecule drug screens reveal that tumor cells harboring the fusion gene are selectively sensitive to IGF-1 receptor (IGF-1R) inhibition. Furthermore, this dependence on autocrine regulation of IGF-1 transcription renders MEC cells susceptible to PPARγ inhibition with inverse agonists. These results yield insights into the aberrant coregulatory functions of C1/M2 and identify a specific vulnerability that can be exploited for precision therapy.
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Affiliation(s)
- Adele M Musicant
- Graduate Curriculum in Genetics and Molecular Biology, Biological and Biomedical Sciences Program, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kshitij Parag-Sharma
- Graduate Curriculum in Cell Biology and Physiology, Biological and Biomedical Sciences Program, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Weida Gong
- Bioinformatics Core, Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Monideepa Sengupta
- Graduate Curriculum in Pharmacological and Physiological Sciences, School of Medicine, Saint Louis University, Saint Louis, MO, USA
| | - Arindam Chatterjee
- Department of Pharmacology and Physiology, School of Medicine, Saint Louis University, Saint Louis, MO, USA
| | - Erin C Henry
- Division of Oral and Craniofacial Health Sciences, UNC Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yi-Hsuan Tsai
- Bioinformatics Core, Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michele C Hayward
- Lineberger Comprehensive Cancer Center, Cancer Genetics Program, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Siddharth Sheth
- Division of Hematology/Oncology, Department of Medicine, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Renee Betancourt
- Department of Pathology and Laboratory Medicine, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Trevor G Hackman
- Department of Otolaryngology/Head and Neck Surgery, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ricardo J Padilla
- Division of Diagnostic Sciences, UNC Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, Cancer Genetics Program, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jimena Giudice
- Department of Cell Biology and Physiology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; McAllister Heart Institute, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Colin A Flaveny
- Department of Pharmacology and Physiology, School of Medicine, Saint Louis University, Saint Louis, MO, USA
| | - David N Hayes
- Lineberger Comprehensive Cancer Center, Cancer Genetics Program, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medical Oncology, University of Tennessee Health Sciences West Cancer Center, Memphis, TN, USA
| | - Antonio L Amelio
- Division of Oral and Craniofacial Health Sciences, UNC Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Biomedical Research Imaging Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, Cancer Cell Biology Program, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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166
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Mani I. Genome editing in cardiovascular diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:289-308. [PMID: 34127197 DOI: 10.1016/bs.pmbts.2021.01.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genetic modification at the molecular level in somatic cells, germline, and animal models requires for different purposes, such as introducing desired mutation, deletion of alleles, and insertion of novel genes in the genome. Various genome-editing tools are available to accomplish these alterations, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated (Cas) system. CRISPR-Cas system is an emerging technology, which is being used in biological and medical sciences, including in the cardiovascular field. It assists to identify the mechanism of various cardiovascular disease occurrence, such as hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), and arrhythmogenic cardiomyopathy (ACM). Furthermore, it has been advantages to edit various genes simultaneously and can also be used to treat and prevent several human diseases. This chapter explores the use of the scientific and therapeutic potential of a CRISPR-Cas system to edit the various cardiovascular disease-associated genes to understand the pathways involved in disease progression and treatment.
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Affiliation(s)
- Indra Mani
- Department of Microbiology, Gargi College, University of Delhi, New Delhi, India.
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167
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Sarkar E, Khan A. Erratic journey of CRISPR/Cas9 in oncology from bench-work to successful-clinical therapy. Cancer Treat Res Commun 2021; 27:100289. [PMID: 33667951 DOI: 10.1016/j.ctarc.2020.100289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/02/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
CRISPR is a customized molecular scissor, comprising genetic guide made of RNA and an enzyme, Cas9 which snips DNA in simpler, cheaper and more precise way than any other gene editing tools. In recent years CRISPR/Cas has taken the research world by storm being go-to genome editor for potential gene therapy to fix cancer as well as several hereditary disorders. This review explores the literature around the mechanism of Nobel winning CRISPR/Cas9 and its journey from its discovery to various pre-clinical and clinical trials in oncology, focusing mostly on PD-1 knockout CAR-T cell therapy. It also discusses the hurdles and ethical dispute associated with CRISPR, such as unintended on-target and off-target cuts, embryonic germ-line editing. Despite the controversies regarding the safety of this technique, many studies reported promising results on targeting cancer and other diseases using CRISPR/Cas9. Outcomes from the first successful clinical trial showed the beneficial long term effect on genetically modified T-cells in targeting cancer cells which opens the door for CRISPR to be the most preferred technique to help treating cancer and other diseases in future. As far as germ-line editing is concerned, further studies are needed to support the safety of this technique in humans fixing genetic disorders and mutations. Therefore till date only somatic cell editing is ethically approved.
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Affiliation(s)
- Esha Sarkar
- Department of Biochemistry, Era's Lucknow Medical College and hospital, Era University, Lucknow, Uttar Pradesh, India
| | - Afreen Khan
- Department of Biochemistry, Era's Lucknow Medical College and hospital, Era University, Lucknow, Uttar Pradesh, India.
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168
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Kathiriya IS, Rao KS, Iacono G, Devine WP, Blair AP, Hota SK, Lai MH, Garay BI, Thomas R, Gong HZ, Wasson LK, Goyal P, Sukonnik T, Hu KM, Akgun GA, Bernard LD, Akerberg BN, Gu F, Li K, Speir ML, Haeussler M, Pu WT, Stuart JM, Seidman CE, Seidman JG, Heyn H, Bruneau BG. Modeling Human TBX5 Haploinsufficiency Predicts Regulatory Networks for Congenital Heart Disease. Dev Cell 2021; 56:292-309.e9. [PMID: 33321106 PMCID: PMC7878434 DOI: 10.1016/j.devcel.2020.11.020] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/23/2020] [Accepted: 11/18/2020] [Indexed: 01/10/2023]
Abstract
Haploinsufficiency of transcriptional regulators causes human congenital heart disease (CHD); however, the underlying CHD gene regulatory network (GRN) imbalances are unknown. Here, we define transcriptional consequences of reduced dosage of the CHD transcription factor, TBX5, in individual cells during cardiomyocyte differentiation from human induced pluripotent stem cells (iPSCs). We discovered highly sensitive dysregulation of TBX5-dependent pathways-including lineage decisions and genes associated with heart development, cardiomyocyte function, and CHD genetics-in discrete subpopulations of cardiomyocytes. Spatial transcriptomic mapping revealed chamber-restricted expression for many TBX5-sensitive transcripts. GRN analysis indicated that cardiac network stability, including vulnerable CHD-linked nodes, is sensitive to TBX5 dosage. A GRN-predicted genetic interaction between Tbx5 and Mef2c, manifesting as ventricular septation defects, was validated in mice. These results demonstrate exquisite and diverse sensitivity to TBX5 dosage in heterogeneous subsets of iPSC-derived cardiomyocytes and predicts candidate GRNs for human CHDs, with implications for quantitative transcriptional regulation in disease.
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Affiliation(s)
- Irfan S Kathiriya
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA.
| | - Kavitha S Rao
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Giovanni Iacono
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - W Patrick Devine
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Pathology, University of California, San Francisco, CA 94158, USA
| | - Andrew P Blair
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Swetansu K Hota
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Michael H Lai
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Bayardo I Garay
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | | | - Henry Z Gong
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Lauren K Wasson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Piyush Goyal
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Tatyana Sukonnik
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Kevin M Hu
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Gunes A Akgun
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Laure D Bernard
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Fei Gu
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kai Li
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Matthew L Speir
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | | | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02115, USA
| | - Joshua M Stuart
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Universitat Pompeu Fabra, 08028 Barcelona, Spain
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, CA 94158, USA.
