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Boczki P, Colombo M, Weiner J, Rapöhn I, Lacher M, Kiess W, Hanschkow M, Körner A, Landgraf K. Inhibition of AHCY impedes proliferation and differentiation of mouse and human adipocyte progenitor cells. Adipocyte 2024; 13:2290218. [PMID: 38064408 PMCID: PMC10732623 DOI: 10.1080/21623945.2023.2290218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
S-adenosyl-homocysteine-hydrolase (AHCY) plays an important role in the methionine cycle regulating cellular methylation levels. AHCY has been reported to influence proliferation and differentiation processes in different cell types, e.g. in cancer cells and mouse embryonic stem cells. In the development of adipose tissue, both the proliferation and differentiation of adipocyte progenitor cells (APCs) are important processes, which in the context of obesity are often dysregulated. To assess whether AHCY might also be involved in cell proliferation and differentiation of APCs, we investigated the effect of reduced AHCY activity on human and mouse APCs in vitro. We show that the inhibition of AHCY using adenosine dialdehyde (AdOx) and the knockdown of AHCY using gene-specific siRNAs reduced APC proliferation and number. Inhibition of AHCY further reduced APC differentiation into mature adipocytes and the expression of adipogenic differentiation markers. Global DNA methylation profiling in human APCs revealed that inhibition of AHCY is associated with alterations in CpG methylation levels of genes involved in fat cell differentiation and pathways related to cellular growth. Our findings suggest that AHCY is necessary for the maintenance of APC proliferation and differentiation and inhibition of AHCY alters DNA methylation processes leading to a dysregulation of the expression of genes involved in the regulation of these processes.
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Affiliation(s)
- Paula Boczki
- Center for Pediatric Research Leipzig (CPL), Hospital for Children & Adolescents, University of Leipzig, Leipzig, Germany
| | - Marco Colombo
- Center for Pediatric Research Leipzig (CPL), Hospital for Children & Adolescents, University of Leipzig, Leipzig, Germany
| | - Juliane Weiner
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Inka Rapöhn
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Martin Lacher
- Department of Pediatric Surgery, University of Leipzig, Leipzig, Germany
| | - Wieland Kiess
- Center for Pediatric Research Leipzig (CPL), Hospital for Children & Adolescents, University of Leipzig, Leipzig, Germany
| | - Martha Hanschkow
- Center for Pediatric Research Leipzig (CPL), Hospital for Children & Adolescents, University of Leipzig, Leipzig, Germany
| | - Antje Körner
- Center for Pediatric Research Leipzig (CPL), Hospital for Children & Adolescents, University of Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Kathrin Landgraf
- Center for Pediatric Research Leipzig (CPL), Hospital for Children & Adolescents, University of Leipzig, Leipzig, Germany
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Li Z, Hu T, Li R, Li J, Wang Y, Li Y, Lin Y, Wang Y, Jiani X. Effect of DHCR7 on adipocyte differentiation in goats. Anim Biotechnol 2024; 35:2298399. [PMID: 38157229 DOI: 10.1080/10495398.2023.2298399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Cholesterol is regarded as a signaling molecule in regulating the metabolism and function of fat cells, in which 7-Dehydrocholesterol reductase (DHCR7) is a key enzyme that catalyzes the conversion of 7-dehydrocholesterol to cholesterol, however, the exact function of DHCR7 in goat adipocytes remains unknown. Here, the effect of DHCR7 on the formation of subcutaneous and intramuscular fat in goats was investigated in vitro, and the result indicated that the mRNA level of DHCR7 showed a gradual downward trend in subcutaneous adipogenesis, but an opposite trend in intramuscular adipogenesis. In the process of subcutaneous preadipocytes differentiation, overexpression of DHCR7 inhibited the expression of adipocytes differentiation marker genes (CEBP/α, CEBP/β, SREBP1 and AP2), lipid metabolism-related genes (AGPAT6, FASN, SCD1 and LPL), and the lipid accumulation. However, in intramuscular preadipocyte differentiation, DHCR7 overexpression showed a promoting effect on adipocyte differentiation marker genes (CEBP/α, CEBP/β, PPARγ and SREBP1) and lipid metabolism-related genes (GPAM, AGPAT6, DGAT1 and SCD1) expression, and on lipid accumulation. In summary, our work demonstrated that DHCR7 played an important role in regulating adipogenic differentiation and lipid metabolism in preadipocytes in goats, which is of great significance for uncovering the underlying molecular mechanism of adipocyte differentiation and improving goat meat quality.
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Affiliation(s)
- Zhibin Li
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Tingting Hu
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ruiwen Li
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jinlan Li
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Youli Wang
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yanyan Li
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yaqiu Lin
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yong Wang
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xing Jiani
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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Wang J, Yang L, Du Y, Wang J, Weng Q, Liu X, Nicholson E, Xin M, Lu QR. BRG1 programs PRC2-complex repression and controls oligodendrocyte differentiation and remyelination. J Cell Biol 2024; 223:e202310143. [PMID: 38652118 DOI: 10.1083/jcb.202310143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/01/2024] [Accepted: 03/28/2024] [Indexed: 04/25/2024] Open
Abstract
Chromatin-remodeling protein BRG1/SMARCA4 is pivotal for establishing oligodendrocyte (OL) lineage identity. However, its functions for oligodendrocyte-precursor cell (OPC) differentiation within the postnatal brain and during remyelination remain elusive. Here, we demonstrate that Brg1 loss profoundly impairs OPC differentiation in the brain with a comparatively lesser effect in the spinal cord. Moreover, BRG1 is critical for OPC remyelination after injury. Integrative transcriptomic/genomic profiling reveals that BRG1 exhibits a dual role by promoting OPC differentiation networks while repressing OL-inhibitory cues and proneuronal programs. Furthermore, we find that BRG1 interacts with EED/PRC2 polycomb-repressive-complexes to enhance H3K27me3-mediated repression at gene loci associated with OL-differentiation inhibition and neurogenesis. Notably, BRG1 depletion decreases H3K27me3 deposition, leading to the upregulation of BMP/WNT signaling and proneurogenic genes, which suppresses OL programs. Thus, our findings reveal a hitherto unexplored spatiotemporal-specific role of BRG1 for OPC differentiation in the developing CNS and underscore a new insight into BRG1/PRC2-mediated epigenetic regulation that promotes and safeguards OL lineage commitment and differentiation.
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Affiliation(s)
- Jiajia Wang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lijun Yang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yiwen Du
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Jincheng Wang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Qinjie Weng
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xuezhao Liu
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Eva Nicholson
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mei Xin
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Qing Richard Lu
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA
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Salerno D, Peruzzi G, Giuseppe Rubens Pascucci, Levrero M, Belloni L, Pediconi N. miRNA-27a-3p is involved in the plasticity of differentiated hepatocytes. Gene 2024; 913:148387. [PMID: 38499211 DOI: 10.1016/j.gene.2024.148387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/01/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND Epigenetic mechanisms, including DNA methylation, histone modifications, and chromatin remodeling, are highly involved in the regulation of hepatocyte viability, proliferation, and plasticity. We have previously demonstrated that repression of H3K27 methylation in differentiated hepatic HepaRG cells by treatment with GSK-J4, an inhibitor of JMJD3 and UTX H3K27 demethylase activity, changed their phenotype, inducing differentiated hepatocytes to proliferate. In addition to the epigenetic enzymatic role in the regulation of the retro-differentiation process, emerging evidence indicate that microRNAs (miRNAs) are involved in controlling hepatocyte proliferation during liver regeneration. Hence, the aim of this work is to investigate the impact of H3K27 methylation on miRNAs expression profile and its role in the regulation of the differentiation status of human hepatic progenitors HepaRG cells. METHODS A miRNA-sequencing was carried out in differentiated HepaRG cells treated or not with GSK-J4. Target searching and Gene Ontology analysis were performed to identify the molecular processes modulated by differentially expressed miRNAs. The biological functions of selected miRNAs was further investigated by transfection of miRNAs inhibitors or mimics in differentiated HepaRG cells followed by qPCR analysis, albumin ELISA assay, CD49a FACS analysis and EdU staining. RESULTS We identified 12 miRNAs modulated by GSK-J4; among these, miR-27a-3p and miR- 423-5p influenced the expression of several proliferation genes in differentiated HepaRG cells. MiR-27a-3p overexpression increased the number of hepatic cells reentering proliferation. Interestingly, both miR-27a-3p and miR-423-5p did not affect the expression levels of genes involved in the differentiation of progenitors HepaRG cells. CONCLUSIONS Modulation of H3K27me3 methylation in differentiated HepaRG cells, by GSK-J4 treatment, influenced miRNA' s expression profile pushing liver cells towards a proliferating phenotype. We demonstrated the involvement of miR-27a-3p in reinducing proliferation of differentiated hepatocytes suggesting a potential role in liver plasticity.
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Affiliation(s)
- Debora Salerno
- Dept. of Molecular Medicine, Sapienza University of Rome, Italy; Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Giuseppe Rubens Pascucci
- Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Systems Medicine, University of Rome "Tor Vergata", Italy
| | - Massimo Levrero
- Cancer Research Center of Lyon (CRCL), INSERM U1052, CNRS UMR5286, Lyon, France
| | - Laura Belloni
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; Dept. of Medical and Surgical Sciences and Translational Medicine, Sapienza University of Rome, Via Giorgio Nicola Papanicolau, 00189 Rome, Italy.
| | - Natalia Pediconi
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; Dept. of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy.
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5
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Weng W, Deng Y, Deviatiiarov R, Hamidi S, Kajikawa E, Gusev O, Kiyonari H, Zhang G, Sheng G. ETV2 induces endothelial, but not hematopoietic, lineage specification in birds. Life Sci Alliance 2024; 7:e202402694. [PMID: 38570190 PMCID: PMC10992995 DOI: 10.26508/lsa.202402694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024] Open
Abstract
Cardiovascular system develops from the lateral plate mesoderm. Its three primary cell lineages (hematopoietic, endothelial, and muscular) are specified by the sequential actions of conserved transcriptional factors. ETV2, a master regulator of mammalian hemangioblast development, however, is absent in the chicken genome and acts downstream of NPAS4L in zebrafish. Here, we investigated the epistatic relationship between NPAS4L and ETV2 in avian hemangioblast development. We showed that ETV2 is deleted in all 363 avian genomes analyzed. Mouse ETV2 induced LMO2, but not NPAS4L or SCL, expression in chicken mesoderm. Squamate (lizards, geckos, and snakes) genomes contain both NPAS4L and ETV2 In Madagascar ground gecko, both genes were expressed in developing hemangioblasts. Gecko ETV2 induced only LMO2 in chicken mesoderm. We propose that both NPAS4L and ETV2 were present in ancestral amniote, with ETV2 acting downstream of NPAS4L in endothelial lineage specification. ETV2 may have acted as a pioneer factor by promoting chromatin accessibility of endothelial-specific genes and, in parallel with NPAS4L loss in ancestral mammals, has gained similar function in regulating blood-specific genes.
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Affiliation(s)
- Wei Weng
- https://ror.org/02cgss904 International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yuan Deng
- Beijing Genome Institute (BGI), Shenzhen, China
| | - Ruslan Deviatiiarov
- https://ror.org/02cgss904 International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Sofiane Hamidi
- https://ror.org/02cgss904 International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | | | - Oleg Gusev
- https://ror.org/02cgss904 International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Life Improvement by Future Technologies (LIFT) Center, Moscow, Russia
| | | | - Guojie Zhang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou, China
| | - Guojun Sheng
- https://ror.org/02cgss904 International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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6
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Ding L, Chen D, Li Y, Xie Y, Sun X, Wang D. Saracatinib prompts hemin-induced K562 erythroid differentiation but suppresses erythropoiesis of hematopoietic stem cells. Hum Cell 2024; 37:648-665. [PMID: 38388899 PMCID: PMC11016514 DOI: 10.1007/s13577-024-01034-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/17/2024] [Indexed: 02/24/2024]
Abstract
Human myeloid leukemia cells (such as K562) could be used for the study of erythropoiesis, and mature erythroid markers and globins could be induced during leukemia cell differentiation; however, the pathways involved are different compared with those of hematopoietic stem cells (HSCs).We identified the differentially expressed genes (DEGs) of K562 cells and HSCs associated with stem cells and erythroid differentiation. Furthermore, we showed that hemin-induced differentiation of K562 cells could be induced by serum starvation or treatment with the tyrosine kinase inhibitor saracatinib. However, erythroid differentiation of HSCs was inhibited by the deprivation of the important serum component erythropoietin (EPO) or treatment with saracatinib. Finally, we found that the mRNA expression of K562 cells and HSCs was different during saracatinib-treated erythroid differentiation, and the DEGs of K562 cells and HSCs associated with tyrosine-protein kinase were identified.These findings elucidated the cellular phenomenon of saracatinib induction during erythroid differentiation of K562 cells and HSCs, and the potential mechanism is the different mRNA expression profile of tyrosine-protein kinase in K562 cells and HSCs.
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Affiliation(s)
- Lina Ding
- Department of Obstetrics, Dongguan Songshan Lake Central Hospital, Dongguan Third People's Hospital, Dongguan, 523326, Guangdong, China
| | - Diyu Chen
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Guangzhou, 510150, Guangdong, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Guangzhou, 510150, Guangdong, China
| | - Yuanshuai Li
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Guangzhou, 510150, Guangdong, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Guangzhou, 510150, Guangdong, China
| | - Yingjun Xie
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Guangzhou, 510150, Guangdong, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Guangzhou, 510150, Guangdong, China
| | - Xiaofang Sun
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Guangzhou, 510150, Guangdong, China.
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Guangzhou, 510150, Guangdong, China.
| | - Ding Wang
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Guangzhou, 510150, Guangdong, China.
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Guangzhou, 510150, Guangdong, China.
