1
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Chand S, Tripathi AS, Dewani AP, Sheikh NWA. Molecular targets for management of diabetes: Remodelling of white adipose to brown adipose tissue. Life Sci 2024; 345:122607. [PMID: 38583857 DOI: 10.1016/j.lfs.2024.122607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/09/2024]
Abstract
Diabetes mellitus is a disorder characterised metabolic dysfunction that results in elevated glucose level in the bloodstream. Diabetes is of two types, type1 and type 2 diabetes. Obesity is considered as one of the major reasons intended for incidence of diabetes hence it turns out to be essential to study about the adipose tissue which is responsible for fat storage in body. Adipose tissues play significant role in maintaining the balance between energy stabilization and homeostasis. The three forms of adipose tissue are - White adipose tissue (WAT), Brown adipose tissue (BAT) and Beige adipose tissue (intermediate form). The amount of BAT gets reduced, and WAT starts to increase with the age. WAT when exposed to certain stimuli gets converted to BAT by the help of certain transcriptional regulators. The browning of WAT has been a matter of study to treat the metabolic disorders and to initiate the expenditure of energy. The three main regulators responsible for the browning of WAT are PRDM16, PPARγ and PGC-1α via various cellular and molecular mechanism. Presented review article includes the detailed elaborative aspect of genes and proteins involved in conversion of WAT to BAT.
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Affiliation(s)
- Shushmita Chand
- Amity Institute of Pharmacy, Amity University, Sector 125, Noida, Uttar Pradesh, India
| | - Alok Shiomurti Tripathi
- Department of Pharmacology, ERA College of Pharmacy, ERA University, Lucknow, Uttar Pradesh, India.
| | - Anil P Dewani
- Department of Pharmacology, P. Wadhwani College of Pharmacy, Yavatmal, Maharashtra, India
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2
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Leite DJ, Schönauer A, Blakeley G, Harper A, Garcia-Castro H, Baudouin-Gonzalez L, Wang R, Sarkis N, Nikola AG, Koka VSP, Kenny NJ, Turetzek N, Pechmann M, Solana J, McGregor AP. An atlas of spider development at single-cell resolution provides new insights into arthropod embryogenesis. EvoDevo 2024; 15:5. [PMID: 38730509 PMCID: PMC11083766 DOI: 10.1186/s13227-024-00224-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/15/2024] [Indexed: 05/13/2024] Open
Abstract
Spiders are a diverse order of chelicerates that diverged from other arthropods over 500 million years ago. Research on spider embryogenesis, particularly studies using the common house spider Parasteatoda tepidariorum, has made important contributions to understanding the evolution of animal development, including axis formation, segmentation, and patterning. However, we lack knowledge about the cells that build spider embryos, their gene expression profiles and fate. Single-cell transcriptomic analyses have been revolutionary in describing these complex landscapes of cellular genetics in a range of animals. Therefore, we carried out single-cell RNA sequencing of P. tepidariorum embryos at stages 7, 8 and 9, which encompass the establishment and patterning of the body plan, and initial differentiation of many tissues and organs. We identified 20 cell clusters, from 18.5 k cells, which were marked by many developmental toolkit genes, as well as a plethora of genes not previously investigated. We found differences in the cell cycle transcriptional signatures, suggestive of different proliferation dynamics, which related to distinctions between endodermal and some mesodermal clusters, compared with ectodermal clusters. We identified many Hox genes as markers of cell clusters, and Hox gene ohnologs were often present in different clusters. This provided additional evidence of sub- and/or neo-functionalisation of these important developmental genes after the whole genome duplication in an arachnopulmonate ancestor (spiders, scorpions, and related orders). We also examined the spatial expression of marker genes for each cluster to generate a comprehensive cell atlas of these embryonic stages. This revealed new insights into the cellular basis and genetic regulation of head patterning, hematopoiesis, limb development, gut development, and posterior segmentation. This atlas will serve as a platform for future analysis of spider cell specification and fate, and studying the evolution of these processes among animals at cellular resolution.
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Affiliation(s)
- Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK.