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169
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A comprehensive phenotypic CRISPR-Cas9 screen of the ubiquitin pathway uncovers roles of ubiquitin ligases in mitosis. Mol Cell 2021; 81:1319-1336.e9. [PMID: 33539788 DOI: 10.1016/j.molcel.2021.01.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 10/20/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
The human ubiquitin proteasome system, composed of over 700 ubiquitin ligases (E3s) and deubiquitinases (DUBs), has been difficult to characterize systematically and phenotypically. We performed chemical-genetic CRISPR-Cas9 screens to identify E3s/DUBs whose loss renders cells sensitive or resistant to 41 compounds targeting a broad range of biological processes, including cell cycle progression, genome stability, metabolism, and vesicular transport. Genes and compounds clustered functionally, with inhibitors of related pathways interacting similarly with E3s/DUBs. Some genes, such as FBXW7, showed interactions with many of the compounds. Others, such as RNF25 and FBXO42, showed interactions primarily with a single compound (methyl methanesulfonate for RNF25) or a set of related compounds (the mitotic cluster for FBXO42). Mutation of several E3s with sensitivity to mitotic inhibitors led to increased aberrant mitoses, suggesting a role for these genes in cell cycle regulation. Our comprehensive CRISPR-Cas9 screen uncovered 466 gene-compound interactions covering 25% of the interrogated E3s/DUBs.
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170
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Hu M, Cebola I, Carrat G, Jiang S, Nawaz S, Khamis A, Canouil M, Froguel P, Schulte A, Solimena M, Ibberson M, Marchetti P, Cardenas-Diaz FL, Gadue PJ, Hastoy B, Almeida-Souza L, McMahon H, Rutter GA. Chromatin 3D interaction analysis of the STARD10 locus unveils FCHSD2 as a regulator of insulin secretion. Cell Rep 2021; 34:108703. [PMID: 33535042 PMCID: PMC7856552 DOI: 10.1016/j.celrep.2021.108703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/10/2019] [Accepted: 01/08/2021] [Indexed: 12/26/2022] Open
Abstract
Using chromatin conformation capture, we show that an enhancer cluster in the STARD10 type 2 diabetes (T2D) locus forms a defined 3-dimensional (3D) chromatin domain. A 4.1-kb region within this locus, carrying 5 T2D-associated variants, physically interacts with CTCF-binding regions and with an enhancer possessing strong transcriptional activity. Analysis of human islet 3D chromatin interaction maps identifies the FCHSD2 gene as an additional target of the enhancer cluster. CRISPR-Cas9-mediated deletion of the variant region, or of the associated enhancer, from human pancreas-derived EndoC-βH1 cells impairs glucose-stimulated insulin secretion. Expression of both STARD10 and FCHSD2 is reduced in cells harboring CRISPR deletions, and lower expression of STARD10 and FCHSD2 is associated, the latter nominally, with the possession of risk variant alleles in human islets. Finally, CRISPR-Cas9-mediated loss of STARD10 or FCHSD2, but not ARAP1, impairs regulated insulin secretion. Thus, multiple genes at the STARD10 locus influence β cell function.
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Affiliation(s)
- Ming Hu
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Gaelle Carrat
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Shuying Jiang
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Sameena Nawaz
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LE, UK
| | - Amna Khamis
- Université de Lille, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 8199 - EGID, 59000 Lille, France
| | - Mickaël Canouil
- Université de Lille, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 8199 - EGID, 59000 Lille, France
| | - Philippe Froguel
- Université de Lille, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 8199 - EGID, 59000 Lille, France
| | - Anke Schulte
- Sanofi-Aventis Deutschland GmbH, 65926 Frankfurt am Main, Germany
| | - Michele Solimena
- Paul Langerhans Institute of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany
| | - Mark Ibberson
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Piero Marchetti
- Department of Endocrinology and Metabolism, University of Pisa, 56126 Pisa, Italy
| | - Fabian L Cardenas-Diaz
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Centre for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul J Gadue
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Centre for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Benoit Hastoy
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LE, UK
| | - Leonardo Almeida-Souza
- HiLIFE Institute of Biotechnology & Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Harvey McMahon
- MRC MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK; Lee Kong Chian School of Medicine, Nan Yang Technological University, Singapore, Singapore.
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171
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Willsey HR, Exner CRT, Xu Y, Everitt A, Sun N, Wang B, Dea J, Schmunk G, Zaltsman Y, Teerikorpi N, Kim A, Anderson AS, Shin D, Seyler M, Nowakowski TJ, Harland RM, Willsey AJ, State MW. Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience. Neuron 2021; 109:788-804.e8. [PMID: 33497602 DOI: 10.1016/j.neuron.2021.01.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 12/02/2020] [Accepted: 01/04/2021] [Indexed: 12/29/2022]
Abstract
Gene Ontology analyses of autism spectrum disorders (ASD) risk genes have repeatedly highlighted synaptic function and transcriptional regulation as key points of convergence. However, these analyses rely on incomplete knowledge of gene function across brain development. Here we leverage Xenopus tropicalis to study in vivo ten genes with the strongest statistical evidence for association with ASD. All genes are expressed in developing telencephalon at time points mapping to human mid-prenatal development, and mutations lead to an increase in the ratio of neural progenitor cells to maturing neurons, supporting previous in silico systems biological findings implicating cortical neurons in ASD vulnerability, but expanding the range of convergent functions to include neurogenesis. Systematic chemical screening identifies that estrogen, via Sonic hedgehog signaling, rescues this convergent phenotype in Xenopus and human models of brain development, suggesting a resilience factor that may mitigate a range of ASD genetic risks.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cameron R T Exner
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yuxiao Xu
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Amanda Everitt
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nawei Sun
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeanselle Dea
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Galina Schmunk
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yefim Zaltsman
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nia Teerikorpi
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Albert Kim
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Aoife S Anderson
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David Shin
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Meghan Seyler
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tomasz J Nowakowski
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA 94143, USA.
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172
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Liu SJ, Horlbeck MA, Weissman JS, Lim DA. Genome-Scale Perturbation of Long Noncoding RNA Expression Using CRISPR Interference. Methods Mol Biol 2021; 2254:323-338. [PMID: 33326085 PMCID: PMC7917014 DOI: 10.1007/978-1-0716-1158-6_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
CRISPR-mediated interference (CRISPRi), a robust and specific system for programmably repressing transcription, provides a versatile tool for systematically characterizing the function of long noncoding RNAs (lncRNAs). When used with highly parallel, lentiviral pooled screening approaches, CRISPRi enables the targeted knockdown of tens of thousands of lncRNA-expressing loci in a single screen. Here we describe the use of CRISPRi to target lncRNA loci in a pooled screen, using cell growth and proliferation as an example of a phenotypic readout. Considerations for custom lncRNA-targeting libraries, alternative phenotypic readouts, and orthogonal validation approaches are also discussed.
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Affiliation(s)
- S John Liu
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA, USA
- Center for RNA Systems Biology, University of California, San Francisco, CA, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA, USA
- Center for RNA Systems Biology, University of California, San Francisco, CA, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, CA, USA.
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA.
- San Francisco Veterans Affairs Medical Center, University of California, San Francisco, CA, USA.
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173
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Libby ARG, Joy DA, McDevitt TC. Engineering the Spatiotemporal Mosaic Self-Patterning of Pluripotent Stem Cells. Methods Mol Biol 2021; 2258:105-116. [PMID: 33340357 DOI: 10.1007/978-1-0716-1174-6_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Pluripotent stem cells (PSCs) possess the ability to self-organize into complex tissue-like structures; however, the genetic mechanisms and multicellular dynamics that direct such patterning are difficult to control. Here, we pair live imaging with controlled induction of gene knockdown by CRISPR interference (CRISPRi) to generate changes within subpopulations of human PSCs, allowing for control over organization and analysis of emergent behaviors. Specifically, we use forced aggregation of mixtures of cells with and without an inducible CRISPRi system to knockdown molecular regulators of tissue symmetry. We then track the resulting multicellular organization through fluorescence live imaging concurrent with the induction of knockdown. Overall, this technique allows for controlled initiation of symmetry breaking by CRISPRi to produce changes in cellular behavior that can be tracked over time within high-density pluripotent stem cell colonies.
