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Tapia-Rojas S, García-Paitán M, Rosario-Chavarri JD, Santiani A, Alvarez-Vega S, Amiel-Pérez J, Mayanga-Herrera A. Medicinal plant extracts interfere in gastric cancer stem cells fluorescence-based assays. Saudi J Biol Sci 2024; 31:104000. [PMID: 38706720 PMCID: PMC11066463 DOI: 10.1016/j.sjbs.2024.104000] [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: 11/15/2023] [Revised: 04/06/2024] [Accepted: 04/14/2024] [Indexed: 05/07/2024] Open
Abstract
Fluorescence is used in various biological assays due to its high sensitivity, versatility, and precision. In recent years, studies using medicinal plant extracts have increased. However, fluorescence-based assays could be biased by plant metabolites autofluorescence. To address this issue, this study investigated the interference caused by methanolic extracts and chloroform fractions of three medicinal plants in three fluorescence-based assays on gastric cancer stem cells(CSC): resazurin reduction, confocal microscopy, and flow cytometry. CSC were isolated based on CD44 surface marker, incubated with methanolic extracts and chloroform fractions of Buddleja incana, Dracontium spruceanum, Piper aduncum. Resazurin assay evidenced that CSC exposed to extracts and fractions from the three plants showed significant differences in relative fluorescence units (RFU) levels (p < 0.001) compared to the unexposed groups after a 3-hour incubation. In addition, DMSO-treated CSC exposed to extracts and fractions had significantly lower fluorescence levels than living ones, but higher than extracts and fractions without cells. In confocal microscopy, cancer stem cells exposed to extracts and fractions of B. incana and P. aduncum were observed in the same emission spectra of the CSC markers. In flow cytometry, CSC exposed to extracts and fractions without any fluorescent dyes were detected in the double positive quadrants for CSC markers (CD44+/CD133 + ). Among the three plants, D. spruceanum exhibited the least interference. These results show that methanolic extracts and chloroform fractions contain autofluorescent metabolites that interfere with fluorescence-based assays. These results highlight the importance of a prior evaluation for possible fluorescence interference to avoid interpretation biases in fluorescence assays.
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Affiliation(s)
- Salyoc Tapia-Rojas
- Cell Culture and Immunology Lab, Universidad Científica del Sur, Antigua Panamericana Sur km 19, Lima, 15067, Perú
| | | | - Jorge Del Rosario-Chavarri
- Plant Biology System Lab, Pontificia Universidad Católica de Chile, Libertador Bernardo O’higgins AV. 340, Santiago, 8331150, Chile
| | - Alexei Santiani
- Animal Reproduction Lab, Universidad Nacional Mayor de San Marcos, Circunvalación Av 28, San Borja, Lima, 15021, Perú
| | - Santiago Alvarez-Vega
- Cell Culture and Immunology Lab, Universidad Científica del Sur, Antigua Panamericana Sur km 19, Lima, 15067, Perú
| | - José Amiel-Pérez
- Cell Culture and Immunology Lab, Universidad Científica del Sur, Antigua Panamericana Sur km 19, Lima, 15067, Perú
| | - Ana Mayanga-Herrera
- Cell Culture and Immunology Lab, Universidad Científica del Sur, Antigua Panamericana Sur km 19, Lima, 15067, Perú
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2
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Chowdhury MM, Zimmerman S, Leeson H, Nefzger CM, Mar JC, Laslett A, Polo JM, Wolvetang E, Cooper-White JJ. Superior Induced Pluripotent Stem Cell Generation through Phactr3-Driven Mechanomodulation of Both Early and Late Phases of Cell Reprogramming. Biomater Res 2024; 28:0025. [PMID: 38774128 PMCID: PMC11106629 DOI: 10.34133/bmr.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/25/2024] [Indexed: 05/24/2024] Open
Abstract
Human cell reprogramming traditionally involves time-intensive, multistage, costly tissue culture polystyrene-based cell culture practices that ultimately produce low numbers of reprogrammed cells of variable quality. Previous studies have shown that very soft 2- and 3-dimensional hydrogel substrates/matrices (of stiffnesses ≤ 1 kPa) can drive ~2× improvements in human cell reprogramming outcomes. Unfortunately, these similarly complex multistage protocols lack intrinsic scalability, and, furthermore, the associated underlying molecular mechanisms remain to be fully elucidated, limiting the potential to further maximize reprogramming outcomes. In screening the largest range of polyacrylamide (pAAm) hydrogels of varying stiffness to date (1 kPa to 1.3 MPa), we have found that a medium stiffness gel (~100 kPa) increased the overall number of reprogrammed cells by up to 10-fold (10×), accelerated reprogramming kinetics, improved both early and late phases of reprogramming, and produced induced pluripotent stem cells (iPSCs) having more naïve characteristics and lower remnant transgene expression, compared to the gold standard tissue culture polystyrene practice. Functionalization of these pAAm hydrogels with poly-l-dopamine enabled, for the first-time, continuous, single-step reprogramming of fibroblasts to iPSCs on hydrogel substrates (noting that even the tissue culture polystyrene practice is a 2-stage process). Comparative RNA sequencing analyses coupled with experimental validation revealed that a novel reprogramming regulator, protein phosphatase and actin regulator 3, up-regulated under the gel condition at a very early time point, was responsible for the observed enhanced reprogramming outcomes. This study provides a novel culture protocol and substrate for continuous hydrogel-based cell reprogramming and previously unattained clarity of the underlying mechanisms via which substrate stiffness modulates reprogramming kinetics and iPSC quality outcomes.
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Affiliation(s)
- Mohammad Mahfuz Chowdhury
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Hannah Leeson
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Jessica Cara Mar
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
- Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Andrew Laslett
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jose Maria Polo
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute and the Australian Regenerative Medicine Institute,
Monash University, Clayton, VIC 3800, Australia
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences,
The University of Adelaide, Adelaide, SA 5005, Australia
| | - Ernst Wolvetang
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Justin John Cooper-White
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
- School of Chemical Engineering, Andrew N. Liveris Building,
The University of Queensland, St. Lucia, QLD 4072, Australia
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3
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Chen KG, Johnson KR, Park K, Maric D, Yang F, Liu WF, Fann YC, Mallon BS, Robey PG. Resistance to Naïve and Formative Pluripotency Conversion in RSeT Human Embryonic Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580778. [PMID: 38410444 PMCID: PMC10896352 DOI: 10.1101/2024.02.16.580778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
One of the most important properties of human embryonic stem cells (hESCs) is related to their primed and naïve pluripotent states. Our previous meta-analysis indicates the existence of heterogeneous pluripotent states derived from diverse naïve protocols. In this study, we have characterized a commercial medium (RSeT)-based pluripotent state under various growth conditions. Notably, RSeT hESCs can circumvent hypoxic growth conditions as required by naïve hESCs, in which some RSeT cells (e.g., H1 cells) exhibit much lower single cell plating efficiency, having altered or much retarded cell growth under both normoxia and hypoxia. Evidently, hPSCs lack many transcriptomic hallmarks of naïve and formative pluripotency (a phase between naive and primed states). Integrative transcriptome analysis suggests our primed and RSeT hESCs are close to the early stage of post-implantation embryos, similar to the previously reported primary hESCs and early hESC cultures. Moreover, RSeT hESCs did not express naïve surface markers such as CD75, SUSD2, and CD130 at a significant level. Biochemically, RSeT hESCs exhibit a differential dependency of FGF2 and co-independency of both Janus kinase (JAK) and TGFβ signaling in a cell-line-specific manner. Thus, RSeT hESCs represent a previously unrecognized pluripotent state downstream of formative pluripotency. Our data suggest that human naïve pluripotent potentials may be restricted in RSeT medium. Hence, this study provides new insights into pluripotent state transitions in vitro.
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Affiliation(s)
| | - Kory R. Johnson
- Intramural IT and Bioinformatics Program, Bethesda, Maryland 20892, USA
| | - Kyeyoon Park
- NIH Stem Cell Unit, Bethesda, Maryland 20892, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Forest Yang
- NIH Stem Cell Unit, Bethesda, Maryland 20892, USA
| | - Wen Fang Liu
- NIH Stem Cell Unit, Bethesda, Maryland 20892, USA
| | - Yang C. Fann
- Intramural IT and Bioinformatics Program, Bethesda, Maryland 20892, USA
| | | | - Pamela G. Robey
- Skeletal Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, USA
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4
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Hu B, Jin H, Shi Y, Yu H, Wu X, Wang S, Zhang K. Single-cell RNA-Seq reveals the earliest lineage specification and X chromosome dosage compensation in bovine preimplantation embryos. FASEB J 2024; 38:e23492. [PMID: 38363564 DOI: 10.1096/fj.202302035rr] [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: 10/08/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
Lineage specification and X chromosome dosage compensation are two crucial biological processes that occur during preimplantation embryonic development. Although extensively studied in mice, the timing and regulation of these processes remain elusive in other species, including humans. Previous studies have suggested conserved principles of human and bovine early development. This study aims to provide fundamental insights into these programs and the regulation using a bovine embryo model by employing single-cell transcriptomics and genome editing approaches. The study analyzes the transcriptomes of 286 individual cells and reveals that bovine trophectoderm/inner cell mass transcriptomes diverge at the early blastocyst stage, after cavitation but before blastocyst expansion. The study also identifies transcriptomic markers and provides the timing of lineage specification events in the bovine embryo. Importantly, we find that SOX2 is required for the first cell decision program in bovine embryos. Moreover, the study shows the occurrence of X chromosome dosage compensation from morula to late blastocyst and reveals that this compensation results from downregulation of X-linked genes in female embryonic cells. The transcriptional atlas generated by this study is expected to be widely useful in improving our understanding of mammalian early embryo development.
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Affiliation(s)
- Bingjie Hu
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Jin
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Shi
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haotian Yu
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaotong Wu
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shaohua Wang
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kun Zhang
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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5
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Chen KG, Park K, Maric D, Johnson KR, Robey PG, Mallon BS. Metabolic Quadrivalency in RSeT Human Embryonic Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.21.581486. [PMID: 38496581 PMCID: PMC10942463 DOI: 10.1101/2024.02.21.581486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
One of the most important properties of human embryonic stem cells (hESCs) is related to their pluripotent states. In our recent study, we identified a previously unrecognized pluripotent state induced by RSeT medium. This state makes primed hESCs resistant to conversion to naïve pluripotent state. In this study, we have further characterized the metabolic features in these RSeT hESCs, including metabolic gene expression, metabolomic analysis, and various functional assays. The commonly reported metabolic modes include glycolysis or both glycolysis and oxidative phosphorylation (i.e., metabolic bivalency) in pluripotent stem cells. However, besides the presence of metabolic bivalency, RSeT hESCs exhibited a unique metabolome with additional fatty acid oxidation and imbalanced nucleotide metabolism. This metabolic quadrivalency is linked to hESC growth independent of oxygen tension and restricted capacity for naïve reprogramming in these cells. Thus, this study provides new insights into pluripotent state transitions and metabolic stress-associated hPSC growth in vitro.
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Affiliation(s)
- Kevin G. Chen
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kyeyoon Park
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kory R. Johnson
- Intramural IT and Bioinformatics Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Pamela G. Robey
- Skeletal Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Barbara S. Mallon
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
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6
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Sinenko SA, Tomilin AN. Metabolic control of induced pluripotency. Front Cell Dev Biol 2024; 11:1328522. [PMID: 38274274 PMCID: PMC10808704 DOI: 10.3389/fcell.2023.1328522] [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: 10/26/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
Pluripotent stem cells of the mammalian epiblast and their cultured counterparts-embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs)-have the capacity to differentiate in all cell types of adult organisms. An artificial process of reactivation of the pluripotency program in terminally differentiated cells was established in 2006, which allowed for the generation of induced pluripotent stem cells (iPSCs). This iPSC technology has become an invaluable tool in investigating the molecular mechanisms of human diseases and therapeutic drug development, and it also holds tremendous promise for iPSC applications in regenerative medicine. Since the process of induced reprogramming of differentiated cells to a pluripotent state was discovered, many questions about the molecular mechanisms involved in this process have been clarified. Studies conducted over the past 2 decades have established that metabolic pathways and retrograde mitochondrial signals are involved in the regulation of various aspects of stem cell biology, including differentiation, pluripotency acquisition, and maintenance. During the reprogramming process, cells undergo major transformations, progressing through three distinct stages that are regulated by different signaling pathways, transcription factor networks, and inputs from metabolic pathways. Among the main metabolic features of this process, representing a switch from the dominance of oxidative phosphorylation to aerobic glycolysis and anabolic processes, are many critical stage-specific metabolic signals that control the path of differentiated cells toward a pluripotent state. In this review, we discuss the achievements in the current understanding of the molecular mechanisms of processes controlled by metabolic pathways, and vice versa, during the reprogramming process.
