1
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Huang B, Zeng Z, Kim S, Fausto CC, Koppitch K, Li H, Li Z, Chen X, Guo J, Zhang CC, Ma T, Medina P, Schreiber ME, Xia MW, Vonk AC, Xiang T, Patel T, Li Y, Parvez RK, Der B, Chen JH, Liu Z, Thornton ME, Grubbs BH, Diao Y, Dou Y, Gnedeva K, Ying Q, Pastor-Soler NM, Fei T, Hallows KR, Lindström NO, McMahon AP, Li Z. Long-term expandable mouse and human-induced nephron progenitor cells enable kidney organoid maturation and modeling of plasticity and disease. Cell Stem Cell 2024; 31:921-939.e17. [PMID: 38692273 PMCID: PMC11162329 DOI: 10.1016/j.stem.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 02/07/2024] [Accepted: 04/01/2024] [Indexed: 05/03/2024]
Abstract
Nephron progenitor cells (NPCs) self-renew and differentiate into nephrons, the functional units of the kidney. Here, manipulation of p38 and YAP activity allowed for long-term clonal expansion of primary mouse and human NPCs and induced NPCs (iNPCs) from human pluripotent stem cells (hPSCs). Molecular analyses demonstrated that cultured iNPCs closely resemble primary human NPCs. iNPCs generated nephron organoids with minimal off-target cell types and enhanced maturation of podocytes relative to published human kidney organoid protocols. Surprisingly, the NPC culture medium uncovered plasticity in human podocyte programs, enabling podocyte reprogramming to an NPC-like state. Scalability and ease of genome editing facilitated genome-wide CRISPR screening in NPC culture, uncovering genes associated with kidney development and disease. Further, NPC-directed modeling of autosomal-dominant polycystic kidney disease (ADPKD) identified a small-molecule inhibitor of cystogenesis. These findings highlight a broad application for the reported iNPC platform in the study of kidney development, disease, plasticity, and regeneration.
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Affiliation(s)
- Biao Huang
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Zipeng Zeng
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Sunghyun Kim
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Connor C Fausto
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Kari Koppitch
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Hui Li
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Zexu Li
- College of Life and Health Sciences, Northeastern University, Shenyang 110819, P.R. China
| | - Xi Chen
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Chennan C Zhang
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Tianyi Ma
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Pedro Medina
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Megan E Schreiber
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Mateo W Xia
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ariel C Vonk
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Tianyuan Xiang
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Tadrushi Patel
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yidan Li
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Riana K Parvez
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Balint Der
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Urology, Faculty of Medicine, Semmelweis University, Budapest 3170, Hungary
| | - Jyun Hao Chen
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Zhenqing Liu
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Matthew E Thornton
- Division of Maternal Fetal Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Brendan H Grubbs
- Division of Maternal Fetal Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yali Dou
- Department of Medicine, Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ksenia Gnedeva
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Tina and Rick Caruso Department of Otolaryngology - Head and Neck Surgery, University of Southern California, Los Angeles, CA 90033, USA
| | - Qilong Ying
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Nuria M Pastor-Soler
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Teng Fei
- College of Life and Health Sciences, Northeastern University, Shenyang 110819, P.R. China
| | - Kenneth R Hallows
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Zhongwei Li
- USC/UKRO Kidney Research Center, Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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2
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Vieira R, Mariani JN, Huynh NPT, Stephensen HJT, Solly R, Tate A, Schanz S, Cotrupi N, Mousaei M, Sporring J, Benraiss A, Goldman SA. Young glial progenitor cells competitively replace aged and diseased human glia in the adult chimeric mouse brain. Nat Biotechnol 2024; 42:719-730. [PMID: 37460676 PMCID: PMC11098747 DOI: 10.1038/s41587-023-01798-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 04/20/2023] [Indexed: 08/26/2023]
Abstract
Competition among adult brain cells has not been extensively researched. To investigate whether healthy glia can outcompete diseased human glia in the adult forebrain, we engrafted wild-type (WT) human glial progenitor cells (hGPCs) produced from human embryonic stem cells into the striata of adult mice that had been neonatally chimerized with mutant Huntingtin (mHTT)-expressing hGPCs. The WT hGPCs outcompeted and ultimately eliminated their human Huntington's disease (HD) counterparts, repopulating the host striata with healthy glia. Single-cell RNA sequencing revealed that WT hGPCs acquired a YAP1/MYC/E2F-defined dominant competitor phenotype upon interaction with the host HD glia. WT hGPCs also outcompeted older resident isogenic WT cells that had been transplanted neonatally, suggesting that competitive success depended primarily on the relative ages of competing populations, rather than on the presence of mHTT. These data indicate that aged and diseased human glia may be broadly replaced in adult brain by younger healthy hGPCs, suggesting a therapeutic strategy for the replacement of aged and diseased human glia.
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Affiliation(s)
- Ricardo Vieira
- Center for Translational Neuromedicine, University of Copenhagen Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - John N Mariani
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Nguyen P T Huynh
- Center for Translational Neuromedicine, University of Copenhagen Faculty of Health and Medical Sciences, Copenhagen, Denmark
- Sana Biotechnology, Inc, Cambridge, MA, USA
| | - Hans J T Stephensen
- Center for Translational Neuromedicine, University of Copenhagen Faculty of Health and Medical Sciences, Copenhagen, Denmark
- Department of Computer Science, University of Copenhagen Faculty of Science, Copenhagen, Denmark
| | - Renee Solly
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, USA
- Sana Biotechnology, Inc, Cambridge, MA, USA
| | - Ashley Tate
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, USA
- Sana Biotechnology, Inc, Cambridge, MA, USA
| | - Steven Schanz
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Natasha Cotrupi
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Marzieh Mousaei
- Center for Translational Neuromedicine, University of Copenhagen Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Jon Sporring
- Department of Computer Science, University of Copenhagen Faculty of Science, Copenhagen, Denmark
| | - Abdellatif Benraiss
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Steven A Goldman
- Center for Translational Neuromedicine, University of Copenhagen Faculty of Health and Medical Sciences, Copenhagen, Denmark.
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, USA.
- Sana Biotechnology, Inc, Cambridge, MA, USA.
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3
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Husser MC, Pham NP, Law C, Araujo FRB, Martin VJJ, Piekny A. Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies. eLife 2024; 12:RP92819. [PMID: 38652106 PMCID: PMC11037917 DOI: 10.7554/elife.92819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Endogenous tags have become invaluable tools to visualize and study native proteins in live cells. However, generating human cell lines carrying endogenous tags is difficult due to the low efficiency of homology-directed repair. Recently, an engineered split mNeonGreen protein was used to generate a large-scale endogenous tag library in HEK293 cells. Using split mNeonGreen for large-scale endogenous tagging in human iPSCs would open the door to studying protein function in healthy cells and across differentiated cell types. We engineered an iPS cell line to express the large fragment of the split mNeonGreen protein (mNG21-10) and showed that it enables fast and efficient endogenous tagging of proteins with the short fragment (mNG211). We also demonstrate that neural network-based image restoration enables live imaging studies of highly dynamic cellular processes such as cytokinesis in iPSCs. This work represents the first step towards a genome-wide endogenous tag library in human stem cells.
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Affiliation(s)
| | - Nhat P Pham
- Biology Department, Concordia University, Montreal, Canada
| | - Chris Law
- Biology Department, Concordia University, Montreal, Canada
- Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Canada
| | - Flavia R B Araujo
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| | - Vincent J J Martin
- Biology Department, Concordia University, Montreal, Canada
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| | - Alisa Piekny
- Biology Department, Concordia University, Montreal, Canada
- Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Canada
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
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4
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Yan J, Oyler-Castrillo P, Ravisankar P, Ward CC, Levesque S, Jing Y, Simpson D, Zhao A, Li H, Yan W, Goudy L, Schmidt R, Solley SC, Gilbert LA, Chan MM, Bauer DE, Marson A, Parsons LR, Adamson B. Improving prime editing with an endogenous small RNA-binding protein. Nature 2024; 628:639-647. [PMID: 38570691 PMCID: PMC11023932 DOI: 10.1038/s41586-024-07259-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 02/29/2024] [Indexed: 04/05/2024]
Abstract
Prime editing enables the precise modification of genomes through reverse transcription of template sequences appended to the 3' ends of CRISPR-Cas guide RNAs1. To identify cellular determinants of prime editing, we developed scalable prime editing reporters and performed genome-scale CRISPR-interference screens. From these screens, a single factor emerged as the strongest mediator of prime editing: the small RNA-binding exonuclease protection factor La. Further investigation revealed that La promotes prime editing across approaches (PE2, PE3, PE4 and PE5), edit types (substitutions, insertions and deletions), endogenous loci and cell types but has no consistent effect on genome-editing approaches that rely on standard, unextended guide RNAs. Previous work has shown that La binds polyuridine tracts at the 3' ends of RNA polymerase III transcripts2. We found that La functionally interacts with the 3' ends of polyuridylated prime editing guide RNAs (pegRNAs). Guided by these results, we developed a prime editor protein (PE7) fused to the RNA-binding, N-terminal domain of La. This editor improved prime editing with expressed pegRNAs and engineered pegRNAs (epegRNAs), as well as with synthetic pegRNAs optimized for La binding. Together, our results provide key insights into how prime editing components interact with the cellular environment and suggest general strategies for stabilizing exogenous small RNAs therein.
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Affiliation(s)
- Jun Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Paul Oyler-Castrillo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Purnima Ravisankar
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Carl C Ward
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Sébastien Levesque
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Yangwode Jing
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Danny Simpson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Anqi Zhao
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Hui Li
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Weihao Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Laine Goudy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
| | - Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Sabrina C Solley
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Luke A Gilbert
- Arc Institute, Palo Alto, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Michelle M Chan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Lance R Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Britt Adamson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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5
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Pinheiro EA, DeKeyser JM, Lenny B, Sapkota Y, Burridge PW. Nilotinib-induced alterations in endothelial cell function recapitulate clinical vascular phenotypes independent of ABL1. Sci Rep 2024; 14:7123. [PMID: 38532120 DOI: 10.1038/s41598-024-57686-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/20/2024] [Indexed: 03/28/2024] Open
Abstract
Nilotinib is a highly effective treatment for chronic myeloid leukemia but has been consistently associated with the development of nilotinib-induced arterial disease (NAD) in a subset of patients. To date, which cell types mediate this effect and whether NAD results from on-target mechanisms is unknown. We utilized human induced pluripotent stem cells (hiPSCs) to generate endothelial cells and vascular smooth muscle cells for in vitro study of NAD. We found that nilotinib adversely affects endothelial proliferation and migration, in addition to increasing intracellular nitric oxide. Nilotinib did not alter endothelial barrier function or lipid uptake. No effect of nilotinib was observed in vascular smooth muscle cells, suggesting that NAD is primarily mediated through endothelial cells. To evaluate whether NAD results from enhanced inhibition of ABL1, we generated multiple ABL1 knockout lines. The effects of nilotinib remained unchanged in the absence of ABL1, suggesting that NAD results from off- rather than on-target signaling. The model established in the present study can be applied to future mechanistic and patient-specific pharmacogenomic studies.
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Affiliation(s)
- Emily A Pinheiro
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, 320 E Superior St, Searle 8-525, Chicago, IL, 60611, USA
| | - Jean-Marc DeKeyser
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, 320 E Superior St, Searle 8-525, Chicago, IL, 60611, USA
| | - Brian Lenny
- Department of Epidemiology and Cancer Control, St. Jude Children's Hospital, Memphis, TN, 38105, USA
| | - Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Hospital, Memphis, TN, 38105, USA
| | - Paul W Burridge
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, 320 E Superior St, Searle 8-525, Chicago, IL, 60611, USA.
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6
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Tsujimoto H, Hoshina A, Mae SI, Araoka T, Changting W, Ijiri Y, Nakajima-Koyama M, Sakurai S, Okita K, Mizuta K, Niwa A, Saito MK, Saitou M, Yamamoto T, Graneli C, Woollard KJ, Osafune K. Selective induction of human renal interstitial progenitor-like cell lineages from iPSCs reveals development of mesangial and EPO-producing cells. Cell Rep 2024; 43:113602. [PMID: 38237600 DOI: 10.1016/j.celrep.2023.113602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/13/2023] [Accepted: 12/05/2023] [Indexed: 03/02/2024] Open
Abstract
Recent regenerative studies using human pluripotent stem cells (hPSCs) have developed multiple kidney-lineage cells and organoids. However, to further form functional segments of the kidney, interactions of epithelial and interstitial cells are required. Here we describe a selective differentiation of renal interstitial progenitor-like cells (IPLCs) from human induced pluripotent stem cells (hiPSCs) by modifying our previous induction method for nephron progenitor cells (NPCs) and analyzing mouse embryonic interstitial progenitor cell (IPC) development. Our IPLCs combined with hiPSC-derived NPCs and nephric duct cells form nephrogenic niche- and mesangium-like structures in vitro. Furthermore, we successfully induce hiPSC-derived IPLCs to differentiate into mesangial and erythropoietin-producing cell lineages in vitro by screening differentiation-inducing factors and confirm that p38 MAPK, hypoxia, and VEGF signaling pathways are involved in the differentiation of mesangial-lineage cells. These findings indicate that our IPC-lineage induction method contributes to kidney regeneration and developmental research.
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Affiliation(s)
- Hiraku Tsujimoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Rege Nephro Co., Ltd., Med-Pharm Collaboration Building, Kyoto University, 46-29 Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Azusa Hoshina
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shin-Ichi Mae
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Toshikazu Araoka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Wang Changting
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yoshihiro Ijiri
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - May Nakajima-Koyama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Satoko Sakurai
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kazusa Okita
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Ken Mizuta
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Akira Niwa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Megumu K Saito
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Mitinori Saitou
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Takuya Yamamoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan; Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
| | - Cecilia Graneli
- BioPharmaceuticals R&D Cell Therapy, Research and Early Development, Cardiovascular, Renal and Metabolic (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Kevin J Woollard
- Bioscience Renal, Research and Early Development, Cardiovascular, Renal and Metabolic, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Kenji Osafune
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.