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Affiliation(s)
- Ashley R G Libby
- Developmental and Stem Cell Biology PhD Program, University of California, San Francisco, CA, USA
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
| | - David A Joy
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, San Francisco, CA, USA
| | - Todd C McDevitt
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
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174
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Abstract
Identifying causative genes in a given phenotype or disease model is important for biological discovery and drug development. The recent development of the CRISPR/Cas9 system has enabled unbiased and large-scale genetic perturbation screens to identify causative genes by knocking out many genes in parallel and selecting cells with desired phenotype of interest. However, compared to cancer cell lines, human somatic cells including cardiomyocytes (CMs), neuron cells, and endothelial cells are not easy targets of CRISPR screens because CRISPR screens require a large number of isogenic cells to be cultured and thus primary cells from patients are not ideal. The combination of CRISPR screens with induced pluripotent stem cell (iPSC) technology would be a powerful tool to identify causative genes and pathways because iPSCs can be expanded easily and differentiated to any cell type in principle. Here we describe a robust protocol for CRISPR screening using human iPSCs. Because each screening is different and needs to be customized depending on the cell types and phenotypes of interest, we show an example of CRISPR knockdown screening using CRISPRi system to identify essential genes to differentiate iPSCs to CMs.
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Affiliation(s)
- Masataka Nishiga
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.
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175
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Chung SH, Sin TN, Ngo T, Yiu G. CRISPR Technology for Ocular Angiogenesis. Front Genome Ed 2020; 2:594984. [PMID: 34713223 PMCID: PMC8525361 DOI: 10.3389/fgeed.2020.594984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/01/2020] [Indexed: 12/24/2022] Open
Abstract
Among genome engineering tools, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based approaches have been widely adopted for translational studies due to their robustness, precision, and ease of use. When delivered to diseased tissues with a viral vector such as adeno-associated virus, direct genome editing can be efficiently achieved in vivo to treat different ophthalmic conditions. While CRISPR has been actively explored as a strategy for treating inherited retinal diseases, with the first human trial recently initiated, its applications for complex, multifactorial conditions such as ocular angiogenesis has been relatively limited. Currently, neovascular retinal diseases such as retinopathy of prematurity, proliferative diabetic retinopathy, and neovascular age-related macular degeneration, which together constitute the majority of blindness in developed countries, are managed with frequent and costly injections of anti-vascular endothelial growth factor (anti-VEGF) agents that are short-lived and burdensome for patients. By contrast, CRISPR technology has the potential to suppress angiogenesis permanently, with the added benefit of targeting intracellular signals or regulatory elements, cell-specific delivery, and multiplexing to disrupt different pro-angiogenic factors simultaneously. However, the prospect of permanently suppressing physiologic pathways, the unpredictability of gene editing efficacy, and concerns for off-target effects have limited enthusiasm for these approaches. Here, we review the evolution of gene therapy and advances in adapting CRISPR platforms to suppress retinal angiogenesis. We discuss different Cas9 orthologs, delivery strategies, and different genomic targets including VEGF, VEGF receptor, and HIF-1α, as well as the advantages and disadvantages of genome editing vs. conventional gene therapies for multifactorial disease processes as compared to inherited monogenic retinal disorders. Lastly, we describe barriers that must be overcome to enable effective adoption of CRISPR-based strategies for the management of ocular angiogenesis.
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Affiliation(s)
| | | | | | - Glenn Yiu
- Department of Ophthalmology and Vision Science, University of California, Davis, Sacramento, CA, United States
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176
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Ayala-Sarmiento AE, Kobritz N, Breunig JJ. De Novo Generation of Murine and Human MADR Recipient Cell Lines for Locus-Specific, Stable Integration of Transgenic Elements. STAR Protoc 2020; 1:100184. [PMID: 33377078 PMCID: PMC7757409 DOI: 10.1016/j.xpro.2020.100184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Mosaic analysis by dual recombinase-mediated cassette exchange (MADR) is a technology that allows stable and locus-specific integration of transgenic elements into recipient cells carrying loxP and FRT sites. Nevertheless, most cell lines lack these recombination-specific sites. This protocol describes a method to introduce the minimum requirements into cells, leading to the generation of de novo primary MADR recipient cells or MADR "Proxy" cells. These cell lines allow the combinatorial use of a wide range of transgenic elements through MADR. For complete details on the use and execution of this protocol, please refer to Kim et al. (2019).
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Affiliation(s)
- Alberto E. Ayala-Sarmiento
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Naomi Kobritz
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joshua J. Breunig
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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177
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Shim WJ, Sinniah E, Xu J, Vitrinel B, Alexanian M, Andreoletti G, Shen S, Sun Y, Balderson B, Boix C, Peng G, Jing N, Wang Y, Kellis M, Tam PPL, Smith A, Piper M, Christiaen L, Nguyen Q, Bodén M, Palpant NJ. Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity. Cell Syst 2020; 11:625-639.e13. [PMID: 33278344 PMCID: PMC7781436 DOI: 10.1016/j.cels.2020.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/31/2020] [Accepted: 11/09/2020] [Indexed: 01/06/2023]
Abstract
Determining genes that orchestrate cell differentiation in development and disease remains a fundamental goal of cell biology. This study establishes a genome-wide metric based on the gene-repressive trimethylation of histone H3 at lysine 27 (H3K27me3) across hundreds of diverse cell types to identify genetic regulators of cell differentiation. We introduce a computational method, TRIAGE, which uses discordance between gene-repressive tendency and expression to identify genetic drivers of cell identity. We apply TRIAGE to millions of genome-wide single-cell transcriptomes, diverse omics platforms, and eukaryotic cells and tissue types. Using a wide range of data, we validate the performance of TRIAGE in identifying cell-type-specific regulatory factors across diverse species including human, mouse, boar, bird, fish, and tunicate. Using CRISPR gene editing, we use TRIAGE to experimentally validate RNF220 as a regulator of Ciona cardiopharyngeal development and SIX3 as required for differentiation of endoderm in human pluripotent stem cells. A record of this paper’s transparent peer review process is included in the Supplemental Information. Perturbing genes controlling cell decisions have major implications in development or disease. However, identifying key regulatory genes from the thousands expressed in a cell is challenging. TRIAGE is a computational method that distills patterns of epigenetic repression across diverse cell types to infer regulatory genes using input gene expression data from any cell type. Demonstrating its utility, we combine single-cell RNA-seq and TRIAGE to identify and experimentally confirm novel regulators of heart development in evolutionarily distant species.
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Affiliation(s)
- Woo Jun Shim
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Enakshi Sinniah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jun Xu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Burcu Vitrinel
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
| | - Michael Alexanian
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA
| | - Gaia Andreoletti
- Institute for Computational Health Sciences, University of California, San Francisco, CA 94158, USA
| | - Sophie Shen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Yuliangzi Sun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Brad Balderson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Carles Boix
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Guangdun Peng
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences and Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China; State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Naihe Jing
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences and Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China; State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yuliang Wang
- Paul G. Allen School of Computer Science and Engineering and Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA
| | | | - Patrick P L Tam
- The University of Sydney, Children's Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, Westmead, NSW 2145, Australia
| | - Aaron Smith
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia; Translational Research Institute, Woolloongabba, Brisbane, Australia
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
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178
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Mizushima N, Murphy LO. Autophagy Assays for Biological Discovery and Therapeutic Development. Trends Biochem Sci 2020; 45:1080-1093. [DOI: 10.1016/j.tibs.2020.07.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/08/2020] [Accepted: 07/24/2020] [Indexed: 12/14/2022]
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179
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Integrative analyses prioritize GNL3 as a risk gene for bipolar disorder. Mol Psychiatry 2020; 25:2672-2684. [PMID: 32826963 DOI: 10.1038/s41380-020-00866-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 07/30/2020] [Accepted: 08/06/2020] [Indexed: 12/14/2022]
Abstract
Genome-wide association studies (GWASs) have identified numerous single nucleotide polymorphisms (SNPs) associated with bipolar disorder (BD), but what the causal variants are and how they contribute to BD is largely unknown. In this study, we used FUMA, a GWAS annotation tool, to pinpoint potential causal variants and genes from the latest BD GWAS findings, and performed integrative analyses, including brain expression quantitative trait loci (eQTL), gene coexpression network, differential gene expression, protein-protein interaction, and brain intermediate phenotype association analysis to identify the functions of a prioritized gene and its connection to BD. Convergent lines of evidence prioritized protein-coding gene G Protein Nucleolar 3 (GNL3) as a BD risk gene, with integrative analyses revealing GNL3's roles in cell proliferation, neuronal functions, and brain phenotypes. We experimentally revealed that BD-related eQTL SNPs rs10865973, rs12635140, and rs4687644 regulate GNL3 expression using dual luciferase reporter assay and CRISPR interference experiment in human neural progenitor cells. We further identified that GNL3 knockdown and overexpression led to aberrant neuronal proliferation and differentiation, using two-dimensional human neural cell cultures and three-dimensional forebrain organoid model. This study gathers evidence that BD-related genetic variants regulate GNL3 expression which subsequently affects neuronal proliferation and differentiation.