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Affiliation(s)
- Sergey A. Sinenko
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
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7
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Dror I, Chitiashvili T, Tan SYX, Cano CT, Sahakyan A, Markaki Y, Chronis C, Collier AJ, Deng W, Liang G, Sun Y, Afasizheva A, Miller J, Xiao W, Black DL, Ding F, Plath K. XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells. Cell 2024; 187:110-129.e31. [PMID: 38181737 PMCID: PMC10783549 DOI: 10.1016/j.cell.2023.11.033] [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: 12/21/2020] [Revised: 04/01/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024]
Abstract
X chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X chromosome in cis to mediate gene silencing chromosome-wide. In female naive human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration, and XCI does not occur, raising questions about XIST's function. We found that XIST spreads across the X chromosome and induces dampening of X-linked gene expression in naive hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences in autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.
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Affiliation(s)
- Iris Dror
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tsotne Chitiashvili
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shawn Y X Tan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Clara T Cano
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anna Sahakyan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yolanda Markaki
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Constantinos Chronis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Amanda J Collier
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Weixian Deng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Guohao Liang
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA
| | - Yu Sun
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anna Afasizheva
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jarrett Miller
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wen Xiao
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fangyuan Ding
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA; Department of Developmental and Cell Biology, Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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8
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Tran ANT, Kim HY, Oh SY, Kim HS. CD49f and CD146: A Possible Crosstalk Modulates Adipogenic Differentiation Potential of Mesenchymal Stem Cells. Cells 2023; 13:55. [PMID: 38201259 PMCID: PMC10778538 DOI: 10.3390/cells13010055] [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: 10/21/2023] [Revised: 12/07/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND The lack of appropriate mesenchymal stem cells (MSCs) selection methods has given the challenges for standardized harvesting, processing, and phenotyping procedures of MSCs. Genetic engineering coupled with high-throughput proteomic studies of MSC surface markers arises as a promising strategy to identify stem cell-specific markers. However, the technical limitations are the key factors making it less suitable to provide an appropriate starting material for the screening platform. A more accurate, easily accessible approach is required to solve the issues. METHODS This study established a high-throughput screening strategy with forward versus side scatter gating to identify the adipogenesis-associated markers of bone marrow-derived MSCs (BMSCs) and tonsil-derived MSCs (TMSCs). We classified the MSC-derived adipogenic differentiated cells into two clusters: lipid-rich cells as side scatter (SSC)-high population and lipid-poor cells as SSC-low population. By screening the expression of 242 cell surface proteins, we identified the surface markers which exclusively found in lipid-rich subpopulation as the specific markers for BMSCs and TMSCs. RESULTS High-throughput screening of the expression of 242 cell surface proteins indicated that CD49f and CD146 were specific for BMSCs and TMSCs. Subsequent immunostaining confirmed the consistent specific expression of CD49f and CD146 and in BMSCs and TMSCs. Enrichment of MSCs by CD49f and CD146 surface markers demonstrated that the simultaneous expression of CD49f and CD146 is required for adipogenesis and osteogenesis of mesenchymal stem cells. Furthermore, the fate decision of MSCs from different sources is regulated by distinct responses of cells to differentiation stimulations despite sharing a common CD49f+CD146+ immunophenotype. CONCLUSIONS We established an accurate, robust, transgene-free method for screening adipogenesis associated cell surface proteins. This provided a valuable tool to investigate MSC-specific markers. Additionally, we showed a possible crosstalk between CD49f and CD146 modulates the adipogenesis of MSCs.
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Affiliation(s)
- An Nguyen-Thuy Tran
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Ewha Womans University, Seoul 07985, Republic of Korea; (A.N.-T.T.); (H.Y.K.)
- Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ha Yeong Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Ewha Womans University, Seoul 07985, Republic of Korea; (A.N.-T.T.); (H.Y.K.)
| | - Se-Young Oh
- Department of Convergence Medicine, Ewha Womans University Mokdong Hospital, Ewha Womans University, Seoul 07985, Republic of Korea;
| | - Han Su Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Ewha Womans University, Seoul 07985, Republic of Korea; (A.N.-T.T.); (H.Y.K.)
- Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
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9
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Yan T, Boatner LM, Cui L, Tontonoz PJ, Backus KM. Defining the Cell Surface Cysteinome Using Two-Step Enrichment Proteomics. JACS AU 2023; 3:3506-3523. [PMID: 38155636 PMCID: PMC10751780 DOI: 10.1021/jacsau.3c00707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
The plasma membrane proteome is a rich resource of functionally important and therapeutically relevant protein targets. Distinguished by high hydrophobicity, heavy glycosylation, disulfide-rich sequences, and low overall abundance, the cell surface proteome remains undersampled in established proteomic pipelines, including our own cysteine chemoproteomics platforms. Here, we paired cell surface glycoprotein capture with cysteine chemoproteomics to establish a two-stage enrichment method that enables chemoproteomic profiling of cell Surface Cysteinome. Our "Cys-Surf" platform captures >2,800 total membrane protein cysteines in 1,046 proteins, including 1,907 residues not previously captured by bulk proteomic analysis. By pairing Cys-Surf with an isotopic chemoproteomic readout, we uncovered 821 total ligandable cysteines, including known and novel sites. Cys-Surf also robustly delineates redox-sensitive cysteines, including cysteines prone to activation-dependent changes to cysteine oxidation state and residues sensitive to addition of exogenous reductants. Exemplifying the capacity of Cys-Surf to delineate functionally important cysteines, we identified a redox sensitive cysteine in the low-density lipoprotein receptor (LDLR) that impacts both the protein localization and uptake of low-density lipoprotein (LDL) particles. Taken together, the Cys-Surf platform, distinguished by its two-stage enrichment paradigm, represents a tailored approach to delineate the functional and therapeutic potential of the plasma membrane cysteinome.
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Affiliation(s)
- Tianyang Yan
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Lisa M. Boatner
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Liujuan Cui
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, Los Angeles, California 90095, United States
| | - Peter J. Tontonoz
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, Los Angeles, California 90095, United States
| | - Keriann M. Backus
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- DOE
Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, United States
- Jonsson
Comprehensive Cancer Center, UCLA, Los Angeles, California 90095, United States
- Eli
and Edythe
Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, California 90095, United States
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10
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Ware CB, Jonlin EC, Anderson DJ, Cavanaugh C, Hesson J, Sidhu S, Cook S, Villagomez-Olea G, Horwitz MS, Wang Y, Mathieu J. Derivation of Naïve Human Embryonic Stem Cells Using a CHK1 Inhibitor. Stem Cell Rev Rep 2023; 19:2980-2990. [PMID: 37702917 PMCID: PMC10662141 DOI: 10.1007/s12015-023-10613-2] [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] [Accepted: 08/21/2023] [Indexed: 09/14/2023]
Abstract
Embryonic development is a continuum in vivo. Transcriptional analysis can separate established human embryonic stem cells (hESC) into at least four distinct developmental pluripotent stages, two naïve and two primed, early and late relative to the intact epiblast. In this study we primarily show that exposure of frozen human blastocysts to an inhibitor of checkpoint kinase 1 (CHK1) upon thaw greatly enhances establishment of karyotypically normal late naïve hESC cultures. These late naïve cells are plastic and can be toggled back to early naïve and forward to early primed pluripotent stages. The early primed cells are transcriptionally equivalent to the post inner cell mass intermediate (PICMI) stage seen one day following transfer of human blastocysts into in vitro culture and are stable at an earlier stage than conventional primed hESC.
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Affiliation(s)
- Carol B Ware
- Department of Comparative Medicine, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Erica C Jonlin
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Donovan J Anderson
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Christopher Cavanaugh
- Department of Comparative Medicine, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Jennifer Hesson
- Department of Comparative Medicine, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Sonia Sidhu
- Department of Comparative Medicine, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Savannah Cook
- Department of Comparative Medicine, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Guillermo Villagomez-Olea
- Department of Comparative Medicine, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Laboratory of Tissue Engineering and Regenerative Medicine, Facultad de Odontología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Marshall S Horwitz
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Yuliang Wang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
- Department of Computer Science and Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Julie Mathieu
- Department of Comparative Medicine, University of Washington, Seattle, WA, 98195, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA.
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11
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Tangherloni A, Riva SG, Myers B, Buffa FM, Cazzaniga P. MAGNETO: Cell type marker panel generator from single-cell transcriptomic data. J Biomed Inform 2023; 147:104510. [PMID: 37797704 DOI: 10.1016/j.jbi.2023.104510] [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: 02/28/2023] [Revised: 09/12/2023] [Accepted: 09/29/2023] [Indexed: 10/07/2023]
Abstract
Single-cell RNA sequencing experiments produce data useful to identify different cell types, including uncharacterized and rare ones. This enables us to study the specific functional roles of these cells in different microenvironments and contexts. After identifying a (novel) cell type of interest, it is essential to build succinct marker panels, composed of a few genes referring to cell surface proteins and clusters of differentiation molecules, able to discriminate the desired cells from the other cell populations. In this work, we propose a fully-automatic framework called MAGNETO, which can help construct optimal marker panels starting from a single-cell gene expression matrix and a cell type identity for each cell. MAGNETO builds effective marker panels solving a tailored bi-objective optimization problem, where the first objective regards the identification of the genes able to isolate a specific cell type, while the second conflicting objective concerns the minimization of the total number of genes included in the panel. Our results on three public datasets show that MAGNETO can identify marker panels that identify the cell populations of interest better than state-of-the-art approaches. Finally, by fine-tuning MAGNETO, our results demonstrate that it is possible to obtain marker panels with different specificity levels.
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Affiliation(s)
- Andrea Tangherloni
- Department of Computing Sciences, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Bocconi Institute for Data Science and Analytics, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Department of Human and Social Sciences, University of Bergamo, Piazzale S. Agostino 2, Bergamo, 24129, Italy.
| | - Simone G Riva
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Brynelle Myers
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Francesca M Buffa
- Department of Computing Sciences, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Bocconi Institute for Data Science and Analytics, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, United Kingdom
| | - Paolo Cazzaniga
- Department of Human and Social Sciences, University of Bergamo, Piazzale S. Agostino 2, Bergamo, 24129, Italy; Bicocca Bioinformatics, Biostatistics, and Bioimaging Centre - B4, Via Follereau 3, Vedano al Lambro, 20854, Italy
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12
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Yan T, Boatner LM, Cui L, Tontonoz P, Backus KM. Defining the Cell Surface Cysteinome using Two-step Enrichment Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562832. [PMID: 37904933 PMCID: PMC10614875 DOI: 10.1101/2023.10.17.562832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
The plasma membrane proteome is a rich resource of functional and therapeutically relevant protein targets. Distinguished by high hydrophobicity, heavy glycosylation, disulfide-rich sequences, and low overall abundance, the cell surface proteome remains undersampled in established proteomic pipelines, including our own cysteine chemoproteomics platforms. Here we paired cell surface glycoprotein capture with cysteine chemoproteomics to establish a two-stage enrichment method that enables chemoproteomic profiling of cell Surface Cysteinome. Our "Cys-Surf" platform captures >2,800 total membrane protein cysteines in 1,046 proteins, including 1,907 residues not previously captured by bulk proteomic analysis. By pairing Cys-Surf with an isotopic chemoproteomic readout, we uncovered 821 total ligandable cysteines, including known and novel sites. Cys-Surf also robustly delineates redox-sensitive cysteines, including cysteines prone to activation-dependent changes to cysteine oxidation state and residues sensitive to addition of exogenous reductants. Exemplifying the capacity of Cys-Surf to delineate functionally important cysteines, we identified a redox sensitive cysteine in the low-density lipoprotein receptor (LDLR) that impacts both the protein localization and uptake of LDL particles. Taken together, the Cys-Surf platform, distinguished by its two-stage enrichment paradigm, represents a tailored approach to delineate the functional and therapeutic potential of the plasma membrane cysteinome.