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Grace Blakeley
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Amber Harper
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Helena Garcia-Castro
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | | | - Ruixun Wang
- Institute for Zoology, Biocenter, University of Cologne, Zuelpicher Str. 47B, 50674, Cologne, Germany
| | - Naïra Sarkis
- Institute for Zoology, Biocenter, University of Cologne, Zuelpicher Str. 47B, 50674, Cologne, Germany
| | - Alexander Günther Nikola
- Evolutionary Ecology, Faculty of Biology, Biocenter, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Venkata Sai Poojitha Koka
- Evolutionary Ecology, Faculty of Biology, Biocenter, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Nathan J Kenny
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
- Department of Biochemistry Te Tari Matū Koiora, University of Otago, Dunedin, New Zealand
| | - Natascha Turetzek
- Evolutionary Ecology, Faculty of Biology, Biocenter, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Matthias Pechmann
- Institute for Zoology, Biocenter, University of Cologne, Zuelpicher Str. 47B, 50674, Cologne, Germany
| | - Jordi Solana
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK.
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3
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Zhang J, Kong J, Cao J, Dai P, Chen B, Tan J, Meng X, Luo K, Fu Q, Wei P, Luan S, Sui J. Reproductive Ability Disparity in the Pacific Whiteleg Shrimp ( Penaeus vannamei): Insights from Ovarian Cellular and Molecular Levels. BIOLOGY 2024; 13:218. [PMID: 38666830 PMCID: PMC11048709 DOI: 10.3390/biology13040218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
The Pacific whiteleg shrimp (Penaeus vannamei) is a highly significant species in shrimp aquaculture. In the production of shrimp larvae, noticeable variations in the reproductive capacity among female individuals have been observed. Some females experience slow gonadal development, resulting in the inability to spawn, while others undergo multiple maturations and contribute to the majority of larval supply. Despite numerous studies that have been conducted on the regulatory mechanisms of ovarian development in shrimp, the factors contributing to the differences in reproductive capacity among females remain unclear. To elucidate the underlying mechanisms, this study examined the differences in the ovarian characteristics between high and low reproductive bulks at different maturity stages, focusing on the cellular and molecular levels. Transmission electron microscopy analysis revealed that the abundance of the endoplasmic reticulum, ribosomes, mitochondria, and mitochondrial cristae in oocytes of high reproductive bulk was significantly higher than that of the low reproductive bulk in the early stages of ovarian maturation (stages I and II). As the ovaries progressed to late-stage maturation (stages III and IV), differences in the internal structures of oocytes between females with different reproductive capacities gradually diminished. Transcriptome analysis identified differentially expressed genes (DEGs) related to the mitochondria between two groups, suggesting that energy production processes might play a crucial role in the observed variations in ovary development. The expression levels of the ETS homology factor (EHF) and PRDI-BF1 and RIZ homology domain containing 9 (PRDM9), which were significantly different between the two groups, were compared using qRT-PCR in individuals at different stages of ovarian maturation. The results showed a significantly higher expression of the EHF gene in the ovaries of high reproductive bulk at the II and IV maturity stages compared to the low reproductive bulk, while almost no expression was detected in the eyestalk tissue of the high reproductive bulk. The PRDM9 gene was exclusively expressed in ovarian tissue, with significantly higher expression in the ovaries of the high reproductive bulk at the four maturity stages compared to the low reproductive bulk. Fluorescence in situ hybridization further compared the expression patterns of EHF and PRDM9 in the ovaries of individuals with different fertility levels, with both genes showing stronger positive signals in the high reproductive bulk at the four ovarian stages. These findings not only contribute to our understanding of the regulatory mechanisms involved in shrimp ovarian development, but also provide valuable insights for the cultivation of new varieties aimed at improving shrimp fecundity.