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180
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Li R, Xia X, Wang X, Sun X, Dai Z, Huo D, Zheng H, Xiong H, He A, Wu X. Generation and validation of versatile inducible CRISPRi embryonic stem cell and mouse model. PLoS Biol 2020; 18:e3000749. [PMID: 33253175 PMCID: PMC7728392 DOI: 10.1371/journal.pbio.3000749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 12/10/2020] [Accepted: 11/02/2020] [Indexed: 01/09/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated (Cas) 9 has been widely used far beyond genome editing. Fusions of deactivated Cas9 (dCas9) to transcription effectors enable interrogation of the epigenome and controlling of gene expression. However, the large transgene size of dCas9-fusion hinders its applications especially in somatic tissues. Here, we develop a robust CRISPR interference (CRISPRi) system by transgenic expression of doxycycline (Dox) inducible dCas9-KRAB in mouse embryonic stem cells (iKRAB ESC). After introduction of specific single-guide RNAs (sgRNAs), the induced dCas9-KRAB efficiently maintains gene inactivation, although it modestly down-regulates the expression of active genes. The proper timing of Dox addition during cell differentiation or reprogramming allows us to study or screen spatiotemporally activated promoters or enhancers and thereby the gene functions. Furthermore, taking the ESC for blastocyst injection, we generate an iKRAB knock-in (KI) mouse model that enables the shutdown of gene expression and loss-of-function (LOF) studies ex vivo and in vivo by a simple transduction of gRNAs. Thus, our inducible CRISPRi ESC line and KI mouse provide versatile and convenient platforms for functional interrogation and high-throughput screens of specific genes and potential regulatory elements in the setting of development or diseases.
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Affiliation(s)
- Rui Li
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xianyou Xia
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xing Wang
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiaoyu Sun
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhongye Dai
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Dawei Huo
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Huimin Zheng
- Department of Prosthodontics, School and Hospital of Stomatology, Tianjin Medical University, Tianjin, China
| | - Haiqing Xiong
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Aibin He
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xudong Wu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin, China
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181
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Santos-Moreno J, Schaerli Y. CRISPR-based gene expression control for synthetic gene circuits. Biochem Soc Trans 2020; 48:1979-1993. [PMID: 32964920 PMCID: PMC7609024 DOI: 10.1042/bst20200020] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/22/2022]
Abstract
Synthetic gene circuits allow us to govern cell behavior in a programmable manner, which is central to almost any application aiming to harness engineered living cells for user-defined tasks. Transcription factors (TFs) constitute the 'classic' tool for synthetic circuit construction but some of their inherent constraints, such as insufficient modularity, orthogonality and programmability, limit progress in such forward-engineering endeavors. Here we review how CRISPR (clustered regularly interspaced short palindromic repeats) technology offers new and powerful possibilities for synthetic circuit design. CRISPR systems offer superior characteristics over TFs in many aspects relevant to a modular, predictable and standardized circuit design. Thus, the choice of CRISPR technology as a framework for synthetic circuit design constitutes a valid alternative to complement or replace TFs in synthetic circuits and promises the realization of more ambitious designs.
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Affiliation(s)
- Javier Santos-Moreno
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Yolanda Schaerli
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
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182
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Chu D, Nguyen A, Smith SS, Vavrušová Z, Schneider RA. Stable integration of an optimized inducible promoter system enables spatiotemporal control of gene expression throughout avian development. Biol Open 2020; 9:bio055343. [PMID: 32917762 PMCID: PMC7561481 DOI: 10.1242/bio.055343] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/27/2020] [Indexed: 01/18/2023] Open
Abstract
Precisely altering gene expression is critical for understanding molecular processes of embryogenesis. Although some tools exist for transgene misexpression in developing chick embryos, we have refined and advanced them by simplifying and optimizing constructs for spatiotemporal control. To maintain expression over the entire course of embryonic development we use an enhanced piggyBac transposon system that efficiently integrates sequences into the host genome. We also incorporate a DNA targeting sequence to direct plasmid translocation into the nucleus and a D4Z4 insulator sequence to prevent epigenetic silencing. We designed these constructs to minimize their size and maximize cellular uptake, and to simplify usage by placing all of the integrating sequences on a single plasmid. Following electroporation of stage HH8.5 embryos, our tetracycline-inducible promoter construct produces robust transgene expression in the presence of doxycycline at any point during embryonic development in ovo or in culture. Moreover, expression levels can be modulated by titrating doxycycline concentrations and spatial control can be achieved using beads or gels. Thus, we have generated a novel, sensitive, tunable, and stable inducible-promoter system for high-resolution gene manipulation in vivo.
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Affiliation(s)
- Daniel Chu
- Department of Orthopaedic Surgery, University of California at San Francisco, 513 Parnassus Avenue, S-1164, San Francisco, CA 94143-0514, USA
| | - An Nguyen
- Department of Orthopaedic Surgery, University of California at San Francisco, 513 Parnassus Avenue, S-1164, San Francisco, CA 94143-0514, USA
| | - Spenser S Smith
- Department of Orthopaedic Surgery, University of California at San Francisco, 513 Parnassus Avenue, S-1164, San Francisco, CA 94143-0514, USA
| | - Zuzana Vavrušová
- Department of Orthopaedic Surgery, University of California at San Francisco, 513 Parnassus Avenue, S-1164, San Francisco, CA 94143-0514, USA
| | - Richard A Schneider
- Department of Orthopaedic Surgery, University of California at San Francisco, 513 Parnassus Avenue, S-1164, San Francisco, CA 94143-0514, USA
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183
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Ide S, Imai R, Ochi H, Maeshima K. Transcriptional suppression of ribosomal DNA with phase separation. SCIENCE ADVANCES 2020; 6:6/42/eabb5953. [PMID: 33055158 PMCID: PMC7556839 DOI: 10.1126/sciadv.abb5953] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/25/2020] [Indexed: 05/21/2023]
Abstract
The nucleolus is a nuclear body with multiphase liquid droplets for ribosomal RNA (rRNA) transcription. How rRNA transcription is regulated in the droplets remains unclear. Here, using single-molecule tracking of RNA polymerase I (Pol I) and chromatin-bound upstream binding factor (UBF), we reveal suppression of transcription with phase separation. For transcription, active Pol I formed small clusters/condensates that constrained rDNA chromatin in the nucleolus fibrillar center (FC). Treatment with a transcription inhibitor induced Pol I to dissociate from rDNA chromatin and to move like a liquid within the nucleolar cap that transformed from the FC. Expression of a Pol I mutant associated with a craniofacial disorder inhibited transcription by competing with wild-type Pol I clusters and transforming the FC into the nucleolar cap. The cap droplet excluded an initiation factor, ensuring robust silencing. Our findings suggest a mechanism of rRNA transcription suppression via phase separation of intranucleolar molecules governed by Pol I.