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Affiliation(s)
- Tianyang Yan
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
| | - Lisa M. Boatner
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
| | - Liujuan Cui
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles; Los Angeles, CA 90095, USA
| | - Peter Tontonoz
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles; Los Angeles, CA 90095, USA
| | - Keriann M. Backus
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095 (USA)
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095 (USA)
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095 (USA)
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13
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Liu R, Wubulikasimu Z, Cai R, Meng F, Cui Q, Zhou Y, Li Y. NAT10-mediated N4-acetylcytidine mRNA modification regulates self-renewal in human embryonic stem cells. Nucleic Acids Res 2023; 51:8514-8531. [PMID: 37497776 PMCID: PMC10484679 DOI: 10.1093/nar/gkad628] [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: 10/05/2022] [Revised: 07/05/2023] [Accepted: 07/15/2023] [Indexed: 07/28/2023] Open
Abstract
NAT10-catalyzed N4-acetylcytidine (ac4C) has emerged as a vital post-transcriptional modulator on the coding transcriptome by promoting mRNA stability. However, its role in mammalian development remains unclear. Here, we found that NAT10 expression positively correlates with pluripotency in vivo and in vitro. High throughput ac4C-targeted RNA immunoprecipitation sequencing (ac4C-RIP-seq), NaCNBH3-based chemical ac4C sequencing (ac4C-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays revealed noticeable ac4C modifications in transcriptome of hESCs, among which transcripts encoding core pluripotency transcription factors are favorable targets of ac4C modification. Further validation assays demonstrate that genetic inactivation of NAT10, the ac4C writer enzyme, led to ac4C level decrease on target genes, promoted the core pluripotency regulator OCT4 (POU5F1) transcript decay, and finally impaired self-renewal and promoted early differentiation in hESCs. Together, our work presented here elucidates a previously unrecognized interconnectivity between the core pluripotent transcriptional network for the maintenance of human ESC self-renewal and NAT10-catalyzed ac4C RNA epigenetic modification.
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Affiliation(s)
- Rucong Liu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
- Department of Biomedical Informatics, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Zibaguli Wubulikasimu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Runze Cai
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Fanyi Meng
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Qinghua Cui
- Department of Biomedical Informatics, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Yuan Zhou
- Department of Biomedical Informatics, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Yang Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
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14
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Patterson B, Yang B, Tanaka Y, Kim KY, Cakir B, Xiang Y, Kim J, Wang S, Park IH. Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations. SCIENCE ADVANCES 2023; 9:eadf2245. [PMID: 37540754 PMCID: PMC10403202 DOI: 10.1126/sciadv.adf2245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 07/06/2023] [Indexed: 08/06/2023]
Abstract
Three-dimensional (3D) genomics shows immense promise for studying X chromosome inactivation (XCI) by interrogating changes to the X chromosomes' 3D states. Here, we sought to characterize the 3D state of the X chromosome in naïve and primed human pluripotent stem cells (hPSCs). Using chromatin tracing, we analyzed X chromosome folding conformations in these cells with megabase genomic resolution. X chromosomes in female naïve hPSCs exhibit folding conformations similar to the active X chromosome (Xa) and the inactive X chromosome (Xi) in somatic cells. However, naïve X chromosomes do not exhibit the chromatin compaction typically associated with these somatic X chromosome states. In H7 naïve human embryonic stem cells, XIST accumulation observed on damaged X chromosomes demonstrates the potential for naïve hPSCs to activate XCI-related mechanisms. Overall, our findings provide insight into the X chromosome status of naïve hPSCs with a single-chromosome resolution and are critical in understanding the unique epigenetic regulation in early embryonic cells.
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Affiliation(s)
- Benjamin Patterson
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Bing Yang
- Department of Genetics, and Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yoshiaki Tanaka
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Bilal Cakir
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yangfei Xiang
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jonghun Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Siyuan Wang
- Department of Genetics, and Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
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15
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Glass MR, Waxman EA, Yamashita S, Lafferty M, Beltran A, Farah T, Patel NK, Matoba N, Ahmed S, Srivastava M, Drake E, Davis LT, Yeturi M, Sun K, Love MI, Hashimoto-Torii K, French DL, Stein JL. Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.550873. [PMID: 37546772 PMCID: PMC10402155 DOI: 10.1101/2023.07.28.550873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Background Reproducibility of human cortical organoid (hCO) phenotypes remains a concern for modeling neurodevelopmental disorders. While guided hCO protocols reproducibly generate cortical cell types in multiple cell lines at one site, variability across sites using a harmonized protocol has not yet been evaluated. We present an hCO cross-site reproducibility study examining multiple phenotypes. Methods Three independent research groups generated hCOs from one induced pluripotent stem cell (iPSC) line using a harmonized miniaturized spinning bioreactor protocol. scRNA-seq, 3D fluorescent imaging, phase contrast imaging, qPCR, and flow cytometry were used to characterize the 3 month differentiations across sites. Results In all sites, hCOs were mostly cortical progenitor and neuronal cell types in reproducible proportions with moderate to high fidelity to the in vivo brain that were consistently organized in cortical wall-like buds. Cross-site differences were detected in hCO size and morphology. Differential gene expression showed differences in metabolism and cellular stress across sites. Although iPSC culture conditions were consistent and iPSCs remained undifferentiated, primed stem cell marker expression prior to differentiation correlated with cell type proportions in hCOs. Conclusions We identified hCO phenotypes that are reproducible across sites using a harmonized differentiation protocol. Previously described limitations of hCO models were also reproduced including off-target differentiations, necrotic cores, and cellular stress. Improving our understanding of how stem cell states influence early hCO cell types may increase reliability of hCO differentiations. Cross-site reproducibility of hCO cell type proportions and organization lays the foundation for future collaborative prospective meta-analytic studies modeling neurodevelopmental disorders in hCOs.
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Affiliation(s)
- Madison R Glass
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Elisa A Waxman
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Satoshi Yamashita
- Center for Neuroscience Research, Children's National Hospital, Washington, DC
| | - Michael Lafferty
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alvaro Beltran
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Tala Farah
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Niyanta K Patel
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Nana Matoba
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sara Ahmed
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Mary Srivastava
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Emma Drake
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Liam T Davis
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Meghana Yeturi
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kexin Sun
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Departments of Pediatrics, and Pharmacology & Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC
| | - Kazue Hashimoto-Torii
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Deborah L French
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jason L Stein
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
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16
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Cuesta-Gomez N, Verhoeff K, Dadheech N, Dang T, Jasra IT, de Leon MB, Pawlick R, Marfil-Garza B, Anwar P, Razavy H, Zapata-Morin PA, Jickling G, Thiesen A, O'Gorman D, Kallos MS, Shapiro AMJ. Suspension culture improves iPSC expansion and pluripotency phenotype. Stem Cell Res Ther 2023; 14:154. [PMID: 37280707 DOI: 10.1186/s13287-023-03382-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 05/18/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Induced pluripotent stem cells (iPSCs) offer potential to revolutionize regenerative medicine as a renewable source for islets, dopaminergic neurons, retinal cells, and cardiomyocytes. However, translation of these regenerative cell therapies requires cost-efficient mass manufacturing of high-quality human iPSCs. This study presents an improved three-dimensional Vertical-Wheel® bioreactor (3D suspension) cell expansion protocol with comparison to a two-dimensional (2D planar) protocol. METHODS Sendai virus transfection of human peripheral blood mononuclear cells was used to establish mycoplasma and virus free iPSC lines without common genetic duplications or deletions. iPSCs were then expanded under 2D planar and 3D suspension culture conditions. We comparatively evaluated cell expansion capacity, genetic integrity, pluripotency phenotype, and in vitro and in vivo pluripotency potential of iPSCs. RESULTS Expansion of iPSCs using Vertical-Wheel® bioreactors achieved 93.8-fold (IQR 30.2) growth compared to 19.1 (IQR 4.0) in 2D (p < 0.0022), the largest expansion potential reported to date over 5 days. 0.5 L Vertical-Wheel® bioreactors achieved similar expansion and further reduced iPSC production cost. 3D suspension expanded cells had increased proliferation, measured as Ki67+ expression using flow cytometry (3D: 69.4% [IQR 5.5%] vs. 2D: 57.4% [IQR 10.9%], p = 0.0022), and had a higher frequency of pluripotency marker (Oct4+Nanog+Sox2+) expression (3D: 94.3 [IQR 1.4] vs. 2D: 52.5% [IQR 5.6], p = 0.0079). q-PCR genetic analysis demonstrated a lack of duplications or deletions at the 8 most commonly mutated regions within iPSC lines after long-term passaging (> 25). 2D-cultured cells displayed a primed pluripotency phenotype, which transitioned to naïve after 3D-culture. Both 2D and 3D cells were capable of trilineage differentiation and following teratoma, 2D-expanded cells generated predominantly solid teratomas, while 3D-expanded cells produced more mature and predominantly cystic teratomas with lower Ki67+ expression within teratomas (3D: 16.7% [IQR 3.2%] vs.. 2D: 45.3% [IQR 3.0%], p = 0.002) in keeping with a naïve phenotype. CONCLUSION This study demonstrates nearly 100-fold iPSC expansion over 5-days using our 3D suspension culture protocol in Vertical-Wheel® bioreactors, the largest cell growth reported to date. 3D expanded cells showed enhanced in vitro and in vivo pluripotency phenotype that may support more efficient scale-up strategies and safer clinical implementation.
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Affiliation(s)
- Nerea Cuesta-Gomez
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2T9, Canada
- Department of Surgery, University of Alberta, Edmonton, AB, T6G 2B7, Canada
| | - Kevin Verhoeff
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2T9, Canada
- Department of Surgery, University of Alberta, Edmonton, AB, T6G 2B7, Canada
| | - Nidheesh Dadheech
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2T9, Canada.
- Department of Surgery, University of Alberta, Edmonton, AB, T6G 2B7, Canada.
| | - Tiffany Dang
- Pharmaceutical Production Research Facility (PPRF), Schulich School of Engineering, University of Calgary, Calgary, AB, T2N1N4, Canada
- Department of Biomedical Engineering, Schulich School of Engineering, University of Calgary, Calgary, AB, T2N1N4, Canada
| | - Ila Tewari Jasra
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2T9, Canada
- Department of Surgery, University of Alberta, Edmonton, AB, T6G 2B7, Canada
| | - Mario Bermudez de Leon
- Department of Molecular Biology, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, 64720, Monterrey, Nuevo Leon, Mexico
| | - Rena Pawlick
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2T9, Canada
- Department of Surgery, University of Alberta, Edmonton, AB, T6G 2B7, Canada
| | - Braulio Marfil-Garza
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2T9, Canada
- National Institute of Medical Sciences and Nutrition Salvador Zubiran, 14080, Mexico City, Mexico
- CHRISTUS-LatAm Hub - Excellence and Innovation Center, 66260, Monterrey, Mexico
| | - Perveen Anwar
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2T9, Canada
- Department of Surgery, University of Alberta, Edmonton, AB, T6G 2B7, Canada
| | - Haide Razavy
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2T9, Canada
- Department of Surgery, University of Alberta, Edmonton, AB, T6G 2B7, Canada
| | - Patricio Adrián Zapata-Morin
- Laboratory of Mycology and Phytopathology, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, 66451, San Nicolás de los Garza, Nuevo León, Mexico
| | - Glen Jickling
- Department of Medicine, Division of Neurology, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Aducio Thiesen
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2B7, Canada
| | - Doug O'Gorman
- Clinical Islet Transplant Program, University of Alberta, Edmonton, AB, T6G 2J3, Canada
| | - Michael S Kallos
- Pharmaceutical Production Research Facility (PPRF), Schulich School of Engineering, University of Calgary, Calgary, AB, T2N1N4, Canada
- Department of Biomedical Engineering, Schulich School of Engineering, University of Calgary, Calgary, AB, T2N1N4, Canada
| | - A M James Shapiro
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2T9, Canada.