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7
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Karbassi E, Padgett R, Bertero A, Reinecke H, Klaiman JM, Yang X, Hauschka SD, Murry CE. Targeted CRISPR activation is functional in engineered human pluripotent stem cells but undergoes silencing after differentiation into cardiomyocytes and endothelium. Cell Mol Life Sci 2024; 81:95. [PMID: 38372898 PMCID: PMC10876724 DOI: 10.1007/s00018-023-05101-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 02/20/2024]
Abstract
Human induced pluripotent stem cells (hiPSCs) offer opportunities to study human biology where primary cell types are limited. CRISPR technology allows forward genetic screens using engineered Cas9-expressing cells. Here, we sought to generate a CRISPR activation (CRISPRa) hiPSC line to activate endogenous genes during pluripotency and differentiation. We first targeted catalytically inactive Cas9 fused to VP64, p65 and Rta activators (dCas9-VPR) regulated by the constitutive CAG promoter to the AAVS1 safe harbor site. These CRISPRa hiPSC lines effectively activate target genes in pluripotency, however the dCas9-VPR transgene expression is silenced after differentiation into cardiomyocytes and endothelial cells. To understand this silencing, we systematically tested different safe harbor sites and different promoters. Targeting to safe harbor sites hROSA26 and CLYBL loci also yielded hiPSCs that expressed dCas9-VPR in pluripotency but silenced during differentiation. Muscle-specific regulatory cassettes, derived from cardiac troponin T or muscle creatine kinase promoters, were also silent after differentiation when dCas9-VPR was introduced. In contrast, in cell lines where the dCas9-VPR sequence was replaced with cDNAs encoding fluorescent proteins, expression persisted during differentiation in all loci and with all promoters. Promoter DNA was hypermethylated in CRISPRa-engineered lines, and demethylation with 5-azacytidine enhanced dCas9-VPR gene expression. In summary, the dCas9-VPR cDNA is readily expressed from multiple loci during pluripotency but induces silencing in a locus- and promoter-independent manner during differentiation to mesoderm derivatives. Researchers intending to use this CRISPRa strategy during stem cell differentiation should pilot their system to ensure it remains active in their population of interest.
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Affiliation(s)
- Elaheh Karbassi
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Ruby Padgett
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alessandro Bertero
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Molecular Biotechnology Center "Guido Tarone", Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy
| | - Hans Reinecke
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Jordan M Klaiman
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Xiulan Yang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Stephen D Hauschka
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Center for Translational Muscle Research, University of Washington, Seattle, WA, 98109, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98109, USA
| | - Charles E Murry
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA.
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA.
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, 98195, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
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8
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Matsui S, Granitto M, Buckley M, Ludwig K, Koigi S, Shiley J, Zacharias WJ, Mayhew CN, Lim HW, Iwafuchi M. Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate. Mol Cell 2024; 84:476-489.e10. [PMID: 38211589 PMCID: PMC10872272 DOI: 10.1016/j.molcel.2023.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/30/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024]
Abstract
Pioneer transcription factors (TFs) regulate cell fate by establishing transcriptionally primed and active states. However, cell fate control requires the coordination of both lineage-specific gene activation and repression of alternative-lineage programs, a process that is poorly understood. Here, we demonstrate that the pioneer TF FOXA coordinates with PRDM1 TF to recruit nucleosome remodeling and deacetylation (NuRD) complexes and Polycomb repressive complexes (PRCs), which establish highly occupied, accessible nucleosome conformation with bivalent epigenetic states, thereby preventing precocious and alternative-lineage gene expression during human endoderm differentiation. Similarly, the pioneer TF OCT4 coordinates with PRDM14 to form bivalent enhancers and repress cell differentiation programs in human pluripotent stem cells, suggesting that this may be a common and critical function of pioneer TFs. We propose that pioneer and PRDM TFs coordinate to safeguard cell fate through epigenetic repression mechanisms.
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Affiliation(s)
- Satoshi Matsui
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Marissa Granitto
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Morgan Buckley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Katie Ludwig
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Sandra Koigi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Joseph Shiley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - William J Zacharias
- Division of Pulmonary Biology and Pulmonary and Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Christopher N Mayhew
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
| | - Makiko Iwafuchi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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9
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Humphreys PEA, Woods S, Bates N, Rooney KM, Mancini FE, Barclay C, O'Flaherty J, Martial FP, Domingos MAN, Kimber SJ. Optogenetic manipulation of BMP signaling to drive chondrogenic differentiation of hPSCs. Cell Rep 2023; 42:113502. [PMID: 38032796 DOI: 10.1016/j.celrep.2023.113502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/23/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Optogenetics is a rapidly advancing technology combining photochemical, optical, and synthetic biology to control cellular behavior. Together, sensitive light-responsive optogenetic tools and human pluripotent stem cell differentiation models have the potential to fine-tune differentiation and unpick the processes by which cell specification and tissue patterning are controlled by morphogens. We used an optogenetic bone morphogenetic protein (BMP) signaling system (optoBMP) to drive chondrogenic differentiation of human embryonic stem cells (hESCs). We engineered light-sensitive hESCs through CRISPR-Cas9-mediated integration of the optoBMP system into the AAVS1 locus. The activation of optoBMP with blue light, in lieu of BMP growth factors, resulted in the activation of BMP signaling mechanisms and upregulation of a chondrogenic phenotype, with significant transcriptional differences compared to cells in the dark. Furthermore, cells differentiated with light could form chondrogenic pellets consisting of a hyaline-like cartilaginous matrix. Our findings indicate the applicability of optogenetics for understanding human development and tissue engineering.
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Affiliation(s)
- Paul E A Humphreys
- Division of Cell Matrix & Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Steven Woods
- Division of Cell Matrix & Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Nicola Bates
- Division of Cell Matrix & Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Kirsty M Rooney
- Division of Cell Matrix & Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Fabrizio E Mancini
- Division of Cell Matrix & Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK; Department of Mechanical, Aerospace, and Civil Engineering, Faculty of Science and Engineering, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Cerys Barclay
- Division of Cell Matrix & Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Julieta O'Flaherty
- Division of Cell Matrix & Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Franck P Martial
- Division of Neuroscience & Experimental Psychology, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Marco A N Domingos
- Department of Mechanical, Aerospace, and Civil Engineering, Faculty of Science and Engineering, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Susan J Kimber
- Division of Cell Matrix & Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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10
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Min AK, Javidfar B, Missall R, Doanman D, Durens M, Graziani M, Mordelt A, Marro SG, de Witte L, Chen BK, Swartz TH, Akbarian S. HIV-1 infection of genetically engineered iPSC-derived central nervous system-engrafted microglia in a humanized mouse model. J Virol 2023; 97:e0159523. [PMID: 38032195 PMCID: PMC10734545 DOI: 10.1128/jvi.01595-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/05/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Our mouse model is a powerful tool for investigating the genetic mechanisms governing central nervous system (CNS) human immunodeficiency virus type-1 (HIV-1) infection and latency in the CNS at a single-cell level. A major advantage of our model is that it uses induced pluripotent stem cell-derived microglia, which enables human genetics, including gene function and therapeutic gene manipulation, to be explored in vivo, which is more challenging to study with current hematopoietic stem cell-based models for neuroHIV. Our transgenic tracing of xenografted human cells will provide a quantitative medium to develop new molecular and epigenetic strategies for reducing the HIV-1 latent reservoir and to test the impact of therapeutic inflammation-targeting drug interventions on CNS HIV-1 latency.
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Affiliation(s)
- Alice K. Min
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Behnam Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Roy Missall
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Donald Doanman
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Madel Durens
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mara Graziani
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Annika Mordelt
- Department of Human Genetics and Department of Cognitive Neuroscience, Radboud UMC, Nijmegen, the Netherlands
- Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, the Netherlands
| | - Samuele G. Marro
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lotje de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Human Genetics and Department of Cognitive Neuroscience, Radboud UMC, Nijmegen, the Netherlands
- Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, the Netherlands
| | - Benjamin K. Chen
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Talia H. Swartz
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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11
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Ra EA, Kim MS, Lee G. Optogenetic induction of alpha-synuclein aggregation in human dopaminergic neurons to model Parkinson's disease pathology. STAR Protoc 2023; 4:102609. [PMID: 37742181 PMCID: PMC10522986 DOI: 10.1016/j.xpro.2023.102609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/12/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023] Open
Abstract
Alpha-synuclein (α-syn) aggregation is a principal factor in Parkinson's disease (PD) onset. Here, we present a protocol for optogenetic induction of α-syn aggregation in human midbrain dopaminergic (mDA) neurons, facilitating a detailed PD pathology study. We describe steps for nucleofection of the opto-α-syn construct, single colony selection and validation, alongside mDA neuron differentiation and rapid induction of toxic α-syn aggregates via blue light. This establishes a potent human induced pluripotent-stem-cell-based platform for PD drug testing and validation. For complete details on the use and execution of this protocol, please refer to Kim et al. (2023).1.
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Affiliation(s)
- Eun A Ra
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Min Seong Kim
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gabsang Lee
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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12
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Pellegrino E, Aylan B, Bussi C, Fearns A, Bernard EM, Athanasiadi N, Santucci P, Botella L, Gutierrez MG. Peroxisomal ROS control cytosolic Mycobacterium tuberculosis replication in human macrophages. J Cell Biol 2023; 222:e202303066. [PMID: 37737955 PMCID: PMC10515436 DOI: 10.1083/jcb.202303066] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/27/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Peroxisomes are organelles involved in many metabolic processes including lipid metabolism, reactive oxygen species (ROS) turnover, and antimicrobial immune responses. However, the cellular mechanisms by which peroxisomes contribute to bacterial elimination in macrophages remain elusive. Here, we investigated peroxisome function in iPSC-derived human macrophages (iPSDM) during infection with Mycobacterium tuberculosis (Mtb). We discovered that Mtb-triggered peroxisome biogenesis requires the ESX-1 type 7 secretion system, critical for cytosolic access. iPSDM lacking peroxisomes were permissive to Mtb wild-type (WT) replication but were able to restrict an Mtb mutant missing functional ESX-1, suggesting a role for peroxisomes in the control of cytosolic but not phagosomal Mtb. Using genetically encoded localization-dependent ROS probes, we found peroxisomes increased ROS levels during Mtb WT infection. Thus, human macrophages respond to the infection by increasing peroxisomes that generate ROS primarily to restrict cytosolic Mtb. Our data uncover a peroxisome-controlled, ROS-mediated mechanism that contributes to the restriction of cytosolic bacteria.
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Affiliation(s)
- Enrica Pellegrino
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Beren Aylan
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Claudio Bussi
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Antony Fearns
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Elliott M. Bernard
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Natalia Athanasiadi
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Pierre Santucci
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Laure Botella
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
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13
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Meier AB, Zawada D, De Angelis MT, Martens LD, Santamaria G, Zengerle S, Nowak-Imialek M, Kornherr J, Zhang F, Tian Q, Wolf CM, Kupatt C, Sahara M, Lipp P, Theis FJ, Gagneur J, Goedel A, Laugwitz KL, Dorn T, Moretti A. Epicardioid single-cell genomics uncovers principles of human epicardium biology in heart development and disease. Nat Biotechnol 2023; 41:1787-1800. [PMID: 37012447 PMCID: PMC10713454 DOI: 10.1038/s41587-023-01718-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 02/22/2023] [Indexed: 04/05/2023]
Abstract
The epicardium, the mesothelial envelope of the vertebrate heart, is the source of multiple cardiac cell lineages during embryonic development and provides signals that are essential to myocardial growth and repair. Here we generate self-organizing human pluripotent stem cell-derived epicardioids that display retinoic acid-dependent morphological, molecular and functional patterning of the epicardium and myocardium typical of the left ventricular wall. By combining lineage tracing, single-cell transcriptomics and chromatin accessibility profiling, we describe the specification and differentiation process of different cell lineages in epicardioids and draw comparisons to human fetal development at the transcriptional and morphological levels. We then use epicardioids to investigate the functional cross-talk between cardiac cell types, gaining new insights into the role of IGF2/IGF1R and NRP2 signaling in human cardiogenesis. Finally, we show that epicardioids mimic the multicellular pathogenesis of congenital or stress-induced hypertrophy and fibrotic remodeling. As such, epicardioids offer a unique testing ground of epicardial activity in heart development, disease and regeneration.
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Affiliation(s)
- Anna B Meier
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany
| | - Dorota Zawada
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany
| | - Maria Teresa De Angelis
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany
- Department of Experimental and Clinical Medicine, University 'Magna Graecia', Catanzaro, Italy
| | - Laura D Martens
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
- Helmholtz Association-Munich School for Data Science (MUDS), Munich, Germany
| | - Gianluca Santamaria
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany
- Department of Experimental and Clinical Medicine, University 'Magna Graecia', Catanzaro, Italy
| | - Sophie Zengerle
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany
| | - Monika Nowak-Imialek
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany
| | - Jessica Kornherr
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany
| | - Fangfang Zhang
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany
| | - Qinghai Tian
- Center for Molecular Signaling (PZMS), Institute for Molecular Cell Biology, Research Center for Molecular Imaging and Screening, Medical Faculty, Saarland University, Homburg, Germany
| | - Cordula M Wolf
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany
- Department of Congenital Heart Defects and Pediatric Cardiology, German Heart Center Munich, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Christian Kupatt
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Makoto Sahara
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Peter Lipp
- Center for Molecular Signaling (PZMS), Institute for Molecular Cell Biology, Research Center for Molecular Imaging and Screening, Medical Faculty, Saarland University, Homburg, Germany
| | - Fabian J Theis
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Alexander Goedel
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Karl-Ludwig Laugwitz
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Tatjana Dorn
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany
| | - Alessandra Moretti
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany.
- Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany.
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany.
- Department of Surgery, Yale University School of Medicine, New Haven, CT, USA.
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14
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Hadiloo K, Taremi S, Heidari M, Esmaeilzadeh A. The CAR macrophage cells, a novel generation of chimeric antigen-based approach against solid tumors. Biomark Res 2023; 11:103. [PMID: 38017494 PMCID: PMC10685521 DOI: 10.1186/s40364-023-00537-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/02/2023] [Indexed: 11/30/2023] Open
Abstract
Today, adoptive cell therapy has many successes in cancer therapy, and this subject is brilliant in using chimeric antigen receptor T cells. The CAR T cell therapy, with its FDA-approved drugs, could treat several types of hematological malignancies and thus be very attractive for treating solid cancer. Unfortunately, the CAR T cell cannot be very functional in solid cancers due to its unique features. This treatment method has several harmful adverse effects that limit their applications, so novel treatments must use new cells like NK cells, NKT cells, and macrophage cells. Among these cells, the CAR macrophage cells, due to their brilliant innate features, are more attractive for solid tumor therapy and seem to be a better candidate for the prior treatment methods. The CAR macrophage cells have vital roles in the tumor microenvironment and, with their direct effect, can eliminate tumor cells efficiently. In addition, the CAR macrophage cells, due to being a part of the innate immune system, attended the tumor sites. With the high infiltration, their therapy modulations are more effective. This review investigates the last achievements in CAR-macrophage cells and the future of this immunotherapy treatment method.
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Affiliation(s)
- Kaveh Hadiloo
- Student Research Committee, School of Medicine, Zanjan University of Medical Sciences, Department of Immunology, Zanjan, Iran
| | - Siavash Taremi
- School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mahmood Heidari
- School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Abdolreza Esmaeilzadeh
- Department of Immunology, Zanjan University of Medical Sciences, Zanjan, Iran.