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Affiliation(s)
- Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Shizuoka 411-8540, Japan
| | - Ryosuke Imai
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Shizuoka 411-8540, Japan
| | - Hiroko Ochi
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Shizuoka 411-8540, Japan
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184
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Liu X, Fang Z, Wen J, Tang F, Liao B, Jing N, Lai D, Jin Y. SOX1 Is Required for the Specification of Rostral Hindbrain Neural Progenitor Cells from Human Embryonic Stem Cells. iScience 2020; 23:101475. [PMID: 32905879 PMCID: PMC7486433 DOI: 10.1016/j.isci.2020.101475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 07/11/2020] [Accepted: 08/17/2020] [Indexed: 01/09/2023] Open
Abstract
Region-specific neural progenitor cells (NPCs) can be generated from human embryonic stem cells (hESCs) by modulating signaling pathways. However, how intrinsic transcriptional factors contribute to the neural regionalization is not well characterized. Here, we generate region-specific NPCs from hESCs and find that SOX1 is highly expressed in NPCs with the rostral hindbrain identity. Moreover, we find that OTX2 inhibits SOX1 expression, displaying exclusive expression between the two factors. Furthermore, SOX1 knockout (KO) leads to the upregulation of midbrain genes and downregulation of rostral hindbrain genes, indicating that SOX1 is required for specification of rostral hindbrain NPCs. Our SOX1 chromatin immunoprecipitation sequencing analysis reveals that SOX1 binds to the distal region of GBX2 to activate its expression. Overexpression of GBX2 largely abrogates SOX1-KO-induced aberrant gene expression. Taken together, this study uncovers previously unappreciated role of SOX1 in early neural regionalization and provides new information for the precise control of the OTX2/GBX2 interface.
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Affiliation(s)
- Xinyuan Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Zhuoqing Fang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Jing Wen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Fan Tang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, Shanghai 200025, China
| | - Bing Liao
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, Shanghai 200025, China
| | - Naihe Jing
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
| | - Dongmei Lai
- International Peace Maternity and Child Health Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200030, China
| | - Ying Jin
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, Shanghai 200025, China
- Basic Clinical Research Center, Renji Hospital, Shanghai JiaoTong University School of Medicine, 160 Pujian Road, Shanghai 200127, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
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185
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Xia S, Wang X, Yue P, Li Y, Zhang D. Establishment of induced pluripotent stem cell lines from a family of an ARVC patient receiving heart transplantation in infant age carrying compound heterozygous mutations in DSP gene. Stem Cell Res 2020; 48:101977. [PMID: 32942234 DOI: 10.1016/j.scr.2020.101977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 11/19/2022] Open
Abstract
The mutations of desmoplakin (DSP) lead to arrhythmia right ventricular cardiomyopathy (ARVC) which is a kind of progressive cardiomyopathy characterized by arrhythmia, heart failure and sudden cardiac death. The human induced pluripotent stem (iPS) cell line HUBUi001-A was generated from a patient carrying the compound DSP heterozygous mutations (c.104G > T p.G35V; c.5617C > T p.R1873C), which were inherited from his parents (HUBUi002-A, HUBUi003- A), who presented a normal phenotype. We have derived the iPSC cell lines through peripheral blood mononuclear (PBMCs) cell reprogramming technology. Pluripotency and differentiation capacity have been confirmed by RT-PCR, immunocytochemistry and teratoma experiment. These cell lines can help us understand the pathogenic mechanism and screening potential therapeutic options.
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Affiliation(s)
- Shutao Xia
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, Wuhan, Hubei 430062, China
| | - Xvdong Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, Wuhan, Hubei 430062, China
| | - Peng Yue
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Donghui Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, Wuhan, Hubei 430062, China.
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186
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Sharanek A, Burban A, Laaper M, Heckel E, Joyal JS, Soleimani VD, Jahani-Asl A. OSMR controls glioma stem cell respiration and confers resistance of glioblastoma to ionizing radiation. Nat Commun 2020; 11:4116. [PMID: 32807793 PMCID: PMC7431428 DOI: 10.1038/s41467-020-17885-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma contains a rare population of self-renewing brain tumor stem cells (BTSCs) which are endowed with properties to proliferate, spur the growth of new tumors, and at the same time, evade ionizing radiation (IR) and chemotherapy. However, the drivers of BTSC resistance to therapy remain unknown. The cytokine receptor for oncostatin M (OSMR) regulates BTSC proliferation and glioblastoma tumorigenesis. Here, we report our discovery of a mitochondrial OSMR that confers resistance to IR via regulation of oxidative phosphorylation, independent of its role in cell proliferation. Mechanistically, OSMR is targeted to the mitochondrial matrix via the presequence translocase-associated motor complex components, mtHSP70 and TIM44. OSMR interacts with NADH ubiquinone oxidoreductase 1/2 (NDUFS1/2) of complex I and promotes mitochondrial respiration. Deletion of OSMR impairs spare respiratory capacity, increases reactive oxygen species, and sensitizes BTSCs to IR-induced cell death. Importantly, suppression of OSMR improves glioblastoma response to IR and prolongs lifespan. The suppression of the receptor for oncostatin M (OSMR) can prevent glioblastoma cell growth. Here, the authors demonstrate a role for OSMR in modulating glioma stem cell respiration and its impact on resistance to ionizing radiation.
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Affiliation(s)
- Ahmad Sharanek
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada
| | - Audrey Burban
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada
| | - Matthew Laaper
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada.,Integrated program in Neuroscience, Montreal Neurological Institute, 3801 University Street, Montréal, QC, H3A 2B4, Canada
| | - Emilie Heckel
- Departments of Pediatrics, Pharmacology and Ophthalmology, Université de Montréal, CHU Sainte-Justine, Montréal, QC, H3T 1C5, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC, H3G 1Y6, Canada
| | - Jean-Sebastien Joyal
- Departments of Pediatrics, Pharmacology and Ophthalmology, Université de Montréal, CHU Sainte-Justine, Montréal, QC, H3T 1C5, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC, H3G 1Y6, Canada
| | - Vahab D Soleimani
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada.,Department of Human Genetics, McGill University, 3640 Rue University, Montréal, QC, H3A OC7, Canada
| | - Arezu Jahani-Asl
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada. .,Integrated program in Neuroscience, Montreal Neurological Institute, 3801 University Street, Montréal, QC, H3A 2B4, Canada. .,Gerald Bronfman Department of Oncology and Division of Experimental Medicine, McGill University, 5100 Maisonneuve Blvd West, Suite 720, H4A3T2, Montréal, QC, Canada.
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187
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Gao Y, Gao K, Yang H. CRISPR/Cas: a potential gene-editing tool in the nervous system. CELL REGENERATION (LONDON, ENGLAND) 2020; 9:12. [PMID: 32761306 PMCID: PMC7406588 DOI: 10.1186/s13619-020-00044-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023]
Abstract
The rapidly developmental RNA-guided CRISPR/Cas system is a powerful tool for RNA and DNA editing in a variety of cells from different species and makes a great contribution to gene function research, disease model generation and gene therapy development in the past few years. The ease of use, low cost and high efficiency of CRISPR/Cas make it commonly used in various conditions. In this review, we introduce the CRISPR/Cas system and its diverse applications in nervous system briefly, which provides a better understanding for its potential application values.
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Affiliation(s)
- Yanxia Gao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Kexin Gao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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188
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Werley CA, Boccardo S, Rigamonti A, Hansson EM, Cohen AE. Multiplexed Optical Sensors in Arrayed Islands of Cells for multimodal recordings of cellular physiology. Nat Commun 2020; 11:3881. [PMID: 32753572 PMCID: PMC7403318 DOI: 10.1038/s41467-020-17607-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 07/07/2020] [Indexed: 11/29/2022] Open
Abstract
Cells typically respond to chemical or physical perturbations via complex signaling cascades which can simultaneously affect multiple physiological parameters, such as membrane voltage, calcium, pH, and redox potential. Protein-based fluorescent sensors can report many of these parameters, but spectral overlap prevents more than ~4 modalities from being recorded in parallel. Here we introduce the technique, MOSAIC, Multiplexed Optical Sensors in Arrayed Islands of Cells, where patterning of fluorescent sensor-encoding lentiviral vectors with a microarray printer enables parallel recording of multiple modalities. We demonstrate simultaneous recordings from 20 sensors in parallel in human embryonic kidney (HEK293) cells and in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), and we describe responses to metabolic and pharmacological perturbations. Together, these results show that MOSAIC can provide rich multi-modal data on complex physiological responses in multiple cell types.