- Department of Surgery, University of Alberta, Edmonton, AB, T6G 2B7, Canada.
- Clinical Islet Transplant Program, University of Alberta, Edmonton, AB, T6G 2J3, Canada.
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17
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Vallabhaneni H, Shah T, Shah P, Hursh DA. Suspension culture on microcarriers and as aggregates enables expansion and differentiation of pluripotent stem cells (PSCs). Cytotherapy 2023:S1465-3249(23)00933-7. [PMID: 37256241 DOI: 10.1016/j.jcyt.2023.05.002] [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: 12/19/2022] [Revised: 04/02/2023] [Accepted: 05/08/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND AIMS Human pluripotent stem cells (PSCs) hold a great promise for promoting regenerative medical therapies due to their ability to generate multiple mature cell types and for their high expansion potential. However, cell therapies require large numbers of cells to achieve desired therapeutic effects, and traditional two-dimensional static culture methods cannot meet the required production demand for cellular therapies. One solution to this problem is scaling up expansion of PSCs in bioreactors using culture strategies such as growing cells on microcarriers or as aggregates in suspension culture. METHODS In this study, we directly compared PSC expansion and quality parameters in microcarrier- and aggregate-cultures grown in single-use vertical-wheel bioreactors. RESULTS We showed comparable expansion of cells on microcarriers and as aggregates by day 6 with a cell density reaching 2.2 × 106 cells/mL and 1.8 × 106 cells/mL and a fold-expansion of 22- and 18-fold, respectively. PSCs cultured on microcarriers and as aggregates were comparable with parallel two-dimensional cultures and with each other in terms of pluripotency marker expression and retention of other pluripotency characteristics as well as differentiation potential into three germ layers, neural precursor cells and cardiomyocytes. CONCLUSIONS Our study did not demonstrate a clear advantage between the two three-dimensional methods for the quality parameters assessed. This analysis adds support to the use of bioreactor systems for large scale expansion of PSCs, demonstrating that the cells retain key characteristics of PSCs and differentiation potential in suspension culture.
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Affiliation(s)
- Haritha Vallabhaneni
- Division of Cellular and Gene Therapies, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA.
| | - Tanvi Shah
- Division of Cellular and Gene Therapies, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Parthiv Shah
- Division of Cellular and Gene Therapies, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Deborah A Hursh
- Division of Cellular and Gene Therapies, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA.
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18
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Zhou J, Hu J, Wang Y, Gao S. Induction and application of human naive pluripotency. Cell Rep 2023; 42:112379. [PMID: 37043354 DOI: 10.1016/j.celrep.2023.112379] [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: 06/25/2022] [Revised: 12/18/2022] [Accepted: 03/26/2023] [Indexed: 04/13/2023] Open
Abstract
Over the past few decades, many attempts have been made to capture different states of pluripotency in vitro. Naive and primed pluripotent stem cells, corresponding to the pluripotency states of pre- and post-implantation epiblasts, respectively, have been well characterized in mice and can be interconverted in vitro. Here, we summarize the recently reported strategies to generate human naive pluripotent stem cells in vitro. We discuss their applications in studies of regulatory mechanisms involved in early developmental processes, including identification of molecular features, X chromosome inactivation modeling, transposable elements regulation, metabolic characteristics, and cell fate regulation, as well as potential for extraembryonic differentiation and blastoid construction for embryogenesis modeling. We further discuss the naive pluripotency-related research, including 8C-like cell establishment and disease modeling. We also highlight limitations of current naive pluripotency studies, such as imperfect culture conditions and inadequate responsiveness to differentiation signals.
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Affiliation(s)
- Jianfeng Zhou
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Jindian Hu
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yixuan Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Shaorong Gao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
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19
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Zorzan I, Betto RM, Rossignoli G, Arboit M, Drusin A, Corridori C, Martini P, Martello G. Chemical conversion of human conventional PSCs to TSCs following transient naive gene activation. EMBO Rep 2023; 24:e55235. [PMID: 36847616 PMCID: PMC10074076 DOI: 10.15252/embr.202255235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 03/01/2023] Open
Abstract
In human embryos, naive pluripotent cells of the inner cell mass (ICM) generate epiblast, primitive endoderm and trophectoderm (TE) lineages, whence trophoblast cells derive. In vitro, naive pluripotent stem cells (PSCs) retain this potential and efficiently generate trophoblast stem cells (TSCs), while conventional PSCs form TSCs at low efficiency. Transient histone deacetylase and MEK inhibition combined with LIF stimulation is used to chemically reset conventional to naive PSCs. Here, we report that chemical resetting induces the expression of both naive and TSC markers and of placental imprinted genes. A modified chemical resetting protocol allows for the fast and efficient conversion of conventional PSCs into TSCs, entailing shutdown of pluripotency genes and full activation of the trophoblast master regulators, without induction of amnion markers. Chemical resetting generates a plastic intermediate state, characterised by co-expression of naive and TSC markers, after which cells steer towards one of the two fates in response to the signalling environment. The efficiency and rapidity of our system will be useful to study cell fate transitions and to generate models of placental disorders.
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Affiliation(s)
- Irene Zorzan
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | | | | | - Mattia Arboit
- Department of Biology, University of Padua, Padua, Italy
| | - Andrea Drusin
- Department of Biology, University of Padua, Padua, Italy
| | | | - Paolo Martini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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20
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Heidari Khoei H, Javali A, Kagawa H, Sommer TM, Sestini G, David L, Slovakova J, Novatchkova M, Scholte Op Reimer Y, Rivron N. Generating human blastoids modeling blastocyst-stage embryos and implantation. Nat Protoc 2023; 18:1584-1620. [PMID: 36792779 DOI: 10.1038/s41596-023-00802-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 12/08/2022] [Indexed: 02/17/2023]
Abstract
Human early development sets the stage for embryonic and adult life but remains difficult to investigate. A solution came from the ability of stem cells to organize into structures resembling preimplantation embryos-blastocysts-that we termed blastoids. This embryo model is available in unlimited numbers and could thus support scientific and medical advances. However, its predictive power depends on how faithfully it recapitulates the blastocyst. Here, we describe how we formed human blastoids that (1) efficiently achieve the morphology of the blastocyst and (2) form lineages according to the pace and sequence of blastocyst development, (3) ultimately forming cells that transcriptionally reflect the blastocyst (preimplantation stage). We employ three different commercially available 96- and 24-well microwell plates with results similar to our custom-made ones, and show that blastoids form in clinical in vitro fertilization medium and can be cryopreserved for shipping. Finally, we explain how blastoids replicate the directional process of implantation into endometrial organoids, specifically when these are hormonally stimulated. It takes 4 d for human blastoids to form and 10 d to prepare the endometrial implantation assay, and we have cultured blastoids up to 6 d (time-equivalent of day 13). On the basis of our experience, we anticipate that a person with ~1 year of human pluripotent stem cell culture experience and of organoid culture should be able to perform the protocol. Altogether, blastoids offer an opportunity to establish scientific and biomedical discovery programs for early pregnancy, and an ethical alternative to the use of embryos.
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Affiliation(s)
- Heidar Heidari Khoei
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Alok Javali
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Harunobu Kagawa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Theresa Maria Sommer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Giovanni Sestini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Laurent David
- Université de Nantes, CHU Nantes, Inserm, CR2TI, UMR 1064, Nantes, France.,Université de Nantes, CHU Nantes, Inserm, CNRS, BioCore, Nantes, France
| | - Jana Slovakova
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), IMBA Stem Cell Core Facility (ISCCF), Vienna BioCenter (VBC), Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.,Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Yvonne Scholte Op Reimer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Nicolas Rivron
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
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21
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Koo KM, Go YH, Kim SM, Kim CD, Do JT, Kim TH, Cha HJ. Label-free and non-destructive identification of naïve and primed embryonic stem cells based on differences in cellular metabolism. Biomaterials 2023; 293:121939. [PMID: 36521427 DOI: 10.1016/j.biomaterials.2022.121939] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/25/2022] [Accepted: 12/02/2022] [Indexed: 12/07/2022]
Abstract
Pluripotent stem cells (PSCs) exist in naïve or primed states based on their origin. For in vitro culture, these PSCs require different supplements and growth factors. However, owing to their similar phenotypic features, identifying both cell types without harming cellular functions is challenging. This study reports an electrochemical method that enables simple, label-free, and non-destructive detection of naïve embryonic stem cells (ESCs) derived from mouse ESCs, based on the differences in cellular metabolism. Two major metabolic pathways to generate adenosine triphosphate (ATP)-glycolysis and oxidative phosphorylation (OXPHOS)-were blocked, and it was found that mitochondrial energy generation is the origin of the strong electrochemical signals of naïve ESCs. The number of ESCs is quantified when mixed with primed ESCs or converted from naïve-primed switchable metastable ESCs. The mouse PSCs derived from doxycycline-inducible mouse embryonic fibroblasts (MEFs) are also sensitively identified among other cell types such as unconverted MEFs and primed PSCs. The developed sensing platform operates in a non-invasive and label-free manner. Thus, it can be useful in the development of stem cell-derived therapeutics.
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Affiliation(s)
- Kyeong-Mo Koo
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Young-Hyun Go
- Research Institute of Pharmaceutical Science, Seoul National University, Seoul, 08826, Republic of Korea; College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seong-Min Kim
- College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chang-Dae Kim
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biology, College of Animal Bioscience and Technology, Konkuk University, Seoul, Republic of Korea
| | - Tae-Hyung Kim
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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22
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Alves-Lopes JP, Wong FCK, Tang WWC, Gruhn WH, Ramakrishna NB, Jowett GM, Jahnukainen K, Surani MA. Specification of human germ cell fate with enhanced progression capability supported by hindgut organoids. Cell Rep 2023; 42:111907. [PMID: 36640324 DOI: 10.1016/j.celrep.2022.111907] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 10/04/2022] [Accepted: 12/09/2022] [Indexed: 01/07/2023] Open
Abstract
Human primordial germ cells (hPGCs), the precursors of sperm and eggs, are specified during weeks 2-3 after fertilization. Few studies on ex vivo and in vitro cultured human embryos reported plausible hPGCs on embryonic day (E) 12-13 and in an E16-17 gastrulating embryo. In vitro, hPGC-like cells (hPGCLCs) can be specified from the intermediary pluripotent stage or peri-gastrulation precursors. Here, we explore the broad spectrum of hPGCLC precursors and how different precursors impact hPGCLC development. We show that resetting precursors can give rise to hPGCLCs (rhPGCLCs) in response to BMP. Strikingly, rhPGCLCs co-cultured with human hindgut organoids progress at a pace reminiscent of in vivo hPGC development, unlike those derived from peri-gastrulation precursors. Moreover, rhPGCLC specification depends on both EOMES and TBXT, not just on EOMES as for peri-gastrulation hPGCLCs. Importantly, our study provides the foundation for developing efficient in vitro models of human gametogenesis.