- Cancer Gene Therapy Research Center (CGRC), Zanjan University of Medical Sciences, Zanjan, Iran.
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15
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Matsui K, Yamanaka S, Chen S, Matsumoto N, Morimoto K, Kinoshita Y, Inage Y, Saito Y, Takamura T, Fujimoto T, Tajiri S, Matsumoto K, Kobayashi E, Yokoo T. Long-term viable chimeric nephrons generated from progenitor cells are a reliable model in cisplatin-induced toxicity. Commun Biol 2023; 6:1097. [PMID: 37898693 PMCID: PMC10613230 DOI: 10.1038/s42003-023-05484-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/18/2023] [Indexed: 10/30/2023] Open
Abstract
Kidney organoids have shown promise as evaluation tools, but their in vitro maturity remains limited. Transplantation into adult mice has aided in maturation; however, their lack of urinary tract connection limits long-term viability. Thus, long-term viable generated nephrons have not been demonstrated. In this study, we present an approachable method in which mouse and rat renal progenitor cells are injected into the developing kidneys of neonatal mice, resulting in the generation of chimeric nephrons integrated with the host urinary tracts. These chimeric nephrons exhibit similar maturation to the host nephrons, long-term viability with excretion and reabsorption functions, and cisplatin-induced renal injury in both acute and chronic phases, as confirmed by single-cell RNA-sequencing. Additionally, induced human nephron progenitor cells differentiate into nephrons within the neonatal kidneys. Collectively, neonatal injection represents a promising approach for in vivo nephron generation, with potential applications in kidney regeneration, drug screening, and pathological analysis.
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Affiliation(s)
- Kenji Matsui
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Shuichiro Yamanaka
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan.
| | - Sandy Chen
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Naoto Matsumoto
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Keita Morimoto
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Yoshitaka Kinoshita
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8654, Japan
| | - Yuka Inage
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
- Department of Pediatrics, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Yatsumu Saito
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Tsuyoshi Takamura
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Toshinari Fujimoto
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Susumu Tajiri
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Kei Matsumoto
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Eiji Kobayashi
- Department of Kidney Regenerative Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Takashi Yokoo
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan.
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16
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Kawakami E, Saiki N, Yoneyama Y, Moriya C, Maezawa M, Kawamura S, Kinebuchi A, Kono T, Funata M, Sakoda A, Kondo S, Ebihara T, Matsumoto H, Togami Y, Ogura H, Sugihara F, Okuzaki D, Kojima T, Deguchi S, Vallee S, McQuade S, Islam R, Natarajan M, Ishigaki H, Nakayama M, Nguyen CT, Kitagawa Y, Wu Y, Mori K, Hishiki T, Takasaki T, Itoh Y, Takayama K, Nio Y, Takebe T. Complement factor D targeting protects endotheliopathy in organoid and monkey models of COVID-19. Cell Stem Cell 2023; 30:1315-1330.e10. [PMID: 37802037 PMCID: PMC10575686 DOI: 10.1016/j.stem.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 07/04/2023] [Accepted: 09/01/2023] [Indexed: 10/08/2023]
Abstract
COVID-19 is linked to endotheliopathy and coagulopathy, which can result in multi-organ failure. The mechanisms causing endothelial damage due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain elusive. Here, we developed an infection-competent human vascular organoid from pluripotent stem cells for modeling endotheliopathy. Longitudinal serum proteome analysis identified aberrant complement signature in critically ill patients driven by the amplification cycle regulated by complement factor B and D (CFD). This deviant complement pattern initiates endothelial damage, neutrophil activation, and thrombosis specific to organoid-derived human blood vessels, as verified through intravital imaging. We examined a new long-acting, pH-sensitive (acid-switched) antibody targeting CFD. In both human and macaque COVID-19 models, this long-acting anti-CFD monoclonal antibody mitigated abnormal complement activation, protected endothelial cells, and curtailed the innate immune response post-viral exposure. Collectively, our findings suggest that the complement alternative pathway exacerbates endothelial injury and inflammation. This underscores the potential of CFD-targeted therapeutics against severe viral-induced inflammathrombotic outcomes.
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Affiliation(s)
- Eri Kawakami
- T-CiRA Discovery & Innovation, Takeda Pharmaceutical Company Ltd, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan; Organoid Medicine Project, T-CiRA Joint Program, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Norikazu Saiki
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Organoid Medicine Project, T-CiRA Joint Program, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Yosuke Yoneyama
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Chiharu Moriya
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Mari Maezawa
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Shuntaro Kawamura
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Akiko Kinebuchi
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Tamaki Kono
- T-CiRA Discovery & Innovation, Takeda Pharmaceutical Company Ltd, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan; Organoid Medicine Project, T-CiRA Joint Program, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Masaaki Funata
- T-CiRA Discovery & Innovation, Takeda Pharmaceutical Company Ltd, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan; Organoid Medicine Project, T-CiRA Joint Program, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Ayaka Sakoda
- T-CiRA Discovery & Innovation, Takeda Pharmaceutical Company Ltd, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Shigeru Kondo
- T-CiRA Discovery & Innovation, Takeda Pharmaceutical Company Ltd, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Takeshi Ebihara
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, 2-15, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Hisatake Matsumoto
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, 2-15, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yuki Togami
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, 2-15, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Ogura
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, 2-15, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center and Research Institute for Microbial Diseases, Osaka University, 3-3-1, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Disease, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Takashi Kojima
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, 2-15, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Sebastien Vallee
- Rare Disease DDU, Takeda Pharmaceutical Company Ltd, 125 Binney Street, Cambridge, MA 02139, USA
| | - Susan McQuade
- Rare Disease DDU, Takeda Pharmaceutical Company Ltd, 125 Binney Street, Cambridge, MA 02139, USA; BPS Biosciences Inc., 6405 Mira Mesa Blvd. Suite 100, San Diego, CA 92121, USA
| | - Rizwana Islam
- Rare Disease DDU, Takeda Pharmaceutical Company Ltd, 125 Binney Street, Cambridge, MA 02139, USA
| | - Madhusudan Natarajan
- Rare Disease DDU, Takeda Pharmaceutical Company Ltd, 125 Binney Street, Cambridge, MA 02139, USA
| | - Hirohito Ishigaki
- Department of Pathology, Shiga University of Medical Science, Setatsukinowa, Otsu, Shiga 520-2192, Japan
| | - Misako Nakayama
- Department of Pathology, Shiga University of Medical Science, Setatsukinowa, Otsu, Shiga 520-2192, Japan
| | - Cong Thanh Nguyen
- Department of Pathology, Shiga University of Medical Science, Setatsukinowa, Otsu, Shiga 520-2192, Japan
| | - Yoshinori Kitagawa
- Department of Pathology, Shiga University of Medical Science, Setatsukinowa, Otsu, Shiga 520-2192, Japan
| | - Yunheng Wu
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kensaku Mori
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Information Technology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Research Center for Medical Bigdata, National Institute of Informatics, Tokyo 100-0003, Japan
| | - Takayuki Hishiki
- Kanagawa Prefectural Institute of Public Health, 1-3-1, Shimomachiya, Chigasaki, Kanagawa 253-0087, Japan; Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tomohiko Takasaki
- Kanagawa Prefectural Institute of Public Health, 1-3-1, Shimomachiya, Chigasaki, Kanagawa 253-0087, Japan; Advanced Technology and Development Division, BML, INC, 1361-1, Matoba, Kawagoe-shi, Saitama 350-1101, Japan
| | - Yasushi Itoh
- Department of Pathology, Shiga University of Medical Science, Setatsukinowa, Otsu, Shiga 520-2192, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Yasunori Nio
- T-CiRA Discovery & Innovation, Takeda Pharmaceutical Company Ltd, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan; Organoid Medicine Project, T-CiRA Joint Program, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan.
| | - Takanori Takebe
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Organoid Medicine Project, T-CiRA Joint Program, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan; Division of Gastroenterology, Hepatology and Nutrition & Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA; The Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA; Communication Design Center, Advanced Medical Research Center, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan; Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe) and Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.
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17
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Fujimori T, Rios-Martinez C, Thurm AR, Hinks MM, Doughty BR, Sinha J, Le D, Hafner A, Greenleaf WJ, Boettiger AN, Bintu L. Single-cell chromatin state transitions during epigenetic memory formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560616. [PMID: 37873344 PMCID: PMC10592931 DOI: 10.1101/2023.10.03.560616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Repressive chromatin modifications are thought to compact chromatin to silence transcription. However, it is unclear how chromatin structure changes during silencing and epigenetic memory formation. We measured gene expression and chromatin structure in single cells after recruitment and release of repressors at a reporter gene. Chromatin structure is heterogeneous, with open and compact conformations present in both active and silent states. Recruitment of repressors associated with epigenetic memory produces chromatin compaction across 10-20 kilobases, while reversible silencing does not cause compaction at this scale. Chromatin compaction is inherited, but changes molecularly over time from histone methylation (H3K9me3) to DNA methylation. The level of compaction at the end of silencing quantitatively predicts epigenetic memory weeks later. Similarly, chromatin compaction at the Nanog locus predicts the degree of stem-cell fate commitment. These findings suggest that the chromatin state across tens of kilobases, beyond the gene itself, is important for epigenetic memory formation.
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Affiliation(s)
- Taihei Fujimori
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Abby R. Thurm
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Michaela M. Hinks
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Joydeb Sinha
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA, USA
| | - Derek Le
- Department of Dermatology, Program in Epithelial Biology, Stanford University, Stanford, CA, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Antonina Hafner
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Current address: Department of Discovery Oncology, Genentech, CA, USA
| | - William J. Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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18
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Balmas E, Sozza F, Bottini S, Ratto ML, Savorè G, Becca S, Snijders KE, Bertero A. Manipulating and studying gene function in human pluripotent stem cell models. FEBS Lett 2023; 597:2250-2287. [PMID: 37519013 DOI: 10.1002/1873-3468.14709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are uniquely suited to study human development and disease and promise to revolutionize regenerative medicine. These applications rely on robust methods to manipulate gene function in hPSC models. This comprehensive review aims to both empower scientists approaching the field and update experienced stem cell biologists. We begin by highlighting challenges with manipulating gene expression in hPSCs and their differentiated derivatives, and relevant solutions (transfection, transduction, transposition, and genomic safe harbor editing). We then outline how to perform robust constitutive or inducible loss-, gain-, and change-of-function experiments in hPSCs models, both using historical methods (RNA interference, transgenesis, and homologous recombination) and modern programmable nucleases (particularly CRISPR/Cas9 and its derivatives, i.e., CRISPR interference, activation, base editing, and prime editing). We further describe extension of these approaches for arrayed or pooled functional studies, including emerging single-cell genomic methods, and the related design and analytical bioinformatic tools. Finally, we suggest some directions for future advancements in all of these areas. Mastering the combination of these transformative technologies will empower unprecedented advances in human biology and medicine.
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Affiliation(s)
- Elisa Balmas
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Federica Sozza
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Sveva Bottini
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Maria Luisa Ratto
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Giulia Savorè
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Silvia Becca
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Kirsten Esmee Snijders
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Alessandro Bertero
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
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19
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Tamura R, Miyoshi H, Imaizumi K, Yo M, Kase Y, Sato T, Sato M, Morimoto Y, Sampetrean O, Kohyama J, Shinozaki M, Miyawaki A, Yoshida K, Saya H, Okano H, Toda M. Gene therapy using genome-edited iPS cells for targeting malignant glioma. Bioeng Transl Med 2023; 8:e10406. [PMID: 37693056 PMCID: PMC10487333 DOI: 10.1002/btm2.10406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/23/2022] [Accepted: 08/28/2022] [Indexed: 11/08/2022] Open
Abstract
Glioblastoma is characterized by diffuse infiltration into the normal brain. Invasive glioma stem cells (GSCs) are an underlying cause of treatment failure. Despite the use of multimodal therapies, the prognosis remains dismal. New therapeutic approach targeting invasive GSCs is required. Here, we show that neural stem cells (NSCs) derived from CRISRP/Cas9-edited human-induced pluripotent stem cell (hiPSC) expressing a suicide gene had higher tumor-trophic migratory capacity compared with mesenchymal stem cells (MSCs), leading to marked in vivo antitumor effects. High migratory capacity in iPSC-NSCs was related to self-repulsive action and pathotropism involved in EphB-ephrinB and CXCL12-CXCR4 signaling. The gene insertion to ACTB provided higher and stable transgene expression than other common insertion sites, such as GAPDH or AAVS1. Ferroptosis was associated with enhanced antitumor immune responses. The thymidylate synthase and dihydroprimidine dehydrogenase expressions predicted the treatment efficacy of therapeutic hiPSC-NSCs. Our results indicate the potential benefit of genome-edited iPS cells based gene therapy for invasive GSCs. Furthermore, the present research concept may become a platform to promote clinical studies using hiPSC.
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Affiliation(s)
- Ryota Tamura
- Department of NeurosurgeryKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | | | - Kent Imaizumi
- Department of PhysiologyKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Masahiro Yo
- Laboratory for Cell Function and Dynamics, RIKEN Center for Brain ScienceWako, SaitamaJapan
| | - Yoshitaka Kase
- Department of PhysiologyKeio University School of MedicineShinjuku‐ku, TokyoJapan
- Department of Geriatric MedicineGraduate School of Medicine, The University of TokyoBunkyo‐ku, TokyoJapan
| | - Tsukika Sato
- Department of PhysiologyKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Mizuto Sato
- Department of NeurosurgeryKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Yukina Morimoto
- Department of NeurosurgeryKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Oltea Sampetrean
- Division of Gene RegulationKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Jun Kohyama
- Department of PhysiologyKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Munehisa Shinozaki
- Department of PhysiologyKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Atsushi Miyawaki
- Laboratory for Cell Function and Dynamics, RIKEN Center for Brain ScienceWako, SaitamaJapan
| | - Kazunari Yoshida
- Department of NeurosurgeryKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Hideyuki Saya
- Division of Gene RegulationKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Hideyuki Okano
- Department of PhysiologyKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Masahiro Toda
- Department of NeurosurgeryKeio University School of MedicineShinjuku‐ku, TokyoJapan
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20
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Dabiri H, Safarzadeh Kozani P, Habibi Anbouhi M, Mirzaee Godarzee M, Haddadi MH, Basiri M, Ziaei V, Sadeghizadeh M, Hajizadeh Saffar E. Site-specific transgene integration in chimeric antigen receptor (CAR) T cell therapies. Biomark Res 2023; 11:67. [PMID: 37403182 DOI: 10.1186/s40364-023-00509-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/09/2023] [Indexed: 07/06/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cells and natural killer (NK) cells are genetically engineered immune cells that can detect target antigens on the surface of target cells and eliminate them following adoptive transfer. Recent progress in CAR-based therapies has led to outstanding clinical success in certain patients with leukemias and lymphomas and offered therapeutic benefits to those resistant to conventional therapies. The universal approach to stable CAR transgene delivery into the T/NK cells is the use of viral particles. Such approaches mediate semi-random transgene insertions spanning the entire genome with a high preference for integration into sites surrounding highly-expressed genes and active loci. Regardless of the variable CAR expression level based on the integration site of the CAR transgene, foreign integrated DNA fragments may affect the neighboring endogenous genes and chromatin structure and potentially change a transduced T/NK cell behavior and function or even favor cellular transformation. In contrast, site-specific integration of CAR constructs using recent genome-editing technologies could overcome the limitations and disadvantages of universal random gene integration. Herein, we explain random and site-specific integration of CAR transgenes in CAR-T/NK cell therapies. Also, we tend to summarize the methods for site-specific integration as well as the clinical outcomes of certain gene disruptions or enhancements due to CAR transgene integration. Also, the advantages and limitations of using site-specific integration methods are discussed in this review. Ultimately, we will introduce the genomic safe harbor (GSH) standards and suggest some appropriate safety prospects for CAR integration in CAR-T/NK cell therapies.