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Tan L, Chen X, Yan S, Guo A, Gao L, Zhou L, Zhou Y, Zeng J, Lu J. WTAP-Mediated N6-Methyladenosine of RNAs Facilitate the Pathophysiology of Atopic Dermatitis. J Invest Dermatol 2024; 144:1058-1070.e4. [PMID: 38029838 DOI: 10.1016/j.jid.2023.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/21/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant dynamic and reversible internal chemical modification of RNA in eukaryotic cells and is essential in multiple pathophysiological processes. However, it has not been reported in atopic dermatitis (AD). We used Arraystar m6A-mRNA epitranscriptomic microarray to screen for differentially expressed genes and their m6A levels and m6A-related enzymes in patients with AD. We confirmed that the m6A RNA methyltransferase WTAP and 2 candidate differentially expressed genes (S100A9 and SERPINB3) were significantly upregulated in keratinocytes in public data and epidermal lesions of patients with AD. In vitro cell experiments confirmed that WTAP influenced the expression of the 2 candidate differentially expressed genes and promoted primary human epidermal keratinocyte proliferation while inhibiting human epidermal keratinocyte differentiation. Furthermore, we showed that WTAP, S100A9, and SERPINB3 expression correlated with AD severity. Our findings revealed that WTAP-mediated m6A modification promoted the expression of S100A9 and SERPINB3 to aggravate human epidermal keratinocyte proliferation and dysdifferentiation contributing to the pathophysiological development of AD.
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Affiliation(s)
- Lina Tan
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China; Medical Ozone Research Center, Central South University, Changsha, China
| | - Xue Chen
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China; Medical Ozone Research Center, Central South University, Changsha, China
| | - Siyu Yan
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China; Medical Ozone Research Center, Central South University, Changsha, China
| | - Aiyuan Guo
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China; Medical Ozone Research Center, Central South University, Changsha, China
| | - Lihua Gao
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China; Medical Ozone Research Center, Central South University, Changsha, China
| | - Lu Zhou
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China; Medical Ozone Research Center, Central South University, Changsha, China
| | - Yanping Zhou
- Department of Operating Room, Third Xiangya Hospital, Central South University, Changsha, China
| | - Jinrong Zeng
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China; Medical Ozone Research Center, Central South University, Changsha, China.
| | - Jianyun Lu
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China; Medical Ozone Research Center, Central South University, Changsha, China.
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8
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Kidder BL. Decoding the universal human chromatin landscape through teratoma-based profiling. Nucleic Acids Res 2024; 52:3589-3606. [PMID: 38281248 DOI: 10.1093/nar/gkae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 12/15/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
Teratoma formation is key for evaluating differentiation of human pluripotent stem cells into embryonic germ layers and serves as a model for understanding stem cell differentiation and developmental processes. Its potential for insights into epigenome and transcriptome profiling is significant. This study integrates the analysis of the epigenome and transcriptome of hESC-generated teratomas, comparing transcriptomes between hESCs and teratomas. It employs cell type-specific expression patterns from single-cell data to deconvolve RNA-Seq data and identify cell types within teratomas. Our results provide a catalog of activating and repressive histone modifications, while also elucidating distinctive features of chromatin states. Construction of an epigenetic signature matrix enabled the quantification of diverse cell populations in teratomas and enhanced the ability to unravel the epigenetic landscape in heterogeneous tissue contexts. This study also includes a single cell multiome atlas of expression (scRNA-Seq) and chromatin accessibility (scATAC-Seq) of human teratomas, further revealing the complexity of these tissues. A histology-based digital staining tool further complemented the annotation of cell types in teratomas, enhancing our understanding of their cellular composition. This research is a valuable resource for examining teratoma epigenomic and transcriptomic landscapes and serves as a model for epigenetic data comparison.
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Affiliation(s)
- Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
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9
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Lorenzo JP, Molla L, Amro EM, Ibarra IL, Ruf S, Neber C, Gkougkousis C, Ridani J, Subramani PG, Boulais J, Harjanto D, Vonica A, Di Noia JM, Dieterich C, Zaugg JB, Papavasiliou FN. APOBEC2 safeguards skeletal muscle cell fate through binding chromatin and regulating transcription of non-muscle genes during myoblast differentiation. Proc Natl Acad Sci U S A 2024; 121:e2312330121. [PMID: 38625936 DOI: 10.1073/pnas.2312330121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 03/07/2024] [Indexed: 04/18/2024] Open
Abstract
The apolipoprotein B messenger RNA editing enzyme, catalytic polypeptide (APOBEC) family is composed of nucleic acid editors with roles ranging from antibody diversification to RNA editing. APOBEC2, a member of this family with an evolutionarily conserved nucleic acid-binding cytidine deaminase domain, has neither an established substrate nor function. Using a cellular model of muscle differentiation where APOBEC2 is inducibly expressed, we confirmed that APOBEC2 does not have the attributed molecular functions of the APOBEC family, such as RNA editing, DNA demethylation, and DNA mutation. Instead, we found that during muscle differentiation APOBEC2 occupied a specific motif within promoter regions; its removal from those regions resulted in transcriptional changes. Mechanistically, these changes reflect the direct interaction of APOBEC2 with histone deacetylase (HDAC) transcriptional corepressor complexes. We also found that APOBEC2 could bind DNA directly, in a sequence-specific fashion, suggesting that it functions as a recruiter of HDAC to specific genes whose promoters it occupies. These genes are normally suppressed during muscle cell differentiation, and their suppression may contribute to the safeguarding of muscle cell fate. Altogether, our results reveal a unique role for APOBEC2 within the APOBEC family.
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Affiliation(s)
- J Paulo Lorenzo
- Division of Immune Diversity, German Cancer Research Center, Heidelberg 69120, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg 69120, Germany
| | - Linda Molla
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY 10065
| | - Elias Moris Amro
- Division of Immune Diversity, German Cancer Research Center, Heidelberg 69120, Germany
| | - Ignacio L Ibarra
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Sandra Ruf
- Division of Immune Diversity, German Cancer Research Center, Heidelberg 69120, Germany
| | - Cedrik Neber
- Division of Immune Diversity, German Cancer Research Center, Heidelberg 69120, Germany
| | - Christos Gkougkousis
- Division of Immune Diversity, German Cancer Research Center, Heidelberg 69120, Germany
| | - Jana Ridani
- Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Poorani Ganesh Subramani
- Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Jonathan Boulais
- Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
| | - Dewi Harjanto
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY 10065
| | - Alin Vonica
- Department of Biology, Nazareth University, Rochester, NY 14618
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H4A 3J1, Canada
- Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg 69120, Germany
- German Center for Cardiovascular Research (DZHK) - Partner site Heidelberg/Mannheim, Heidelberg 69120, Germany
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - F Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Center, Heidelberg 69120, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg 69120, Germany
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY 10065
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10
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Xue G, Zhang X, Li W, Zhang L, Zhang Z, Zhou X, Zhang D, Zhang L, Li Z. A logic-incorporated gene regulatory network deciphers principles in cell fate decisions. eLife 2024; 12:RP88742. [PMID: 38652107 DOI: 10.7554/elife.88742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Organisms utilize gene regulatory networks (GRN) to make fate decisions, but the regulatory mechanisms of transcription factors (TF) in GRNs are exceedingly intricate. A longstanding question in this field is how these tangled interactions synergistically contribute to decision-making procedures. To comprehensively understand the role of regulatory logic in cell fate decisions, we constructed a logic-incorporated GRN model and examined its behavior under two distinct driving forces (noise-driven and signal-driven). Under the noise-driven mode, we distilled the relationship among fate bias, regulatory logic, and noise profile. Under the signal-driven mode, we bridged regulatory logic and progression-accuracy trade-off, and uncovered distinctive trajectories of reprogramming influenced by logic motifs. In differentiation, we characterized a special logic-dependent priming stage by the solution landscape. Finally, we applied our findings to decipher three biological instances: hematopoiesis, embryogenesis, and trans-differentiation. Orthogonal to the classical analysis of expression profile, we harnessed noise patterns to construct the GRN corresponding to fate transition. Our work presents a generalizable framework for top-down fate-decision studies and a practical approach to the taxonomy of cell fate decisions.
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Affiliation(s)
- Gang Xue
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaoyi Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Wanqi Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Lu Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Zongxu Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaolin Zhou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Di Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Lei Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing International Center for Mathematical Research, Center for Machine Learning Research, Peking University, Beijing, China
| | - Zhiyuan Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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11
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Hu P, Zhang G, Ba H, Ren J, Li J, Wang Z, Li C. Reciprocal negative feedback between Prrx1 and miR-140-3p regulates rapid chondrogenesis in the regenerating antler. Cell Mol Biol Lett 2024; 29:56. [PMID: 38643083 PMCID: PMC11031908 DOI: 10.1186/s11658-024-00573-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/05/2024] [Indexed: 04/22/2024] Open
Abstract
During growth phase, antlers exhibit a very rapid rate of chondrogenesis. The antler is formed from its growth center reserve mesenchyme (RM) cells, which have been found to be the derivatives of paired related homeobox 1 (Prrx1)-positive periosteal cells. However, the underlying mechanism that drives rapid chondrogenesis is not known. Herein, the miRNA expression profiles and chromatin states of three tissue layers (RM, precartilage, and cartilage) at different stages of differentiation within the antler growth center were analyzed by RNA-sequencing and ATAC-sequencing. We found that miR-140-3p was the miRNA that exhibited the greatest degree of upregulation in the rapidly growing antler, increasing from the RM to the cartilage layer. We also showed that Prrx1 was a key upstream regulator of miR-140-3p, which firmly confirmed by Prrx1 CUT&Tag sequencing of RM cells. Through multiple approaches (three-dimensional chondrogenic culture and xenogeneic antler model), we demonstrated that Prrx1 and miR-140-3p functioned as reciprocal negative feedback in the antler growth center, and downregulating PRRX1/upregulating miR-140-3p promoted rapid chondrogenesis of RM cells and xenogeneic antler. Thus, we conclude that the reciprocal negative feedback between Prrx1 and miR-140-3p is essential for balancing mesenchymal proliferation and chondrogenic differentiation in the regenerating antler. We further propose that the mechanism underlying chondrogenesis in the regenerating antler would provide a reference for helping understand the regulation of human cartilage regeneration and repair.
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Affiliation(s)
- Pengfei Hu
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun, China.
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China.
| | - Guokun Zhang
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun, China
| | - Hengxing Ba
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun, China
| | - Jing Ren
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun, China
| | - Jiping Li
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun, China
| | - Zhen Wang
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun, China
| | - Chunyi Li
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun, China.
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12
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Li Y, Duan J, Li Y, Zhang M, Wu J, Wang G, Li S, Hu Z, Qu Y, Li Y, Hu X, Guo F, Cao L, Lu J. Transcriptomic profiling across human serotonin neuron differentiation via the FEV reporter system. Stem Cell Res Ther 2024; 15:107. [PMID: 38637896 PMCID: PMC11027224 DOI: 10.1186/s13287-024-03728-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND The detailed transcriptomic profiles during human serotonin neuron (SN) differentiation remain elusive. The establishment of a reporter system based on SN terminal selector holds promise to produce highly-purified cells with an early serotonergic fate and help elucidate the molecular events during human SN development process. METHODS A fifth Ewing variant (FEV)-EGFP reporter system was established by CRISPR/Cas9 technology to indicate SN since postmitotic stage. FACS was performed to purify SN from the heterogeneous cell populations. RNA-sequencing analysis was performed for cells at four key stages of differentiation (pluripotent stem cells, serotonergic neural progenitors, purified postmitotic SN and purifed mature SN) to explore the transcriptomic dynamics during SN differentiation. RESULTS We found that human serotonergic fate specification may commence as early as day 21 of differentiation from human pluripotent stem cells. Furthermore, the transcriptional factors ZIC1, HOXA2 and MSX2 were identified as the hub genes responsible for orchestrating serotonergic fate determination. CONCLUSIONS For the first time, we exposed the developmental transcriptomic profiles of human SN via FEV reporter system, which will further our understanding for the development process of human SN.
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Affiliation(s)
- Yingqi Li
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinjin Duan
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - You Li
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Meihui Zhang
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiaan Wu
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Guanhao Wang
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shuanqing Li
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhangsen Hu
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yi Qu
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yunhe Li
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiran Hu
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Fei Guo
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Lining Cao
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Jianfeng Lu
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
- Suzhou Institute of Tongji University, Suzhou, China.
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13
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Larouche JD, Laumont CM, Trofimov A, Vincent K, Hesnard L, Brochu S, Côté C, Humeau JF, Bonneil É, Lanoix J, Durette C, Gendron P, Laverdure JP, Richie ER, Lemieux S, Thibault P, Perreault C. Transposable elements regulate thymus development and function. eLife 2024; 12:RP91037. [PMID: 38635416 PMCID: PMC11026094 DOI: 10.7554/elife.91037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Transposable elements (TEs) are repetitive sequences representing ~45% of the human and mouse genomes and are highly expressed by medullary thymic epithelial cells (mTECs). In this study, we investigated the role of TEs on T-cell development in the thymus. We performed multiomic analyses of TEs in human and mouse thymic cells to elucidate their role in T-cell development. We report that TE expression in the human thymus is high and shows extensive age- and cell lineage-related variations. TE expression correlates with multiple transcription factors in all cell types of the human thymus. Two cell types express particularly broad TE repertoires: mTECs and plasmacytoid dendritic cells (pDCs). In mTECs, transcriptomic data suggest that TEs interact with transcription factors essential for mTEC development and function (e.g., PAX1 and REL), and immunopeptidomic data showed that TEs generate MHC-I-associated peptides implicated in thymocyte education. Notably, AIRE, FEZF2, and CHD4 regulate small yet non-redundant sets of TEs in murine mTECs. Human thymic pDCs homogenously express large numbers of TEs that likely form dsRNA, which can activate innate immune receptors, potentially explaining why thymic pDCs constitutively secrete IFN ɑ/β. This study highlights the diversity of interactions between TEs and the adaptive immune system. TEs are genetic parasites, and the two thymic cell types most affected by TEs (mTEcs and pDCs) are essential to establishing central T-cell tolerance. Therefore, we propose that orchestrating TE expression in thymic cells is critical to prevent autoimmunity in vertebrates.