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Affiliation(s)
- Christopher A Werley
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Q-State Biosciences, Cambridge, MA, 02139, USA
| | - Stefano Boccardo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Nobel Biocare AG, Kloten, Switzerland
| | - Alessandra Rigamonti
- Integrated Cardio Metabolic Centre, Department of Medicine Huddinge, Karolinska Institute, Huddinge, Sweden
| | - Emil M Hansson
- Integrated Cardio Metabolic Centre, Department of Medicine Huddinge, Karolinska Institute, Huddinge, Sweden
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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189
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Replogle JM, Norman TM, Xu A, Hussmann JA, Chen J, Cogan JZ, Meer EJ, Terry JM, Riordan DP, Srinivas N, Fiddes IT, Arthur JG, Alvarado LJ, Pfeiffer KA, Mikkelsen TS, Weissman JS, Adamson B. Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing. Nat Biotechnol 2020; 38:954-961. [PMID: 32231336 PMCID: PMC7416462 DOI: 10.1038/s41587-020-0470-y] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/26/2020] [Indexed: 12/13/2022]
Abstract
Single-cell CRISPR screens enable the exploration of mammalian gene function and genetic regulatory networks. However, use of this technology has been limited by reliance on indirect indexing of single-guide RNAs (sgRNAs). Here we present direct-capture Perturb-seq, a versatile screening approach in which expressed sgRNAs are sequenced alongside single-cell transcriptomes. Direct-capture Perturb-seq enables detection of multiple distinct sgRNA sequences from individual cells and thus allows pooled single-cell CRISPR screens to be easily paired with combinatorial perturbation libraries that contain dual-guide expression vectors. We demonstrate the utility of this approach for high-throughput investigations of genetic interactions and, leveraging this ability, dissect epistatic interactions between cholesterol biogenesis and DNA repair. Using direct capture Perturb-seq, we also show that targeting individual genes with multiple sgRNAs per cell improves efficacy of CRISPR interference and activation, facilitating the use of compact, highly active CRISPR libraries for single-cell screens. Last, we show that hybridization-based target enrichment permits sensitive, specific sequencing of informative transcripts from single-cell RNA-seq experiments.
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Affiliation(s)
- Joseph M Replogle
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
| | - Thomas M Norman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Albert Xu
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jin Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
| | - J Zachery Cogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA.
| | - Britt Adamson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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190
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Najm R, Zalocusky KA, Zilberter M, Yoon SY, Hao Y, Koutsodendris N, Nelson M, Rao A, Taubes A, Jones EA, Huang Y. In Vivo Chimeric Alzheimer's Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons. Cell Rep 2020; 32:107962. [PMID: 32726626 PMCID: PMC7430173 DOI: 10.1016/j.celrep.2020.107962] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/15/2020] [Accepted: 07/03/2020] [Indexed: 02/08/2023] Open
Abstract
Despite its clear impact on Alzheimer's disease (AD) risk, apolipoprotein (apo) E4's contributions to AD etiology remain poorly understood. Progress in answering this and other questions in AD research has been limited by an inability to model human-specific phenotypes in an in vivo environment. Here we transplant human induced pluripotent stem cell (hiPSC)-derived neurons carrying normal apoE3 or pathogenic apoE4 into human apoE3 or apoE4 knockin mouse hippocampi, enabling us to disentangle the effects of apoE4 produced in human neurons and in the brain environment. Using single-nucleus RNA sequencing (snRNA-seq), we identify key transcriptional changes specific to human neuron subtypes in response to endogenous or exogenous apoE4. We also find that Aβ from transplanted human neurons forms plaque-like aggregates, with differences in localization and interaction with microglia depending on the transplant and host apoE genotype. These findings highlight the power of in vivo chimeric disease modeling for studying AD.
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Affiliation(s)
- Ramsey Najm
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kelly A Zalocusky
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Gladstone Center for Translational Advancement, San Francisco, CA 94158, USA
| | - Misha Zilberter
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Seo Yeon Yoon
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Yanxia Hao
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Gladstone Center for Translational Advancement, San Francisco, CA 94158, USA
| | - Nicole Koutsodendris
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Maxine Nelson
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Antara Rao
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alice Taubes
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emily A Jones
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yadong Huang
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Center for Translational Advancement, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Departments of Neurology and Pathology, University of California, San Francisco, San Francisco, CA 94143, USA.
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191
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Shakirova KM, Ovchinnikova VY, Dashinimaev EB. Cell Reprogramming With CRISPR/Cas9 Based Transcriptional Regulation Systems. Front Bioeng Biotechnol 2020; 8:882. [PMID: 32850737 PMCID: PMC7399070 DOI: 10.3389/fbioe.2020.00882] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/09/2020] [Indexed: 12/22/2022] Open
Abstract
The speed of reprogramming technologies evolution is rising dramatically in modern science. Both the scientific community and health workers depend on such developments due to the lack of safe autogenic cells and tissues for regenerative medicine, genome editing tools and reliable screening techniques. To perform experiments efficiently and to propel the fundamental science it is important to keep up with novel modifications and techniques that are being discovered almost weekly. One of them is CRISPR/Cas9 based genome and transcriptome editing. The aim of this article is to summarize currently existing CRISPR/Cas9 applications for cell reprogramming, mainly, to compare them with other non-CRISPR approaches and to highlight future perspectives and opportunities.
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Affiliation(s)
- Ksenia M Shakirova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Viktoriia Y Ovchinnikova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Erdem B Dashinimaev
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
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192
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Cheng CL, Yang SC, Lai CY, Wang CK, Chang CF, Lin CY, Chen WJ, Lin PY, Wu HC, Ma N, Lu FL, Lu J. CXCL14 Maintains hESC Self-Renewal through Binding to IGF-1R and Activation of the IGF-1R Pathway. Cells 2020; 9:cells9071706. [PMID: 32708730 PMCID: PMC7407311 DOI: 10.3390/cells9071706] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 01/04/2023] Open
Abstract
Human embryonic stem cells (hESCs) have important roles in regenerative medicine, but only a few studies have investigated the cytokines secreted by hESCs. We screened and identified chemokine (C-X-C motif) ligand 14 (CXCL14), which plays crucial roles in hESC renewal. CXCL14, a C-X-C motif chemokine, is also named as breast and kidney-expressed chemokine (BRAK), B cell and monocyte-activated chemokine (BMAC), and macrophage inflammatory protein-2γ (MIP-2γ). Knockdown of CXCL14 disrupted the hESC self-renewal, changed cell cycle distribution, and further increased the expression levels of mesoderm and endoderm differentiated markers. Interestingly, we demonstrated that CXCL14 is the ligand for the insulin-like growth factor 1 receptor (IGF-1R), and it can activate IGF-1R signal transduction to support hESC renewal. Currently published literature indicates that all receptors in the CXCL family are G protein-coupled receptors (GPCRs). This report is the first to demonstrate that a CXCL protein can bind to and activate a receptor tyrosine kinase (RTK), and also the first to show that IGF-1R has another ligand in addition to IGFs. These findings broaden our understanding of stem cell biology and signal transduction.
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Affiliation(s)
- Chih-Lun Cheng
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan; (C.-L.C.); (H.-C.W.)