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Affiliation(s)
- João Pedro Alves-Lopes
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK; NORDFERTIL Research Lab Stockholm, Childhood Cancer Research Unit, J9:30, Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, Visionsgatan 4, Solna, 17164 Stockholm, Sweden.
| | - Frederick C K Wong
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Walfred W C Tang
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Wolfram H Gruhn
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Navin B Ramakrishna
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK; Genome Institute of Singapore, A(∗)STAR, Biopolis, Singapore 138672, Singapore
| | - Geraldine M Jowett
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Kirsi Jahnukainen
- NORDFERTIL Research Lab Stockholm, Childhood Cancer Research Unit, J9:30, Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, Visionsgatan 4, Solna, 17164 Stockholm, Sweden; New Children's Hospital, Paediatric Research Centre, University of Helsinki and Helsinki University Hospital, Pl 281, 00029 Helsinki, Finland
| | - M Azim Surani
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
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23
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Maskalenka K, Alagöz G, Krueger F, Wright J, Rostovskaya M, Nakhuda A, Bendall A, Krueger C, Walker S, Scally A, Rugg-Gunn PJ. NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naïve pluripotent stem cells. Development 2023; 150:286291. [PMID: 36621005 PMCID: PMC10110494 DOI: 10.1242/dev.201155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/16/2022] [Indexed: 01/10/2023]
Abstract
Gene duplication events can drive evolution by providing genetic material for new gene functions, and they create opportunities for diverse developmental strategies to emerge between species. To study the contribution of duplicated genes to human early development, we examined the evolution and function of NANOGP1, a tandem duplicate of the transcription factor NANOG. We found that NANOGP1 and NANOG have overlapping but distinct expression profiles, with high NANOGP1 expression restricted to early epiblast cells and naïve-state pluripotent stem cells. Sequence analysis and epitope-tagging revealed that NANOGP1 is protein coding with an intact homeobox domain. The duplication that created NANOGP1 occurred earlier in primate evolution than previously thought and has been retained only in great apes, whereas Old World monkeys have disabled the gene in different ways, including homeodomain point mutations. NANOGP1 is a strong inducer of naïve pluripotency; however, unlike NANOG, it is not required to maintain the undifferentiated status of human naïve pluripotent cells. By retaining expression, sequence and partial functional conservation with its ancestral copy, NANOGP1 exemplifies how gene duplication and subfunctionalisation can contribute to transcription factor activity in human pluripotency and development.
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Affiliation(s)
| | - Gökberk Alagöz
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | - Joshua Wright
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Asif Nakhuda
- Gene Targeting Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | - Adam Bendall
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Christel Krueger
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Simon Walker
- Imaging Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
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24
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Karvas RM, David L, Theunissen TW. Accessing the human trophoblast stem cell state from pluripotent and somatic cells. Cell Mol Life Sci 2022; 79:604. [PMID: 36434136 PMCID: PMC9702929 DOI: 10.1007/s00018-022-04549-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/26/2022]
Abstract
Trophoblasts are specialized epithelial cells that perform critical functions during blastocyst implantation and mediate maternal-fetal communication during pregnancy. However, our understanding of human trophoblast biology remains limited since access to first-trimester placental tissue is scarce, especially between the first and fourth weeks of development. Moreover, animal models inadequately recapitulate unique aspects of human placental physiology. In the mouse system, the isolation of self-renewing trophoblast stem cells has provided a valuable in vitro model system of placental development, but the derivation of analogous human trophoblast stem cells (hTSCs) has remained elusive until recently. Building on a landmark study reporting the isolation of bona fide hTSCs from blastocysts and first-trimester placental tissues in 2018, several groups have developed methods to derive hTSCs from pluripotent and somatic cell sources. Here we review the biological and molecular properties that define authentic hTSCs, the trophoblast potential of distinct pluripotent states, and methods for inducing hTSCs in somatic cells by direct reprogramming. The generation of hTSCs from pluripotent and somatic cells presents exciting opportunities to elucidate the molecular mechanisms of human placental development and the etiology of pregnancy-related diseases.
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Affiliation(s)
- Rowan M Karvas
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Laurent David
- Nantes Université, CHU Nantes, INSERM, CR2TI, UMR 1064, 44000, Nantes, France.
- Nantes Université, CHU Nantes, INSERM, CNRS, Biocore, US 016, UAR 3556, 44000, Nantes, France.
| | - Thorold W Theunissen
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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25
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Waldhorn I, Turetsky T, Steiner D, Gil Y, Benyamini H, Gropp M, Reubinoff BE. Modeling sex differences in humans using isogenic induced pluripotent stem cells. Stem Cell Reports 2022; 17:2732-2744. [PMID: 36427492 PMCID: PMC9768579 DOI: 10.1016/j.stemcr.2022.10.017] [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: 11/15/2021] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 11/27/2022] Open
Abstract
Biological sex is a fundamental trait influencing development, reproduction, pathogenesis, and medical treatment outcomes. Modeling sex differences is challenging because of the masking effect of genetic variability and the hurdle of differentiating chromosomal versus hormonal effects. In this work we developed a cellular model to study sex differences in humans. Somatic cells from a mosaic Klinefelter syndrome patient were reprogrammed to generate isogenic induced pluripotent stem cell (iPSC) lines with different sex chromosome complements: 47,XXY/46,XX/46,XY/45,X0. Transcriptional analysis of the hiPSCs revealed novel and known genes and pathways that are sexually dimorphic in the pluripotent state and during early neural development. Female hiPSCs more closely resembled the naive pluripotent state than their male counterparts. Moreover, the system enabled differentiation between the contributions of X versus Y chromosome to these differences. Taken together, isogenic hiPSCs present a novel platform for studying sex differences in humans and bear potential to promote gender-specific medicine in the future.
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Affiliation(s)
- Ithai Waldhorn
- Hadassah Stem Cell Research Center, Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Tikva Turetsky
- Hadassah Stem Cell Research Center, Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Debora Steiner
- Hadassah Stem Cell Research Center, Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Yaniv Gil
- Hadassah Stem Cell Research Center, Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Hadar Benyamini
- Bioinformatics Unit of the I-CORE at Hebrew University and Hadassah Medical Center, Jerusalem, Israel
| | - Michal Gropp
- Hadassah Stem Cell Research Center, Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Benjamin E. Reubinoff
- Hadassah Stem Cell Research Center, Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel,Department of Obstetrics and Gynecology, Ein Kerem, Hadassah Hebrew University Medical Center, Jerusalem, Israel,Corresponding author
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26
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Ávila-González D, Portillo W, Barragán-Álvarez CP, Hernandez-Montes G, Flores-Garza E, Molina-Hernández A, Diaz-Martinez NE, Diaz NF. The human amniotic epithelium confers a bias to differentiate toward the neuroectoderm lineage in human embryonic stem cells. eLife 2022; 11:68035. [PMID: 35815953 PMCID: PMC9313526 DOI: 10.7554/elife.68035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/08/2022] [Indexed: 11/28/2022] Open
Abstract
Human embryonic stem cells (hESCs) derive from the epiblast and have pluripotent potential. To maintain the conventional conditions of the pluripotent potential in an undifferentiated state, inactivated mouse embryonic fibroblast (iMEF) is used as a feeder layer. However, it has been suggested that hESC under this conventional condition (hESC-iMEF) is an artifact that does not correspond to the in vitro counterpart of the human epiblast. Our previous studies demonstrated the use of an alternative feeder layer of human amniotic epithelial cells (hAECs) to derive and maintain hESC. We wondered if the hESC-hAEC culture could represent a different pluripotent stage than that of naïve or primed conventional conditions, simulating the stage in which the amniotic epithelium derives from the epiblast during peri-implantation. Like the conventional primed hESC-iMEF, hESC-hAEC has the same levels of expression as the ‘pluripotency core’ and does not express markers of naïve pluripotency. However, it presents a downregulation of HOX genes and genes associated with the endoderm and mesoderm, and it exhibits an increase in the expression of ectoderm lineage genes, specifically in the anterior neuroectoderm. Transcriptome analysis showed in hESC-hAEC an upregulated signature of genes coding for transcription factors involved in neural induction and forebrain development, and the ability to differentiate into a neural lineage was superior in comparison with conventional hESC-iMEF. We propose that the interaction of hESC with hAEC confers hESC a biased potential that resembles the anteriorized epiblast, which is predisposed to form the neural ectoderm.
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Affiliation(s)
- Daniela Ávila-González
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
| | - Wendy Portillo
- Behavioral and Cognitive Neurobiology, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Carla P Barragán-Álvarez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico
| | | | - Eliezer Flores-Garza
- Departamento de Biología Molecular y Biotecnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Anayansi Molina-Hernández
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
| | | | - Nestor F Diaz
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
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27
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Yu H, Chen M, Hu Y, Ou S, Yu X, Liang S, Li N, Yang M, Kong X, Sun C, Jia S, Zhang Q, Liu L, Hurst LD, Li R, Wang W, Wang J. Dynamic reprogramming of H3K9me3 at hominoid-specific retrotransposons during human preimplantation development. Cell Stem Cell 2022; 29:1031-1050.e12. [PMID: 35803225 DOI: 10.1016/j.stem.2022.06.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022]
Abstract
Reprogramming of H3K9me3-dependent heterochromatin is required for early development. How H3K9me3 is involved in early human development remains, however, largely unclear. Here, we resolve the temporal landscape of H3K9me3 during human preimplantation development and its regulation for diverse hominoid-specific retrotransposons. At the 8-cell stage, H3K9me3 reprogramming at hominoid-specific retrotransposons termed SINE-VNTR-Alu (SVA) facilitates interaction between certain promoters and SVA-derived enhancers, promoting the zygotic genome activation. In trophectoderm, de novo H3K9me3 domains prevent pluripotent transcription factors from binding to hominoid-specific retrotransposons-derived regulatory elements for inner cell mass (ICM)-specific genes. H3K9me3 re-establishment at SVA elements in the ICM is associated with higher transcription of DNA repair genes, when compared with naive human pluripotent stem cells. Our data demonstrate that species-specific reorganization of H3K9me3-dependent heterochromatin at hominoid-specific retrotransposons plays important roles during early human development, shedding light on how the epigenetic regulation for early development has evolved in mammals.
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Affiliation(s)
- Hanwen Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Manqi Chen
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Yuanlang Hu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Songbang Ou
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xiu Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Shiqi Liang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Niannian Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Mingzhu Yang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Xuhui Kong
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Chuanbo Sun
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Shiqi Jia
- The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Qingxue Zhang
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Laurence D Hurst
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Ruiqi Li
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Wenjun Wang
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Jichang Wang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.
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Haldar B, Hwang J, Narimatsu Y, Clausen H, Bellis SL. The incorrect use of CD75 as a synonym for ST6GAL1 has fostered the expansion of commercial "ST6GAL1" antibodies that do not recognize ST6GAL1. Glycobiology 2022; 32:736-742. [PMID: 35789385 PMCID: PMC9387509 DOI: 10.1093/glycob/cwac043] [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: 06/02/2022] [Revised: 06/02/2022] [Accepted: 06/27/2022] [Indexed: 12/24/2022] Open
Abstract
The ST6GAL1 Golgi sialyltransferase is upregulated in many human malignancies, however, detection of ST6GAL1 protein in cancer tissues has been hindered by the prior lack of antibodies. Recently, numerous commercial antibodies for ST6GAL1 have become available, however, many of these do not, in fact, recognize ST6GAL1. Decades ago, the CD75 cell-surface epitope was mistakenly suggested to be the same molecule as ST6GAL1. While this was rapidly disproven, the use of CD75 as a synonym for ST6GAL1 has persisted, particularly by companies selling "ST6GAL1" antibodies. CD75 is reportedly a sialylated epitope which appears to encompass a range of glycan structures and glycan carriers. In this study, we evaluated the LN1 and ZB55 monoclonal antibodies, which are advertised as ST6GAL1 antibodies but were initially developed as CD75-recognizing antibodies (neither was raised against ST6GAL1 as the immunogen). Importantly, the LN1 and ZB55 antibodies have been widely used by investigators, as well as the Human Protein Atlas database, to characterize ST6GAL1 expression. Herein, we used cell and mouse models with controlled expression of ST6GAL1 to compare LN1 and ZB55 with an extensively validated polyclonal antibody to ST6GAL1. We find that LN1 and ZB55 do not recognize ST6GAL1, and furthermore, these 2 antibodies recognize different targets. Additionally, we utilized the well-validated ST6GAL1 antibody to determine that ST6GAL1 is overexpressed in bladder cancer, a finding that contradicts prior studies which employed LN1 to suggest ST6GAL1 is downregulated in bladder cancer. Collectively, our studies underscore the need for careful validation of antibodies purported to recognize ST6GAL1.