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Affiliation(s)
- Hamed Dabiri
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Pooria Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Mohadeseh Mirzaee Godarzee
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Mohsen Basiri
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Vahab Ziaei
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran
| | - Majid Sadeghizadeh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ensiyeh Hajizadeh Saffar
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
- Advanced Therapy Medicinal Product Technology Development Center (ATMP-TDC), Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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21
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Dabiri H, Safarzadeh Kozani P, Habibi Anbouhi M, Mirzaee Godarzee M, Haddadi MH, Basiri M, Ziaei V, Sadeghizadeh M, Hajizadeh Saffar E. Site-specific transgene integration in chimeric antigen receptor (CAR) T cell therapies. Biomark Res 2023; 11:67. [DOI: https:/doi.org/10.1186/s40364-023-00509-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/09/2023] [Indexed: 09/15/2023] Open
Abstract
AbstractChimeric antigen receptor (CAR) T cells and natural killer (NK) cells are genetically engineered immune cells that can detect target antigens on the surface of target cells and eliminate them following adoptive transfer. Recent progress in CAR-based therapies has led to outstanding clinical success in certain patients with leukemias and lymphomas and offered therapeutic benefits to those resistant to conventional therapies. The universal approach to stable CAR transgene delivery into the T/NK cells is the use of viral particles. Such approaches mediate semi-random transgene insertions spanning the entire genome with a high preference for integration into sites surrounding highly-expressed genes and active loci. Regardless of the variable CAR expression level based on the integration site of the CAR transgene, foreign integrated DNA fragments may affect the neighboring endogenous genes and chromatin structure and potentially change a transduced T/NK cell behavior and function or even favor cellular transformation. In contrast, site-specific integration of CAR constructs using recent genome-editing technologies could overcome the limitations and disadvantages of universal random gene integration. Herein, we explain random and site-specific integration of CAR transgenes in CAR-T/NK cell therapies. Also, we tend to summarize the methods for site-specific integration as well as the clinical outcomes of certain gene disruptions or enhancements due to CAR transgene integration. Also, the advantages and limitations of using site-specific integration methods are discussed in this review. Ultimately, we will introduce the genomic safe harbor (GSH) standards and suggest some appropriate safety prospects for CAR integration in CAR-T/NK cell therapies.
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22
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Choi YJ, Kim MS, Rhoades JH, Johnson NM, Berry CT, Root S, Chen Q, Tian Y, Fernandez RJ, Cramer Z, Adams-Tzivelekidis S, Li N, Johnson FB, Lengner CJ. Patient-Induced Pluripotent Stem Cell-Derived Hepatostellate Organoids Establish a Basis for Liver Pathologies in Telomeropathies. Cell Mol Gastroenterol Hepatol 2023; 16:451-472. [PMID: 37302654 PMCID: PMC10404563 DOI: 10.1016/j.jcmgh.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023]
Abstract
BACKGROUND & AIMS Dyskeratosis congenita (DC) is a telomere biology disorder caused primarily by mutations in the DKC1 gene. Patients with DC and related telomeropathies resulting from premature telomere dysfunction experience multiorgan failure. In the liver, DC patients present with nodular hyperplasia, steatosis, inflammation, and cirrhosis. However, the mechanism responsible for telomere dysfunction-induced liver disease remains unclear. METHODS We used isogenic human induced pluripotent stem cells (iPSCs) harboring a causal DC mutation in DKC1 or a CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/Cas9)-corrected control allele to model DC liver pathologies. We differentiated these iPSCs into hepatocytes (HEPs) or hepatic stellate cells (HSCs) followed by generation of genotype-admixed hepatostellate organoids. Single-cell transcriptomics were applied to hepatostellate organoids to understand cell type-specific genotype-phenotype relationships. RESULTS Directed differentiation of iPSCs into HEPs and stellate cells and subsequent hepatostellate organoid formation revealed a dominant phenotype in the parenchyma, with DC HEPs becoming hyperplastic and also eliciting a pathogenic hyperplastic, proinflammatory response in stellate cells independent of stellate cell genotype. Pathogenic phenotypes in DKC1-mutant HEPs and hepatostellate organoids could be rescued via suppression of serine/threonine kinase AKT (protein kinase B) activity, a central regulator of MYC-driven hyperplasia downstream of DKC1 mutation. CONCLUSIONS Isogenic iPSC-derived admixed hepatostellate organoids offer insight into the liver pathologies in telomeropathies and provide a framework for evaluating emerging therapies.
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Affiliation(s)
- Young-Jun Choi
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Melissa S Kim
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Joshua H Rhoades
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nicolette M Johnson
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Corbett T Berry
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sarah Root
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Qijun Chen
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yuhua Tian
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rafael J Fernandez
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zvi Cramer
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephanie Adams-Tzivelekidis
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ning Li
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - F Brad Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Christopher J Lengner
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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23
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Zhao J, Veeranan-Karmegam R, Baker FC, Mysona BA, Bagchi P, Liu Y, Smith SB, Gonsalvez GB, Bollinger KE. Defining the ligand-dependent proximatome of the sigma 1 receptor. Front Cell Dev Biol 2023; 11:1045759. [PMID: 37351276 PMCID: PMC10284605 DOI: 10.3389/fcell.2023.1045759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 05/16/2023] [Indexed: 06/24/2023] Open
Abstract
Sigma 1 Receptor (S1R) is a therapeutic target for a wide spectrum of pathological conditions ranging from neurodegenerative diseases to cancer and COVID-19. S1R is ubiquitously expressed throughout the visceral organs, nervous, immune and cardiovascular systems. It is proposed to function as a ligand-dependent molecular chaperone that modulates multiple intracellular signaling pathways. The purpose of this study was to define the S1R proximatome under native conditions and upon binding to well-characterized ligands. This was accomplished by fusing the biotin ligase, Apex2, to the C terminus of S1R. Cells stably expressing S1R-Apex or a GFP-Apex control were used to map proximal proteins. Biotinylated proteins were labeled under native conditions and in a ligand dependent manner, then purified and identified using quantitative mass spectrometry. Under native conditions, S1R biotinylates over 200 novel proteins, many of which localize within the endomembrane system (endoplasmic reticulum, Golgi, secretory vesicles) and function within the secretory pathway. Under conditions of cellular exposure to either S1R agonist or antagonist, results show enrichment of proteins integral to secretion, extracellular matrix formation, and cholesterol biosynthesis. Notably, Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) displays increased binding to S1R under conditions of treatment with Haloperidol, a well-known S1R antagonist; whereas Low density lipoprotein receptor (LDLR) binds more efficiently to S1R upon treatment with (+)-Pentazocine ((+)-PTZ), a classical S1R agonist. Furthermore, we demonstrate that the ligand bound state of S1R correlates with specific changes to the cellular secretome. Our results are consistent with the postulated role of S1R as an intracellular chaperone and further suggest important and novel functionalities related to secretion and cholesterol metabolism.
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Affiliation(s)
- Jing Zhao
- Department of Ophthalmology, Medical College of Georgia at Augusta University, Augusta, GA, United States
- Culver Vision Discovery Institute, Augusta, GA, United States
| | - Rajalakshmi Veeranan-Karmegam
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Frederick C. Baker
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Barbara A. Mysona
- Department of Ophthalmology, Medical College of Georgia at Augusta University, Augusta, GA, United States
- Culver Vision Discovery Institute, Augusta, GA, United States
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Pritha Bagchi
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA, United States
| | - Yutao Liu
- Culver Vision Discovery Institute, Augusta, GA, United States
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Sylvia B. Smith
- Department of Ophthalmology, Medical College of Georgia at Augusta University, Augusta, GA, United States
- Culver Vision Discovery Institute, Augusta, GA, United States
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Graydon B. Gonsalvez
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Kathryn E. Bollinger
- Department of Ophthalmology, Medical College of Georgia at Augusta University, Augusta, GA, United States
- Culver Vision Discovery Institute, Augusta, GA, United States
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, United States
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24
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Mhatre KN, Mathieu J, Martinson A, Flint G, Blakley LP, Tabesh A, Reinecke H, Yang X, Guan X, Murali E, Klaiman JM, Odom GL, Brown MB, Tian R, Hauschka SD, Raftery D, Moussavi-Harami F, Regnier M, Murry CE. Cell based dATP delivery as a therapy for chronic heart failure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538108. [PMID: 37162854 PMCID: PMC10168250 DOI: 10.1101/2023.04.24.538108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Transplanted human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) improve ventricular performance when delivered acutely post-myocardial infarction but are ineffective in chronic myocardial infarction/heart failure. 2'-deoxy-ATP (dATP) activates cardiac myosin and potently increases contractility. Here we engineered hPSC-CMs to overexpress ribonucleotide reductase, the enzyme controlling dATP production. In vivo, dATP-producing CMs formed new myocardium that transferred dATP to host cardiomyocytes via gap junctions, increasing their dATP levels. Strikingly, when transplanted into chronically infarcted hearts, dATP-producing grafts increased left ventricular function, whereas heart failure worsened with wild-type grafts or vehicle injections. dATP-donor cells recipients had greater voluntary exercise, improved cardiac metabolism, reduced pulmonary congestion and pathological cardiac hypertrophy, and improved survival. This combination of remuscularization plus enhanced host contractility offers a novel approach to treating the chronically failing heart.
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Affiliation(s)
- Ketaki N Mhatre
- Institute for Stem Cell and Regenerative Medicine, University of Washington; Seattle, WA 98109, USA
- Department of Bioengineering, University of Washington; Seattle, WA 98195, USA
- Department of Laboratory Medicine & Pathology, University of Washington; Seattle, WA 98195, USA
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington; Seattle, WA 98109, USA
- Department of Comparative Medicine, University of Washington; Seattle, WA 98195, USA
| | - Amy Martinson
- Institute for Stem Cell and Regenerative Medicine, University of Washington; Seattle, WA 98109, USA
- Center for Cardiovascular Biology, University of Washington; Seattle, WA 98109, USA
- Department of Laboratory Medicine & Pathology, University of Washington; Seattle, WA 98195, USA
| | - Galina Flint
- Department of Bioengineering, University of Washington; Seattle, WA 98195, USA
- Center for Translational Muscle Research, University of Washington; Seattle, WA 98109, USA
| | - Leslie P Blakley
- Institute for Stem Cell and Regenerative Medicine, University of Washington; Seattle, WA 98109, USA
- Center for Cardiovascular Biology, University of Washington; Seattle, WA 98109, USA
- Department of Laboratory Medicine & Pathology, University of Washington; Seattle, WA 98195, USA
| | - Arash Tabesh
- Institute for Stem Cell and Regenerative Medicine, University of Washington; Seattle, WA 98109, USA
- Department of Laboratory Medicine & Pathology, University of Washington; Seattle, WA 98195, USA
| | - Hans Reinecke
- Institute for Stem Cell and Regenerative Medicine, University of Washington; Seattle, WA 98109, USA
- Center for Cardiovascular Biology, University of Washington; Seattle, WA 98109, USA
- Department of Laboratory Medicine & Pathology, University of Washington; Seattle, WA 98195, USA
| | - Xiulan Yang
- Institute for Stem Cell and Regenerative Medicine, University of Washington; Seattle, WA 98109, USA
- Center for Cardiovascular Biology, University of Washington; Seattle, WA 98109, USA
- Department of Laboratory Medicine & Pathology, University of Washington; Seattle, WA 98195, USA
| | - Xuan Guan
- Department of Bioengineering, University of Washington; Seattle, WA 98195, USA
| | - Eesha Murali
- Institute for Stem Cell and Regenerative Medicine, University of Washington; Seattle, WA 98109, USA
- Department of Bioengineering, University of Washington; Seattle, WA 98195, USA
| | - Jordan M Klaiman
- Institute for Stem Cell and Regenerative Medicine, University of Washington; Seattle, WA 98109, USA
- Center for Cardiovascular Biology, University of Washington; Seattle, WA 98109, USA
- Department of Laboratory Medicine & Pathology, University of Washington; Seattle, WA 98195, USA
| | - Guy L Odom
- Institute for Stem Cell and Regenerative Medicine, University of Washington; Seattle, WA 98109, USA
- Center for Cardiovascular Biology, University of Washington; Seattle, WA 98109, USA
- Center for Translational Muscle Research, University of Washington; Seattle, WA 98109, USA
- Department of Neurology, University of Washington; Seattle, WA 98195, USA
| | - Mary Beth Brown
- Center for Translational Muscle Research, University of Washington; Seattle, WA 98109, USA
- Division of Physical Therapy, Department of Rehabilitation Medicine, University of Washington; Seattle, WA 98195, USA
| | - Rong Tian
- Center for Translational Muscle Research, University of Washington; Seattle, WA 98109, USA
- Department of Anesthesiology and Pain Medicine, University of Washington; Seattle, WA 98195, USA
- The Mitochondria and Metabolism Center (MMC), University of Washington; Seattle, WA 98109, USA
| | - Stephen D Hauschka
- Institute for Stem Cell and Regenerative Medicine, University of Washington; Seattle, WA 98109, USA
- Center for Translational Muscle Research, University of Washington; Seattle, WA 98109, USA
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Daniel Raftery
- Department of Anesthesiology and Pain Medicine, University of Washington; Seattle, WA 98195, USA
- The Mitochondria and Metabolism Center (MMC), University of Washington; Seattle, WA 98109, USA
- Northwest Metabolomics Research Center, University of Washington; Seattle, WA 98109, USA
| | - Farid Moussavi-Harami
- Institute for Stem Cell and Regenerative Medicine, University of Washington; Seattle, WA 98109, USA
- Center for Cardiovascular Biology, University of Washington; Seattle, WA 98109, USA
- Department of Laboratory Medicine & Pathology, University of Washington; Seattle, WA 98195, USA
- Center for Translational Muscle Research, University of Washington; Seattle, WA 98109, USA
- Division of Cardiology, University of Washington; Seattle, WA 98195, USA
| | - Michael Regnier
- Institute for Stem Cell and Regenerative Medicine, University of Washington; Seattle, WA 98109, USA
- Department of Bioengineering, University of Washington; Seattle, WA 98195, USA
- Center for Cardiovascular Biology, University of Washington; Seattle, WA 98109, USA
- Center for Translational Muscle Research, University of Washington; Seattle, WA 98109, USA
- Department of Physiology and Biophysics, University of Washington; Seattle, WA 98195, USA
| | - Charles E Murry
- Institute for Stem Cell and Regenerative Medicine, University of Washington; Seattle, WA 98109, USA
- Department of Bioengineering, University of Washington; Seattle, WA 98195, USA
- Center for Cardiovascular Biology, University of Washington; Seattle, WA 98109, USA
- Department of Laboratory Medicine & Pathology, University of Washington; Seattle, WA 98195, USA
- Center for Translational Muscle Research, University of Washington; Seattle, WA 98109, USA
- Division of Cardiology, University of Washington; Seattle, WA 98195, USA
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25
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Min AK, Javidfar B, Missall R, Doanman D, Durens M, Vil SS, Masih Z, Graziani M, Mordelt A, Marro S, de Witte L, Chen BK, Swartz TH, Akbarian S. HIV-1 infection of genetically engineered iPSC-derived central nervous system-engrafted microglia in a humanized mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538461. [PMID: 37162838 PMCID: PMC10168358 DOI: 10.1101/2023.04.26.538461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The central nervous system (CNS) is a major human immunodeficiency virus type 1 reservoir. Microglia are the primary target cell of HIV-1 infection in the CNS. Current models have not allowed the precise molecular pathways of acute and chronic CNS microglial infection to be tested with in vivo genetic methods. Here, we describe a novel humanized mouse model utilizing human-induced pluripotent stem cell-derived microglia to xenograft into murine hosts. These mice are additionally engrafted with human peripheral blood mononuclear cells that served as a medium to establish a peripheral infection that then spread to the CNS microglia xenograft, modeling a trans-blood-brain barrier route of acute CNS HIV-1 infection with human target cells. The approach is compatible with iPSC genetic engineering, including inserting targeted transgenic reporter cassettes to track the xenografted human cells, enabling the testing of novel treatment and viral tracking strategies in a comparatively simple and cost-effective way vivo model for neuroHIV.