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Affiliation(s)
- Jean-David Larouche
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Medicine, Université de MontréalMontréalCanada
| | - Céline M Laumont
- Deeley Research Centre, BC CancerVictoriaCanada
- Department of Medical Genetics, University of British ColumbiaVancouverCanada
| | - Assya Trofimov
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Computer Science and Operations Research, Université de MontréalMontréalCanada
- Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Physics, University of WashingtonSeattleUnited States
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Leslie Hesnard
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Sylvie Brochu
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Caroline Côté
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Juliette F Humeau
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Joel Lanoix
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | | | - Ellen R Richie
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M.D. Anderson Cancer CenterHoustonUnited States
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Biochemistry and Molecular Medicine, Université de MontréalMontrealCanada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Chemistry, Université de MontréalMontréalCanada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Medicine, Université de MontréalMontréalCanada
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14
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Toriseva M, Björkgren I, Junnila A, Mehmood A, Mattsson J, Raimoranta I, Kim B, Laiho A, Nees M, Elo L, Poutanen M, Breton S, Sipilä P. RUNX transcription factors are essential in maintaining epididymal epithelial differentiation. Cell Mol Life Sci 2024; 81:183. [PMID: 38630262 PMCID: PMC11023966 DOI: 10.1007/s00018-024-05211-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 01/06/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
Apart from the androgen receptor, transcription factors (TFs) that are required for the development and formation of the different segments of the epididymis have remained unknown. We identified TF families expressed in the developing epididymides, of which many showed segment specificity. From these TFs, down-regulation of runt related transcription factors (RUNXs) 1 and 2 expression coincides with epithelial regression in Dicer1 cKO mice. Concomitant deletion of both Runx1 and Runx2 in a mouse epididymal epithelial cell line affected cell morphology, adhesion and mobility in vitro. Furthermore, lack of functional RUNXs severely disturbed the formation of 3D epididymal organoid-like structures. Transcriptomic analysis of the epididymal cell organoid-like structures indicated that RUNX1 and RUNX2 are involved in the regulation of MAPK signaling, NOTCH pathway activity, and EMT-related gene expression. This suggests that RUNXs are master regulators of several essential signaling pathways, and necessary for the maintenance of proper differentiation of the epididymal epithelium.
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Affiliation(s)
- Mervi Toriseva
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre Laboratory, University of Turku and Turku University Hospital, Turku, Finland
| | - Ida Björkgren
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Arttu Junnila
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Arfa Mehmood
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Jesse Mattsson
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre Laboratory, University of Turku and Turku University Hospital, Turku, Finland
| | - Inka Raimoranta
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Bongki Kim
- Program in Membrane Biology/Division of Nephrology, Massachusetts General Hospital, Simches Research Center, Boston, MA, 02114, USA
- Department of Animal Resources Science, Kongju National University, Chungcheongnam-do, Yesan, 32439, Republic of Korea
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Matthias Nees
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre Laboratory, University of Turku and Turku University Hospital, Turku, Finland
| | - Laura Elo
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Matti Poutanen
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
- Institute of Medicine, The Sahlgrenska Academy, Gothenburg University, Göteborg, Sweden
| | - Sylvie Breton
- Program in Membrane Biology/Division of Nephrology, Massachusetts General Hospital, Simches Research Center, Boston, MA, 02114, USA
- Department of Obstetrics, Gynecology and Reproduction, Faculty of Medicine, Research Center-CHU de Québec, Université Laval, Québec, QC, Canada
| | - Petra Sipilä
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland.
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15
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Andersson E, Rothenberg EV, Peterson C, Olariu V. T-cell commitment inheritance-an agent-based multi-scale model. NPJ Syst Biol Appl 2024; 10:40. [PMID: 38632273 PMCID: PMC11024127 DOI: 10.1038/s41540-024-00368-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
T-cell development provides an excellent model system for studying lineage commitment from a multipotent progenitor. The intrathymic development process has been thoroughly studied. The molecular circuitry controlling it has been dissected and the necessary steps like programmed shut off of progenitor genes and T-cell genes upregulation have been revealed. However, the exact timing between decision-making and commitment stage remains unexplored. To this end, we implemented an agent-based multi-scale model to investigate inheritance in early T-cell development. Treating each cell as an agent provides a powerful tool as it tracks each individual cell of a simulated T-cell colony, enabling the construction of lineage trees. Based on the lineage trees, we introduce the concept of the last common ancestors (LCA) of committed cells and analyse their relations, both at single-cell level and population level. In addition to simulating wild-type development, we also conduct knockdown analysis. Our simulations predicted that the commitment is a three-step process that occurs on average over several cell generations once a cell is first prepared by a transcriptional switch. This is followed by the loss of the Bcl11b-opposing function approximately two to three generations later. This is when our LCA analysis indicates that the decision to commit is taken even though in general another one to two generations elapse before the cell actually becomes committed by transitioning to the DN2b state. Our results showed that there is decision inheritance in the commitment mechanism.
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Affiliation(s)
- Emil Andersson
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, 156-29, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Carsten Peterson
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Victor Olariu
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden.
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16
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McCauley KB, Kukreja K, Tovar Walker AE, Jaffe AB, Klein AM. A map of signaling responses in the human airway epithelium. Cell Syst 2024; 15:307-321.e10. [PMID: 38508187 PMCID: PMC11031335 DOI: 10.1016/j.cels.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 11/14/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Receptor-mediated signaling plays a central role in tissue regeneration, and it is dysregulated in disease. Here, we build a signaling-response map for a model regenerative human tissue: the airway epithelium. We analyzed the effect of 17 receptor-mediated signaling pathways on organotypic cultures to determine changes in abundance and phenotype of epithelial cell types. This map recapitulates the gamut of known airway epithelial signaling responses to these pathways. It defines convergent states induced by multiple ligands and diverse, ligand-specific responses in basal cell and secretory cell metaplasia. We show that loss of canonical differentiation induced by multiple pathways is associated with cell-cycle arrest, but that arrest is not sufficient to block differentiation. Using the signaling-response map, we show that a TGFB1-mediated response underlies specific aberrant cells found in multiple lung diseases and identify interferon responses in COVID-19 patient samples. Thus, we offer a framework enabling systematic evaluation of tissue signaling responses. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Katherine B McCauley
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Respiratory Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA; Disease Area X, Biomedical Research, Novartis, Cambridge, MA 02139, USA
| | - Kalki Kukreja
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Aron B Jaffe
- Respiratory Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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17
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Lin HT, Takagi M, Kubara K, Yamazaki K, Michikawa F, Okumura T, Naruto T, Morio T, Miyazaki K, Taniguchi H, Otsu M. Monoallelic KRAS (G13C) mutation triggers dysregulated expansion in induced pluripotent stem cell-derived hematopoietic progenitor cells. Stem Cell Res Ther 2024; 15:106. [PMID: 38627844 PMCID: PMC11021011 DOI: 10.1186/s13287-024-03723-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Although oncogenic RAS mutants are thought to exert mutagenic effects upon blood cells, it remains uncertain how a single oncogenic RAS impacts non-transformed multipotent hematopoietic stem or progenitor cells (HPCs). Such potential pre-malignant status may characterize HPCs in patients with RAS-associated autoimmune lymphoproliferative syndrome-like disease (RALD). This study sought to elucidate the biological and molecular alterations in human HPCs carrying monoallelic mutant KRAS (G13C) with no other oncogene mutations. METHODS We utilized induced pluripotent stem cells (iPSCs) derived from two unrelated RALD patients. Isogenic HPC pairs harboring either wild-type KRAS or monoallelic KRAS (G13C) alone obtained following differentiation enabled reliable comparative analyses. The compound screening was conducted with an established platform using KRAS (G13C) iPSCs and differentiated HPCs. RESULTS Cell culture assays revealed that monoallelic KRAS (G13C) impacted both myeloid differentiation and expansion characteristics of iPSC-derived HPCs. Comprehensive RNA-sequencing analysis depicted close clustering of HPC samples within the isogenic group, warranting that comparative studies should be performed within the same genetic background. When compared with no stimulation, iPSC-derived KRAS (G13C)-HPCs showed marked similarity with the wild-type isogenic control in transcriptomic profiles. After stimulation with cytokines, however, KRAS (G13C)-HPCs exhibited obvious aberrant cell-cycle and apoptosis responses, compatible with "dysregulated expansion," demonstrated by molecular and biological assessment. Increased BCL-xL expression was identified amongst other molecular changes unique to mutant HPCs. With screening platforms established for therapeutic intervention, we observed selective activity against KRAS (G13C)-HPC expansion in several candidate compounds, most notably in a MEK- and a BCL-2/BCL-xL-inhibitor. These two compounds demonstrated selective inhibitory effects on KRAS (G13C)-HPCs even with primary patient samples when combined. CONCLUSIONS Our findings indicate that a monoallelic oncogenic KRAS can confer dysregulated expansion characteristics to non-transformed HPCs, which may constitute a pathological condition in RALD hematopoiesis. The use of iPSC-based screening platforms will lead to discovering treatments that enable selective inhibition of RAS-mutated HPC clones.
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Affiliation(s)
- Huan-Ting Lin
- Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Kenji Kubara
- Tsukuba Research Laboratories, Eisai Co., Ltd., Tsukuba, Ibaraki, 300-2635, Japan
| | - Kazuto Yamazaki
- Tsukuba Research Laboratories, Eisai Co., Ltd., Tsukuba, Ibaraki, 300-2635, Japan
| | - Fumiko Michikawa
- Tsukuba Research Laboratories, Eisai Co., Ltd., Tsukuba, Ibaraki, 300-2635, Japan
| | - Takashi Okumura
- Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Takuya Naruto
- Department of Pediatrics and Developmental Biology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Koji Miyazaki
- Department of Transfusion and Cell Transplantation, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan
| | - Hideki Taniguchi
- Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
- Department of Regenerative Medicine, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa, 236-0004, Japan
| | - Makoto Otsu
- Department of Transfusion and Cell Transplantation, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan.
- Division of Hematology, Department of Medical Laboratory Sciences, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0373, Japan.
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18
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Handal T, Juster S, Abu Diab M, Yanovsky-Dagan S, Zahdeh F, Aviel U, Sarel-Gallily R, Michael S, Bnaya E, Sebban S, Buganim Y, Drier Y, Mouly V, Kubicek S, van den Broek WJAA, Wansink DG, Epsztejn-Litman S, Eiges R. Differentiation shifts from a reversible to an irreversible heterochromatin state at the DM1 locus. Nat Commun 2024; 15:3270. [PMID: 38627364 PMCID: PMC11021500 DOI: 10.1038/s41467-024-47217-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
Epigenetic defects caused by hereditary or de novo mutations are implicated in various human diseases. It remains uncertain whether correcting the underlying mutation can reverse these defects in patient cells. Here we show by the analysis of myotonic dystrophy type 1 (DM1)-related locus that in mutant human embryonic stem cells (hESCs), DNA methylation and H3K9me3 enrichments are completely abolished by repeat excision (CTG2000 expansion), whereas in patient myoblasts (CTG2600 expansion), repeat deletion fails to do so. This distinction between undifferentiated and differentiated cells arises during cell differentiation, and can be reversed by reprogramming of gene-edited myoblasts. We demonstrate that abnormal methylation in DM1 is distinctively maintained in the undifferentiated state by the activity of the de novo DNMTs (DNMT3b in tandem with DNMT3a). Overall, the findings highlight a crucial difference in heterochromatin maintenance between undifferentiated (sequence-dependent) and differentiated (sequence-independent) cells, thus underscoring the role of differentiation as a locking mechanism for repressive epigenetic modifications at the DM1 locus.
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Affiliation(s)
- Tayma Handal
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel
| | - Sarah Juster
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel
| | - Manar Abu Diab
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel
| | - Shira Yanovsky-Dagan
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel
| | - Fouad Zahdeh
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
| | - Uria Aviel
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel
| | - Roni Sarel-Gallily
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, 91904, Israel
| | - Shir Michael
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel
| | - Ester Bnaya
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel
| | - Shulamit Sebban
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Yotam Drier
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Vincent Mouly
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, F-75013, Paris, France
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Walther J A A van den Broek
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Derick G Wansink
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Silvina Epsztejn-Litman
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
| | - Rachel Eiges
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel.
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel.
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19
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Guo L, Zou D, Qiu W, Fei F, Chen L, Chen W, Xiong H, Li X, Wang Y, Gao M, Zhu J, Zhang J, He Y, Gao M, Xu R. Linc-NSC affects cell differentiation, apoptosis and proliferation in mouse neural stem cells and embryonic stem cells in vitro and in vivo. Cell Mol Life Sci 2024; 81:182. [PMID: 38615283 PMCID: PMC11016521 DOI: 10.1007/s00018-024-05224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/12/2023] [Accepted: 03/18/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND Stem cell therapy is a promising therapeutic strategy. In a previous study, we evaluated tumorigenicity by the stereotactic transplantation of neural stem cells (NSCs) and embryonic stem cells (ESCs) from experimental mice. Twenty-eight days later, there was no evidence of tumor formation or long-term engraftment in the NSCs transplantation group. In contrast, the transplantation of ESCs caused tumor formation; this was due to their high proliferative capacity. Based on transcriptome sequencing, we found that a long intergenic non-coding RNA (named linc-NSC) with unknown structure and function was expressed at 1100-fold higher levels in NSCs than in ESCs. This finding suggested that linc-NSC is negatively correlated with stem cell pluripotency and tumor development, but positively correlated with neurogenesis. In the present study, we investigated the specific role of linc-NSC in NSCs/ESCs in tumor formation and neurogenesis. METHODS Whole transcriptome profiling by RNA sequencing and bioinformatics was used to predict lncRNAs that are widely associated with enhanced tumorigenicity. The expression of linc-NSC was assessed by quantitative real-time PCR. We also performed a number of in vitro methods, including cell proliferation assays, differentiation assays, immunofluorescence assays, flow cytometry, along with in vivo survival and immunofluorescence assays to investigate the impacts of linc-NSC on tumor formation and neurogenesis in NSCs and ESCs. RESULTS Following the knockdown of linc-NSC in NSCs, NSCs cultured in vitro and those transplanted into the cortex of mice showed stronger survival ability (P < 0.0001), enhanced proliferation(P < 0.001), and reduced apoptosis (P < 0.05); the opposite results were observed when linc-NSC was overexpressed in ESCs. Furthermore, the overexpression of linc-NSC in ECSs induced enhanced apoptosis (P < 0.001) and differentiation (P < 0.01), inhibited tumorigenesis (P < 0.05) in vivo, and led to a reduction in tumor weight (P < 0.0001). CONCLUSIONS Our analyses demonstrated that linc-NSC, a promising gene-edited target, may promote the differentiation of mouse NSCs and inhibit tumorigenesis in mouse ESCs. The knockdown of linc-NSC inhibited the apoptosis in NSCs both in vitro and in vivo, and prevented tumor formation, revealing a new dimension into the effect of lncRNA on low survival NSCs and providing a prospective gene manipulation target prior to transplantation. In parallel, the overexpression of linc-NSC induced apoptosis in ESCs both in vitro and in vivo and attenuated the tumorigenicity of ESCs in vivo, but did not completely prevent tumor formation.
