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Han JL, Entcheva E. Gene Modulation with CRISPR-based Tools in Human iPSC-Cardiomyocytes. Stem Cell Rev Rep 2023; 19:886-905. [PMID: 36656467 PMCID: PMC9851124 DOI: 10.1007/s12015-023-10506-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 01/20/2023]
Abstract
Precise control of gene expression (knock-out, knock-in, knockdown or overexpression) is at the heart of functional genomics - an approach to dissect the contribution of a gene/protein to the system's function. The development of a human in vitro system that can be patient-specific, induced pluripotent stem cells, iPSC, and the ability to obtain various cell types of interest, have empowered human disease modeling and therapeutic development. Scalable tools have been deployed for gene modulation in these cells and derivatives, including pharmacological means, DNA-based RNA interference and standard RNA interference (shRNA/siRNA). The CRISPR/Cas9 gene editing system, borrowed from bacteria and adopted for use in mammalian cells a decade ago, offers cell-specific genetic targeting and versatility. Outside genome editing, more subtle, time-resolved gene modulation is possible by using a catalytically "dead" Cas9 enzyme linked to an effector of gene transcription in combination with a guide RNA. The CRISPRi / CRISPRa (interference/activation) system evolved over the last decade as a scalable technology for performing functional genomics with libraries of gRNAs. Here, we review key developments of these approaches and their deployment in cardiovascular research. We discuss specific use with iPSC-cardiomyocytes and the challenges in further translation of these techniques.
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Affiliation(s)
- Julie Leann Han
- Department of Biomedical Engineering, The George Washington University, 800 22nd St NW, Suite 5000, Washington, DC, 20052, USA
| | - Emilia Entcheva
- Department of Biomedical Engineering, The George Washington University, 800 22nd St NW, Suite 5000, Washington, DC, 20052, USA.
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Gu L, Zheng H, Zhao R, Zhang X, Wang Q. Diosgenin inhibits the proliferation of gastric cancer cells via inducing mesoderm posterior 1 down-regulation-mediated alternative reading frame expression. Hum Exp Toxicol 2021; 40:S632-S645. [PMID: 34806916 DOI: 10.1177/09603271211053292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
INTRODUCTION Whether and how mesoderm posterior 1 (MESP1) plays a role in the proliferation of gastric cancer cells remain unclear. METHODS The expression of MESP1 was compared in 48 human gastric cancer tissues and adjacent normal tissues. Knockdown of MESP1 was performed to investigate the role of MESP1 in the proliferation and apoptosis of BGC-823 and MGC-803 gastric cancer cells. Knockdown of alternative reading frame (ARF) was performed to study the role of ARF in the inhibitory effect of MESP1 knockdown on cell proliferation in gastric cancer cells. Mouse subcutaneous xenograft tumor model bearing BGC-823 cells was used to investigate the role of MESP1 in the growth of gastric tumor in vivo. The effect of seven active ingredients from T. terrestris on MESP1 expression was tested. The anti-cancer effect of diosgenin was confirmed in gastric cancer cells. MESP1 dependence of the anti-cancer effect of diosgenin was confirmed by MESP1 knockdown. RESULTS MESP1 was highly expressed in human gastric cancer tissues (p < 0.05). MESP1 knockdown induced apoptosis and up-regulated the expression of ARF in gastric cancer cells (p < 0.05). Knockdown of ARF attenuated the anti-cancer effect of MESP1 knockdown (p < 0.05). In addition, MESP1 knockdown also suppressed tumor growth in vivo (p < 0.05). Diosgenin inhibits both mRNA and protein expression of MESP1 (p < 0.05). MESP1 knockdown attenuated the anti-cancer effect of diosgenin (p < 0.05). CONCLUSIONS MESP1 promotes the proliferation of gastric cancer cells via inhibiting ARF expression. Diosgenin exerts anti-cancer effect through inhibiting MESP1 expression in gastric cancer cells.