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Affiliation(s)
- Alice K. Min
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Behnam Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Roy Missall
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Donald Doanman
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Madel Durens
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Samantha St Vil
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zahra Masih
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mara Graziani
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Annika Mordelt
- Department of Human Genetics and Department of Cognitive Neuroscience, Radboud UMC, Nijmegen, Netherlands
- Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, Netherlands
| | - Samuele Marro
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lotje de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Human Genetics and Department of Cognitive Neuroscience, Radboud UMC, Nijmegen, Netherlands
- Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, Netherlands
| | - Benjamin K. Chen
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Talia H. Swartz
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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26
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Kawasaki S, Ono H, Hirosawa M, Kuwabara T, Sumi S, Lee S, Woltjen K, Saito H. Programmable mammalian translational modulators by CRISPR-associated proteins. Nat Commun 2023; 14:2243. [PMID: 37076490 PMCID: PMC10115826 DOI: 10.1038/s41467-023-37540-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/21/2023] [Indexed: 04/21/2023] Open
Abstract
Translational modulation based on RNA-binding proteins can be used to construct artificial gene circuits, but RNA-binding proteins capable of regulating translation efficiently and orthogonally remain scarce. Here we report CARTRIDGE (Cas-Responsive Translational Regulation Integratable into Diverse Gene control) to repurpose Cas proteins as translational modulators in mammalian cells. We demonstrate that a set of Cas proteins efficiently and orthogonally repress or activate the translation of designed mRNAs that contain a Cas-binding RNA motif in the 5'-UTR. By linking multiple Cas-mediated translational modulators, we designed and built artificial circuits like logic gates, cascades, and half-subtractor circuits. Moreover, we show that various CRISPR-related technologies like anti-CRISPR and split-Cas9 platforms could be similarly repurposed to control translation. Coupling Cas-mediated translational and transcriptional regulation enhanced the complexity of synthetic circuits built by only introducing a few additional elements. Collectively, CARTRIDGE has enormous potential as a versatile molecular toolkit for mammalian synthetic biology.
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Affiliation(s)
- Shunsuke Kawasaki
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
| | - Hiroki Ono
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Moe Hirosawa
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Takeru Kuwabara
- Faculty of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shunsuke Sumi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Suji Lee
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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27
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Matsumoto N, Yamanaka S, Morimoto K, Matsui K, Nishimura S, Kinoshita Y, Inage Y, Fujimori K, Kuroda T, Saito Y, Takamura T, Fujimoto T, Tajiri S, Matsumoto K, Inoue M, Kobayashi E, Yokoo T. Evaluation of the ability of human induced nephron progenitor cells to form chimeric renal organoids using mouse embryonic renal progenitor cells. Biochem Biophys Res Commun 2023; 662:18-25. [PMID: 37094429 DOI: 10.1016/j.bbrc.2023.04.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/17/2023] [Indexed: 04/26/2023]
Abstract
The number of patients with end-stage renal failure is increasing annually worldwide and the problem is compounded by a shortage of renal transplantation donors. In our previous research, we have shown that transplantation of renal progenitor cells into the nephrogenic region of heterologous fetuses can induce the development of nephrons. We have also developed transgenic mice in which specific renal progenitor cells can be removed by drugs. By combining these two technologies, we have succeeded in generating human-mouse chimeric kidneys in fetal mice. We hope to apply these technologies to regenerative medicine. The quality of nephron progenitor cells (NPCs) derived from human pluripotent stem cells is important for the generation of chimeric kidneys, but there is currently no simple evaluation system for the chimerogenic potential of human NPCs. In this study, we focused on the fact that the re-aggregation of mouse renal progenitor cells can be used for nephron formation, even when merged into single cells. First, we examined the conditions under which nephron formation is likely to occur in mice during re-aggregation. Next, to improve the differentiation potential of human NPCs derived from pluripotent stem cells, NPCs were sorted using Integrin subunit alpha 8 (ITGA8). Finally, we demonstrated chimera formation between different species by mixing mouse cells with purified, selectively-induced human NPCs under optimum conditions. We observed these chimeric organoids at different time points to learn about these human-mouse chimeric structures at various stages of renal development. We found that the rate of chimera formation was affected by the purity of the human NPCs and the cell ratios used. We demonstrated that chimeric nephrons can be generated using a simple model, even between distant species. We believe that this admixture of human and mouse renal progenitor cells is a promising technology with potential application for the evaluation of the chimera formation abilities of NPCs.
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Affiliation(s)
- Naoto Matsumoto
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Shuichiro Yamanaka
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.
| | - Keita Morimoto
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Kenji Matsui
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Sandy Nishimura
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Yoshitaka Kinoshita
- Department of Kidney Regenerative Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan; Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8654, Japan
| | - Yuka Inage
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan; Department of Pediatrics, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Koki Fujimori
- Sumitomo Pharma, Co., Ltd., 2-6-8, Doshomachi, Chuo-ku, Osaka, 541-0045, Japan
| | - Takao Kuroda
- Sumitomo Pharma, Co., Ltd., 2-6-8, Doshomachi, Chuo-ku, Osaka, 541-0045, Japan
| | - Yatsumu Saito
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Tsuyoshi Takamura
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Toshinari Fujimoto
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Susumu Tajiri
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Kei Matsumoto
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Makoto Inoue
- Sumitomo Pharma, Co., Ltd., 2-6-8, Doshomachi, Chuo-ku, Osaka, 541-0045, Japan
| | - Eiji Kobayashi
- Department of Kidney Regenerative Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Takashi Yokoo
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.
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28
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Miao Y, Djeffal Y, De Simone A, Zhu K, Lee JG, Lu Z, Silberfeld A, Rao J, Tarazona OA, Mongera A, Rigoni P, Diaz-Cuadros M, Song LMS, Di Talia S, Pourquié O. Reconstruction and deconstruction of human somitogenesis in vitro. Nature 2023; 614:500-508. [PMID: 36543321 PMCID: PMC10018515 DOI: 10.1038/s41586-022-05655-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
The vertebrate body displays a segmental organization that is most conspicuous in the periodic organization of the vertebral column and peripheral nerves. This metameric organization is first implemented when somites, which contain the precursors of skeletal muscles and vertebrae, are rhythmically generated from the presomitic mesoderm. Somites then become subdivided into anterior and posterior compartments that are essential for vertebral formation and segmental patterning of the peripheral nervous system1-4. How this key somitic subdivision is established remains poorly understood. Here we introduce three-dimensional culture systems of human pluripotent stem cells called somitoids and segmentoids, which recapitulate the formation of somite-like structures with anteroposterior identity. We identify a key function of the segmentation clock in converting temporal rhythmicity into the spatial regularity of anterior and posterior somitic compartments. We show that an initial 'salt and pepper' expression of the segmentation gene MESP2 in the newly formed segment is transformed into compartments of anterior and posterior identity through an active cell-sorting mechanism. Our research demonstrates that the major patterning modules that are involved in somitogenesis, including the clock and wavefront, anteroposterior polarity patterning and somite epithelialization, can be dissociated and operate independently in our in vitro systems. Together, we define a framework for the symmetry-breaking process that initiates somite polarity patterning. Our work provides a platform for decoding general principles of somitogenesis and advancing knowledge of human development.
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Affiliation(s)
- Yuchuan Miao
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Yannis Djeffal
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Kongju Zhu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jong Gwan Lee
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Ziqi Lu
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Andrew Silberfeld
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jyoti Rao
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Oscar A Tarazona
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Alessandro Mongera
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Pietro Rigoni
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Margarete Diaz-Cuadros
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Laura Min Sook Song
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Stefano Di Talia
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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29
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3D osteogenic differentiation of human iPSCs reveals the role of TGFβ signal in the transition from progenitors to osteoblasts and osteoblasts to osteocytes. Sci Rep 2023; 13:1094. [PMID: 36658197 PMCID: PMC9852429 DOI: 10.1038/s41598-023-27556-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/04/2023] [Indexed: 01/21/2023] Open
Abstract
Although the formation of bone-like nodules is regarded as the differentiation process from stem cells to osteogenic cells, including osteoblasts and osteocytes, the precise biological events during nodule formation are unknown. Here we performed the osteogenic induction of human induced pluripotent stem cells using a three-dimensional (3D) culture system using type I collagen gel and a rapid induction method with retinoic acid. Confocal and time-lapse imaging revealed the osteogenic differentiation was initiated with vigorous focal proliferation followed by aggregation, from which cells invaded the gel. Invading cells changed their morphology and expressed osteocyte marker genes, suggesting the transition from osteoblasts to osteocytes. Single-cell RNA sequencing analysis revealed that 3D culture-induced cells with features of periosteal skeletal stem cells, some of which expressed TGFβ-regulated osteoblast-related molecules. The role of TGFβ signal was further analyzed in the transition from osteoblasts to osteocytes, which revealed that modulation of the TGFβ signal changed the morphology and motility of cells isolated from the 3D culture, suggesting that the TGFβ signal maintains the osteoblastic phenotype and the transition into osteocytes requires down-regulation of the TGFβ signal.
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30
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Ueda T, Shiina S, Iriguchi S, Terakura S, Kawai Y, Kabai R, Sakamoto S, Watanabe A, Ohara K, Wang B, Xu H, Minagawa A, Hotta A, Woltjen K, Uemura Y, Kodama Y, Seno H, Nakatsura T, Tamada K, Kaneko S. Optimization of the proliferation and persistency of CAR T cells derived from human induced pluripotent stem cells. Nat Biomed Eng 2023; 7:24-37. [PMID: 36509913 PMCID: PMC9870784 DOI: 10.1038/s41551-022-00969-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 10/21/2022] [Indexed: 12/14/2022]
Abstract
The effectiveness of chimaeric antigen receptor (CAR) T-cell immunotherapies against solid tumours relies on the accumulation, proliferation and persistency of T cells at the tumour site. Here we show that the proliferation of CD8αβ cytotoxic CAR T cells in solid tumours can be enhanced by deriving and expanding them from a single human induced-pluripotent-stem-cell clone bearing a CAR selected for efficient differentiation. We also show that the proliferation and persistency of the effector cells in the tumours can be further enhanced by genetically knocking out diacylglycerol kinase, which inhibits antigen-receptor signalling, and by transducing the cells with genes encoding for membrane-bound interleukin-15 (IL-15) and its receptor subunit IL-15Rα. In multiple tumour-bearing animal models, the engineered hiPSC-derived CAR T cells led to therapeutic outcomes similar to those of primary CD8 T cells bearing the same CAR. The optimization of effector CAR T cells derived from pluripotent stem cells may aid the development of long-lasting antigen-specific T-cell immunotherapies for the treatment of solid tumours.