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Affiliation(s)
- Lili Guo
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Dan Zou
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Wenqiao Qiu
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Fan Fei
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Lihua Chen
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Wenjin Chen
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Huan Xiong
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Xinda Li
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Yangyang Wang
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Mingjun Gao
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Jianwei Zhu
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Jin Zhang
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Yunsen He
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Mou Gao
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Ruxiang Xu
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China.
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20
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Álvarez-Campos P, García-Castro H, Emili E, Pérez-Posada A, Del Olmo I, Peron S, Salamanca-Díaz DA, Mason V, Metzger B, Bely AE, Kenny NJ, Özpolat BD, Solana J. Annelid adult cell type diversity and their pluripotent cellular origins. Nat Commun 2024; 15:3194. [PMID: 38609365 PMCID: PMC11014941 DOI: 10.1038/s41467-024-47401-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Many annelids can regenerate missing body parts or reproduce asexually, generating all cell types in adult stages. However, the putative adult stem cell populations involved in these processes, and the diversity of cell types generated by them, are still unknown. To address this, we recover 75,218 single cell transcriptomes of the highly regenerative and asexually-reproducing annelid Pristina leidyi. Our results uncover a rich cell type diversity including annelid specific types as well as novel types. Moreover, we characterise transcription factors and gene networks that are expressed specifically in these populations. Finally, we uncover a broadly abundant cluster of putative stem cells with a pluripotent signature. This population expresses well-known stem cell markers such as vasa, piwi and nanos homologues, but also shows heterogeneous expression of differentiated cell markers and their transcription factors. We find conserved expression of pluripotency regulators, including multiple chromatin remodelling and epigenetic factors, in piwi+ cells. Finally, lineage reconstruction analyses reveal computational differentiation trajectories from piwi+ cells to diverse adult types. Our data reveal the cell type diversity of adult annelids by single cell transcriptomics and suggest that a piwi+ cell population with a pluripotent stem cell signature is associated with adult cell type differentiation.
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Affiliation(s)
- Patricia Álvarez-Campos
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM) & Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Helena García-Castro
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Elena Emili
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Alberto Pérez-Posada
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Irene Del Olmo
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM) & Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Sophie Peron
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - David A Salamanca-Díaz
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Vincent Mason
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Bria Metzger
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 05432, USA
- Department of Biology, Washington University in St. Louis. 1 Brookings Dr. Saint Louis, Saint Louis, MO, 63130, USA
| | - Alexandra E Bely
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | - Nathan J Kenny
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, Aotearoa, New Zealand
| | - B Duygu Özpolat
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 05432, USA.
- Department of Biology, Washington University in St. Louis. 1 Brookings Dr. Saint Louis, Saint Louis, MO, 63130, USA.
| | - Jordi Solana
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
- Living Systems Institute, University of Exeter, Exeter, UK.
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21
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Shoji M, Ohashi T, Nagase S, Yuri H, Ichihashi K, Takagishi T, Nagata Y, Nomura Y, Fukunaka A, Kenjou S, Miyake H, Hara T, Yoshigai E, Fujitani Y, Sakurai H, Dos Santos HG, Fukada T, Kuzuhara T. Possible involvement of zinc transporter ZIP13 in myogenic differentiation. Sci Rep 2024; 14:8052. [PMID: 38609428 PMCID: PMC11014994 DOI: 10.1038/s41598-024-56912-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/12/2024] [Indexed: 04/14/2024] Open
Abstract
Ehlers-Danlos syndrome spondylodysplastic type 3 (EDSSPD3, OMIM 612350) is an inherited recessive connective tissue disorder that is caused by loss of function of SLC39A13/ZIP13, a zinc transporter belonging to the Slc39a/ZIP family. We previously reported that patients with EDSSPD3 harboring a homozygous loss of function mutation (c.221G > A, p.G64D) in ZIP13 exon 2 (ZIP13G64D) suffer from impaired development of bone and connective tissues, and muscular hypotonia. However, whether ZIP13 participates in the early differentiation of these cell types remains unclear. In the present study, we investigated the role of ZIP13 in myogenic differentiation using a murine myoblast cell line (C2C12) as well as patient-derived induced pluripotent stem cells (iPSCs). We found that ZIP13 gene expression was upregulated by myogenic stimulation in C2C12 cells, and its knockdown disrupted myotubular differentiation. Myocytes differentiated from iPSCs derived from patients with EDSSPD3 (EDSSPD3-iPSCs) also exhibited incomplete myogenic differentiation. Such phenotypic abnormalities of EDSSPD3-iPSC-derived myocytes were corrected by genomic editing of the pathogenic ZIP13G64D mutation. Collectively, our findings suggest the possible involvement of ZIP13 in myogenic differentiation, and that EDSSPD3-iPSCs established herein may be a promising tool to study the molecular basis underlying the clinical features caused by loss of ZIP13 function.
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Affiliation(s)
- Masaki Shoji
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahouji, Yamashirocho, Tokushima-City, Tokushima, 770-8514, Japan.
| | - Takuto Ohashi
- Laboratory of Molecular and Cellular Physiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahouji, Yamashirocho, Tokushima-City, Tokushima, 770-8514, Japan
| | - Saki Nagase
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahouji, Yamashirocho, Tokushima-City, Tokushima, 770-8514, Japan
| | - Haato Yuri
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahouji, Yamashirocho, Tokushima-City, Tokushima, 770-8514, Japan
| | - Kenta Ichihashi
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahouji, Yamashirocho, Tokushima-City, Tokushima, 770-8514, Japan
| | - Teruhisa Takagishi
- Laboratory of Molecular and Cellular Physiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahouji, Yamashirocho, Tokushima-City, Tokushima, 770-8514, Japan
| | - Yuji Nagata
- Laboratory of Molecular and Cellular Physiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahouji, Yamashirocho, Tokushima-City, Tokushima, 770-8514, Japan
| | - Yuki Nomura
- Laboratory of Molecular and Cellular Physiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahouji, Yamashirocho, Tokushima-City, Tokushima, 770-8514, Japan
| | - Ayako Fukunaka
- Laboratory of Developmental Biology and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi-City, Gunma, Japan
| | - Sae Kenjou
- Laboratory of Molecular and Cellular Physiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahouji, Yamashirocho, Tokushima-City, Tokushima, 770-8514, Japan
| | - Hatsuna Miyake
- Laboratory of Molecular and Cellular Physiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahouji, Yamashirocho, Tokushima-City, Tokushima, 770-8514, Japan
| | - Takafumi Hara
- Laboratory of Molecular and Cellular Physiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahouji, Yamashirocho, Tokushima-City, Tokushima, 770-8514, Japan
| | - Emi Yoshigai
- Laboratory of Molecular and Cellular Physiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahouji, Yamashirocho, Tokushima-City, Tokushima, 770-8514, Japan
| | - Yoshio Fujitani
- Laboratory of Developmental Biology and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi-City, Gunma, Japan
| | - Hidetoshi Sakurai
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto-City, Kyoto, Japan
| | | | - Toshiyuki Fukada
- Laboratory of Molecular and Cellular Physiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahouji, Yamashirocho, Tokushima-City, Tokushima, 770-8514, Japan.
| | - Takashi Kuzuhara
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahouji, Yamashirocho, Tokushima-City, Tokushima, 770-8514, Japan.
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22
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He L, Feng X, Hu C, Liu S, Sheng H, Cai B, Ma Y. HOXA9 gene inhibits proliferation and differentiation and promotes apoptosis of bovine preadipocytes. BMC Genomics 2024; 25:358. [PMID: 38605318 PMCID: PMC11007997 DOI: 10.1186/s12864-024-10231-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 03/15/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND Hox gene family is an important transcription factor that regulates cell process, and plays a role in the process of adipocytes differentiation and fat deposition. Previous transcriptome sequencing studies have indicated that the Homeobox A9 gene (HOXA9) is a candidate gene for regulating the process of bovine lipid metabolism, but the function and specific mechanism of action remain unclear. Therefore, this study aims to explore the role of HOXA9 in the proliferation, differentiation and apoptosis of bovine preadipocytes through gain-of-function and lose-of-function. RESULT It found HOXA9 highly expressed in bovine adipose tissue, and its expression level changed significantly during adipocytes differentiation process. It gave a hint that HOXA9 may be involved in the process of bovine lipid metabolism. The results of HOXA9 gain-of-function experiments indicated that HOXA9 appeared to act as a negative regulator not only in the differentiation but also in the proliferation of bovine preadipocytes, which is mainly reflected that overexpression of HOXA9 down-regulate the mRNA and protein expression level of PPARγ, CEBPα and FABP4 (P < 0.05). The mRNA expression level of CDK1, CDK2, PCNA, CCNA2, CCNB1, CCND1 and CCNE2, as well as the protein expression of CDK2 also significantly decreased. The decrease of lipid droplets content was the main characteristic of the phenotype (P < 0.01), which further supported the evidence that HOXA9 was a negative regulator of preadipocytes differentiation. The decrease of cell proliferation rate and EdU positive rate, as well as the limitation of transition of preadipocytes from G0/G1 phase to S phase also provided evidence for the inhibition of proliferation. Apart from this above, we noted an interesting phenomenon that overexpression of HOXA9 showed in a significant upregulation of both mRNA and protein level of apoptosis markers, accompanied by a significant increase in cell apoptosis rate. These data led us not to refute the fact that HOXA9 played an active regulatory role in apoptosis. HOXA9 loss-of-function experiments, however, yielded the opposite results. Considering that HOXA9 acts as a transcription factor, we predicted its target genes. Dual luciferase reporter assay system indicated that overexpression of HOXA9 inhibits activity of PCNA promoter. CONCLUSION Taken together, we demonstrated for the first time that HOXA9 played a role as a negative regulatory factor in the differentiation and proliferation of preadipocytes, but played a positive regulatory role in apoptosis, and it may play a regulatory role by targeting PCNA. This study provides basic data for further exploring the regulatory network of intramuscular fat deposition in bovine.
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Affiliation(s)
- Lixia He
- College of Animal Science and Technology, Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, 750021, Yinchuan, China
| | - Xue Feng
- College of Animal Science and Technology, Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, 750021, Yinchuan, China
| | - Chunli Hu
- College of Animal Science and Technology, Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, 750021, Yinchuan, China
| | - Shuang Liu
- College of Animal Science and Technology, Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, 750021, Yinchuan, China
| | - Hui Sheng
- College of Animal Science and Technology, Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, 750021, Yinchuan, China
| | - Bei Cai
- College of Animal Science and Technology, Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, 750021, Yinchuan, China
| | - Yun Ma
- College of Animal Science and Technology, Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, 750021, Yinchuan, China.
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23
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Li J, Ma R, Wang X, Lu Y, Chen J, Feng D, Zhou J, Xia K, Klein O, Xie H, Lu P. Sprouty genes regulate activated fibroblasts in mammary epithelial development and breast cancer. Cell Death Dis 2024; 15:256. [PMID: 38600092 PMCID: PMC11006910 DOI: 10.1038/s41419-024-06637-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Stromal fibroblasts are a major stem cell niche component essential for organ formation and cancer development. Fibroblast heterogeneity, as revealed by recent advances in single-cell techniques, has raised important questions about the origin, differentiation, and function of fibroblast subtypes. In this study, we show in mammary stromal fibroblasts that loss of the receptor tyrosine kinase (RTK) negative feedback regulators encoded by Spry1, Spry2, and Spry4 causes upregulation of signaling in multiple RTK pathways and increased extracellular matrix remodeling, resulting in accelerated epithelial branching. Single-cell transcriptomic analysis demonstrated that increased production of FGF10 due to Sprouty (Spry) loss results from expansion of a functionally distinct subgroup of fibroblasts with the most potent branching-promoting ability. Compared to their three independent lineage precursors, fibroblasts in this subgroup are "activated," as they are located immediately adjacent to the epithelium that is actively undergoing branching and invasion. Spry genes are downregulated, and activated fibroblasts are expanded, in all three of the major human breast cancer subtypes. Together, our data highlight the regulation of a functional subtype of mammary fibroblasts by Spry genes and their essential role in epithelial morphogenesis and cancer development.