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Affiliation(s)
- Barnita Haldar
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jihye Hwang
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yoshiki Narimatsu
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, DK-1165, Denmark
| | - Henrik Clausen
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, DK-1165, Denmark
| | - Susan L Bellis
- Corresponding author: Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, MCLM 350, 1918 University Boulevard, Birmingham, AL 35294, USA.
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29
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Kim KT, Oh JY, Park S, Kim SM, Benjamin P, Park IH, Chun KH, Chang YT, Cha HJ. Live isolation of naïve ESCs via distinct glucose metabolism and stored glycogen. Metab Eng 2022; 72:97-106. [DOI: 10.1016/j.ymben.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 10/18/2022]
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Yu X, Liang S, Chen M, Yu H, Li R, Qu Y, Kong X, Guo R, Zheng R, Izsvák Z, Sun C, Yang M, Wang J. Recapitulating early human development with 8C-like cells. Cell Rep 2022; 39:110994. [PMID: 35732112 DOI: 10.1016/j.celrep.2022.110994] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/21/2022] [Accepted: 05/31/2022] [Indexed: 11/17/2022] Open
Abstract
In human embryos, major zygotic genome activation (ZGA) initiates at the eight-cell (8C) stage. Abnormal ZGA leads to developmental defects and even contributes to the failure of human blastocyst formation or implantation. An in vitro cell model mimicking human 8C blastomeres would be invaluable to understanding the mechanisms regulating key biological events during early human development. Using the non-canonical promoter of LEUTX that putatively regulates human ZGA, we developed an 8C::mCherry reporter, which specifically marks the 8C state, to isolate rare 8C-like cells (8CLCs) from human preimplantation epiblast-like stem cells. The 8CLCs express a panel of human ZGA genes and have a unique transcriptome resembling that of the human 8C embryo. Using the 8C::mCherry reporter, we further optimize the chemical-based culture condition to increase and maintain the 8CLC population. Functionally, 8CLCs can self-organize to form blastocyst-like structures. The discovery and maintenance of 8CLCs provide an opportunity to recapitulate early human development.
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Affiliation(s)
- Xiu Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Shiqi Liang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Manqi Chen
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Hanwen Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Ruiqi Li
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yuliang Qu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Xuhui Kong
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Ruirui Guo
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Rongyan Zheng
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Zsuzsanna Izsvák
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Chuanbo Sun
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China.
| | - Mingzhu Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
| | - Jichang Wang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China.
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31
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Choi HS, Lee HM, Kim MK, Ryu CJ. Role of heat shock protein 60 in primed and naïve states of human pluripotent stem cells. PLoS One 2022; 17:e0269547. [PMID: 35679330 PMCID: PMC9182300 DOI: 10.1371/journal.pone.0269547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/23/2022] [Indexed: 11/19/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) exist in at least two distinct states in mammals: naïve pluripotency that represents several molecular characteristics in pre-implantation epiblast and primed pluripotency that corresponds to cells poised for differentiation in post-implantation epiblast. To identify and characterize the surface molecules that are necessary for the maintenance of naïve hPSCs, we generated a panel of murine monoclonal antibodies (MAbs) specific to the naïve state of hPSCs. Flow cytometry showed that N1-A4, one of the MAbs, bound to naïve hPSCs but not to primed hPSCs. Cell surface biotinylation and immunoprecipitation analysis identified that N1-A4 recognized heat shock protein 60 (HSP60) expressed on the surface of naïve hPSCs. Quantitative polymerase chain reaction (qPCR) analysis showed that HSP60 expression was rapidly downregulated during the embryoid body (EB) differentiation of primed hPSCs. HSP60 knockdown led to a decrease in the expression of pluripotency genes in primed hPSCs. HSP60 depletion also led to a decrease in the expression of pluripotency genes and representative naïve-state-specific genes in naïve hPSCs. Taken together, the results suggest that HSP60 is downregulated during differentiation of hPSCs and is required for the maintenance of pluripotency genes in both primed and naïve hPSCs, suggesting that HSP60 is a regulator of hPSC pluripotency and differentiation.
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Affiliation(s)
- Hong Seo Choi
- Department of Integrative Bioscience and Biotechnology, Institute of Anticancer Medicine Development, Sejong University, Seoul, Korea
| | - Hyun Min Lee
- Department of Integrative Bioscience and Biotechnology, Institute of Anticancer Medicine Development, Sejong University, Seoul, Korea
| | - Min Kyu Kim
- Department of Integrative Bioscience and Biotechnology, Institute of Anticancer Medicine Development, Sejong University, Seoul, Korea
| | - Chun Jeih Ryu
- Department of Integrative Bioscience and Biotechnology, Institute of Anticancer Medicine Development, Sejong University, Seoul, Korea
- * E-mail:
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32
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Romayor I, Herrera L, Burón M, Martin-Inaraja M, Prieto L, Etxaniz J, Inglés-Ferrándiz M, Pineda JR, Eguizabal C. A Comparative Study of Cell Culture Conditions during Conversion from Primed to Naive Human Pluripotent Stem Cells. Biomedicines 2022; 10:biomedicines10061358. [PMID: 35740381 PMCID: PMC9219795 DOI: 10.3390/biomedicines10061358] [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: 05/12/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 11/16/2022] Open
Abstract
The successful reprogramming of human somatic cells into induced pluripotent stem cells (hiPSCs) represented a turning point in the stem cell research field, owing to their ability to differentiate into any cell type with fewer ethical issues than human embryonic stem cells (hESCs). In mice, PSCs are thought to exist in a naive state, the cell culture equivalent of the immature pre-implantation embryo, whereas in humans, PSCs are in a primed state, which is a more committed pluripotent state than a naive state. Recent studies have focused on capturing a similar cell stage in human cells. Given their earlier developmental stage and therefore lack of cell-of-origin epigenetic memory, these cells would be better candidates for further re-differentiation, use in disease modeling, regenerative medicine and drug discovery. In this study, we used primed hiPSCs and hESCs to evaluate the successful establishment and maintenance of a naive cell stage using three different naive-conversion media, both in the feeder and feeder-free cells conditions. In addition, we compared the directed differentiation capacity of primed and naive cells into the three germ layers and characterized these different cell stages with commonly used pluripotent and lineage-specific markers. Our results show that, in general, naive culture NHSM medium (in both feeder and feeder-free systems) confers greater hiPSCs and hESCs viability and the highest naive pluripotency markers expression. This medium also allows better cell differentiation cells toward endoderm and mesoderm.
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Affiliation(s)
- Irene Romayor
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
| | - Lara Herrera
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
| | - Maria Burón
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
| | - Myriam Martin-Inaraja
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
| | - Laura Prieto
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
| | - Jone Etxaniz
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
| | - Marta Inglés-Ferrándiz
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
| | - Jose Ramon Pineda
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
- Achucarro Basque Center for Neuroscience, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Cristina Eguizabal
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
- Correspondence: ; Tel.: +34-944-007-151
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Cell fate roadmap of human primed-to-naive transition reveals preimplantation cell lineage signatures. Nat Commun 2022; 13:3147. [PMID: 35672317 PMCID: PMC9174176 DOI: 10.1038/s41467-022-30924-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Human naive pluripotent stem cells offer a unique window into early embryogenesis studies. Recent studies have reported several strategies to obtain cells in the naive state. However, cell fate transitions and the underlying mechanisms remain poorly understood. Here, by a dual fluorescent reporter system, we depict the cell fate dynamics from primed state toward naive pluripotency with ALPG activation followed by the activation of OCT4-distal enhancer. Integration of transcription profiles and the chromatin accessibility landscape reveals the appearance of primitive endoderm and trophectoderm signatures in the transitioning subpopulations, with the capacities for derivation of extra-embryonic endoderm and trophoblast stem cell lines, respectively. Furthermore, despite different fluorescent dynamics, all transitioning intermediates are capable of reaching the naive state with prolonged induction, showing their developmental plasticity and potential. Overall, our study describes a global cell roadmap toward naive pluripotency and provides hints for embryo modeling-related studies. Cell fate dynamics during human naïve pluripotency establishment remain poorly understood. Here, Bi et al. depict a high-resolution cell roadmap of the primed-to-naïve pluripotency transition, providing hints for embryo modeling-related studies.
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34
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Kumar B, Navarro C, Winblad N, Schell JP, Zhao C, Weltner J, Baqué-Vidal L, Salazar Mantero A, Petropoulos S, Lanner F, Elsässer SJ. Polycomb repressive complex 2 shields naïve human pluripotent cells from trophectoderm differentiation. Nat Cell Biol 2022; 24:845-857. [PMID: 35637409 PMCID: PMC9203276 DOI: 10.1038/s41556-022-00916-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 04/13/2022] [Indexed: 12/12/2022]
Abstract
The first lineage choice in human embryo development separates trophectoderm from the inner cell mass. Naïve human embryonic stem cells are derived from the inner cell mass and offer possibilities to explore how lineage integrity is maintained. Here, we discover that polycomb repressive complex 2 (PRC2) maintains naïve pluripotency and restricts differentiation to trophectoderm and mesoderm lineages. Through quantitative epigenome profiling, we found that a broad gain of histone H3 lysine 27 trimethylation (H3K27me3) is a distinct feature of naïve pluripotency. We define shared and naïve-specific bivalent promoters featuring PRC2-mediated H3K27me3 concomitant with H3K4me3. Naïve bivalency maintains key trophectoderm and mesoderm transcription factors in a transcriptionally poised state. Inhibition of PRC2 forces naïve human embryonic stem cells into an ‘activated’ state, characterized by co-expression of pluripotency and lineage-specific transcription factors, followed by differentiation into either trophectoderm or mesoderm lineages. In summary, PRC2-mediated repression provides a highly adaptive mechanism to restrict lineage potential during early human development. Two side-by-side papers report that H3K27me3 deposited by polycomb repressive complex 2 represents an epigenetic barrier that restricts naïve human pluripotent cell differentiation into alternative lineages including trophoblasts.
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35
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Large-Scale Analysis of X Inactivation Variations between Primed and Naïve Human Embryonic Stem Cells. Cells 2022; 11:cells11111729. [PMID: 35681423 PMCID: PMC9179337 DOI: 10.3390/cells11111729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/22/2022] [Accepted: 05/23/2022] [Indexed: 12/04/2022] Open
Abstract
X chromosome inactivation is a mammalian dosage compensation mechanism, where one of two X chromosomes is randomly inactivated in female cells. Previous studies have suggested that primed human embryonic stem cells (hESCs) maintain an eroded state of the X chromosome and do not express XIST, while in naïve transition, both XIST and the eroded X chromosome are reactivated. However, the pattern of chromosome X reactivation in naïve hESCs remains mainly unknown. In this study, we examine the variations in the status of X chromosome between primed and naïve hESCs by analyzing RNA sequencing samples from different studies. We show that most samples of naïve hESCs indeed reactivate XIST and there is an increase in gene expression levels on chromosome X. However, most of the naïve samples do not fully activate chromosome X in a uniform manner and present a distinct eroded pattern, probably as a result of XIST reactivation and initiation of re-inactivation of chromosome X. This large-scale analysis provides a higher-resolution description of the changes occurring in chromosome X during primed-to-naïve transition and emphasizes the importance of taking these variations into consideration when studying X inactivation in embryonic development.