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (S.-C.Y.); (C.-Y.L.); (C.-K.W.); (C.-F.C.); (C.-Y.L.); (W.-J.C.); (P.-Y.L.)
| | - Shang-Chih Yang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (S.-C.Y.); (C.-Y.L.); (C.-K.W.); (C.-F.C.); (C.-Y.L.); (W.-J.C.); (P.-Y.L.)
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Chien-Ying Lai
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (S.-C.Y.); (C.-Y.L.); (C.-K.W.); (C.-F.C.); (C.-Y.L.); (W.-J.C.); (P.-Y.L.)
| | - Cheng-Kai Wang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (S.-C.Y.); (C.-Y.L.); (C.-K.W.); (C.-F.C.); (C.-Y.L.); (W.-J.C.); (P.-Y.L.)
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Ching-Fang Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (S.-C.Y.); (C.-Y.L.); (C.-K.W.); (C.-F.C.); (C.-Y.L.); (W.-J.C.); (P.-Y.L.)
| | - Chun-Yu Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (S.-C.Y.); (C.-Y.L.); (C.-K.W.); (C.-F.C.); (C.-Y.L.); (W.-J.C.); (P.-Y.L.)
| | - Wei-Ju Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (S.-C.Y.); (C.-Y.L.); (C.-K.W.); (C.-F.C.); (C.-Y.L.); (W.-J.C.); (P.-Y.L.)
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Po-Yu Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (S.-C.Y.); (C.-Y.L.); (C.-K.W.); (C.-F.C.); (C.-Y.L.); (W.-J.C.); (P.-Y.L.)
| | - Han-Chung Wu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan; (C.-L.C.); (H.-C.W.)
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan
| | - Nianhan Ma
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan City 320, Taiwan;
| | - Frank Leigh Lu
- Department of Pediatrics, National Taiwan University Children’s Hospital, National Taiwan University Hospital, and National Taiwan University Medical College, Taipei 100, Taiwan
- Correspondence: (F.L.L.); (J.L.)
| | - Jean Lu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan; (C.-L.C.); (H.-C.W.)
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (S.-C.Y.); (C.-Y.L.); (C.-K.W.); (C.-F.C.); (C.-Y.L.); (W.-J.C.); (P.-Y.L.)
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei 106, Taiwan
- National Core Facility Program for Biotechnology, National RNAi Platform, Taipei 112, Taiwan
- Department of Life Science, Tzu Chi University, Hualien 970, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan
- Correspondence: (F.L.L.); (J.L.)
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193
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Zhu Y, Yan Z, Tang Z, Li W. Novel Approaches to Profile Functional Long Noncoding RNAs Associated with Stem Cell Pluripotency. Curr Genomics 2020; 21:37-45. [PMID: 32655297 PMCID: PMC7324891 DOI: 10.2174/1389202921666200210142840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/17/2020] [Accepted: 01/31/2020] [Indexed: 12/11/2022] Open
Abstract
The pluripotent state of stem cells depends on the complicated network orchestrated by thousands of factors and genes. Long noncoding RNAs (lncRNAs) are a class of RNA longer than 200 nt without a protein-coding function. Single-cell sequencing studies have identified hundreds of lncRNAs with dynamic changes in somatic cell reprogramming. Accumulating evidence suggests that they participate in the initiation of reprogramming, maintenance of pluripotency, and developmental processes by cis and/or trans mechanisms. In particular, they may interact with proteins, RNAs, and chromatin modifier complexes to form an intricate pluripotency-associated network. In this review, we focus on recent progress in approaches to profiling functional lncRNAs in somatic cell reprogramming and cell differentiation.
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Affiliation(s)
- Yanbo Zhu
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
| | - Zi Yan
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
| | - Ze Tang
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
| | - Wei Li
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
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194
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RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells. Nat Genet 2020; 52:931-938. [PMID: 32632336 DOI: 10.1038/s41588-020-0662-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/08/2020] [Indexed: 12/11/2022]
Abstract
Many chromatin-binding proteins and protein complexes that regulate transcription also bind RNA. One of these, Polycomb repressive complex 2 (PRC2), deposits the H3K27me3 mark of facultative heterochromatin and is required for stem cell differentiation. PRC2 binds RNAs broadly in vivo and in vitro. Yet, the biological importance of this RNA binding remains unsettled. Here, we tackle this question in human induced pluripotent stem cells by using multiple complementary approaches. Perturbation of RNA-PRC2 interaction by RNase A, by a chemical inhibitor of transcription or by an RNA-binding-defective mutant all disrupted PRC2 chromatin occupancy and localization genome wide. The physiological relevance of PRC2-RNA interactions is further underscored by a cardiomyocyte differentiation defect upon genetic disruption. We conclude that PRC2 requires RNA binding for chromatin localization in human pluripotent stem cells and in turn for defining cellular state.
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195
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Gopal S, Rodrigues AL, Dordick JS. Exploiting CRISPR Cas9 in Three-Dimensional Stem Cell Cultures to Model Disease. Front Bioeng Biotechnol 2020; 8:692. [PMID: 32671050 PMCID: PMC7326781 DOI: 10.3389/fbioe.2020.00692] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/03/2020] [Indexed: 12/14/2022] Open
Abstract
Three-dimensional (3D) cell culture methods have been widely used on a range of cell types, including stem cells to modulate precisely the cellular biophysical and biochemical microenvironment and control various cell signaling cues. As a result, more in vivo-like microenvironments are recapitulated, particularly through the formation of multicellular spheroids and organoids, which may yield more valid mechanisms of disease. Recently, genome-engineering tools such as CRISPR Cas9 have expanded the repertoire of techniques to control gene expression, which complements external signaling cues with intracellular control elements. As a result, the combination of CRISPR Cas9 and 3D cell culture methods enhance our understanding of the molecular mechanisms underpinning several disease phenotypes and may lead to developing new therapeutics that may advance more quickly and effectively into clinical candidates. In addition, using CRISPR Cas9 tools to rescue genes brings us one step closer to its use as a gene therapy tool for various degenerative diseases. Herein, we provide an overview of bridging of CRISPR Cas9 genome editing with 3D spheroid and organoid cell culture to better understand disease progression in both patient and non-patient derived cells, and we address potential remaining gaps that must be overcome to gain widespread use.
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Affiliation(s)
- Sneha Gopal
- Department of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - André Lopes Rodrigues
- Department of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Jonathan S. Dordick
- Department of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
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196
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Wheelwright M, Mikkila J, Bedada FB, Mandegar MA, Thompson BR, Metzger JM. Advancing physiological maturation in human induced pluripotent stem cell-derived cardiac muscle by gene editing an inducible adult troponin isoform switch. Stem Cells 2020; 38:1254-1266. [PMID: 32497296 DOI: 10.1002/stem.3235] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/11/2020] [Indexed: 01/11/2023]
Abstract
Advancing maturation of stem cell-derived cardiac muscle represents a major barrier to progress in cardiac regenerative medicine. Cardiac muscle maturation involves a myriad of gene, protein, and cell-based transitions, spanning across all aspects of cardiac muscle form and function. We focused here on a key developmentally controlled transition in the cardiac sarcomere, the functional unit of the heart. Using a gene-editing platform, human induced pluripotent stem cell (hiPSCs) were engineered with a drug-inducible expression cassette driving the adult cardiac troponin I (cTnI) regulatory isoform, a transition shown to be a rate-limiting step in advancing sarcomeric maturation of hiPSC cardiac muscle (hiPSC-CM) toward the adult state. Findings show that induction of the adult cTnI isoform resulted in the physiological acquisition of adult-like cardiac contractile function in hiPSC-CMs in vitro. Specifically, cTnI induction accelerated relaxation kinetics at baseline conditions, a result independent of alterations in the kinetics of the intracellular Ca2+ transient. In comparison, isogenic unedited hiPSC-CMs had no cTnI induction and no change in relaxation function. Temporal control of adult cTnI isoform induction did not alter other developmentally regulated sarcomere transitions, including myosin heavy chain isoform expression, nor did it affect expression of SERCA2a or phospholamban. Taken together, precision genetic targeting of sarcomere maturation via inducible TnI isoform switching enables physiologically relevant adult myocardium-like contractile adaptations that are essential for beat-to-beat modulation of adult human heart performance. These findings have relevance to hiPSC-CM structure-function and drug-discovery studies in vitro, as well as for potential future clinical applications of physiologically optimized hiPSC-CM in cardiac regeneration/repair.