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Affiliation(s)
- Jiyong Li
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Hu Nan Sheng, China
- Institute of Cell Biology, University of South China, Hu Nan Sheng, China
- Institute for Future Sciences, Hengyang Medical School, University of South China, Hu Nan Sheng, China
| | - Rongze Ma
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Hu Nan Sheng, China
- Institute of Cell Biology, University of South China, Hu Nan Sheng, China
- Institute for Future Sciences, Hengyang Medical School, University of South China, Hu Nan Sheng, China
| | - Xuebing Wang
- Institute of Aix-Marseille, Wuhan University of Technology, Wuhan, 430070, China
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070, China
| | - Yunzhe Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jing Chen
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Hu Nan Sheng, China
- Institute of Cell Biology, University of South China, Hu Nan Sheng, China
- Institute for Future Sciences, Hengyang Medical School, University of South China, Hu Nan Sheng, China
| | - Deyi Feng
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Hu Nan Sheng, China
- Institute of Cell Biology, University of South China, Hu Nan Sheng, China
- Institute for Future Sciences, Hengyang Medical School, University of South China, Hu Nan Sheng, China
| | - Jiecan Zhou
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Hu Nan Sheng, China
- The First Affiliated Hospital, Pharmacy Department, Hengyang Medical School, University of South China, Hu Nan Sheng, China
| | - Kun Xia
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Hu Nan Sheng, China
- Institute of Cell Biology, University of South China, Hu Nan Sheng, China
| | - Ophir Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, UCSF Box 0422, 513 Parnassus Avenue, HSE1508, San Francisco, CA, 94143, California, USA
- Department of Pediatrics and Guerin Children's, Cedars-Sinai Medical Center, 8700 Gracie Allen Dr., Los Angeles, CA, USA
| | - Hao Xie
- Institute of Aix-Marseille, Wuhan University of Technology, Wuhan, 430070, China
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070, China
| | - Pengfei Lu
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Hu Nan Sheng, China.
- Institute of Cell Biology, University of South China, Hu Nan Sheng, China.
- Institute for Future Sciences, Hengyang Medical School, University of South China, Hu Nan Sheng, China.
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24
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Bergamasco MI, Ranathunga N, Abeysekera W, Li-Wai-Suen CSN, Garnham AL, Willis SN, McRae HM, Yang Y, D'Amico A, Di Rago L, Wilcox S, Nutt SL, Alexander WS, Smyth GK, Voss AK, Thomas T. The histone acetyltransferase KAT6B is required for hematopoietic stem cell development and function. Stem Cell Reports 2024; 19:469-485. [PMID: 38518784 DOI: 10.1016/j.stemcr.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/24/2024] Open
Abstract
The histone lysine acetyltransferase KAT6B (MYST4, MORF, QKF) is the target of recurrent chromosomal translocations causing hematological malignancies with poor prognosis. Using Kat6b germline deletion and overexpression in mice, we determined the role of KAT6B in the hematopoietic system. We found that KAT6B sustained the fetal hematopoietic stem cell pool but did not affect viability or differentiation. KAT6B was essential for normal levels of histone H3 lysine 9 (H3K9) acetylation but not for a previously proposed target, H3K23. Compound heterozygosity of Kat6b and the closely related gene, Kat6a, abolished hematopoietic reconstitution after transplantation. KAT6B and KAT6A cooperatively promoted transcription of genes regulating hematopoiesis, including the Hoxa cluster, Pbx1, Meis1, Gata family, Erg, and Flt3. In conclusion, we identified the hematopoietic processes requiring Kat6b and showed that KAT6B and KAT6A synergistically promoted HSC development, function, and transcription. Our findings are pertinent to current clinical trials testing KAT6A/B inhibitors as cancer therapeutics.
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Affiliation(s)
- Maria I Bergamasco
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Nishika Ranathunga
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Waruni Abeysekera
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Connie S N Li-Wai-Suen
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Alexandra L Garnham
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Simon N Willis
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Helen M McRae
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Yuqing Yang
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Angela D'Amico
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Ladina Di Rago
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Stephen Wilcox
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Warren S Alexander
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Anne K Voss
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia.
| | - Tim Thomas
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia.
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25
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Lei Y, Al Delbany D, Krivec N, Regin M, Couvreu de Deckersberg E, Janssens C, Ghosh M, Sermon K, Spits C. SALL3 mediates the loss of neuroectodermal differentiation potential in human embryonic stem cells with chromosome 18q loss. Stem Cell Reports 2024; 19:562-578. [PMID: 38552632 DOI: 10.1016/j.stemcr.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 04/12/2024] Open
Abstract
Human pluripotent stem cell (hPSC) cultures are prone to genetic drift, because cells that have acquired specific genetic abnormalities experience a selective advantage in vitro. These abnormalities are highly recurrent in hPSC lines worldwide, but their functional consequences in differentiating cells are scarcely described. In this work, we show that the loss of chromosome 18q impairs neuroectoderm commitment and that downregulation of SALL3, a gene located in the common 18q loss region, is responsible for this failed neuroectodermal differentiation. Knockdown of SALL3 in control lines impaired differentiation in a manner similar to the loss of 18q, and transgenic overexpression of SALL3 in hESCs with 18q loss rescued the differentiation capacity of the cells. Finally, we show that loss of 18q and downregulation of SALL3 leads to changes in the expression of genes involved in pathways regulating pluripotency and differentiation, suggesting that these cells are in an altered state of pluripotency.
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Affiliation(s)
- Yingnan Lei
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Diana Al Delbany
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Nuša Krivec
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Marius Regin
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Edouard Couvreu de Deckersberg
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Charlotte Janssens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Manjusha Ghosh
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Karen Sermon
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium.
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26
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Ream MW, Randolph LN, Jiang Y, Chang Y, Bao X, Lian XL. Direct programming of human pluripotent stem cells into endothelial progenitors with SOX17 and FGF2. Stem Cell Reports 2024; 19:579-595. [PMID: 38518781 DOI: 10.1016/j.stemcr.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/24/2024] Open
Abstract
Transcription factors (TFs) are pivotal in guiding stem cell behavior, including their maintenance and differentiation. Using single-cell RNA sequencing, we investigated TFs expressed in endothelial progenitors (EPs) derived from human pluripotent stem cells (hPSCs) and identified upregulated expression of SOXF factors SOX7, SOX17, and SOX18 in the EP population. To test whether overexpression of these factors increases differentiation efficiency, we established inducible hPSC lines for each SOXF factor and found only SOX17 overexpression robustly increased the percentage of cells expressing CD34 and vascular endothelial cadherin (VEC). Conversely, SOX17 knockdown via CRISPR-Cas13d significantly compromised EP differentiation. Intriguingly, we discovered SOX17 overexpression alone was sufficient to generate CD34+VEC+CD31- cells, and, when combined with FGF2 treatment, more than 90% of CD34+VEC+CD31+ EP was produced. These cells are capable of further differentiating into endothelial cells. These findings underscore an undiscovered role of SOX17 in programming hPSCs toward an EP lineage, illuminating pivotal mechanisms in EP differentiation.
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Affiliation(s)
- Michael W Ream
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Lauren N Randolph
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Yuqian Jiang
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Yun Chang
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Xiaoping Bao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA.
| | - Xiaojun Lance Lian
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA; The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
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27
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Zhang Y, Zhou Y, Li X, Pan X, Bai J, Chen Y, Lai Z, Chen Q, Ma F, Dong Y. Small-molecule α-lipoic acid targets ELK1 to balance human neutrophil and erythrocyte differentiation. Stem Cell Res Ther 2024; 15:100. [PMID: 38589882 PMCID: PMC11003016 DOI: 10.1186/s13287-024-03711-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 03/31/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Erythroid and myeloid differentiation disorders are commonly occurred in leukemia. Given that the relationship between erythroid and myeloid lineages is still unclear. To find the co-regulators in erythroid and myeloid differentiation might help to find new target for therapy of myeloid leukemia. In hematopoiesis, ALA (alpha lipoic acid) is reported to inhibit neutrophil lineage determination by targeting transcription factor ELK1 in granulocyte-monocyte progenitors via splicing factor SF3B1. However, further exploration is needed to determine whether ELK1 is a common regulatory factor for erythroid and myeloid differentiation. METHODS In vitro culture of isolated CD34+, CMPs (common myeloid progenitors) and CD34+ CD371- HSPCs (hematopoietic stem progenitor cells) were performed to assay the differentiation potential of monocytes, neutrophils, and erythrocytes. Overexpression lentivirus of long isoform (L-ELK1) or the short isoform (S-ELK1) of ELK1 transduced CD34+ HSPCs were transplanted into NSG mice to assay the human lymphocyte and myeloid differentiation differences 3 months after transplantation. Knocking down of SRSF11, which was high expressed in CD371+GMPs (granulocyte-monocyte progenitors), upregulated by ALA and binding to ELK1-RNA splicing site, was performed to analyze the function in erythroid differentiation derived from CD34+ CD123mid CD38+ CD371- HPCs (hematopoietic progenitor cells). RNA sequencing of L-ELK1 and S-ELK1 overexpressed CD34+ CD123mid CD38+ CD371- HPCs were performed to assay the signals changed by ELK1. RESULTS Here, we presented new evidence that ALA promoted erythroid differentiation by targeting the transcription factor ELK1 in CD34+ CD371- hematopoietic stem progenitor cells (HSPCs). Overexpression of either the long isoform (L-ELK1) or the short isoform (S-ELK1) of ELK1 inhibited erythroid-cell differentiation, but knockdown of ELK1 did not affect erythroid-cell differentiation. RNAseq analysis of CD34+ CD123mid CD38+ CD371- HPCs showed that L-ELK1 upregulated the expression of genes related to neutrophil activity, phosphorylation, and hypoxia signals, while S-ELK1 mainly regulated hypoxia-related signals. However, most of the genes that were upregulated by L-ELK1 were only moderately upregulated by S-ELK1, which might be due to a lack of serum response factor interaction and regulation domains in S-ELK1 compared to L-ELK1. In summary, the differentiation of neutrophils and erythrocytes might need to rely on the dose of L-ELK1 and S-ELK1 to achieve precise regulation via RNA splicing signals at early lineage commitment. CONCLUSIONS ALA and ELK1 are found to regulate both human granulopoiesis and erythropoiesis via RNA spliceosome, and ALA-ELK1 signal might be the target of human leukemia therapy.
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Affiliation(s)
- Yimeng Zhang
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Xindu Road 783, Chengdu, 610500, China
- Center for Stem Cell Research and Application, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Chengdu, China
| | - Ya Zhou
- Center for Stem Cell Research and Application, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Chengdu, China
| | - Xiaohong Li
- Center for Stem Cell Research and Application, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Chengdu, China
| | - Xu Pan
- Center for Stem Cell Research and Application, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Chengdu, China
| | - Ju Bai
- Center for Stem Cell Research and Application, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Chengdu, China
| | - Yijin Chen
- Center for Stem Cell Research and Application, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Chengdu, China
| | | | - Qiang Chen
- Center for Stem Cell Research and Application, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Chengdu, China
| | - Feng Ma
- Center for Stem Cell Research and Application, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Chengdu, China.
| | - Yong Dong
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Xindu Road 783, Chengdu, 610500, China.
- Center for Stem Cell Research and Application, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Chengdu, China.
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28
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Ketchum HC, Suzuki M, Dawlaty MM. Catalytic-dependent and -independent roles of TET3 in the regulation of specific genetic programs during neuroectoderm specification. Commun Biol 2024; 7:415. [PMID: 38580843 PMCID: PMC10997653 DOI: 10.1038/s42003-024-06120-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/28/2024] [Indexed: 04/07/2024] Open
Abstract
The ten-eleven-translocation family of proteins (TET1/2/3) are epigenetic regulators of gene expression. They regulate genes by promoting DNA demethylation (i.e., catalytic activity) and by partnering with regulatory proteins (i.e., non-catalytic functions). Unlike Tet1 and Tet2, Tet3 is not expressed in mouse embryonic stem cells (ESCs) but is induced upon ESC differentiation. However, the significance of its dual roles in lineage specification is less defined. By generating TET3 catalytic-mutant (Tet3m/m) and knockout (Tet3-/-) mouse ESCs and differentiating them to neuroectoderm (NE), we identify distinct catalytic-dependent and independent roles of TET3 in NE specification. We find that the catalytic activity of TET3 is important for activation of neural genes while its non-catalytic functions are involved in suppressing mesodermal programs. Interestingly, the vast majority of differentially methylated regions (DMRs) in Tet3m/m and Tet3-/- NE cells are hypomethylated. The hypo-DMRs are associated to aberrantly upregulated genes while the hyper-DMRs are linked to downregulated neural genes. We find the maintenance methyltransferase Dnmt1 as a direct target of TET3, which is downregulated in TET3-deficient NE cells and may contribute to the increased DNA hypomethylation. Our findings establish that the catalytic-dependent and -independent roles of TET3 have distinct contributions to NE specification with potential implications in development.
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Affiliation(s)
- Harmony C Ketchum
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Masako Suzuki
- Department of Nutrition, Texas A&M University, College Station, Texas, USA
| | - Meelad M Dawlaty
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, USA.
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA.
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, USA.
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29
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Shirasawa A, Hayashi M, Shono M, Ideta A, Yoshino T, Hayashi K. Efficient derivation of embryonic stem cells and primordial germ cell-like cells in cattle. J Reprod Dev 2024; 70:82-95. [PMID: 38355134 PMCID: PMC11017101 DOI: 10.1262/jrd.2023-087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/06/2024] [Indexed: 02/16/2024] Open
Abstract
The induction of the germ cell lineage from pluripotent stem cells (in vitro gametogenesis) will help understand the mechanisms underlying germ cell differentiation and provide an alternative source of gametes for reproduction. This technology is especially important for cattle, which are among the most important livestock species for milk and meat production. Here, we developed a new method for robust induction of primordial germ cell-like cells (PGCLCs) from newly established bovine embryonic stem (bES) cells. First, we refined the pluripotent culture conditions for pre-implantation embryos and ES cells. Inhibition of RHO increased the number of epiblast cells in the pre-implantation embryos and dramatically improved the efficiency of ES cell establishment. We then determined suitable culture conditions for PGCLC differentiation using bES cells harboring BLIMP1-tdTomato and TFAP2C-mNeonGreen (BTTN) reporter constructs. After a 24-h culture with bone morphogenetic protein 4 (BMP4), followed by three-dimensional culture with BMP4 and a chemical agonist and WNT signaling chemical antagonist, bES cells became positive for the reporters. A set of primordial germ cells (PGC) marker genes, including PRDM1/BLIMP1, TFAP2C, SOX17, and NANOS3, were expressed in BTTN-positive cells. These bovine PGCLCs (bPGCLCs) were isolated as KIT/CD117-positive and CD44-negative cell populations. We anticipate that this method for the efficient establishment of bES cells and induction of PGCLCs will be useful for stem cell-based reproductive technologies in cattle.