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36
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Dong C, Fu S, Karvas RM, Chew B, Fischer LA, Xing X, Harrison JK, Popli P, Kommagani R, Wang T, Zhang B, Theunissen TW. A genome-wide CRISPR-Cas9 knockout screen identifies essential and growth-restricting genes in human trophoblast stem cells. Nat Commun 2022; 13:2548. [PMID: 35538076 PMCID: PMC9090837 DOI: 10.1038/s41467-022-30207-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/21/2022] [Indexed: 12/26/2022] Open
Abstract
The recent derivation of human trophoblast stem cells (hTSCs) provides a scalable in vitro model system of human placental development, but the molecular regulators of hTSC identity have not been systematically explored thus far. Here, we utilize a genome-wide CRISPR-Cas9 knockout screen to comprehensively identify essential and growth-restricting genes in hTSCs. By cross-referencing our data to those from similar genetic screens performed in other cell types, as well as gene expression data from early human embryos, we define hTSC-specific and -enriched regulators. These include both well-established and previously uncharacterized trophoblast regulators, such as ARID3A, GATA2, and TEAD1 (essential), and GCM1, PTPN14, and TET2 (growth-restricting). Integrated analysis of chromatin accessibility, gene expression, and genome-wide location data reveals that the transcription factor TEAD1 regulates the expression of many trophoblast regulators in hTSCs. In the absence of TEAD1, hTSCs fail to complete faithful differentiation into extravillous trophoblast (EVT) cells and instead show a bias towards syncytiotrophoblast (STB) differentiation, thus indicating that this transcription factor safeguards the bipotent lineage potential of hTSCs. Overall, our study provides a valuable resource for dissecting the molecular regulation of human placental development and diseases.
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Affiliation(s)
- Chen Dong
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Shuhua Fu
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rowan M Karvas
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Brian Chew
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Laura A Fischer
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Xiaoyun Xing
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Genetics, Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jessica K Harrison
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Genetics, Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Pooja Popli
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ramakrishna Kommagani
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ting Wang
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Genetics, Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Bo Zhang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Thorold W Theunissen
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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37
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Collier AJ, Bendall A, Fabian C, Malcolm AA, Tilgner K, Semprich CI, Wojdyla K, Nisi PS, Kishore K, Roamio Franklin VN, Mirshekar-Syahkal B, D’Santos C, Plath K, Yusa K, Rugg-Gunn PJ. Genome-wide screening identifies Polycomb repressive complex 1.3 as an essential regulator of human naïve pluripotent cell reprogramming. SCIENCE ADVANCES 2022; 8:eabk0013. [PMID: 35333572 PMCID: PMC8956265 DOI: 10.1126/sciadv.abk0013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Uncovering the mechanisms that establish naïve pluripotency in humans is crucial for the future applications of pluripotent stem cells including the production of human blastoids. However, the regulatory pathways that control the establishment of naïve pluripotency by reprogramming are largely unknown. Here, we use genome-wide screening to identify essential regulators as well as major impediments of human primed to naïve pluripotent stem cell reprogramming. We discover that factors essential for cell state change do not typically undergo changes at the level of gene expression but rather are repurposed with new functions. Mechanistically, we establish that the variant Polycomb complex PRC1.3 and PRDM14 jointly repress developmental and gene regulatory factors to ensure naïve cell reprogramming. In addition, small-molecule inhibitors of reprogramming impediments improve naïve cell reprogramming beyond current methods. Collectively, this work defines the principles controlling the establishment of human naïve pluripotency and also provides new insights into mechanisms that destabilize and reconfigure cell identity during cell state transitions.
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Affiliation(s)
- Amanda J. Collier
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Adam Bendall
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | | | - Andrew A. Malcolm
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Katarzyna Tilgner
- Stem Cell Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | | | - Kamal Kishore
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | - Clive D’Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Kosuke Yusa
- Stem Cell Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Stem Cell Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Peter J. Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
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38
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Xiang X, Tao Y, DiRusso J, Hsu FM, Zhang J, Xue Z, Pontis J, Trono D, Liu W, Clark AT. Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections. Nat Commun 2022; 13:463. [PMID: 35075135 PMCID: PMC8786967 DOI: 10.1038/s41467-022-28105-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/16/2021] [Indexed: 12/26/2022] Open
Abstract
Germ cells are essential to pass DNA from one generation to the next. In human reproduction, germ cell development begins with the specification of primordial germ cells (PGCs) and a failure to specify PGCs leads to human infertility. Recent studies have revealed that the transcription factor network required for PGC specification has diverged in mammals, and this has a significant impact on our understanding of human reproduction. Here, we reveal that the Hominidae-specific Transposable Elements (TEs) LTR5Hs, may serve as TEENhancers (TE Embedded eNhancers) to facilitate PGC specification. LTR5Hs TEENhancers become transcriptionally active during PGC specification both in vivo and in vitro with epigenetic reprogramming leading to increased chromatin accessibility, localized DNA demethylation, enrichment of H3K27ac, and occupation of key hPGC transcription factors. Inactivation of LTR5Hs TEENhancers with KRAB mediated CRISPRi has a significant impact on germ cell specification. In summary, our data reveals the essential role of Hominidae-specific LTR5Hs TEENhancers in human germ cell development. The transcription factor network required for primordial germ cell (PGC) specification is known to diverge in mammals. Here the authors show that hominidae-specific transposable element (TE) LTR5Hs becomes transcriptionally active during PGC specification, and LTR5Hs inactivation abrogates human PGC specification
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Affiliation(s)
- Xinyu Xiang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Yu Tao
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jonathan DiRusso
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Fei-Man Hsu
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jinchun Zhang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Ziwei Xue
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Julien Pontis
- School of Life Sciences, Ecole Polytechnique Fe ́de ́rale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fe ́de ́rale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Wanlu Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China. .,Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310029, China. .,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China. .,Alibaba-Zhejiang University Joint Research Center of Future DigitalHealthcare, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Amander T Clark
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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39
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Sheng J, Hod EA, Vlad G, Chavez A. Quantifying protein abundance on single cells using split-pool sequencing on DNA-barcoded antibodies for diagnostic applications. Sci Rep 2022; 12:884. [PMID: 35042926 PMCID: PMC8766443 DOI: 10.1038/s41598-022-04842-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/03/2022] [Indexed: 12/11/2022] Open
Abstract
Proteins play critical roles across all facets of biology, with their abundance frequently used as markers of cell identity and state. The most popular method for detecting proteins on single cells, flow cytometry, is limited by considerations of fluorescent spectral overlap. While mass cytometry (CyTOF) allows for the detection of upwards of 40 epitopes simultaneously, it requires local access to specialized instrumentation not commonly accessible to many laboratories. To overcome these limitations, we independently developed a method to quantify multiple protein targets on single cells without the need for specialty equipment other than access to widely available next generation sequencing (NGS) services. We demonstrate that this combinatorial indexing method compares favorably to traditional flow-cytometry, and allows over two dozen target proteins to be assayed at a time on single cells. To showcase the potential of the technique, we analyzed peripheral blood and bone marrow aspirates from human clinical samples, and identified pathogenic cellular subsets with high fidelity. The ease of use of this technique makes it a promising technology for high-throughput proteomics and for interrogating complex samples such as those from patients with leukemia.
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Affiliation(s)
- Jenny Sheng
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Eldad A Hod
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - George Vlad
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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40
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Abstract
Prior to implantation, the cells in the mammalian epiblast constitute a naïve pluripotent state, which is distinguished by absence of lineage priming, freedom from epigenetic restriction, and expression of a unique set of transcription factors. However, human embryonic stem cells (hESCs) derived under conventional conditions have exited this naïve state and acquired a more advanced "primed" pluripotent state that corresponds to the post-implantation epiblast. We have developed a cocktail comprising five kinase inhibitors and two growth factors (5i/L/A) that enables induction of defining features of naïve pluripotency in primed hESCs. These conditions can also be applied to induce naïve pluripotency in patient-specific induced pluripotent stem cells (iPSCs). Here, we provide a detailed protocol for inducing naïve pluripotency in primed hESCs and iPSCs and methods for the routine validation of naïve identity. We also outline the use of two fluorescent reporter systems to track acquisition of naïve identity in live cells: (a) a GFP reporter linked to an endogenous OCT4 allele in which the primed-specific proximal enhancer has been deleted (OCT4-ΔPE-GFP); and (b) a dual-color reporter system targeted to both alleles of an X-linked gene that reports on the status of the X chromosome in female cells (MECP2-GFP/tdTomato). The conditions described herein have given insight into various aspects of naïve human pluripotent stem cells (hPSCs), including their unique transposon transcription profile, X chromosome status, and extraembryonic potential.
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Affiliation(s)
- Laura A Fischer
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Shafqat A Khan
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Thorold W Theunissen
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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41
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Rugg-Gunn PJ. Flow Cytometry Analysis of Cell-Surface Markers to Identify Human Naïve Pluripotent Stem Cells. Methods Mol Biol 2022; 2416:257-265. [PMID: 34870841 DOI: 10.1007/978-1-0716-1908-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell-surface proteins provide excellent biomarkers to identify specific cell types and resolve heterogeneous cell populations. The analysis of cell-surface proteins by flow cytometry produces robust and quantitative information with single-cell resolution, and allows live target cells to be purified and characterized or re-cultured. Studies using antibody screens, proteomics, and candidate analysis have identified a comprehensive set of proteins that are expressed on the surface of naïve and primed human pluripotent stem cells. These findings have led to the development of suitable protein markers and antibodies to accurately distinguish between these two cell types. Here, a detailed protocol is provided that uses multi-color flow cytometry to analyze cell-surface protein expression in naïve and primed human pluripotent stem cells. This method enables the unambiguous identification of pluripotent cell types and the opportunity to sort target cells including during cell state transitions. The protocol can be combined to additionally investigate the expression of reporter genes and other informative features, such as DNA content.
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42
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Cinkornpumin JK, Hossain I, Pastor WA. Mapping Chromatin Accessibility in Human Naïve Pluripotent Stem Cells Using ATAC-Seq. Methods Mol Biol 2022; 2416:201-211. [PMID: 34870838 DOI: 10.1007/978-1-0716-1908-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Regulatory elements, such as promoters and enhancers, typically show reduced nucleosome occupancy, which is a feature that is commonly referred to as "open chromatin". The distribution of open chromatin sites can provide important clues about the transcription factors and regulatory networks that drive gene expression in a given cell. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a rapid and robust method for mapping open chromatin sites. ATAC-seq data can also discern the binding sites of nucleosomes and transcription factors. In this chapter, we describe how to produce and assess the quality of ATAC-seq libraries that are generated from naïve human pluripotent stem cells.
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Affiliation(s)
| | | | - William A Pastor
- Department of Biochemistry, McGill University, Montreal, QC, Canada.
- The Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada.
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43
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Sokka J, Yoshihara M, Kvist J, Laiho L, Warren A, Stadelmann C, Jouhilahti EM, Kilpinen H, Balboa D, Katayama S, Kyttälä A, Kere J, Otonkoski T, Weltner J, Trokovic R. CRISPR activation enables high-fidelity reprogramming into human pluripotent stem cells. Stem Cell Reports 2022; 17:413-426. [PMID: 35063129 PMCID: PMC8828555 DOI: 10.1016/j.stemcr.2021.12.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/19/2022] Open
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44
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Lea RA, McCarthy A, Boeing S, Fallesen T, Elder K, Snell P, Christie L, Adkins S, Shaikly V, Taranissi M, Niakan KK. KLF17 promotes human naïve pluripotency but is not required for its establishment. Development 2021; 148:272511. [PMID: 34661235 PMCID: PMC8645209 DOI: 10.1242/dev.199378] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 10/11/2021] [Indexed: 12/11/2022]
Abstract
Current knowledge of the transcriptional regulation of human pluripotency is incomplete, with lack of interspecies conservation observed. Single-cell transcriptomics analysis of human embryos previously enabled us to identify transcription factors, including the zinc-finger protein KLF17, that are enriched in the human epiblast and naïve human embryonic stem cells (hESCs). Here, we show that KLF17 is expressed coincident with the known pluripotency-associated factors NANOG and SOX2 across human blastocyst development. We investigate the function of KLF17 using primed and naïve hESCs for gain- and loss-of-function analyses. We find that ectopic expression of KLF17 in primed hESCs is sufficient to induce a naïve-like transcriptome and that KLF17 can drive transgene-mediated resetting to naïve pluripotency. This implies a role for KLF17 in establishing naïve pluripotency. However, CRISPR-Cas9-mediated knockout studies reveal that KLF17 is not required for naïve pluripotency acquisition in vitro. Transcriptome analysis of naïve hESCs identifies subtle effects on metabolism and signalling pathways following KLF17 loss of function, and possible redundancy with other KLF paralogues. Overall, we show that KLF17 is sufficient, but not necessary, for naïve pluripotency under the given in vitro conditions. Summary: Given that KLF17 was shown to be sufficient, but not necessary, to establish naïve pluripotent hESCs, KLF17 might function as a peripheral regulator of human pluripotent stem cells.