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Affiliation(s)
- Matthew Wheelwright
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Jennifer Mikkila
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Fikru B Bedada
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Mohammad A Mandegar
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA
| | - Brian R Thompson
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Joseph M Metzger
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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197
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Hunkler HJ, Hoepfner J, Huang CK, Chatterjee S, Jara-Avaca M, Gruh I, Bolesani E, Zweigerdt R, Thum T, Bär C. The Long Non-coding RNA Cyrano Is Dispensable for Pluripotency of Murine and Human Pluripotent Stem Cells. Stem Cell Reports 2020; 15:13-21. [PMID: 32531193 PMCID: PMC7363876 DOI: 10.1016/j.stemcr.2020.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 01/29/2023] Open
Abstract
Pluripotency is tightly regulated and is crucial for stem cells and their implementation for regenerative medicine. Non-coding RNAs, especially long non-coding RNAs (lncRNAs) emerged as orchestrators of versatile (patho)-physiological processes on the transcriptional and post-transcriptional level. Cyrano, a well-conserved lncRNA, is highly expressed in stem cells suggesting an important role in pluripotency, which we aimed to investigate in loss-off-function (LOF) experiments. Cyrano was described previously to be essential for the maintenance of mouse embryonic stem cell (ESC) pluripotency. In contrast, using different genetic models, we here found Cyrano to be dispensable in murine and human iPSCs and in human ESCs. RNA sequencing revealed only a moderate influence of Cyrano on the global transcriptome. In line, Cyrano-depleted iPSCs retained the potential to differentiate into the three germ layers. In conclusion, different methods were applied for LOF studies to rule out potential off-target effects. These approaches revealed that Cyrano does not impact pluripotency. lncRNA Cyrano does not impact pluripotency and differentiation capacity of PSCs Genetic deletion of Cyrano has no pluripotency phenotype in mouse iPSCs CRISPRi- and siRNA-mediated knockdown revealed same effects in human PSCs
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Affiliation(s)
- Hannah J Hunkler
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Jeannine Hoepfner
- 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
| | - Shambhabi Chatterjee
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Monica Jara-Avaca
- REBIRTH-Centre for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany; Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic-, Transplantation and Vascular Surgery, Hannover Medical School, Hannover, Germany
| | - Ina Gruh
- REBIRTH-Centre for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany; Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic-, Transplantation and Vascular Surgery, Hannover Medical School, Hannover, Germany
| | - Emiliano Bolesani
- REBIRTH-Centre for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany; Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic-, Transplantation and Vascular Surgery, Hannover Medical School, Hannover, Germany
| | - Robert Zweigerdt
- REBIRTH-Centre for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany; Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic-, Transplantation and Vascular Surgery, Hannover Medical School, Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany; REBIRTH-Centre for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Christian Bär
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany; REBIRTH-Centre for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany.
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198
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Breunig CT, Köferle A, Neuner AM, Wiesbeck MF, Baumann V, Stricker SH. CRISPR Tools for Physiology and Cell State Changes: Potential of Transcriptional Engineering and Epigenome Editing. Physiol Rev 2020; 101:177-211. [PMID: 32525760 DOI: 10.1152/physrev.00034.2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Given the large amount of genome-wide data that have been collected during the last decades, a good understanding of how and why cells change during development, homeostasis, and disease might be expected. Unfortunately, the opposite is true; triggers that cause cellular state changes remain elusive, and the underlying molecular mechanisms are poorly understood. Although genes with the potential to influence cell states are known, the historic dependency on methods that manipulate gene expression outside the endogenous chromatin context has prevented us from understanding how cells organize, interpret, and protect cellular programs. Fortunately, recent methodological innovations are now providing options to answer these outstanding questions, by allowing to target and manipulate individual genomic and epigenomic loci. In particular, three experimental approaches are now feasible due to DNA targeting tools, namely, activation and/or repression of master transcription factors in their endogenous chromatin context; targeting transcription factors to endogenous, alternative, or inaccessible sites; and finally, functional manipulation of the chromatin context. In this article, we discuss the molecular basis of DNA targeting tools and review the potential of these new technologies before we summarize how these have already been used for the manipulation of cellular states and hypothesize about future applications.
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Affiliation(s)
- Christopher T Breunig
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Anna Köferle
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Andrea M Neuner
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Maximilian F Wiesbeck
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Valentin Baumann
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Stefan H Stricker
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
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199
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Kim GB, Rincon Fernandez Pacheco D, Saxon D, Yang A, Sabet S, Dutra-Clarke M, Levy R, Watkins A, Park H, Abbasi Akhtar A, Linesch PW, Kobritz N, Chandra SS, Grausam K, Ayala-Sarmiento A, Molina J, Sedivakova K, Hoang K, Tsyporin J, Gareau DS, Filbin MG, Bannykh S, Santiskulvong C, Wang Y, Tang J, Suva ML, Chen B, Danielpour M, Breunig JJ. Rapid Generation of Somatic Mouse Mosaics with Locus-Specific, Stably Integrated Transgenic Elements. Cell 2020; 179:251-267.e24. [PMID: 31539496 DOI: 10.1016/j.cell.2019.08.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 05/24/2019] [Accepted: 08/06/2019] [Indexed: 12/11/2022]
Abstract
In situ transgenesis methods such as viruses and electroporation can rapidly create somatic transgenic mice but lack control over copy number, zygosity, and locus specificity. Here we establish mosaic analysis by dual recombinase-mediated cassette exchange (MADR), which permits stable labeling of mutant cells expressing transgenic elements from precisely defined chromosomal loci. We provide a toolkit of MADR elements for combination labeling, inducible and reversible transgene manipulation, VCre recombinase expression, and transgenesis of human cells. Further, we demonstrate the versatility of MADR by creating glioma models with mixed reporter-identified zygosity or with "personalized" driver mutations from pediatric glioma. MADR is extensible to thousands of existing mouse lines, providing a flexible platform to democratize the generation of somatic mosaic mice. VIDEO ABSTRACT.
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Affiliation(s)
- Gi Bum Kim
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - David Saxon
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Amy Yang
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sara Sabet
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Marina Dutra-Clarke
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Rachelle Levy
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ashley Watkins
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Hannah Park
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Aslam Abbasi Akhtar
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Paul W Linesch
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Naomi Kobritz
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Swasty S Chandra
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Katie Grausam
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Alberto Ayala-Sarmiento
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jessica Molina
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kristyna Sedivakova
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kendy Hoang
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Jeremiah Tsyporin
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Daniel S Gareau
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY 10065, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Serguei Bannykh
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Chintda Santiskulvong
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yizhou Wang
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jie Tang
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Bin Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Moise Danielpour
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joshua J Breunig
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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200
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Harnessing targeted DNA methylation and demethylation using dCas9. Essays Biochem 2020; 63:813-825. [PMID: 31724704 DOI: 10.1042/ebc20190029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022]
Abstract
DNA methylation is an essential DNA modification that plays a crucial role in genome regulation during differentiation and development, and is disrupted in a range of disease states. The recent development of CRISPR/catalytically dead CRISPR/Cas9 (dCas9)-based targeted DNA methylation editing tools has enabled new insights into the roles and functional relevance of this modification, including its importance at regulatory regions and the role of aberrant methylation in various diseases. However, while these tools are advancing our ability to understand and manipulate this regulatory layer of the genome, they still possess a variety of limitations in efficacy, implementation, and targeting specificity. Effective targeted DNA methylation editing will continue to advance our fundamental understanding of the role of this modification in different genomic and cellular contexts, and further improvements may enable more accurate disease modeling and possible future treatments. In this review, we discuss strategies, considerations, and future directions for targeted DNA methylation editing.
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