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Affiliation(s)
- Atsushi Shirasawa
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Zen-noh Embryo Transfer Center, Fukuoka 810-0001, Japan
| | - Masafumi Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Mayumi Shono
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Atsushi Ideta
- Zen-noh Embryo Transfer Center, Fukuoka 810-0001, Japan
| | - Takashi Yoshino
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Katsuhiko Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Osaka 565-0871, Japan
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30
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Wang W, Zhou L, Li H, Sun T, Wen X, Li W, Esteban MA, Hoffman AR, Hu JF, Cui J. Profiling the role of m6A effectors in the regulation of pluripotent reprogramming. Hum Genomics 2024; 18:33. [PMID: 38566168 PMCID: PMC10986062 DOI: 10.1186/s40246-024-00597-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
The N6-methyladenosine (m6A) RNA modification plays essential roles in multiple biological processes, including stem cell fate determination. To explore the role of the m6A modification in pluripotent reprogramming, we used RNA-seq to map m6A effectors in human iPSCs, fibroblasts, and H9 ESCs, as well as in mouse ESCs and fibroblasts. By integrating the human and mouse RNA-seq data, we found that 19 m6A effectors were significantly upregulated in reprogramming. Notably, IGF2BPs, particularly IGF2BP1, were among the most upregulated genes in pluripotent cells, while YTHDF3 had high levels of expression in fibroblasts. Using quantitative PCR and Western blot, we validated the pluripotency-associated elevation of IGF2BPs. Knockdown of IGF2BP1 induced the downregulation of stemness genes and exit from pluripotency. Proteome analysis of cells collected at both the beginning and terminal states of the reprogramming process revealed that the IGF2BP1 protein was positively correlated with stemness markers SOX2 and OCT4. The eCLIP-seq target analysis showed that IGF2BP1 interacted with the coding sequence (CDS) and 3'UTR regions of the SOX2 transcripts, in agreement with the location of m6A modifications. This study identifies IGF2BP1 as a vital pluripotency-associated m6A effector, providing new insight into the interplay between m6A epigenetic modifications and pluripotent reprogramming.
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Affiliation(s)
- Wenjun Wang
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- VA Palo Alto Health Care System, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - Lei Zhou
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Hui Li
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Tingge Sun
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Xue Wen
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Wei Li
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Miguel A Esteban
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, PR China
| | - Andrew R Hoffman
- VA Palo Alto Health Care System, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - Ji-Fan Hu
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin, 130021, China.
- VA Palo Alto Health Care System, Stanford University School of Medicine, Palo Alto, CA, 94304, USA.
| | - Jiuwei Cui
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin, 130021, China.
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31
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González-Iglesias A, Arcas A, Domingo-Muelas A, Mancini E, Galcerán J, Valcárcel J, Fariñas I, Nieto MA. Intron detention tightly regulates the stemness/differentiation switch in the adult neurogenic niche. Nat Commun 2024; 15:2837. [PMID: 38565566 PMCID: PMC10987655 DOI: 10.1038/s41467-024-47092-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
The adult mammalian brain retains some capacity to replenish neurons and glia, holding promise for brain regeneration. Thus, understanding the mechanisms controlling adult neural stem cell (NSC) differentiation is crucial. Paradoxically, adult NSCs in the subependymal zone transcribe genes associated with both multipotency maintenance and neural differentiation, but the mechanism that prevents conflicts in fate decisions due to these opposing transcriptional programmes is unknown. Here we describe intron detention as such control mechanism. In NSCs, while multiple mRNAs from stemness genes are spliced and exported to the cytoplasm, transcripts from differentiation genes remain unspliced and detained in the nucleus, and the opposite is true under neural differentiation conditions. We also show that m6A methylation is the mechanism that releases intron detention and triggers nuclear export, enabling rapid and synchronized responses. m6A RNA methylation operates as an on/off switch for transcripts with antagonistic functions, tightly controlling the timing of NSCs commitment to differentiation.
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Affiliation(s)
| | - Aida Arcas
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
| | - Ana Domingo-Muelas
- Departamento de Biología Celular, Biología Funcional y Antropología Física and Instituto de Biotecnología y Biomedicina, Universidad de Valencia, Burjassot, 46100, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
- Carlos Simon Foundation, 46980, Paterna, Valencia, Spain
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Igenomix Foundation, 46980, Paterna, Valencia, Spain
| | - Estefania Mancini
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Joan Galcerán
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER), 28029, Madrid, Spain
| | - Juan Valcárcel
- Carlos Simon Foundation, 46980, Paterna, Valencia, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Isabel Fariñas
- Departamento de Biología Celular, Biología Funcional y Antropología Física and Instituto de Biotecnología y Biomedicina, Universidad de Valencia, Burjassot, 46100, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
| | - M Angela Nieto
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain.
- Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER), 28029, Madrid, Spain.
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Yin T, Qian Y, Zhang X, Liao Y, Wu B, Wang S, Wang H. Derivation of an induced pluripotent stem cell line (FDCHi014-A) from PBMCs of a seven-year-old patient with a truncating NOVA2 variant (c.625del). Stem Cell Res 2024; 76:103369. [PMID: 38430735 DOI: 10.1016/j.scr.2024.103369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024] Open
Abstract
Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities (NEDASB) is a rare autosomal dominant disorder caused by a heterozygous mutation in the NOVA2 gene on chromosome 19q13. Here, we describe the generation and characterization of an iPSC line derived from the peripheral blood of a 7-year-old patient carrying a novel heterozygous mutation in NOVA2 (c.625 del). The iPSCs with the confirmed patient-specific mutation were demonstrated by pluripotency markers, a normal karyotype, and the ability to differentiate into three germ layers. This NOVA2-mutant iPSC line could facilitate disease modeling and therapy development studies for NEDASB.
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Affiliation(s)
- Tingting Yin
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Yanyan Qian
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Xi Zhang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Yunfei Liao
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Sujuan Wang
- Department of Rehabilitation, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China.
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33
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Xu Y, Mao S, Fan H, Wan J, Wang L, Zhang M, Zhu S, Yuan J, Lu Y, Wang Z, Yu B, Jiang Z, Huang Y. LINC MIR503HG Controls SC-β Cell Differentiation and Insulin Production by Targeting CDH1 and HES1. Adv Sci (Weinh) 2024; 11:e2305631. [PMID: 38243869 PMCID: PMC10987150 DOI: 10.1002/advs.202305631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/03/2024] [Indexed: 01/22/2024]
Abstract
Stem cell-derived pancreatic progenitors (SC-PPs), as an unlimited source of SC-derived β (SC-β) cells, offers a robust tool for diabetes treatment in stem cell-based transplantation, disease modeling, and drug screening. Whereas, PDX1+/NKX6.1+ PPs enhances the subsequent endocrine lineage specification and gives rise to glucose-responsive SC-β cells in vivo and in vitro. To identify the regulators that promote induction efficiency and cellular function maturation, single-cell RNA-sequencing is performed to decipher the transcriptional landscape during PPs differentiation. The comprehensive evaluation of functionality demonstrated that manipulating LINC MIR503HG using CRISPR in PP cell fate decision can improve insulin synthesis and secretion in mature SC-β cells, without effects on liver lineage specification. Importantly, transplantation of MIR503HG-/- SC-β cells in recipients significantly restored blood glucose homeostasis, accompanied by serum C-peptide release and an increase in body weight. Mechanistically, by releasing CtBP1 occupying the CDH1 and HES1 promoters, the decrease in MIR503HG expression levels provided an excellent extracellular niche and appropriate Notch signaling activation for PPs following differentiation. Furthermore, this exhibited higher crucial transcription factors and mature epithelial markers in CDH1High expressed clusters. Altogether, these findings highlighted MIR503HG as an essential and exclusive PP cell fate specification regulator with promising therapeutic potential for patients with diabetes.
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Affiliation(s)
- Yang Xu
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
- Center of Gallbladder DiseaseShanghai East HospitalInstitute of Gallstone DiseaseSchool of MedicineTongji UniversityShanghai200092China
- Research Center of Clinical MedicineAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
| | - Susu Mao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of EducationNMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology ProductsCo‐innovation Center of NeuroregenerationNantong UniversityNantong226001China
| | - Haowen Fan
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
- Research Center of Clinical MedicineAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
| | - Jian Wan
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
- Research Center of Clinical MedicineAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
| | - Lin Wang
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
- Department of Graduate SchoolDalian Medical UniversityDalianLiaoning116000China
| | - Mingyu Zhang
- Department of Nuclear MedicineBeijing Friendship HospitalAffiliated to Capital Medical UniversityBeijing100050China
| | - Shajun Zhu
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
| | - Jin Yuan
- Department of Endocrinology and MetabolismAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
| | - Yuhua Lu
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
| | - Zhiwei Wang
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
| | - Bin Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of EducationNMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology ProductsCo‐innovation Center of NeuroregenerationNantong UniversityNantong226001China
| | - Zhaoyan Jiang
- Center of Gallbladder DiseaseShanghai East HospitalInstitute of Gallstone DiseaseSchool of MedicineTongji UniversityShanghai200092China
| | - Yan Huang
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
- Research Center of Clinical MedicineAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of EducationNMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology ProductsCo‐innovation Center of NeuroregenerationNantong UniversityNantong226001China
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Stallings CE, Das P, Athul SW, Ukagwu AE, Jensik PJ, Ellsworth BS. FOXO1 regulates expression of Neurod4 in the pituitary gland. Mol Cell Endocrinol 2024; 583:112128. [PMID: 38142853 PMCID: PMC10922409 DOI: 10.1016/j.mce.2023.112128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/26/2023]
Abstract
Pituitary gland function is regulated by the activity of various transcription factors that control cell fate decisions leading to cellular differentiation and hormone production. FOXO1 is necessary for normal somatotrope differentiation and function. Recent in vivo data implicate FOXO1 in the regulation of genes important for somatotrope differentiation including Gh1, Neurod4, and Pou1f1. In the current study, the somatotrope-like cell line GH3 was treated with a FOXO1 inhibitor, resulting in significant reduction in Neurod4 and Gh1 expression. Consistent with these findings, CRISPR/Cas9-mediated deletion of Foxo1 in GH3 cells significantly reduced expression of Gh1 and Neurod4. Chromatin immunoprecipitation sequencing identifies novel FOXO1 binding sites associated with the Neurod4, Gh1, and Pou1f1 genes. The FOXO1 binding site in the Neurod4 gene exhibits enhancer activity in somatotrope-like cells but not in gonadotrope-like cells. These data strongly suggest FOXO1 directly contributes to the transcriptional control of genes important for somatotrope differentiation.
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Affiliation(s)
| | - Pratyusa Das
- Department of Physiology, Southern Illinois University, Carbondale, IL, USA
| | - Sandria W Athul
- Department of Physiology, Southern Illinois University, Carbondale, IL, USA
| | - Arnold E Ukagwu
- Department of Physiology, Southern Illinois University, Carbondale, IL, USA
| | - Philip J Jensik
- Department of Physiology, Southern Illinois University, Carbondale, IL, USA
| | - Buffy S Ellsworth
- Department of Physiology, Southern Illinois University, Carbondale, IL, USA.
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35
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Arunachal G, Milind Nimonkar M, Raghavendra K, Chetan GK, Mehta B, Markandeya YS. Generation of induced pluripotent stem cell line, NIMHi009-A, from PBMCs of an adult healthy male. Stem Cell Res 2024; 76:103349. [PMID: 38368738 DOI: 10.1016/j.scr.2024.103349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024] Open
Abstract
Human induced pluripotent stem cells provide an exceptional platform for studying pathogenesis in vitro. We, therefore, have generated and characterized human induced pluripotent stem cell (iPSC) line NIMHi009-A derived from peripheral blood mononuclear cells (PBMCs) of healthy adult male control for an epileptic patient carrying voltage gated sodium channel mutation, using Sendai virus-based reprogramming. The generated iPSCs express pluripotency genes and can spontaneously differentiate into three germ layers. These cells display a normal karyotype and are free of mycoplasma. The iPSC line NIMHi009-A can be used as healthy control for modelling various diseases and screening for drugs.
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Affiliation(s)
- Gautham Arunachal
- Department of Human Genetics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, Karnataka, India
| | - Madhura Milind Nimonkar
- Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Kenchaiah Raghavendra
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Ghati K Chetan
- Department of Human Genetics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, Karnataka, India
| | - Bhupesh Mehta
- Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Yogananda S Markandeya
- Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India.
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36
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Xu C, Zhou L, Jiang H, Song T, Liu Z, Duan X, Fang F. Establishment of an iPSC line (BCHNDi001-A) from a patient with nicotinamide nucleotide repair system deficiency caused by biallelic NAXD mutations. Stem Cell Res 2024; 76:103346. [PMID: 38387170 DOI: 10.1016/j.scr.2024.103346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/04/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024] Open
Abstract
NAD(P)HX dehydratase (NAXD) gene is one of the key enzymes encoding the nicotinamide nucleotide repair system, reportedly associated with Encephalopathy, progressive, early-onset, with brain edema and/or leukoencephalopathy, 2 (PEBEL2). Here, we generated an induced pluripotent stem cell (iPSC) line from the dermal fibroblasts (HDFs) of a PEBEL2 patient who carried biallelic mutations, c.101_102delTA(p.Thr35Phefs*63) and c.318C > G (p.Ile160Met) in NAXD. These iPSCs showed stable amplification in vitro, expressed pluripotent markers, and differentiated spontaneously into three germ layers, as well as NAXD mutations with normal karyotype.
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Affiliation(s)
- Chaolong Xu
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Ling Zhou
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Huafang Jiang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Tianyu Song
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Zhimei Liu
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Xin Duan
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Fang Fang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China.