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Affiliation(s)
- Tatsuki Ueda
- grid.258799.80000 0004 0372 2033Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan ,grid.258799.80000 0004 0372 2033Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Sara Shiina
- grid.258799.80000 0004 0372 2033Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan ,Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Japan
| | - Shoichi Iriguchi
- grid.258799.80000 0004 0372 2033Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan ,Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Japan
| | - Seitaro Terakura
- grid.27476.300000 0001 0943 978XDepartment of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yohei Kawai
- grid.258799.80000 0004 0372 2033Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ryotaro Kabai
- grid.258799.80000 0004 0372 2033Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Satoko Sakamoto
- grid.258799.80000 0004 0372 2033Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Akira Watanabe
- grid.258799.80000 0004 0372 2033Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kohei Ohara
- grid.258799.80000 0004 0372 2033Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Bo Wang
- grid.258799.80000 0004 0372 2033Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan ,Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Japan
| | - Huaigeng Xu
- grid.258799.80000 0004 0372 2033Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Atsutaka Minagawa
- grid.258799.80000 0004 0372 2033Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Akitsu Hotta
- grid.258799.80000 0004 0372 2033Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Knut Woltjen
- grid.258799.80000 0004 0372 2033Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Yasushi Uemura
- grid.272242.30000 0001 2168 5385Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Yuzo Kodama
- grid.31432.370000 0001 1092 3077Department of Gastroenterology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hiroshi Seno
- grid.258799.80000 0004 0372 2033Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tetsuya Nakatsura
- grid.272242.30000 0001 2168 5385Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Koji Tamada
- grid.268397.10000 0001 0660 7960Department of Immunology, Yamaguchi University Graduate School of Medicine, Yamaguchi, Japan
| | - Shin Kaneko
- grid.258799.80000 0004 0372 2033Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan ,Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Japan
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31
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Schjeide BMM, Püschel GP. Determining On-Target, Off-Target, and Copy Number Status of Transgenic Events After CRISPR/Cas9 Targeted AAVS1 Safe-Harbor Modification of iPSCs Using Double-Control Quantitative Copy Number PCR. Curr Protoc 2023; 3:e635. [PMID: 36598341 DOI: 10.1002/cpz1.635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Double-control quantitative copy number PCR (dc-qcnPCR) is a recently described tool that can be used to quantify donor DNA insertions in genetically modified monoclonal cell lines. In conjunction with an insert-confirmation PCR, the technique can quickly and easily identify clones containing on-target heterozygous or homozygous donor DNA integrations and exclude off-target insertions. The genetic manipulation of immortal cell lines is a versatile tool to elucidate cellular signaling pathways and protein functions. Despite recent advances in the precision of genetic engineering tools such as CRISPR/Cas9, transcription-activator-like effector nucleases (TALENs), and zinc-finger nucleases (ZFNs), it is still essential to verify the accurate insertion of the sequence of interest (donor DNA) into the targeted genomic DNA (gDNA) locus. This precise integration into a genetic safe harbor, and exclusion of the donor DNA from functionally relevant genes, can ensure normal cellular functionality. Current methods to analyze the specificity of donor DNA insertions either are cost-prohibitive or create dependency on manufacturers for assay design and production. The dc-qcnPCR method is a simple, yet powerful, approach that can be prepared and carried out in any laboratory equipped with standard molecular biology supplies. Here we provide step-by-step instructions to prepare and perform the dc-qcnPCR, and its companion insert-confirmation PCR, to determine donor DNA insertion numbers in monoclonal cell lines genetically modified through CRISPR/Cas9. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Genetic modification at AAVS1 safe harbor in induced pluripotent stem cells (IMR90-4) using CRISPR/Cas9: from plasmid design to monoclonal expansion Support Protocol 1: Measurement of Gaussia luciferase activity to verify reporter protein functionality Support Protocol 2: Verification of monoclonal expansion using immunofluorescence. Basic Protocol 2: Insert-confirmation PCR Basic Protocol 3: Design and preparation of double-control quantitative copy number PCR reagents and quantification of donor DNA integrations in genetically modified monoclonal cells.
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Affiliation(s)
- Brit-Maren Michaud Schjeide
- Department of Nutritional Biochemistry, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,Department of Nutritional Biochemistry, Faculty of Life Sciences: Food, Nutrition and Health, University of Bayreuth, Kulmbach, Germany
| | - Gerhard Paul Püschel
- Department of Nutritional Biochemistry, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
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32
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Diaz-Cuadros M, Miettinen TP, Skinner OS, Sheedy D, Díaz-García CM, Gapon S, Hubaud A, Yellen G, Manalis SR, Oldham WM, Pourquié O. Metabolic regulation of species-specific developmental rates. Nature 2023; 613:550-557. [PMID: 36599986 PMCID: PMC9944513 DOI: 10.1038/s41586-022-05574-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/18/2022] [Indexed: 01/06/2023]
Abstract
Animals display substantial inter-species variation in the rate of embryonic development despite a broad conservation of the overall sequence of developmental events. Differences in biochemical reaction rates, including the rates of protein production and degradation, are thought to be responsible for species-specific rates of development1-3. However, the cause of differential biochemical reaction rates between species remains unknown. Here, using pluripotent stem cells, we have established an in vitro system that recapitulates the twofold difference in developmental rate between mouse and human embryos. This system provides a quantitative measure of developmental speed as revealed by the period of the segmentation clock, a molecular oscillator associated with the rhythmic production of vertebral precursors. Using this system, we show that mass-specific metabolic rates scale with the developmental rate and are therefore higher in mouse cells than in human cells. Reducing these metabolic rates by inhibiting the electron transport chain slowed down the segmentation clock by impairing the cellular NAD+/NADH redox balance and, further downstream, lowering the global rate of protein synthesis. Conversely, increasing the NAD+/NADH ratio in human cells by overexpression of the Lactobacillus brevis NADH oxidase LbNOX increased the translation rate and accelerated the segmentation clock. These findings represent a starting point for the manipulation of developmental rate, with multiple translational applications including accelerating the differentiation of human pluripotent stem cells for disease modelling and cell-based therapies.
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Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
| | - Teemu P Miettinen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Owen S Skinner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Dylan Sheedy
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Carlos Manlio Díaz-García
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Svetlana Gapon
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Alexis Hubaud
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Gary Yellen
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Scott R Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - William M Oldham
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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33
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Viana MP, Chen J, Knijnenburg TA, Vasan R, Yan C, Arakaki JE, Bailey M, Berry B, Borensztejn A, Brown EM, Carlson S, Cass JA, Chaudhuri B, Cordes Metzler KR, Coston ME, Crabtree ZJ, Davidson S, DeLizo CM, Dhaka S, Dinh SQ, Do TP, Domingus J, Donovan-Maiye RM, Ferrante AJ, Foster TJ, Frick CL, Fujioka G, Fuqua MA, Gehring JL, Gerbin KA, Grancharova T, Gregor BW, Harrylock LJ, Haupt A, Hendershott MC, Hookway C, Horwitz AR, Hughes HC, Isaac EJ, Johnson GR, Kim B, Leonard AN, Leung WW, Lucas JJ, Ludmann SA, Lyons BM, Malik H, McGregor R, Medrash GE, Meharry SL, Mitcham K, Mueller IA, Murphy-Stevens TL, Nath A, Nelson AM, Oluoch SA, Paleologu L, Popiel TA, Riel-Mehan MM, Roberts B, Schaefbauer LM, Schwarzl M, Sherman J, Slaton S, Sluzewski MF, Smith JE, Sul Y, Swain-Bowden MJ, Tang WJ, Thirstrup DJ, Toloudis DM, Tucker AP, Valencia V, Wiegraebe W, Wijeratna T, Yang R, Zaunbrecher RJ, Labitigan RLD, Sanborn AL, Johnson GT, Gunawardane RN, Gaudreault N, Theriot JA, Rafelski SM. Integrated intracellular organization and its variations in human iPS cells. Nature 2023; 613:345-354. [PMID: 36599983 PMCID: PMC9834050 DOI: 10.1038/s41586-022-05563-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 11/15/2022] [Indexed: 01/06/2023]
Abstract
Understanding how a subset of expressed genes dictates cellular phenotype is a considerable challenge owing to the large numbers of molecules involved, their combinatorics and the plethora of cellular behaviours that they determine1,2. Here we reduced this complexity by focusing on cellular organization-a key readout and driver of cell behaviour3,4-at the level of major cellular structures that represent distinct organelles and functional machines, and generated the WTC-11 hiPSC Single-Cell Image Dataset v1, which contains more than 200,000 live cells in 3D, spanning 25 key cellular structures. The scale and quality of this dataset permitted the creation of a generalizable analysis framework to convert raw image data of cells and their structures into dimensionally reduced, quantitative measurements that can be interpreted by humans, and to facilitate data exploration. This framework embraces the vast cell-to-cell variability that is observed within a normal population, facilitates the integration of cell-by-cell structural data and allows quantitative analyses of distinct, separable aspects of organization within and across different cell populations. We found that the integrated intracellular organization of interphase cells was robust to the wide range of variation in cell shape in the population; that the average locations of some structures became polarized in cells at the edges of colonies while maintaining the 'wiring' of their interactions with other structures; and that, by contrast, changes in the location of structures during early mitotic reorganization were accompanied by changes in their wiring.
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Affiliation(s)
| | - Jianxu Chen
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Ritvik Vasan
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Calysta Yan
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Matte Bailey
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Ben Berry
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Eva M Brown
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Sara Carlson
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Julie A Cass
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | - Thao P Do
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Amanda Haupt
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | - Eric J Isaac
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Brian Kim
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | - Haseeb Malik
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | - Aditya Nath
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Youngmee Sul
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - W Joyce Tang
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | - Ruian Yang
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Ramon Lorenzo D Labitigan
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Adrian L Sanborn
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | | | | | | | - Julie A Theriot
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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34
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Kuzmin AA, Tomilin AN. Building Blocks of Artificial CRISPR-Based Systems beyond Nucleases. Int J Mol Sci 2022; 24:ijms24010397. [PMID: 36613839 PMCID: PMC9820447 DOI: 10.3390/ijms24010397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
Tools developed in the fields of genome engineering, precise gene regulation, and synthetic gene networks have an increasing number of applications. When shared with the scientific community, these tools can be used to further unlock the potential of precision medicine and tissue engineering. A large number of different genetic elements, as well as modifications, have been used to create many different systems and to validate some technical concepts. New studies have tended to optimize or improve existing elements or approaches to create complex synthetic systems, especially those based on the relatively new CRISPR technology. In order to maximize the output of newly developed approaches and to move from proof-of-principle experiments to applications in regenerative medicine, it is important to navigate efficiently through the vast number of genetic elements to choose those most suitable for specific needs. In this review, we have collected information regarding the main genetic elements and their modifications, which can be useful in different synthetic systems with an emphasis of those based on CRISPR technology. We have indicated the most suitable elements and approaches to choose or combine in planning experiments, while providing their deeper understanding, and have also stated some pitfalls that should be avoided.
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35
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Tsujimoto H, Katagiri N, Ijiri Y, Sasaki B, Kobayashi Y, Mima A, Ryosaka M, Furuyama K, Kawaguchi Y, Osafune K. In vitro methods to ensure absence of residual undifferentiated human induced pluripotent stem cells intermingled in induced nephron progenitor cells. PLoS One 2022; 17:e0275600. [PMID: 36378656 PMCID: PMC9665373 DOI: 10.1371/journal.pone.0275600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Cell therapies using human induced pluripotent stem cell (hiPSC)-derived nephron progenitor cells (NPCs) are expected to ameliorate acute kidney injury (AKI). However, using hiPSC-derived NPCs clinically is a challenge because hiPSCs themselves are tumorigenic. LIN28A, ESRG, CNMD and SFRP2 transcripts have been used as a marker of residual hiPSCs for a variety of cell types undergoing clinical trials. In this study, by reanalyzing public databases, we found a baseline expression of LIN28A, ESRG, CNMD and SFRP2 in hiPSC-derived NPCs and several other cell types, suggesting LIN28A, ESRG, CNMD and SFRP2 are not always reliable markers for iPSC detection. As an alternative, we discovered a lncRNA marker gene, MIR302CHG, among many known and unknown iPSC markers, as highly differentially expressed between hiPSCs and NPCs, by RNA sequencing and quantitative RT-PCR (qRT-PCR) analyses. Using MIR302CHG as an hiPSC marker, we constructed two assay methods, a combination of magnetic bead-based enrichment and qRT-PCR and digital droplet PCR alone, to detect a small number of residual hiPSCs in NPC populations. The use of these in vitro assays could contribute to patient safety in treatments using hiPSC-derived cells.
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Affiliation(s)
- Hiraku Tsujimoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Rege Nephro Co., Ltd., Med-Pharm Collaboration Building, Kyoto University, Kyoto, Japan
- * E-mail: (KO); (HT)
| | - Naoko Katagiri
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Rege Nephro Co., Ltd., Med-Pharm Collaboration Building, Kyoto University, Kyoto, Japan
| | - Yoshihiro Ijiri
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Rege Nephro Co., Ltd., Med-Pharm Collaboration Building, Kyoto University, Kyoto, Japan
| | - Ben Sasaki
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Yoshifumi Kobayashi
- Rege Nephro Co., Ltd., Med-Pharm Collaboration Building, Kyoto University, Kyoto, Japan
| | - Akira Mima
- Rege Nephro Co., Ltd., Med-Pharm Collaboration Building, Kyoto University, Kyoto, Japan
| | - Makoto Ryosaka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Rege Nephro Co., Ltd., Med-Pharm Collaboration Building, Kyoto University, Kyoto, Japan
| | - Kenichiro Furuyama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Yoshiya Kawaguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Kenji Osafune
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- * E-mail: (KO); (HT)
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36
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Husser MC, Ozugergin I, Resta T, Martin VJJ, Piekny AJ. Cytokinetic diversity in mammalian cells is revealed by the characterization of endogenous anillin, Ect2 and RhoA. Open Biol 2022; 12:220247. [PMID: 36416720 PMCID: PMC9683116 DOI: 10.1098/rsob.220247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Cytokinesis is required to physically separate the daughter cells at the end of mitosis. This crucial process requires the assembly and ingression of an actomyosin ring, which must occur with high fidelity to avoid aneuploidy and cell fate changes. Most of our knowledge of mammalian cytokinesis was generated using over-expressed transgenes in HeLa cells. Over-expression can introduce artefacts, while HeLa are cancerous human cells that have lost their epithelial identity, and the mechanisms controlling cytokinesis in these cells could be vastly different from other cell types. Here, we tagged endogenous anillin, Ect2 and RhoA with mNeonGreen and characterized their localization during cytokinesis for the first time in live human cells. Comparing anillin localization in multiple cell types revealed cytokinetic diversity with differences in the duration and symmetry of ring closure, and the timing of cortical recruitment. Our findings show that the breadth of anillin correlates with the rate of ring closure, and support models where cell size or ploidy affects the cortical organization, and intrinsic mechanisms control the symmetry of ring closure. This work highlights the need to study cytokinesis in more diverse cell types, which will be facilitated by the reagents generated for this study.
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Affiliation(s)
| | - Imge Ozugergin
- Biology Department, Concordia University, Montreal, Quebec, Canada
| | - Tiziana Resta
- Biology Department, Concordia University, Montreal, Quebec, Canada
| | - Vincent J. J. Martin
- Biology Department, Concordia University, Montreal, Quebec, Canada,Center for Applied Synthetic Biology, Concordia University, Montreal, Quebec, Canada
| | - Alisa J. Piekny
- Biology Department, Concordia University, Montreal, Quebec, Canada,Center for Applied Synthetic Biology, Concordia University, Montreal, Quebec, Canada,Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Quebec, Canada
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37
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Kimura M, Iguchi T, Iwasawa K, Dunn A, Thompson WL, Yoneyama Y, Chaturvedi P, Zorn AM, Wintzinger M, Quattrocelli M, Watanabe-Chailland M, Zhu G, Fujimoto M, Kumbaji M, Kodaka A, Gindin Y, Chung C, Myers RP, Subramanian GM, Hwa V, Takebe T. En masse organoid phenotyping informs metabolic-associated genetic susceptibility to NASH. Cell 2022; 185:4216-4232.e16. [PMID: 36240780 PMCID: PMC9617783 DOI: 10.1016/j.cell.2022.09.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 08/01/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
Genotype-phenotype associations for common diseases are often compounded by pleiotropy and metabolic state. Here, we devised a pooled human organoid-panel of steatohepatitis to investigate the impact of metabolic status on genotype-phenotype association. En masse population-based phenotypic analysis under insulin insensitive conditions predicted key non-alcoholic steatohepatitis (NASH)-genetic factors including the glucokinase regulatory protein (GCKR)-rs1260326:C>T. Analysis of NASH clinical cohorts revealed that GCKR-rs1260326-T allele elevates disease severity only under diabetic state but protects from fibrosis under non-diabetic states. Transcriptomic, metabolomic, and pharmacological analyses indicate significant mitochondrial dysfunction incurred by GCKR-rs1260326, which was not reversed with metformin. Uncoupling oxidative mechanisms mitigated mitochondrial dysfunction and permitted adaptation to increased fatty acid supply while protecting against oxidant stress, forming a basis for future therapeutic approaches for diabetic NASH. Thus, "in-a-dish" genotype-phenotype association strategies disentangle the opposing roles of metabolic-associated gene variant functions and offer a rich mechanistic, diagnostic, and therapeutic inference toolbox toward precision hepatology. VIDEO ABSTRACT.