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Affiliation(s)
- Lin Gu
- Department of Gastroenterology, 74540The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, P. R. China
| | - Hailun Zheng
- Department of Gastroenterology, 74540The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, P. R. China
| | - Rui Zhao
- Department of Gastroenterology, 74540The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, P. R. China
| | - Xiaojing Zhang
- Department of Surgical Oncology, 74540The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, P. R. China
| | - Qizhi Wang
- Department of Gastroenterology, 74540The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, P. R. China
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Haswell JR, Mattioli K, Gerhardinger C, Maass PG, Foster DJ, Peinado P, Wang X, Medina PP, Rinn JL, Slack FJ. Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency. PLoS One 2021; 16:e0252848. [PMID: 34731163 PMCID: PMC8565776 DOI: 10.1371/journal.pone.0252848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/26/2021] [Indexed: 12/26/2022] Open
Abstract
Although many long non-coding RNAs (lncRNAs) exhibit lineage-specific expression, the vast majority remain functionally uncharacterized in the context of development. Here, we report the first described human embryonic stem cell (hESC) lines to repress (CRISPRi) or activate (CRISPRa) transcription during differentiation into all three germ layers, facilitating the modulation of lncRNA expression during early development. We performed an unbiased, genome-wide CRISPRi screen targeting thousands of lncRNA loci expressed during endoderm differentiation. While dozens of lncRNA loci were required for proper differentiation, most differentially expressed lncRNAs were not, supporting the necessity for functional screening instead of relying solely on gene expression analyses. In parallel, we developed a clustering approach to infer mechanisms of action of lncRNA hits based on a variety of genomic features. We subsequently identified and validated FOXD3-AS1 as a functional lncRNA essential for pluripotency and differentiation. Taken together, the cell lines and methodology described herein can be adapted to discover and characterize novel regulators of differentiation into any lineage.
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Affiliation(s)
- Jeffrey R. Haswell
- Department of Pathology, HMS Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Department of Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kaia Mattioli
- Department of Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Chiara Gerhardinger
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Philipp G. Maass
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Daniel J. Foster
- Department of Pathology, HMS Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Department of Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paola Peinado
- Department of Biochemistry and Molecular Biology, University of Granada, Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Xiaofeng Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Pedro P. Medina
- Department of Biochemistry and Molecular Biology, University of Granada, Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - John L. Rinn
- Department of Biochemistry, University of Colorado, BioFrontiers Institute, Boulder, Colorado, United States of America
| | - Frank J. Slack
- Department of Pathology, HMS Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- * E-mail:
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Mohammadinejad R, Biagioni A, Arunkumar G, Shapiro R, Chang KC, Sedeeq M, Taiyab A, Hashemabadi M, Pardakhty A, Mandegary A, Thiery JP, Aref AR, Azimi I. EMT signaling: potential contribution of CRISPR/Cas gene editing. Cell Mol Life Sci 2020; 77:2701-2722. [PMID: 32008085 PMCID: PMC11104910 DOI: 10.1007/s00018-020-03449-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 02/06/2023]
Abstract
Epithelial to mesenchymal transition (EMT) is a complex plastic and reversible cellular process that has critical roles in diverse physiological and pathological phenomena. EMT is involved in embryonic development, organogenesis and tissue repair, as well as in fibrosis, cancer metastasis and drug resistance. In recent years, the ability to edit the genome using the clustered regularly interspaced palindromic repeats (CRISPR) and associated protein (Cas) system has greatly contributed to identify or validate critical genes in pathway signaling. This review delineates the complex EMT networks and discusses recent studies that have used CRISPR/Cas technology to further advance our understanding of the EMT process.
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Affiliation(s)
- Reza Mohammadinejad
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Alessio Biagioni
- Section of Experimental Pathology and Oncology, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Ganesan Arunkumar
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rebecca Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Kun-Che Chang
- Department of Ophthalmology, School of Medicine, Byers Eye Institute, Stanford University, Palo Alto, CA, 94303, USA
| | - Mohammed Sedeeq
- Division of Pharmacy, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Aftab Taiyab
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Mohammad Hashemabadi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University, Kerman, Iran
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Abbas Pardakhty
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Mandegary
- Physiology Research Center, Institute of Neuropharmacology and Department of Toxicology & Pharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Jean-Paul Thiery
- Guangzhou Regenerative Medicine and Health, Guangdong Laboratory, Guangzhou, China
| | - Amir Reza Aref
- Department of Medical Oncology, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
| | - Iman Azimi
- Division of Pharmacy, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia.