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37
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Shi Z, Liu H, Feng F, Huang Z, Chen WX. Generation of an induced pluripotent stem cell line GWCMCi006-A from a patient with autosomal dominant neurodevelopmental disorder with or without hyperkinetic movements and seizures harboring GRIN1 c.389A > G mutation. Stem Cell Res 2024; 76:103371. [PMID: 38452705 DOI: 10.1016/j.scr.2024.103371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/20/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
Autosomal dominant neurodevelopmental disorder with or without hyperkinetic movements and seizures (NDHMSD) is a rare neurological disorder characterized by neurodevelopmental disorder and hyperkinetic movement, with or without seizures. Heterozygous mutation in the GRIN1 encoding the subunit 1 of the N-methyl-D-aspartate receptor caused this disorder. We first established an induced pluripotent stem cell (iPSC) line from a male patient with c.389A > G mutation in the GRIN1, via reprogramming with KLF4, SOX2, OCT3/4, and c-MYC. Through identification examination, the iPSCs (GWCMCi006-A) stably expressed pluripotency-associated stem cell markers, maintained a normal karyotype, and showed proliferative potential for three-germ layers differentiation.
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Affiliation(s)
- Zhen Shi
- Department of Neurology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huan Liu
- Department of Neurology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fangmei Feng
- Department of Neurology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Zhifang Huang
- The Assessment and Intervention Center for Autistic Children, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wen-Xiong Chen
- Department of Neurology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China; The Assessment and Intervention Center for Autistic Children, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
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38
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Pinto SC, Stojilković B, Zhang X, Sablowski R. Plant cell size: Links to cell cycle, differentiation and ploidy. Curr Opin Plant Biol 2024; 78:102527. [PMID: 38484440 DOI: 10.1016/j.pbi.2024.102527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/07/2024]
Abstract
Cell size affects many processes, including exchange of nutrients and external signals, cell division and tissue mechanics. Across eukaryotes, cells have evolved mechanisms that assess their own size to inform processes such as cell cycle progression or gene expression. Here, we review recent progress in understanding plant cell size regulation and its implications, relating these findings to work in other eukaryotes. Highlights include use of DNA contents as reference point to control the cell cycle in shoot meristems, a size-dependent cell fate decision during stomatal development and insights into the interconnection between ploidy, cell size and cell wall mechanics.
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Affiliation(s)
- Sara C Pinto
- Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | | | - Xinyu Zhang
- Cell and Developmental Biology, John Innes Centre, Norwich, UK
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Li Z, Jin S, Xu T, Chen H, Cai W, Du J, Qiu J, Zhuang S, Qi Y, Gu W, Pang L. Effects of Seipin on Mouse Mesenchymal Stem Cell Osteo-Adipogenic Balance. Stem Cells Dev 2024; 33:177-188. [PMID: 38386508 DOI: 10.1089/scd.2023.0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
Seipin deficiency is an important cause of type 2 Berardinelli-Seip congenital dyslipidemia (BSCL2). BSCL2 is a severe lipodystrophy syndrome with lack of adipose tissue, hepatic steatosis, insulin resistance, and normal or higher bone mineral density. Bone marrow mesenchymal stem cells (BMSCs) are believed to maintain bone and fat homeostasis by differentiating into osteoblasts and adipocytes. We aimed to explore the role of seipin in the osteogenic/adipogenic differentiation balance of BMSCs. Seipin loxP/loxP mice are used to explore metabolic disorders caused by seipin gene mutations. Compared with wild-type mice, subcutaneous fat deficiency and ectopic fat accumulation were higher in seipin knockout mice. Microcomputed tomography of the tibia revealed the increased bone content in seipin knockout mice. We generated seipin-deficient BMSCs in vitro and revealed that lipogenic genes are downregulated and osteogenic genes are upregulated in seipin-deficient BMSCs. In addition, peroxisome proliferator-activated receptor gamma (PPARγ) signaling is reduced in seipin-deficient BMSCs, while using the PPARγ activator increased the lipogenic differentiation and decreased osteogenic differentiation of seipin-deficient BMSCs. Our findings indicated that bone and lipid metabolism can be regulated by seipin through modulating the differentiation of mesenchymal stem cells. Thus, a new insight of seipin mutations in lipid metabolism disorders was revealed, providing a prospective strategy for MSC transplantation-based treatment of BSCL2.
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Affiliation(s)
- Zeying Li
- Department of Pathology, Central People's Hospital of Zhanjiang and Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Shan Jin
- Department of Pathology, Central People's Hospital of Zhanjiang and Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Tong Xu
- Department of Pathology, Central People's Hospital of Zhanjiang and Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Hongzhi Chen
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases (First Affiliated Hospital, School of Medicine, Shihezi University) Shihezi, China
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, China
| | - Wenping Cai
- Department of Pathology, Central People's Hospital of Zhanjiang and Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Jin Du
- Department of Pathology, Central People's Hospital of Zhanjiang and Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Jin Qiu
- Department of Pathology, Central People's Hospital of Zhanjiang and Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Sihui Zhuang
- Department of Pathology, Central People's Hospital of Zhanjiang and Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Yan Qi
- Department of Pathology, Central People's Hospital of Zhanjiang and Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Wenyi Gu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Australia
| | - Lijuan Pang
- Department of Pathology, Central People's Hospital of Zhanjiang and Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
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40
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Tu R, Ping Z, Liu J, Tsoi ML, Song X, Liu W, Xie T. Niche Tet maintains germline stem cells independently of dioxygenase activity. EMBO J 2024; 43:1570-1590. [PMID: 38499787 PMCID: PMC11021519 DOI: 10.1038/s44318-024-00074-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Ten-eleven translocation (TET) proteins are dioxygenases that convert 5-methylcytosine (5mC) into 5-hydroxylmethylcytosine (5hmC) in DNA and RNA. However, their involvement in adult stem cell regulation remains unclear. Here, we identify a novel enzymatic activity-independent function of Tet in the Drosophila germline stem cell (GSC) niche. Tet activates the expression of Dpp, the fly homologue of BMP, in the ovary stem cell niche, thereby controlling GSC self-renewal. Depletion of Tet disrupts Dpp production, leading to premature GSC loss. Strikingly, both wild-type and enzyme-dead mutant Tet proteins rescue defective BMP signaling and GSC loss when expressed in the niche. Mechanistically, Tet interacts directly with Bap55 and Stat92E, facilitating recruitment of the Polybromo Brahma associated protein (PBAP) complex to the dpp enhancer and activating Dpp expression. Furthermore, human TET3 can effectively substitute for Drosophila Tet in the niche to support BMP signaling and GSC self-renewal. Our findings highlight a conserved novel catalytic activity-independent role of Tet as a scaffold protein in supporting niche signaling for adult stem cell self-renewal.
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Affiliation(s)
- Renjun Tu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China
| | - Zhaohua Ping
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO, USA
| | - Jian Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Centre, Shenzhen, Guangdong, China
| | - Man Lung Tsoi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, New Territories, Hong Kong Special Administrative Region, China
| | - Xiaoqing Song
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO, USA
| | - Wei Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Centre, Shenzhen, Guangdong, China
| | - Ting Xie
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China.
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO, USA.
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41
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Pollex T, Rabinowitz A, Gambetta MC, Marco-Ferreres R, Viales RR, Jankowski A, Schaub C, Furlong EEM. Enhancer-promoter interactions become more instructive in the transition from cell-fate specification to tissue differentiation. Nat Genet 2024; 56:686-696. [PMID: 38467791 PMCID: PMC11018526 DOI: 10.1038/s41588-024-01678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/31/2024] [Indexed: 03/13/2024]
Abstract
To regulate expression, enhancers must come in proximity to their target gene. However, the relationship between the timing of enhancer-promoter (E-P) proximity and activity remains unclear, with examples of uncoupled, anticorrelated and correlated interactions. To assess this, we selected 600 characterized enhancers or promoters with tissue-specific activity in Drosophila embryos and performed Capture-C in FACS-purified myogenic or neurogenic cells during specification and tissue differentiation. This enabled direct comparison between E-P proximity and activity transitioning from OFF-to-ON and ON-to-OFF states across developmental conditions. This showed remarkably similar E-P topologies between specified muscle and neuronal cells, which are uncoupled from activity. During tissue differentiation, many new distal interactions emerge where changes in E-P proximity reflect changes in activity. The mode of E-P regulation therefore appears to change as embryogenesis proceeds, from largely permissive topologies during cell-fate specification to more instructive regulation during terminal tissue differentiation, when E-P proximity is coupled to activation.
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Affiliation(s)
- Tim Pollex
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Directors' Research Unit, Heidelberg, Germany
| | - Adam Rabinowitz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Maria Cristina Gambetta
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Raquel Marco-Ferreres
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Rebecca R Viales
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Aleksander Jankowski
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Christoph Schaub
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
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Gerosa L, Malvandi AM, Gomarasca M, Verdelli C, Sansoni V, Faraldi M, Ziemann E, Olivieri F, Banfi G, Lombardi G. Murine Myoblasts Exposed to SYUIQ-5 Acquire Senescence Phenotype and Differentiate into Sarcopenic-Like Myotubes, an In Vitro Study. J Gerontol A Biol Sci Med Sci 2024; 79:glae022. [PMID: 38267369 PMCID: PMC10924451 DOI: 10.1093/gerona/glae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Indexed: 01/26/2024] Open
Abstract
The musculoskeletal system is one of the most affected organs by aging that correlates well with an accumulation of senescent cells as for other multiple age-related pathologies. The molecular mechanisms underpinning muscle impairment because of senescent cells are still elusive. The availability of in vitro model of skeletal muscle senescence is limited and restricted to a small panel of phenotypic features of these senescent cells in vivo. Here, we developed a new in vitro model of senescent C2C12 mouse myoblasts that, when subjected to differentiation, the resulting myotubes showed sarcopenic features. To induce senescence, we used SYUIQ-5, a quindoline derivative molecule inhibitor of telomerase activity, leading to the expression of several senescent hallmarks in treated myoblasts. They had increased levels of p21 protein accordingly with the observed cell cycle arrest. Furthermore, they had enhanced SA-βgalactosidase enzyme activity and phosphorylation of p53 and histone H2AX. SYUIQ-5 senescent myoblasts had impaired differentiation potential and the resulting myotubes showed increased levels of ATROGIN-1 and MURF1, ubiquitin ligases components responsible for protein degradation, and decreased mitochondria content, typical features of sarcopenic muscles. Myotubes differentiated from senescent myoblasts cultures release increased levels of MYOSTATIN that could affect skeletal muscle cell growth. Overall, our data suggest that a greater burden of senescent muscle cells could contribute to sarcopenia. This study presents a well-defined in vitro model of muscle cell senescence useful for deeper investigation in the aging research field to discover new putative therapeutic targets and senescence biomarkers associated with the aged musculoskeletal system.
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Affiliation(s)
- Laura Gerosa
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Amir Mohammad Malvandi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Marta Gomarasca
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Chiara Verdelli
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Veronica Sansoni
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Martina Faraldi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Ewa Ziemann
- Department of Athletics, Strength and Conditioning, Poznań University of Physical Education, Poznań, Poland
| | - Fabiola Olivieri
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona, Italy
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Giuseppe Banfi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, Italy
| | - Giovanni Lombardi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
- Department of Athletics, Strength and Conditioning, Poznań University of Physical Education, Poznań, Poland
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Yang Y, Liu C, Liu N, Yang X, Liu Y, Gai Z. Generation and characterization of PBMCs-derived human induced pluripotent stem cell (iPSC) line SDQLCHi055-A from a patient with NEDSDV carrying a heterozygote mutation in the CTNNB1 gene. Stem Cell Res 2024; 76:103335. [PMID: 38364504 DOI: 10.1016/j.scr.2024.103335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/04/2024] [Indexed: 02/18/2024] Open
Abstract
Neurodevelopmental disorder with spastic diplegia and visual defects (NEDSDV, #615075), a rare autosomal dominant genetic disorder caused by heterozygous mutation in the CTNNB1 gene, is characterized by global developmental delay, impaired intellectual development, axial hypotonia, and dysmorphic craniofacial features with microcephaly. Here, we established an iPSC line (SDQLCHi055-A) from a patient with NEDSDV carrying a heterozygote mutation (c.854 T > A, p.L285*) in the CTNNB1 gene. The iPSC line has typical iPSCs characteristics, including pluripotency and trilineage differentiation hallmarks.
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Affiliation(s)
- Yanan Yang
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University (Jinan Children's Hospital), Jinan, Shandong 250022, China; Shandong Province Clinical Research Center for Children's Health and Disease, Jinan, Shandong 250022, China
| | - Chen Liu
- Shandong Province Clinical Research Center for Children's Health and Disease, Jinan, Shandong 250022, China; NICU, Children's Hospital Affiliated to Shandong University (Jinan Children's Hospital), Jinan, Shandong 250022, China
| | - Ning Liu
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University (Jinan Children's Hospital), Jinan, Shandong 250022, China; Shandong Province Clinical Research Center for Children's Health and Disease, Jinan, Shandong 250022, China
| | - Xiaomeng Yang
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University (Jinan Children's Hospital), Jinan, Shandong 250022, China; Shandong Province Clinical Research Center for Children's Health and Disease, Jinan, Shandong 250022, China
| | - Yi Liu
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University (Jinan Children's Hospital), Jinan, Shandong 250022, China; Shandong Province Clinical Research Center for Children's Health and Disease, Jinan, Shandong 250022, China
| | - Zhongtao Gai
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University (Jinan Children's Hospital), Jinan, Shandong 250022, China; Shandong Province Clinical Research Center for Children's Health and Disease, Jinan, Shandong 250022, China
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Su S, Zhao F, Zhang H, Liu Y, Li Z, Zhang H, Wang Y, Fang F, Liu Y. Establishment of a transgene-free iPS cell line (SDCHi003-A) from a young patient bearing a NPRL2 mutation and suffering from Epilepsy. Stem Cell Res 2024; 76:103366. [PMID: 38430737 DOI: 10.1016/j.scr.2024.103366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/13/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024] Open
Abstract
Epilepsy affects ∼ 65 million people worldwide. Status epilepticus can lead to life-threatening if untreated. In this study, peripheral blood mononuclear cells were isolated from a young patient patient bearing a Nitrogen Perntease Regulator Like 2 Protein (NPRL2) mutation and suffering from Epilepsy verified by clinical and genetic diagnosis. Induced pluripotent stem cells (iPSCs) were established by a non-integrative method, using plasmids carrying OCT4, SOX2, KLF4, BCL-XL and C-MYC. The established iPSCs presented typical pluripotent cells morphology, normal karyotype, and potential to differentiate into three germ layers. Our approach offers a useful model to explore pathogenesis and therapy of Epilepsy.