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Affiliation(s)
- Masaki Kimura
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Takuma Iguchi
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kentaro Iwasawa
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrew Dunn
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Wendy L Thompson
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Yosuke Yoneyama
- Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Praneet Chaturvedi
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Aaron M Zorn
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michelle Wintzinger
- Division of Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Mattia Quattrocelli
- Division of Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Miki Watanabe-Chailland
- NMR-Based Metabolomics Core Facility, Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Gaohui Zhu
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Masanobu Fujimoto
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Meenasri Kumbaji
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Asuka Kodaka
- Communication Design Center, Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
| | | | | | - Robert P Myers
- Gilead Sciences, Foster City, CA 94404, USA; The Liver Company, Inc., Palo Alto, CA 94303, USA
| | - G Mani Subramanian
- Gilead Sciences, Foster City, CA 94404, USA; The Liver Company, Inc., Palo Alto, CA 94303, USA
| | - Vivian Hwa
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Takanori Takebe
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Communication Design Center, Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan.
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38
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Zhang F, Meier AB, Poch CM, Tian Q, Engelhardt S, Sinnecker D, Lipp P, Laugwitz KL, Moretti A, Dorn T. High-throughput optical action potential recordings in hiPSC-derived cardiomyocytes with a genetically encoded voltage indicator in the AAVS1 locus. Front Cell Dev Biol 2022; 10:1038867. [PMID: 36274846 PMCID: PMC9585323 DOI: 10.3389/fcell.2022.1038867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/26/2022] [Indexed: 11/22/2022] Open
Abstract
Cardiomyocytes (CMs) derived from human induced pluripotent stem cells (hiPSCs) represent an excellent in vitro model in cardiovascular research. Changes in their action potential (AP) dynamics convey information that is essential for disease modeling, drug screening and toxicity evaluation. High-throughput optical AP recordings utilizing intramolecular Förster resonance energy transfer (FRET) of the voltage-sensitive fluorescent protein (VSFP) have emerged as a substitute or complement to the resource-intensive patch clamp technique. Here, we functionally validated our recently generated voltage indicator hiPSC lines stably expressing CAG-promoter-driven VSFP in the AAVS1 safe harbor locus. By combining subtype-specific cardiomyocyte differentiation protocols, we established optical AP recordings in ventricular, atrial, and nodal CMs in 2D monolayers using fluorescence microscopy. Moreover, we achieved high-throughput optical AP measurements in single hiPSC-derived CMs in a 3D context. Overall, this system greatly expands the spectrum of possibilities for high-throughput, non-invasive and long-term AP analyses in cardiovascular research and drug discovery.
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Affiliation(s)
- Fangfang Zhang
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Anna B. Meier
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Christine M. Poch
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Qinghai Tian
- Molecular Cell Biology, Centre for Molecular Signaling (PZMS), Medical Faculty, Saarland University, Homburg, Germany
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Daniel Sinnecker
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Peter Lipp
- Molecular Cell Biology, Centre for Molecular Signaling (PZMS), Medical Faculty, Saarland University, Homburg, Germany
| | - Karl-Ludwig Laugwitz
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Alessandra Moretti
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- *Correspondence: Alessandra Moretti, ; Tatjana Dorn,
| | - Tatjana Dorn
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- *Correspondence: Alessandra Moretti, ; Tatjana Dorn,
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39
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Möller L, Aird EJ, Schröder MS, Kobel L, Kissling L, van de Venn L, Corn JE. Recursive Editing improves homology-directed repair through retargeting of undesired outcomes. Nat Commun 2022; 13:4550. [PMID: 35931681 PMCID: PMC9356142 DOI: 10.1038/s41467-022-31944-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/11/2022] [Indexed: 12/30/2022] Open
Abstract
CRISPR-Cas induced homology-directed repair (HDR) enables the installation of a broad range of precise genomic modifications from an exogenous donor template. However, applications of HDR in human cells are often hampered by poor efficiency, stemming from a preference for error-prone end joining pathways that yield short insertions and deletions. Here, we describe Recursive Editing, an HDR improvement strategy that selectively retargets undesired indel outcomes to create additional opportunities to produce the desired HDR allele. We introduce a software tool, named REtarget, that enables the rational design of Recursive Editing experiments. Using REtarget-designed guide RNAs in single editing reactions, Recursive Editing can simultaneously boost HDR efficiencies and reduce undesired indels. We also harness REtarget to generate databases for particularly effective Recursive Editing sites across the genome, to endogenously tag proteins, and to target pathogenic mutations. Recursive Editing constitutes an easy-to-use approach without potentially deleterious cell manipulations and little added experimental burden.
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Affiliation(s)
- Lukas Möller
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Eric J Aird
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Markus S Schröder
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Lena Kobel
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Lucas Kissling
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Lilly van de Venn
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Jacob E Corn
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland.
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40
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Naeimi Kararoudi M, Likhite S, Elmas E, Yamamoto K, Schwartz M, Sorathia K, de Souza Fernandes Pereira M, Sezgin Y, Devine RD, Lyberger JM, Behbehani GK, Chakravarti N, Moriarity BS, Meyer K, Lee DA. Optimization and validation of CAR transduction into human primary NK cells using CRISPR and AAV. CELL REPORTS METHODS 2022; 2:100236. [PMID: 35784645 PMCID: PMC9243630 DOI: 10.1016/j.crmeth.2022.100236] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/08/2021] [Accepted: 05/23/2022] [Indexed: 11/22/2022]
Abstract
Human primary natural killer (NK) cells are being widely advanced for cancer immunotherapy. However, methods for gene editing of these cells have suffered low transduction rates, high cell death, and loss of transgene expression after expansion. Here, we developed a highly efficient method for site-specific gene insertion in NK cells using CRISPR (Cas9/RNP) and AAVs. We compared AAV vectors designed to mediate gene insertion by different DNA repair mechanisms, homology arm lengths, and virus concentrations. We then validated the method for site-directed gene insertion of CD33-specific CARs into primary human NK cells. CAR transduction was efficient, its expression remained stable after expansion, and it improved efficacy against AML targets.
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Affiliation(s)
- Meisam Naeimi Kararoudi
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Shibi Likhite
- Center for Gene Therapy, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
| | - Ezgi Elmas
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
- Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Kenta Yamamoto
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Maura Schwartz
- Center for Gene Therapy, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
| | - Kinnari Sorathia
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
| | | | - Yasemin Sezgin
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
| | - Raymond D. Devine
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Justin M. Lyberger
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Gregory K. Behbehani
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Nitin Chakravarti
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | | | - Kathrin Meyer
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- Center for Gene Therapy, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
| | - Dean A. Lee
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
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41
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Chao J, Feng L, Ye P, Chen X, Cui Q, Sun G, Zhou T, Tian E, Li W, Hu W, Riggs AD, Matalon R, Shi Y. Therapeutic development for Canavan disease using patient iPSCs introduced with the wild-type ASPA gene. iScience 2022; 25:104391. [PMID: 35637731 PMCID: PMC9142666 DOI: 10.1016/j.isci.2022.104391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 03/03/2022] [Accepted: 05/06/2022] [Indexed: 12/04/2022] Open
Abstract
Canavan disease (CD) is a devastating neurological disease that lacks effective therapy. Because CD is caused by mutations of the aspartoacylase (ASPA) gene, we introduced the wild-type (WT) ASPA gene into patient iPSCs through lentiviral transduction or CRISPR/Cas9-mediated gene editing. We then differentiated the WT ASPA-expressing patient iPSCs (ASPA-CD iPSCs) into NPCs and showed that the resultant ASPA-CD NPCs exhibited potent ASPA enzymatic activity. The ASPA-CD NPCs were able to survive in brains of transplanted CD mice. The engrafted ASPA-CD NPCs reconstituted ASPA activity in CD mouse brains, reduced the abnormally elevated level of NAA in both brain tissues and cerebrospinal fluid (CSF), and rescued hallmark pathological phenotypes of the disease, including spongy degeneration, myelination defects, and motor function impairment in transplanted CD mice. These genetically modified patient iPSC-derived NPCs represent a promising cell therapy candidate for CD, a disease that has neither a cure nor a standard treatment. The wild-type ASPA gene was introduced into CD patient iPSCs to make ASPA-CD iPSCs ASPA-CD iPSCs were differentiated into ASPA-CD NPCs with potent ASPA activity Engrafted ASPA-CD NPCs could rescue major disease phenotypes in CD mice CSF NAA level can be used as a biomarker to monitor the treatment outcome for CD
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Affiliation(s)
- Jianfei Chao
- Division of Stem Cell Biology Research, Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Lizhao Feng
- Division of Stem Cell Biology Research, Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Peng Ye
- Division of Stem Cell Biology Research, Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Xianwei Chen
- Division of Stem Cell Biology Research, Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Qi Cui
- Division of Stem Cell Biology Research, Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Guihua Sun
- Division of Stem Cell Biology Research, Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA.,Diabetes and Metabolism Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Tao Zhou
- Division of Stem Cell Biology Research, Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - E Tian
- Division of Stem Cell Biology Research, Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Wendong Li
- Division of Stem Cell Biology Research, Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Weidong Hu
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Arthur D Riggs
- Diabetes and Metabolism Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Reuben Matalon
- Department of Pediatrics, The University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555-0359, USA
| | - Yanhong Shi
- Division of Stem Cell Biology Research, Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
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42
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Fehér A, Schnúr A, Muenthaisong S, Bellák T, Ayaydin F, Várady G, Kemter E, Wolf E, Dinnyés A. Establishment and characterization of a novel human induced pluripotent stem cell line stably expressing the iRFP720 reporter. Sci Rep 2022; 12:9874. [PMID: 35701501 PMCID: PMC9198085 DOI: 10.1038/s41598-022-12956-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/19/2022] [Indexed: 11/27/2022] Open
Abstract
Stem cell therapy has great potential for replacing beta-cell loss in diabetic patients. However, a key obstacle to cell therapy’s success is to preserve viability and function of the engrafted cells. While several strategies have been developed to improve engrafted beta-cell survival, tools to evaluate the efficacy within the body by imaging are limited. Traditional labeling tools, such as GFP-like fluorescent proteins, have limited penetration depths in vivo due to tissue scattering and absorption. To circumvent this limitation, a near-infrared fluorescent mutant version of the DrBphP bacteriophytochrome, iRFP720, has been developed for in vivo imaging and stem/progenitor cell tracking. Here, we present the generation and characterization of an iRFP720 expressing human induced pluripotent stem cell (iPSC) line, which can be used for real-time imaging in various biological applications. To generate the transgenic cells, the CRISPR/Cas9 technology was applied. A puromycin resistance gene was inserted into the AAVS1 locus, driven by the endogenous PPP1R12C promoter, along with the CAG-iRFP720 reporter cassette, which was flanked by insulator elements. Proper integration of the transgene into the targeted genomic region was assessed by comprehensive genetic analysis, verifying precise genome editing. Stable expression of iRFP720 in the cells was confirmed and imaged by their near-infrared fluorescence. We demonstrated that the reporter iPSCs exhibit normal stem cell characteristics and can be efficiently differentiated towards the pancreatic lineage. As the genetically modified reporter cells show retained pluripotency and multilineage differentiation potential, they hold great potential as a cellular model in a variety of biological and pharmacological applications.
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Affiliation(s)
- Anita Fehér
- BioTalentum Ltd, Aulich Lajos Street 26, Gödöllő, 2100, Hungary
| | - Andrea Schnúr
- BioTalentum Ltd, Aulich Lajos Street 26, Gödöllő, 2100, Hungary
| | | | - Tamás Bellák
- BioTalentum Ltd, Aulich Lajos Street 26, Gödöllő, 2100, Hungary.,Department of Anatomy, Histology and Embryology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, 6724, Hungary
| | - Ferhan Ayaydin
- Functional Cell Biology and Immunology Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine, University of Szeged (HCEMM-USZ), Szeged, 6720, Hungary.,Laboratory of Cellular Imaging, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - György Várady
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, 1117, Hungary
| | - Elisabeth Kemter
- Chair for Molecular Animal Breeding and Biotechnology, Gene Centre and Department of Veterinary Sciences, LMU Munich, 81377, Munich, Germany.,Centre for Innovative Medical Models (CiMM), Department of Veterinary Sciences, LMU Munich, 85764, Oberschleißheim, Germany.,German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Centre and Department of Veterinary Sciences, LMU Munich, 81377, Munich, Germany.,Centre for Innovative Medical Models (CiMM), Department of Veterinary Sciences, LMU Munich, 85764, Oberschleißheim, Germany.,German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - András Dinnyés
- BioTalentum Ltd, Aulich Lajos Street 26, Gödöllő, 2100, Hungary. .,HCEMM-USZ Stem Cell Research Group, Hungarian Centre of Excellence for Molecular Medicine, Szeged, 6723, Hungary. .,Department of Cell Biology and Molecular Medicine, University of Szeged, Szeged, 6720, Hungary. .,Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary.
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43
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Lensch S, Herschl MH, Ludwig CH, Sinha J, Hinks MM, Mukund A, Fujimori T, Bintu L. Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells. eLife 2022; 11:e75115. [PMID: 35678392 PMCID: PMC9183234 DOI: 10.7554/elife.75115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/23/2022] [Indexed: 12/02/2022] Open
Abstract
In mammalian cells genes that are in close proximity can be transcriptionally coupled: silencing or activating one gene can affect its neighbors. Understanding these dynamics is important for natural processes, such as heterochromatin spreading during development and aging, and when designing synthetic gene regulation circuits. Here, we systematically dissect this process in single cells by recruiting and releasing repressive chromatin regulators at dual-gene synthetic reporters, and measuring how fast gene silencing and reactivation spread as a function of intergenic distance and configuration of insulator elements. We find that silencing by KRAB, associated with histone methylation, spreads between two genes within hours, with a time delay that increases with distance. This fast KRAB-mediated spreading is not blocked by the classical cHS4 insulators. Silencing by histone deacetylase HDAC4 of the upstream gene can also facilitate background silencing of the downstream gene by PRC2, but with a days-long delay that does not change with distance. This slower silencing can sometimes be stopped by insulators. Gene reactivation of neighboring genes is also coupled, with strong promoters and insulators determining the order of reactivation. Our data can be described by a model of multi-gene regulation that builds upon previous knowledge of heterochromatin spreading, where both gene silencing and gene reactivation can act at a distance, allowing for coordinated dynamics via chromatin regulator recruitment.