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Affiliation(s)
- Rebecca A Lea
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Afshan McCarthy
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stefan Boeing
- Bioinformatics and Biostatistics Service, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Todd Fallesen
- Crick Advanced Light Microscopy, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Kay Elder
- Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK
| | - Phil Snell
- Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK
| | | | - Sarah Adkins
- Assisted Reproduction and Gynaecology Centre, London W1G 6LP, UK
| | - Valerie Shaikly
- Assisted Reproduction and Gynaecology Centre, London W1G 6LP, UK
| | | | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,The Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
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45
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Keshet G, Benvenisty N. Large-scale analysis of imprinting in naive human pluripotent stem cells reveals recurrent aberrations and a potential link to FGF signaling. Stem Cell Reports 2021; 16:2520-2533. [PMID: 34597600 PMCID: PMC8514966 DOI: 10.1016/j.stemcr.2021.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 01/21/2023] Open
Abstract
Genomic imprinting is a parent-of-origin dependent monoallelic expression of genes. Previous studies showed that conversion of primed human pluripotent stem cells (hPSCs) into naive pluripotency is accompanied by genome-wide loss of methylation that includes imprinted loci. However, the extent of aberrant biallelic expression of imprinted genes is still unknown. Here, we analyze loss of imprinting (LOI) in a large cohort of both bulk and single-cell RNA sequencing samples of naive and primed hPSCs. We show that naive hPSCs exhibit high levels of non-random LOI, with bias toward paternally methylated imprinting control regions. Importantly, we show that different protocols used for the primed to naive conversion led to different extents of LOI, tightly correlated to FGF signaling. This analysis sheds light on the process of LOI occurring during the conversion to naive pluripotency and highlights the importance of these events when modeling disease and development or when utilizing the cells for therapy.
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Affiliation(s)
- Gal Keshet
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.
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46
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Yu S, Zhang R, Shen Q, Zhu Z, Zhang J, Wu X, Zhao W, Li N, Yang F, Wei H, Hua J. ESRRB Facilitates the Conversion of Trophoblast-Like Stem Cells From Induced Pluripotent Stem Cells by Directly Regulating CDX2. Front Cell Dev Biol 2021; 9:712224. [PMID: 34616727 PMCID: PMC8488167 DOI: 10.3389/fcell.2021.712224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
Porcine-induced pluripotent stem cells (piPSCs) could serve as a great model system for human stem cell preclinical research. However, the pluripotency gene network of piPSCs, especially the function for the core transcription factor estrogen-related receptor beta (ESRRB), was poorly understood. Here, we constructed ESRRB-overexpressing piPSCs (ESRRB-piPSCs). Compared with the control piPSCs (CON-piPSCs), the ESRRB-piPSCs showed flat, monolayered colony morphology. Moreover, the ESRRB-piPSCs showed greater chimeric capacity into trophectoderm than CON-piPSCs. We found that ESRRB could directly regulate the expressions of trophoblast stem cell (TSC)-specific markers, including KRT8, KRT18 and CDX2, through binding to their promoter regions. Mutational analysis proved that the N-terminus zinc finger domain is indispensable for ESRRB to regulate the TSC markers. Furthermore, this regulation needs the participation of OCT4. Accordingly, the cooperation between ESRRB and OCT4 facilitates the conversion from pluripotent state to the trophoblast-like state. Our results demonstrated a unique and crucial role of ESRRB in determining piPSCs fate, and shed new light on the molecular mechanism underlying the segregation of embryonic and extra-embryonic lineages.
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Affiliation(s)
- Shuai Yu
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Shaanxi, China
| | - Rui Zhang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Shaanxi, China
| | - Qiaoyan Shen
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Shaanxi, China
| | - Zhenshuo Zhu
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Shaanxi, China
| | - Juqing Zhang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Shaanxi, China
| | - Xiaolong Wu
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Shaanxi, China
| | - Wenxu Zhao
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Shaanxi, China
| | - Na Li
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Shaanxi, China
| | - Fan Yang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Shaanxi, China
| | - Hongjiang Wei
- Key Laboratory of Animal Gene Editing and Animal Cloning in Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Jinlian Hua
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Shaanxi, China
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47
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Becht E, Tolstrup D, Dutertre CA, Morawski PA, Campbell DJ, Ginhoux F, Newell EW, Gottardo R, Headley MB. High-throughput single-cell quantification of hundreds of proteins using conventional flow cytometry and machine learning. SCIENCE ADVANCES 2021; 7:eabg0505. [PMID: 34550730 PMCID: PMC8457665 DOI: 10.1126/sciadv.abg0505] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 07/14/2021] [Indexed: 06/03/2023]
Abstract
Modern immunologic research increasingly requires high-dimensional analyses to understand the complex milieu of cell types that comprise the tissue microenvironments of disease. To achieve this, we developed Infinity Flow combining hundreds of overlapping flow cytometry panels using machine learning to enable the simultaneous analysis of the coexpression patterns of hundreds of surface-expressed proteins across millions of individual cells. In this study, we demonstrate that this approach allows the comprehensive analysis of the cellular constituency of the steady-state murine lung and the identification of previously unknown cellular heterogeneity in the lungs of melanoma metastasis–bearing mice. We show that by using supervised machine learning, Infinity Flow enhances the accuracy and depth of clustering or dimensionality reduction algorithms. Infinity Flow is a highly scalable, low-cost, and accessible solution to single-cell proteomics in complex tissues.
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Affiliation(s)
- Etienne Becht
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel Tolstrup
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charles-Antoine Dutertre
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
- Program in Emerging Infectious Disease, Duke-NUS Medical School, Singapore, Singapore
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Center, Singapore 169856, Singapore
| | - Peter A. Morawski
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Daniel J. Campbell
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Florent Ginhoux
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Center, Singapore 169856, Singapore
- Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Evan W. Newell
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Raphael Gottardo
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark B. Headley
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
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48
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Osnato A, Brown S, Krueger C, Andrews S, Collier AJ, Nakanoh S, Quiroga Londoño M, Wesley BT, Muraro D, Brumm AS, Niakan KK, Vallier L, Ortmann D, Rugg-Gunn PJ. TGFβ signalling is required to maintain pluripotency of human naïve pluripotent stem cells. eLife 2021; 10:e67259. [PMID: 34463252 PMCID: PMC8410071 DOI: 10.7554/elife.67259] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/26/2021] [Indexed: 12/30/2022] Open
Abstract
The signalling pathways that maintain primed human pluripotent stem cells (hPSCs) have been well characterised, revealing a critical role for TGFβ/Activin/Nodal signalling. In contrast, the signalling requirements of naive human pluripotency have not been fully established. Here, we demonstrate that TGFβ signalling is required to maintain naive hPSCs. The downstream effector proteins - SMAD2/3 - bind common sites in naive and primed hPSCs, including shared pluripotency genes. In naive hPSCs, SMAD2/3 additionally bind to active regulatory regions near to naive pluripotency genes. Inhibiting TGFβ signalling in naive hPSCs causes the downregulation of SMAD2/3-target genes and pluripotency exit. Single-cell analyses reveal that naive and primed hPSCs follow different transcriptional trajectories after inhibition of TGFβ signalling. Primed hPSCs differentiate into neuroectoderm cells, whereas naive hPSCs transition into trophectoderm. These results establish that there is a continuum for TGFβ pathway function in human pluripotency spanning a developmental window from naive to primed states.
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Affiliation(s)
- Anna Osnato
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Stephanie Brown
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Christel Krueger
- Bioinformatics Group, The Babraham InstituteCambridgeUnited Kingdom
| | - Simon Andrews
- Bioinformatics Group, The Babraham InstituteCambridgeUnited Kingdom
| | - Amanda J Collier
- Epigenetics Programme, The Babraham InstituteCambridgeUnited Kingdom
| | - Shota Nakanoh
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
- Division of Embryology, National Institute for Basic BiologyOkazakiJapan
| | - Mariana Quiroga Londoño
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Brandon T Wesley
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Daniele Muraro
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
- Wellcome Sanger Institute, HinxtonCambridgeUnited Kingdom
| | - A Sophie Brumm
- Human Embryo and Stem Cell Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick InstituteLondonUnited Kingdom
- Centre for Trophoblast Research, University of CambridgeCambridgeUnited Kingdom
| | - Ludovic Vallier
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Daniel Ortmann
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Peter J Rugg-Gunn
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Epigenetics Programme, The Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast Research, University of CambridgeCambridgeUnited Kingdom
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49
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OCT4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human. Nat Commun 2021; 12:5123. [PMID: 34446700 PMCID: PMC8390644 DOI: 10.1038/s41467-021-25107-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
Understanding the molecular underpinnings of pluripotency is a prerequisite for optimal maintenance and application of embryonic stem cells (ESCs). While the protein-protein interactions of core pluripotency factors have been identified in mouse ESCs, their interactome in human ESCs (hESCs) has not to date been explored. Here we mapped the OCT4 interactomes in naïve and primed hESCs, revealing extensive connections to mammalian ATP-dependent nucleosome remodeling complexes. In naïve hESCs, OCT4 is associated with both BRG1 and BRM, the two paralog ATPases of the BAF complex. Genome-wide location analyses and genetic studies reveal that these two enzymes cooperate in a functionally redundant manner in the transcriptional regulation of blastocyst-specific genes. In contrast, in primed hESCs, OCT4 cooperates with BRG1 and SOX2 to promote chromatin accessibility at ectodermal genes. This work reveals how a common transcription factor utilizes differential BAF complexes to control distinct transcriptional programs in naïve and primed hESCs. Although the interactors of pluripotency factors have been identified in mouse embryonic stem cells (ESCs), their interactors in human ESCs remain unexplored. Here the authors map OCT4 protein interactions in naïve and primed human ESCs to find specific interactions with BAF subunits that promote an open chromatin architecture at blastocyst-associated genes and ectodermal genes, respectively.
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Amnion signals are essential for mesoderm formation in primates. Nat Commun 2021; 12:5126. [PMID: 34446705 PMCID: PMC8390679 DOI: 10.1038/s41467-021-25186-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/22/2021] [Indexed: 11/26/2022] Open
Abstract
Embryonic development is largely conserved among mammals. However, certain genes show divergent functions. By generating a transcriptional atlas containing >30,000 cells from post-implantation non-human primate embryos, we uncover that ISL1, a gene with a well-established role in cardiogenesis, controls a gene regulatory network in primate amnion. CRISPR/Cas9-targeting of ISL1 results in non-human primate embryos which do not yield viable offspring, demonstrating that ISL1 is critically required in primate embryogenesis. On a cellular level, mutant ISL1 embryos display a failure in mesoderm formation due to reduced BMP4 signaling from the amnion. Via loss of function and rescue studies in human embryonic stem cells we confirm a similar role of ISL1 in human in vitro derived amnion. This study highlights the importance of the amnion as a signaling center during primate mesoderm formation and demonstrates the potential of in vitro primate model systems to dissect the genetics of early human embryonic development. Human and murine embryonic development has disparities, highlighting the need for primate systems. Here, the authors construct a post-implantation transcriptional atlas from non-human primate embryos and show ISL1 controls a gene regulatory network in the amnion required for mesoderm formation.
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