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Affiliation(s)
- Song Su
- Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan, Shandong 250022, China; Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong 250022, China
| | - Fen Zhao
- Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan, Shandong 250022, China; Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong 250022, China
| | - Hongwei Zhang
- Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan, Shandong 250022, China; Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong 250022, China
| | - Yi Liu
- Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan, Shandong 250022, China; Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong 250022, China
| | - Zilong Li
- Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan, Shandong 250022, China; Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong 250022, China
| | - Huan Zhang
- Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan, Shandong 250022, China; Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong 250022, China
| | - Yaping Wang
- Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan, Shandong 250022, China; Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong 250022, China
| | - Fang Fang
- Department of Neurology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing 100045, China.
| | - Yong Liu
- Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan, Shandong 250022, China; Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong 250022, China.
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Das A, Adhikary S, Chowdhury AR, Barui A. Chirality-induced Lineage Enforcement of Mechanosensitive Mesenchymal Stem Cells Across Germ Layer Boundaries. Stem Cell Rev Rep 2024; 20:755-768. [PMID: 37971671 DOI: 10.1007/s12015-023-10656-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
Mesenchymal to epithelial transition (MET) is instrumental in embryogenesis, tissue repair, and wound healing while the epithelial to mesenchymal transition (EMT) plays role in carcinogenesis. Alteration in microenvironment can modulate cellular signaling and induce EMT and MET. However, modulation of microenvironment to induce MET has been relatively less explored. In this work, effect of matrix stiffness in mediating MET in umbilical cord-derived mesenchymal stem cells (UCMSC) is investigated. Differential segregation of cell fate determinant proteins is one of the key factors in mediating altered stem cell fates through MET even though the genesis of apicobasal polarity remains ambiguous. Herein, it is also attempted to decipher if microenvironment-induced asymmetric cell division has a role to play in driving the cells toward MET. UCMSC cultured on stiffer PDMS matrices resulted in significantly (p < 0.05) higher expression of mechanotransduction proteins. It was also observed that stiffer matrices mediated significant (p < 0.05) upregulation of the polarity proteins and cell fate determinant protein, and epithelial marker proteins over lesser stiff substrates. On the contrary, expression of inflammatory and mesenchymal markers was reduced significantly (p < 0.05) on the stiffer matrices. Cell cycle analysis showed a significant increase in the G1 phase among the cells seeded on stiffer matrices. Transcriptomic studies validated higher expression of epithelial markers genes and lower expression of EMT markers. The transition from mesenchymal to epithelial phenotype depending on the gradation in matrix stiffness is successfully demonstrated. A computational machine learning model was developed to validate stiffness-MET correlation with 94% accuracy. The cross-boundary trans-lineage differentiation capability of MSC on bioengineered substrates can be used as a potential tool in tissue regeneration, organogenesis, and wound healing applications. In our present study, we deciphered the correlation between YAP/TAZ mechanotransduction pathway, EMT signaling pathway, and asymmetric cell division in mediating MET in MSC in a substrate stiffness-dependent manner. It is inferred that the stiffer PDMS matrices facilitate the transition from mesenchymal to epithelial state of MSC. Further, our study also proposed a scoring system to sort MSC from an intermediate hybrid E/M population while undergoing graded MET on matrices of different stiffnesses using a machine learning technique. This proposed scoring system can provide information regarding the E/M state of MSC on different bioengineered constructs based on their biophysical properties which may help in the proper choice of biomaterials in complex tissue-engineering applications.
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Affiliation(s)
- Ankita Das
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, India
| | - Shreya Adhikary
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, India
| | - Amit Roy Chowdhury
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, India
- Department of Aerospace and Applied Mechanics, Indian Institute of Engineering Science and Technology, Shibpur, India
| | - Ananya Barui
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, India.
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46
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Samuels TJ, Gui J, Gebert D, Karam Teixeira F. Two distinct waves of transcriptome and translatome changes drive Drosophila germline stem cell differentiation. EMBO J 2024; 43:1591-1617. [PMID: 38480936 PMCID: PMC11021484 DOI: 10.1038/s44318-024-00070-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/18/2024] Open
Abstract
The tight control of fate transitions during stem cell differentiation is essential for proper tissue development and maintenance. However, the challenges in studying sparsely distributed adult stem cells in a systematic manner have hindered efforts to identify how the multilayered regulation of gene expression programs orchestrates stem cell differentiation in vivo. Here, we synchronised Drosophila female germline stem cell (GSC) differentiation in vivo to perform in-depth transcriptome and translatome analyses at high temporal resolution. This characterisation revealed widespread and dynamic changes in mRNA level, promoter usage, exon inclusion, and translation efficiency. Transient expression of the master regulator, Bam, drives a first wave of expression changes, primarily modifying the cell cycle program. Surprisingly, as Bam levels recede, differentiating cells return to a remarkably stem cell-like transcription and translation program, with a few crucial changes feeding into a second phase driving terminal differentiation to form the oocyte. Altogether, these findings reveal that rather than a unidirectional accumulation of changes, the in vivo differentiation of stem cells relies on distinctly regulated and developmentally sequential waves.
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Affiliation(s)
- Tamsin J Samuels
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, CB2 3DY, Cambridge, UK
| | - Jinghua Gui
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, Cambridge, UK
| | - Daniel Gebert
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, CB2 3DY, Cambridge, UK
| | - Felipe Karam Teixeira
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, Cambridge, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, CB2 3DY, Cambridge, UK.
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47
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Xu L, Ramirez-Matias J, Hauptschein M, Sun ED, Lunger JC, Buckley MT, Brunet A. Restoration of neuronal progenitors by partial reprogramming in the aged neurogenic niche. Nat Aging 2024; 4:546-567. [PMID: 38553564 DOI: 10.1038/s43587-024-00594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 02/13/2024] [Indexed: 04/21/2024]
Abstract
Partial reprogramming (pulsed expression of reprogramming transcription factors) improves the function of several tissues in old mice. However, it remains largely unknown how partial reprogramming impacts the old brain. Here we use single-cell transcriptomics to systematically examine how partial reprogramming influences the subventricular zone neurogenic niche in aged mouse brains. Whole-body partial reprogramming mainly improves neuroblasts (cells committed to give rise to new neurons) in the old neurogenic niche, restoring neuroblast proportion to more youthful levels. Interestingly, targeting partial reprogramming specifically to the neurogenic niche also boosts the proportion of neuroblasts and their precursors (neural stem cells) in old mice and improves several molecular signatures of aging, suggesting that the beneficial effects of reprogramming are niche intrinsic. In old neural stem cell cultures, partial reprogramming cell autonomously restores the proportion of neuroblasts during differentiation and blunts some age-related transcriptomic changes. Importantly, partial reprogramming improves the production of new neurons in vitro and in old brains. Our work suggests that partial reprogramming could be used to rejuvenate the neurogenic niche and counter brain decline in old individuals.
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Affiliation(s)
- Lucy Xu
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Max Hauptschein
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Eric D Sun
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Judith C Lunger
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- Glenn Center for the Biology of Aging, Stanford University, Stanford, CA, USA.
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Dashti P, Lewallen EA, Gordon JAR, Montecino MA, Davie JR, Stein GS, van Leeuwen JPTM, van der Eerden BCJ, van Wijnen AJ. Epigenetic regulators controlling osteogenic lineage commitment and bone formation. Bone 2024; 181:117043. [PMID: 38341164 DOI: 10.1016/j.bone.2024.117043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/08/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Bone formation and homeostasis are controlled by environmental factors and endocrine regulatory cues that initiate intracellular signaling pathways capable of modulating gene expression in the nucleus. Bone-related gene expression is controlled by nucleosome-based chromatin architecture that limits the accessibility of lineage-specific gene regulatory DNA sequences and sequence-specific transcription factors. From a developmental perspective, bone-specific gene expression must be suppressed during the early stages of embryogenesis to prevent the premature mineralization of skeletal elements during fetal growth in utero. Hence, bone formation is initially inhibited by gene suppressive epigenetic regulators, while other epigenetic regulators actively support osteoblast differentiation. Prominent epigenetic regulators that stimulate or attenuate osteogenesis include lysine methyl transferases (e.g., EZH2, SMYD2, SUV420H2), lysine deacetylases (e.g., HDAC1, HDAC3, HDAC4, HDAC7, SIRT1, SIRT3), arginine methyl transferases (e.g., PRMT1, PRMT4/CARM1, PRMT5), dioxygenases (e.g., TET2), bromodomain proteins (e.g., BRD2, BRD4) and chromodomain proteins (e.g., CBX1, CBX2, CBX5). This narrative review provides a broad overview of the covalent modifications of DNA and histone proteins that involve hundreds of enzymes that add, read, or delete these epigenetic modifications that are relevant for self-renewal and differentiation of mesenchymal stem cells, skeletal stem cells and osteoblasts during osteogenesis.
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Affiliation(s)
- Parisa Dashti
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands; Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Eric A Lewallen
- Department of Biological Sciences, Hampton University, Hampton, VA, USA
| | | | - Martin A Montecino
- Institute of Biomedical Sciences, Faculty of Medicine, Universidad Andres Bello, Santiago, Chile; Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada; CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, Manitoba R3E 0V9, Canada.
| | - Gary S Stein
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | | | - Bram C J van der Eerden
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Andre J van Wijnen
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands; Department of Biochemistry, University of Vermont, Burlington, VT, USA.
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Wang Q, Yang X, Wang X, Wang X, Zhang J, Gao Y, Pan J, Wang S. Identifying genes for regulating osteogenic differentiation of human periodontal ligament stem cells in inflammatory environments by bioinformatics analysis. J Periodontal Res 2024; 59:311-324. [PMID: 38082497 DOI: 10.1111/jre.13215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 10/03/2023] [Accepted: 11/15/2023] [Indexed: 03/23/2024]
Abstract
BACKGROUND AND OBJECTIVES Periodontitis is an immuno-inflammatory disease caused by dental plaque biofilms and inflammations. The regeneration of bone tissue in inflammatory environment is of great significance for the treatment of periodontal disease, but the specific molecular mechanism of bone formation in periodontitis still needs further exploration. The objective of this study was to identify key osteogenesis-related genes (ORGs) in periodontitis. METHODS We used two datasets from the Gene Expression Omnibus (GEO) database to find differentially expressed mRNAs and miRNAs, further performed Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Then we predicted the downstream genes of the differentially expressed miRNAs (DEMs) by the TargetScan database and established a miRNA-mRNA regulatory network. Finally, the osteogenic mechanism of periodontitis was explored through quantitative real-time PCR (qRT-PCR) by inducing inflammatory environment and osteogenic differentiation of hPDLSCs. RESULTS Through differential expression analysis and prediction of downstream target genes of DEMs, we created a miRNA-mRNA regulatory network consisting of 29 DEMs and 11 differentially expressed osteogenesis-related genes (DEORGs). In addition, the qRT-PCR results demonstrated that BTBD3, PLAT, AKAP12, SGK1, and GLCE expression levels were significantly upregulated, while those of TIMP3, ZCCHC14, LIN7A, DNAH6, NNT, and ITGA6 were downregulated under the dual effects of inflammatory stimulation and osteogenic induction. CONCLUSION DEORGs might be important factors in the osteogenic phase of periodontitis, and the miRNA-mRNA network may shed light on the clarification of the role and mechanism of osteogenesis in periodontitis and contribute to the development of novel therapeutic strategies.
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Affiliation(s)
- Qing Wang
- Department of stomatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaojie Yang
- Department of stomatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuechun Wang
- Department of stomatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuan Wang
- Department of stomatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Zhang
- Department of stomatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ya Gao
- Department of stomatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinsong Pan
- Department of stomatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shiwei Wang
- Department of stomatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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50
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Itoh T, Uehara M, Yura S, Wang JC, Fujii Y, Nakanishi A, Shimizu T, Hibi M. Foxp and Skor family proteins control differentiation of Purkinje cells from Ptf1a- and Neurog1-expressing progenitors in zebrafish. Development 2024; 151:dev202546. [PMID: 38456494 DOI: 10.1242/dev.202546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/01/2024] [Indexed: 03/09/2024]
Abstract
Cerebellar neurons, such as GABAergic Purkinje cells (PCs), interneurons (INs) and glutamatergic granule cells (GCs) are differentiated from neural progenitors expressing proneural genes, including ptf1a, neurog1 and atoh1a/b/c. Studies in mammals previously suggested that these genes determine cerebellar neuron cell fate. However, our studies on ptf1a;neurog1 zebrafish mutants and lineage tracing of ptf1a-expressing progenitors have revealed that the ptf1a/neurog1-expressing progenitors can generate diverse cerebellar neurons, including PCs, INs and a subset of GCs in zebrafish. The precise mechanisms of how each cerebellar neuron type is specified remains elusive. We found that genes encoding the transcriptional regulators Foxp1b, Foxp4, Skor1b and Skor2, which are reportedly expressed in PCs, were absent in ptf1a;neurog1 mutants. foxp1b;foxp4 mutants showed a strong reduction in PCs, whereas skor1b;skor2 mutants completely lacked PCs, and displayed an increase in immature GCs. Misexpression of skor2 in GC progenitors expressing atoh1c suppressed GC fate. These data indicate that Foxp1b/4 and Skor1b/2 function as key transcriptional regulators in the initial step of PC differentiation from ptf1a/neurog1-expressing neural progenitors, and that Skor1b and Skor2 control PC differentiation by suppressing their differentiation into GCs.
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Affiliation(s)
- Tsubasa Itoh
- Department of Biological Science, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Mari Uehara
- Department of Biological Science, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Shinnosuke Yura
- Department of Biological Science, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Jui Chun Wang
- Department of Biological Science, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Yukimi Fujii
- Department of Biological Science, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Akiko Nakanishi
- Department of Biological Science, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Takashi Shimizu
- Department of Biological Science, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Masahiko Hibi
- Department of Biological Science, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8602, Japan
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