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Affiliation(s)
- Jianchun Zhang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Jie Kong
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Jiawang Cao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Ping Dai
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Baolong Chen
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Jian Tan
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Xianhong Meng
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Kun Luo
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Qiang Fu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Peiming Wei
- BLUP Aquabreed Co., Ltd., Weifang 261312, China
| | - Sheng Luan
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Juan Sui
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
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4
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Gautam S, Fenner JL, Wang B, Range RC. Evolutionarily conserved Wnt/Sp5 signaling is critical for anterior-posterior axis patterning in sea urchin embryos. iScience 2024; 27:108616. [PMID: 38179064 PMCID: PMC10765061 DOI: 10.1016/j.isci.2023.108616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/30/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Studies across a diverse group of metazoan embryos indicate that Wnt signaling often activates the transcription factor Sp5, forming a signaling 'cassette' that plays critical roles in many developmental processes. This study explores the role of Wnt/Sp5 signaling during the specification and patterning of the primary germ layers during early anterior-posterior axis formation in the deuterostome sea urchin embryo. Our functional analyses show that Sp5 is critical for endomesoderm specification downstream of Wnt/β-catenin in posterior cells as well as anterior neuroectoderm patterning downstream of non-canonical Wnt/JNK signaling in anterior cells. Interestingly, expression and functional data comparisons show that Wnt/Sp5 signaling often plays similar roles in posterior endomesoderm as well as neuroectoderm patterning along the AP axis of several deuterostome embryos, including vertebrates. Thus, our findings provide strong support for the idea that Wnt-Sp5 signaling cassettes were critical for the establishment of early germ layers in the common deuterostome ancestor.
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Affiliation(s)
- Sujan Gautam
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jennifer L. Fenner
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Boyuan Wang
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ryan C. Range
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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5
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Brand M, Ritzmann F, Kattler K, Milasius D, Yao Y, Herr C, Kirsch SH, Müller R, Yildiz D, Bals R, Beisswenger C. Biochemical and transcriptomic evaluation of a 3D lung organoid platform for pre-clinical testing of active substances targeting senescence. Respir Res 2024; 25:3. [PMID: 38172839 PMCID: PMC10765931 DOI: 10.1186/s12931-023-02636-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Chronic lung diseases such as chronic obstructive pulmonary disease and cystic fibrosis are incurable. Epithelial senescence, a state of dysfunctional cell cycle arrest, contributes to the progression of such diseases. Therefore, lung epithelial cells are a valuable target for therapeutic intervention. Here, we present a 3D airway lung organoid platform for the preclinical testing of active substances with regard to senescence, toxicity, and inflammation under standardized conditions in a 96 well format. Senescence was induced with doxorubicin and measured by activity of senescence associated galactosidase. Pharmaceutical compounds such as quercetin antagonized doxorubicin-induced senescence without compromising organoid integrity. Using single cell sequencing, we identified a subset of cells expressing senescence markers which was decreased by quercetin. Doxorubicin induced the expression of detoxification factors specifically in goblet cells independent of quercetin. In conclusion, our platform enables for the analysis of senescence-related processes and will allow the pre-selection of a wide range of compounds (e.g. natural products) in preclinical studies, thus reducing the need for animal testing.
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Affiliation(s)
- Michelle Brand
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421, Homburg, Germany
| | - Felix Ritzmann
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421, Homburg, Germany
- Department of Drug Delivery (DDEL), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123, Saarbrücken, Germany
| | - Kathrin Kattler
- Department of Genetics/Epigenetics, Saarland University, 66123, Saarbrücken, Germany
| | - Deivydas Milasius
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421, Homburg, Germany
| | - Yiwen Yao
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421, Homburg, Germany
| | - Christian Herr
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421, Homburg, Germany
| | - Susanne H Kirsch
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123, Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Daniela Yildiz
- Experimental and Clinical Pharmacology and Toxicology, PZMS, and Center for Human and Molecular Biology (ZHMB), Saarland University, 66421, Homburg, Germany
| | - Robert Bals
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421, Homburg, Germany
- Department of Drug Delivery (DDEL), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123, Saarbrücken, Germany
| | - Christoph Beisswenger
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421, Homburg, Germany.
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6
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Tsimpos P, Desiderio S, Cabochette P, Poelvoorde P, Kricha S, Vanhamme L, Poulard C, Bellefroid EJ. Loss of G9a does not phenocopy the requirement for Prdm12 in the development of the nociceptive neuron lineage. Neural Dev 2024; 19:1. [PMID: 38167468 PMCID: PMC10759634 DOI: 10.1186/s13064-023-00179-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
Prdm12 is an epigenetic regulator expressed in developing and mature nociceptive neurons, playing a key role in their specification during neurogenesis and modulating pain sensation at adulthood. In vitro studies suggested that Prdm12 recruits the methyltransferase G9a through its zinc finger domains to regulate target gene expression, but how Prdm12 interacts with G9a and whether G9a plays a role in Prdm12's functional properties in sensory ganglia remain unknown. Here we report that Prdm12-G9a interaction is likely direct and that it involves the SET domain of G9a. We show that both proteins are largely co-expressed in dorsal root ganglia during early murine development, opening the possibility that G9a plays a role in DRG and may act as a mediator of Prdm12's function in the development of nociceptive sensory neurons. To test this hypothesis, we conditionally inactivated G9a in neural crest using a Wnt1-Cre transgenic mouse line. We found that the specific loss of G9a in the neural crest lineage does not lead to dorsal root ganglia hypoplasia due to the loss of somatic nociceptive neurons nor to the ectopic expression of the visceral determinant Phox2b as observed upon Prdm12 ablation. These findings suggest that Prdm12 function in the initiation of the nociceptive lineage does not critically involves its interaction with G9a.