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Affiliation(s)
- Sarah Lensch
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Michael H Herschl
- University of California, Berkeley—University of California, San Francisco Graduate Program in BioengineeringBerkeleyUnited States
| | - Connor H Ludwig
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Joydeb Sinha
- Department of Chemical and Systems Biology, Stanford UniversityStanfordUnited States
| | - Michaela M Hinks
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Adi Mukund
- Biophysics Program, Stanford UniversityStanfordUnited States
| | - Taihei Fujimori
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford UniversityStanfordUnited States
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44
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Schjeide BMM, Schenke M, Seeger B, Püschel GP. Validation of a Novel Double Control Quantitative Copy Number PCR Method to Quantify Off-Target Transgene Integration after CRISPR-Induced DNA Modification. Methods Protoc 2022; 5:mps5030043. [PMID: 35736544 PMCID: PMC9229199 DOI: 10.3390/mps5030043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/16/2022] Open
Abstract
In order to improve a recently established cell-based assay to assess the potency of botulinum neurotoxin, neuroblastoma-derived SiMa cells and induced pluripotent stem-cells (iPSC) were modified to incorporate the coding sequence of a reporter luciferase into a genetic safe harbor utilizing CRISPR/Cas9. A novel method, the double-control quantitative copy number PCR (dc-qcnPCR), was developed to detect off-target integrations of donor DNA. The donor DNA insertion success rate and targeted insertion success rate were analyzed in clones of each cell type. The dc-qcnPCR reliably quantified the copy number in both cell lines. The probability of incorrect donor DNA integration was significantly increased in SiMa cells in comparison to the iPSCs. This can possibly be explained by the lower bundled relative gene expression of a number of double-strand repair genes (BRCA1, DNA2, EXO1, MCPH1, MRE11, and RAD51) in SiMa clones than in iPSC clones. The dc-qcnPCR offers an efficient and cost-effective method to detect off-target CRISPR/Cas9-induced donor DNA integrations.
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Affiliation(s)
- Brit-Maren Michaud Schjeide
- Department of Nutritional Biochemistry, Institute of Nutritional Science, University of Potsdam, 14558 Nuthetal, Germany;
- Department of Nutritional Biochemistry, Faculty of Life Sciences: Food, Nutrition and Health, University of Bayreuth, 95326 Kulmbach, Germany
- Correspondence:
| | - Maren Schenke
- Research Group Food Toxicology and Alternative/Complementary Methods to Animal Experiments, Institute for Food Quality and Safety, University of Veterinary Medicine Hannover, 30173 Hannover, Germany; (M.S.); (B.S.)
| | - Bettina Seeger
- Research Group Food Toxicology and Alternative/Complementary Methods to Animal Experiments, Institute for Food Quality and Safety, University of Veterinary Medicine Hannover, 30173 Hannover, Germany; (M.S.); (B.S.)
| | - Gerhard Paul Püschel
- Department of Nutritional Biochemistry, Institute of Nutritional Science, University of Potsdam, 14558 Nuthetal, Germany;
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45
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Nakauchi Y, Azizi A, Thomas D, Corces MR, Reinisch A, Sharma R, Cruz Hernandez D, Kohnke T, Karigane D, Fan A, Martinez-Krams D, Stafford M, Kaur S, Dutta R, Phan P, Ediriwickrema A, McCarthy E, Ning Y, Phillips T, Ellison CK, Guler GD, Bergamaschi A, Ku CJ, Levy S, Majeti R. The cell type specific 5hmC landscape and dynamics of healthy human hematopoiesis and TET2-mutant pre-leukemia. Blood Cancer Discov 2022; 3:346-367. [DOI: 10.1158/2643-3230.bcd-21-0143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 02/07/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
Abstract
The conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) is a key step in DNA demethylation that is mediated by ten-eleven-translocation (TET) enzymes, which require ascorbate/vitamin C. Here, we report the 5hmC landscape of normal hematopoiesis and identify cell type-specific 5hmC profiles associated with active transcription and chromatin accessibility of key hematopoietic regulators. We utilized CRISPR/Cas9 to model TET2 loss-of-function mutations in primary human HSPCs. Disrupted cells exhibited increased colonies in serial replating, defective erythroid/megakaryocytic differentiation, and in vivo competitive advantage and myeloid skewing coupled with reduction of 5hmC at erythroid-associated gene loci. Azacitidine and ascorbate restored 5hmC abundance and slowed or reverted the expansion of TET2-mutant clones in vivo. These results demonstrate the key role of 5hmC in normal hematopoiesis and TET2-mutant phenotypes and raise the possibility of utilizing these agents to further our understanding of pre-leukemia/clonal hematopoiesis.
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Affiliation(s)
- Yusuke Nakauchi
- Stanford University School of Medicine, Stanford, California, United States
| | - Armon Azizi
- Stanford University, Stanford, CA, United States
| | - Daniel Thomas
- University of Adelaide, Adelaide, South Australia, Australia
| | - M. Ryan Corces
- Gladstone Institute of Neurological Disease, San Fransisco, California, United States
| | - Andreas Reinisch
- Stanford University School of Medicine, Stanford, CA, United States
| | - Rajiv Sharma
- Stanford University School of Medicine, Stanford, California, United States
| | - David Cruz Hernandez
- MRC Molecular Haematology Unit and Oxford Centre for Haematology, Weatherall Institute of Molecular Medicine,, Oxford, United Kingdom
| | - Thomas Kohnke
- Stanford University School of Medicine, Stanford, California, United States
| | - Daiki Karigane
- Stanford University School of Medicine, Stanford, California, United States
| | - Amy Fan
- Stanford University, Palo Alto, United States
| | | | | | - Satinder Kaur
- Stanford University School of Medicine, Palo Alto, CA, United States
| | - Ritika Dutta
- Stanford University School of Medicine, Palo Alto, CA, United States
| | - Paul Phan
- Stanford University School of Medicine, Stanford, California, United States
| | | | | | - Yuhong Ning
- Bluestar Genomics Inc., San Diego, CA, United States
| | | | | | | | | | | | - Samuel Levy
- Bluestar Genomics, San Diego, California, United States
| | - Ravindra Majeti
- Stanford University School of Medicine, Palo Alto, CA, United States
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46
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Generation of heterozygous (MRli003-A-5) and homozygous (MRli003-A-6) voltage-sensing knock-in human iPSC lines by CRISPR/Cas9 editing of the AAVS1 locus. Stem Cell Res 2022; 61:102785. [DOI: 10.1016/j.scr.2022.102785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 11/19/2022] Open
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47
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Transposase-CRISPR mediated targeted integration (TransCRISTI) in the human genome. Sci Rep 2022; 12:3390. [PMID: 35232993 PMCID: PMC8888626 DOI: 10.1038/s41598-022-07158-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/08/2022] [Indexed: 11/08/2022] Open
Abstract
Various methods have been used in targeted gene knock-in applications. CRISPR-based knock-in strategies based on homology-independent repair pathways such as CRISPR HITI have been shown to possess the best efficiency for gene knock-in in mammalian cells. However, these methods suffer from the probability of plasmid backbone insertion at the target site. On the other hand, studies trying to combine the targeting ability of the Cas9 molecule and the excision/integration capacity of the PB transposase have shown random integrations. In this study, we introduce a new homology-independent knock-in strategy, Transposase-CRISPR mediated Targeted Integration (TransCRISTI), that exploits a fusion of Cas9 nuclease and a double mutant piggyBac transposase. In isogenic mammalian cell lines, we show that the TransCRISTI method demonstrates higher efficiency (72%) for site-specific insertions than the CRISPR HITI (44%) strategy. Application of the TransCRISTI method resulted in site-directed integration in 4.13% and 3.69% of the initially transfected population in the human AAVS1and PML loci, respectively, while the CRISPR HITI strategy resulted in site-directed integration in the PML locus in only 0.6% of cells. We also observed lower off-target and random insertions in the TransCRISTI group than the CRISPR HITI group. The TransCRISTI technology represents a great potential for the accurate and high-efficiency knock-in of the desired transposable elements into the predetermined genomic locations.
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48
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Takahashi K, Okubo C, Nakamura M, Iwasaki M, Kawahara Y, Tabata T, Miyamoto Y, Woltjen K, Yamanaka S. A stress-reduced passaging technique improves the viability of human pluripotent cells. CELL REPORTS METHODS 2022; 2:100155. [PMID: 35474962 PMCID: PMC9017214 DOI: 10.1016/j.crmeth.2021.100155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/13/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Xeno-free culture systems have expanded the clinical and industrial application of human pluripotent stem cells (PSCs). However, reproducibility issues, often arising from variability during passaging steps, remain. Here, we describe an improved method for the subculture of human PSCs. The revised method significantly enhances the viability of human PSCs by lowering DNA damage and apoptosis, resulting in more efficient and reproducible downstream applications such as gene editing and directed differentiation. Furthermore, the method does not alter PSC characteristics after long-term culture and attenuates the growth advantage of abnormal subpopulations. This robust passaging method minimizes experimental error and reduces the rate of PSCs failing quality control of human PSC research and application.
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Affiliation(s)
- Kazutoshi Takahashi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Chikako Okubo
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Michiko Nakamura
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Mio Iwasaki
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Yuka Kawahara
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Tsuyoshi Tabata
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Yousuke Miyamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Shinya Yamanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
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49
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Ellis MW, Riaz M, Huang Y, Anderson CW, Luo J, Park J, Lopez CA, Batty LD, Gibson KH, Qyang Y. Epigallocatechin gallate facilitates extracellular elastin fiber formation in induced pluripotent stem cell derived vascular smooth muscle cells for tissue engineering. J Mol Cell Cardiol 2022; 163:167-174. [PMID: 34979103 PMCID: PMC8920537 DOI: 10.1016/j.yjmcc.2021.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 02/03/2023]
Abstract
Tissue engineered vascular grafts possess several advantages over synthetic or autologous grafts, including increased availability and reduced rates of infection and thrombosis. Engineered grafts constructed from human induced pluripotent stem cell derivatives further offer enhanced reproducibility in graft production. One notable obstacle to clinical application of these grafts is the lack of elastin in the vessel wall, which would serve to endow compliance in addition to mechanical strength. This study establishes the ability of the polyphenol compound epigallocatechin gallate, a principal component of green tea, to facilitate the extracellular formation of elastin fibers in vascular smooth muscle cells derived from human induced pluripotent stem cells. Further, this study describes the creation of a doxycycline-inducible elastin expression system to uncouple elastin production from vascular smooth muscle cell proliferative capacity to permit fiber formation in conditions conducive to robust tissue engineering.
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Affiliation(s)
- Matthew W Ellis
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06511, USA; Yale Stem Cell Center, New Haven, CT 06520, USA; Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06519, USA
| | - Muhammad Riaz
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06511, USA; Yale Stem Cell Center, New Haven, CT 06520, USA
| | - Yan Huang
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06511, USA; Yale Stem Cell Center, New Haven, CT 06520, USA
| | - Christopher W Anderson
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06511, USA; Yale Stem Cell Center, New Haven, CT 06520, USA; Department of Pathology, Yale University, New Haven, CT 06520, USA
| | - Jiesi Luo
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06511, USA; Yale Stem Cell Center, New Haven, CT 06520, USA
| | - Jinkyu Park
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06511, USA; Yale Stem Cell Center, New Haven, CT 06520, USA
| | - Colleen A Lopez
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06511, USA; Yale Stem Cell Center, New Haven, CT 06520, USA
| | - Luke D Batty
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06511, USA; Yale Stem Cell Center, New Haven, CT 06520, USA; Department of Pathology, Yale University, New Haven, CT 06520, USA
| | - Kimberley H Gibson
- Center for Cellular and Molecular Imaging: Electron Microscopy, Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yibing Qyang
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06511, USA; Yale Stem Cell Center, New Haven, CT 06520, USA; Department of Pathology, Yale University, New Haven, CT 06520, USA; Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520, USA.
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50
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Reijns MAM, Parry DA, Williams TC, Nadeu F, Hindshaw RL, Rios Szwed DO, Nicholson MD, Carroll P, Boyle S, Royo R, Cornish AJ, Xiang H, Ridout K, Schuh A, Aden K, Palles C, Campo E, Stankovic T, Taylor MS, Jackson AP. Signatures of TOP1 transcription-associated mutagenesis in cancer and germline. Nature 2022; 602:623-631. [PMID: 35140396 PMCID: PMC8866115 DOI: 10.1038/s41586-022-04403-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/04/2022] [Indexed: 12/24/2022]
Abstract
The mutational landscape is shaped by many processes. Genic regions are vulnerable to mutation but are preferentially protected by transcription-coupled repair1. In microorganisms, transcription has been demonstrated to be mutagenic2,3; however, the impact of transcription-associated mutagenesis remains to be established in higher eukaryotes4. Here we show that ID4-a cancer insertion-deletion (indel) mutation signature of unknown aetiology5 characterized by short (2 to 5 base pair) deletions -is due to a transcription-associated mutagenesis process. We demonstrate that defective ribonucleotide excision repair in mammals is associated with the ID4 signature, with mutations occurring at a TNT sequence motif, implicating topoisomerase 1 (TOP1) activity at sites of genome-embedded ribonucleotides as a mechanistic basis. Such TOP1-mediated deletions occur somatically in cancer, and the ID-TOP1 signature is also found in physiological settings, contributing to genic de novo indel mutations in the germline. Thus, although topoisomerases protect against genome instability by relieving topological stress6, their activity may also be an important source of mutations in the human genome.
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Affiliation(s)
- Martin A M Reijns
- Disease Mechanisms, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
| | - David A Parry
- Disease Mechanisms, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Thomas C Williams
- Disease Mechanisms, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- Biomedical Genomics, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Rebecca L Hindshaw
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Diana O Rios Szwed
- Disease Mechanisms, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Michael D Nicholson
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Paula Carroll
- Disease Mechanisms, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Shelagh Boyle
- Genome Regulation, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Romina Royo
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Hang Xiang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Kate Ridout
- Department of Oncology, University of Oxford, Oxford, UK
| | - Anna Schuh
- Department of Oncology, University of Oxford, Oxford, UK
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
- Departament de Fonaments Clínics, Universitat de Barcelona, Barcelona, Spain
| | - Tatjana Stankovic
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Martin S Taylor
- Biomedical Genomics, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
| | - Andrew P Jackson
- Disease Mechanisms, MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
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