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Wang L, Zhang F, Duan F, Huang R, Chen X, Ming J, Na J. Homozygous MESP1 knock-in reporter hESCs facilitated cardiovascular cell differentiation and myocardial infarction repair. Theranostics 2020; 10:6898-6914. [PMID: 32550911 PMCID: PMC7295063 DOI: 10.7150/thno.42347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/09/2020] [Indexed: 12/15/2022] Open
Abstract
Different populations of cardiovascular progenitor cells have been shown to possess varying differentiation potentials. They have also been used to facilitate heart repair. However, sensitive reporter cell lines that mark the human cardiovascular progenitors are in short supply. Methods: MESP1 marks the earliest population of cardiovascular progenitor cells during embryo development. Here, we generated a homozygous MESP1 knock-in reporter hESC line where mTomato gene joined to the MESP1 coding region via a 2A peptide, in which both MESP1 alleles were preserved. We performed transcriptome and functional analysis of human MESP1+ cardiovascular progenitor cells and tested their therapeutic potential using a rat model of myocardial infarction. Results: MESP1-mTomato knock-in reporter faithfully recapitulated the endogenous level of MESP1. Transcriptome analysis revealed that MESP1+ cells highly expressed early cardiovascular genes and heart development genes. The activation of MESP1 relied on the strength of canonical Wnt signaling, peak MESP1-mTomato fluorescence correlated with the window of canonical Wnt inhibition during in vitro differentiation. We further showed that MESP1 bound to the promoter of the WNT5A gene and the up-regulation of WNT5A expression suppressed canonical Wnt/β-CATENIN signaling. Moreover, induced MESP1 expression could substitute the canonical Wnt inhibition step and promote robust cardiomyocyte formation. We used a configurable, chemically defined, tri-lineage differentiation system to obtain cardiomyocytes, endothelial cells, and smooth muscle cells from MESP1+ cells at high efficiency. Finally, we showed that the engraftment of MESP1+ cells repaired rat myocardial infarction model. Conclusions: MESP1-mTomato reporter cells offered a useful platform to study cardiovascular differentiation from human pluripotent stem cells and explore their therapeutic potential in regenerative medicine.
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Abstract
PURPOSE OF REVIEW We review the ways in which stem cells are used in psychiatric disease research, including the related advances in gene editing and directed cell differentiation. RECENT FINDINGS The recent development of induced pluripotent stem cell (iPSC) technologies has created new possibilities for the study of psychiatric disease. iPSCs can be derived from patients or controls and differentiated to an array of neuronal and non-neuronal cell types. Their genomes can be edited as desired, and they can be assessed for a variety of phenotypes. This makes them especially interesting for studying genetic variation, which is particularly useful today now that our knowledge on the genetics of psychiatric disease is quickly expanding. The recent advances in cell engineering have led to powerful new methods for studying psychiatric illness including schizophrenia, bipolar disorder, and autism. There is a wide array of possible applications as illustrated by the many examples from the literature, most of which are cited here.
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Affiliation(s)
- Debamitra Das
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kyra Feuer
- Predoctoral Training Program in Human Genetics, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marah Wahbeh
- Predoctoral Training Program in Human Genetics, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dimitrios Avramopoulos
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Tandon N, Goller K, Wang F, Soibam B, Gagea M, Jain AK, Schwartz RJ, Liu Y. Aberrant expression of embryonic mesendoderm factor MESP1 promotes tumorigenesis. EBioMedicine 2019; 50:55-66. [PMID: 31761621 PMCID: PMC6921370 DOI: 10.1016/j.ebiom.2019.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 12/18/2022] Open
Abstract
Background Mesoderm Posterior 1 (MESP1) belongs to the family of basic helix-loop-helix transcription factors. It is a master regulator of mesendoderm development, leading to formation of organs such as heart and lung. However, its role in adult pathophysiology remains unknown. Here, we report for the first time a previously-unknown association of MESP1 with non-small cell lung cancer (NSCLC). Methods MESP1 mRNA and protein levels were measured in NSCLC-derived cells by qPCR and immunoblotting respectively. Colony formation assay, colorimetric cell proliferation assay and soft agar colony formation assays were used to assess the effects of MESP1 knockdown and overexpression in vitro. RNA-sequencing and chromatin immunoprecipitation (ChIP)-qPCR were used to determine direct target genes of MESP1. Subcutaneous injection of MESP1-depleted NSCLC cells in immuno-compromised mice was done to study the effects of MESP1 mediated tumor formation in vivo. Findings We found that MESP1 expression correlates with poor prognosis in NSCLC patients, and is critical for proliferation and survival of NSCLC-derived cells, thus implicating MESP1 as a lung cancer oncogene. Ectopic MESP1 expression cooperates with loss of tumor suppressor ARF to transform murine fibroblasts. Xenografts from MESP1-depleted cells showed decreased tumor growth in vivo. Global transcriptome analysis revealed a MESP1 DNA-binding-dependent gene signature associated with various hallmarks of cancer, suggesting that transcription activity of MESP1 is most likely responsible for its oncogenic abilities. Interpretation Our study demonstrates MESP1 as a previously-unknown lineage-survival oncogene in NSCLC which may serve as a potential prognostic marker and therapeutic target for lung cancer in the future.
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Affiliation(s)
- Neha Tandon
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Kristina Goller
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Fan Wang
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States; Department of Oncology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Benjamin Soibam
- Computer Science and Engineering Technology, University of Houston-Downtown, Houston, TX, United States
| | - Mihai Gagea
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Abhinav K Jain
- Center for Cancer Epigenetics, Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Robert J Schwartz
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Yu Liu
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States.
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