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Affiliation(s)
- Panagiotis Tsimpos
- ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Gosselies, B- 6041, Belgium
| | - Simon Desiderio
- ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Gosselies, B- 6041, Belgium
| | - Pauline Cabochette
- ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Gosselies, B- 6041, Belgium
| | - Philippe Poelvoorde
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Sadia Kricha
- ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Gosselies, B- 6041, Belgium
| | - Luc Vanhamme
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Coralie Poulard
- Cancer Research Cancer of Lyon, Université de Lyon, Lyon, F-69000, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, F-69000, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, F-69000, France
| | - Eric J Bellefroid
- ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Gosselies, B- 6041, Belgium.
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He H, Bell SM, Davis AK, Zhao S, Sridharan A, Na CL, Guo M, Xu Y, Snowball J, Swarr DT, Zacharias WJ, Whitsett JA. PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiation and Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.570481. [PMID: 38187557 PMCID: PMC10769259 DOI: 10.1101/2023.12.20.570481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Differential chromatin accessibility accompanies and mediates transcriptional control of diverse cell fates and their differentiation during embryogenesis. While the critical role of NKX2-1 and its transcriptional targets in lung morphogenesis and pulmonary epithelial cell differentiation is increasingly known, mechanisms by which chromatin accessibility alters the epigenetic landscape and how NKX2-1 interacts with other co-activators required for alveolar epithelial cell differentiation and function are not well understood. Here, we demonstrate that the paired domain zinc finger transcriptional regulators PRDM3 and PRDM16 regulate chromatin accessibility to mediate cell differentiation decisions during lung morphogenesis. Combined deletion of Prdm3 and Prdm16 in early lung endoderm caused perinatal lethality due to respiratory failure from loss of AT2 cell function. Prdm3/16 deletion led to the accumulation of partially differentiated AT1 cells and loss of AT2 cells. Combination of single cell RNA-seq, bulk ATAC-seq, and CUT&RUN demonstrated that PRDM3 and PRDM16 enhanced chromatin accessibility at NKX2-1 transcriptional targets in peripheral epithelial cells, all three factors binding together at a multitude of cell-type specific cis-active DNA elements. Network analysis demonstrated that PRDM3/16 regulated genes critical for perinatal AT2 cell differentiation, surfactant homeostasis, and innate host defense. Lineage specific deletion of PRDM3/16 in AT2 cells led to lineage infidelity, with PRDM3/16 null cells acquiring partial AT1 fate. Together, these data demonstrate that NKX2-1-dependent regulation of alveolar epithelial cell differentiation is mediated by epigenomic modulation via PRDM3/16.
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Affiliation(s)
- Hua He
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, West China Second University Hospital Sichuan University, Chengdu, Sichuan, 610041, China
- NHC Key Laboratory of Chronobiology, Sichuan University, Sichuan 610041, China
| | - Sheila M. Bell
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
| | - Ashley Kuenzi Davis
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
| | - Shuyang Zhao
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
| | - Anusha Sridharan
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
| | - Cheng-Lun Na
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
| | - Minzhe Guo
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - Yan Xu
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - John Snowball
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
| | - Daniel T. Swarr
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - William J. Zacharias
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - Jeffrey A. Whitsett
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
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8
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Yao Z, van Velthoven CTJ, Kunst M, Zhang M, McMillen D, Lee C, Jung W, Goldy J, Abdelhak A, Aitken M, Baker K, Baker P, Barkan E, Bertagnolli D, Bhandiwad A, Bielstein C, Bishwakarma P, Campos J, Carey D, Casper T, Chakka AB, Chakrabarty R, Chavan S, Chen M, Clark M, Close J, Crichton K, Daniel S, DiValentin P, Dolbeare T, Ellingwood L, Fiabane E, Fliss T, Gee J, Gerstenberger J, Glandon A, Gloe J, Gould J, Gray J, Guilford N, Guzman J, Hirschstein D, Ho W, Hooper M, Huang M, Hupp M, Jin K, Kroll M, Lathia K, Leon A, Li S, Long B, Madigan Z, Malloy J, Malone J, Maltzer Z, Martin N, McCue R, McGinty R, Mei N, Melchor J, Meyerdierks E, Mollenkopf T, Moonsman S, Nguyen TN, Otto S, Pham T, Rimorin C, Ruiz A, Sanchez R, Sawyer L, Shapovalova N, Shepard N, Slaughterbeck C, Sulc J, Tieu M, Torkelson A, Tung H, Valera Cuevas N, Vance S, Wadhwani K, Ward K, Levi B, Farrell C, Young R, Staats B, Wang MQM, Thompson CL, Mufti S, Pagan CM, Kruse L, Dee N, Sunkin SM, Esposito L, Hawrylycz MJ, Waters J, Ng L, Smith K, Tasic B, Zhuang X, Zeng H. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature 2023; 624:317-332. [PMID: 38092916 PMCID: PMC10719114 DOI: 10.1038/s41586-023-06812-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
The mammalian brain consists of millions to billions of cells that are organized into many cell types with specific spatial distribution patterns and structural and functional properties1-3. Here we report a comprehensive and high-resolution transcriptomic and spatial cell-type atlas for the whole adult mouse brain. The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.0 million cells passing quality control), and a spatial transcriptomic dataset of approximately 4.3 million cells using multiplexed error-robust fluorescence in situ hybridization (MERFISH). The atlas is hierarchically organized into 4 nested levels of classification: 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters. We present an online platform, Allen Brain Cell Atlas, to visualize the mouse whole-brain cell-type atlas along with the single-cell RNA-sequencing and MERFISH datasets. We systematically analysed the neuronal and non-neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell-type organization in different brain regions-in particular, a dichotomy between the dorsal and ventral parts of the brain. The dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. Our study also uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types. Finally, we found that transcription factors are major determinants of cell-type classification and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole mouse brain transcriptomic and spatial cell-type atlas establishes a benchmark reference atlas and a foundational resource for integrative investigations of cellular and circuit function, development and evolution of the mammalian brain.
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Affiliation(s)
- Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA.
| | | | | | - Meng Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Won Jung
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Pamela Baker
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Daniel Carey
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Min Chen
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Scott Daniel
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - James Gee
- University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Jessica Gloe
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - James Gray
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Windy Ho
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Mike Huang
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kelly Jin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Arielle Leon
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Su Li
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zach Madigan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Zoe Maltzer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Naomi Martin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Rachel McCue
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ryan McGinty
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nicholas Mei
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jose Melchor
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Sven Otto
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Lane Sawyer
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Noah Shepard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Shane Vance
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Rob Young
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Staats
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA.
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9
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Wells AC, Lotfipour S. Prenatal nicotine exposure during pregnancy results in adverse neurodevelopmental alterations and neurobehavioral deficits. ADVANCES IN DRUG AND ALCOHOL RESEARCH 2023; 3:11628. [PMID: 38389806 PMCID: PMC10880762 DOI: 10.3389/adar.2023.11628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/28/2023] [Indexed: 02/24/2024]
Abstract
Maternal tobacco use and nicotine exposure during pregnancy have been associated with adverse birth outcomes in infants and can lead to preventable pregnancy complications. Exposure to nicotine and other compounds in tobacco and electronic cigarettes (e-cigarettes) has been shown to increases the risk of miscarriage, prematurity, stillbirth, low birth weight, perinatal morbidity, and sudden infant death syndrome (SIDS). Additionally, recent data provided by clinical and pre-clinical research demonstrates that nicotine exposure during pregnancy may heighten the risk for adverse neurodevelopmental disorders such as Attention-Deficit Hyperactivity (ADHD), anxiety, and depression along with altering the infants underlying brain circuitry, response to neurotransmitters, and brain volume. In the United States, one in 14 women (7.2%) reported to have smoked cigarettes during their pregnancy with the global prevalence of smoking during pregnancy estimated to be 1.7%. Approximately 1.1% of women in the United States also reported to have used e-cigarettes during the last 3 months of pregnancy. Due to the large percentage of women utilizing nicotine products during pregnancy in the United States and globally, this review seeks to centralize pre-clinical and clinical studies focused on the neurobehavioral and neurodevelopmental complications associated with prenatal nicotine exposure (PNE) such as alterations to the hypothalamic-pituitary-adrenal (HPA) axis and brain regions such as the prefrontal cortex (PFC), ventral tegmental area (VTA), nucleus accumbens (NA), hippocampus, and caudate as well as changes to nAChR and cholinergic receptor signaling, long-term drug seeking behavior following PNE, and other related developmental disorders. Current literature analyzing the association between PNE and the risk for offspring developing schizophrenia, attention-deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD), anxiety, and obesity will also be discussed.
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Affiliation(s)
- Alicia C Wells
- School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Shahrdad Lotfipour
- School of Medicine, University of California, Irvine, Irvine, CA, United States
- Department of Emergency Medicine, Pharmaceutical Sciences, Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, United States
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10
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Lemaître QIB, Bartsch N, Kouzel IU, Busengdal H, Richards GS, Steinmetz PRH, Rentzsch F. NvPrdm14d-expressing neural progenitor cells contribute to non-ectodermal neurogenesis in Nematostella vectensis. Nat Commun 2023; 14:4854. [PMID: 37563174 PMCID: PMC10415408 DOI: 10.1038/s41467-023-39789-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 06/29/2023] [Indexed: 08/12/2023] Open
Abstract
Neurogenesis has been studied extensively in the ectoderm, from which most animals generate the majority of their neurons. Neurogenesis from non-ectodermal tissue is, in contrast, poorly understood. Here we use the cnidarian Nematostella vectensis as a model to provide new insights into the molecular regulation of non-ectodermal neurogenesis. We show that the transcription factor NvPrdm14d is expressed in a subpopulation of NvSoxB(2)-expressing endodermal progenitor cells and their NvPOU4-expressing progeny. Using a new transgenic reporter line, we show that NvPrdm14d-expressing cells give rise to neurons in the body wall and in close vicinity of the longitudinal retractor muscles. RNA-sequencing of NvPrdm14d::GFP-expressing cells and gene knockdown experiments provide candidate genes for the development and function of these neurons. Together, the identification of a population of endoderm-specific neural progenitor cells and of previously undescribed putative motoneurons in Nematostella provide new insights into the regulation of non-ectodermal neurogenesis.
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Affiliation(s)
- Quentin I B Lemaître
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
| | - Natascha Bartsch
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
- Department for Biological Sciences, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
| | - Ian U Kouzel
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
| | - Henriette Busengdal
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
| | - Gemma Sian Richards
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
| | | | - Fabian Rentzsch
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway.
- Department for Biological Sciences, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway.
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11
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Zhao F, Guo X, Li X, Liu F, Fu Y, Sun X, Yang Z, Zhang Z, Qin Z. Identification and Expressional Analysis of Putative PRDI-BF1 and RIZ Homology Domain-Containing Transcription Factors in Mulinia lateralis. BIOLOGY 2023; 12:1059. [PMID: 37626944 PMCID: PMC10451705 DOI: 10.3390/biology12081059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
Mollusca represents one of the ancient bilaterian groups with high morphological diversity, while the formation mechanisms of the precursors of all germ cells, primordial germ cells (PGCs), have not yet been clarified in mollusks. PRDI-BF1 and RIZ homology domain-containing proteins (PRDMs) are a group of transcriptional repressors, and PRDM1 (also known as BLIMP1) and PRDM14 have been reported to be essential for the formation of PGCs. In the present study, we performed a genome-wide retrieval in Mulinia lateralis and identified 11 putative PRDMs, all of which possessed an N-terminal PR domain. Expressional profiles revealed that all these prdm genes showed specifically high expression levels in the given stages, implying that all PRDMs played important roles during early development stages. Specifically, Ml-prdm1 was highly expressed at the gastrula stage, the key period when PGCs arise, and was specifically localized in the cytoplasm of two or three cells of blastula, gastrula, or trochophore larvae, matching the typical characteristics of PGCs. These results suggested that Ml-prdm1-positive cells may be PGCs and that Ml-prdm1 could be a candidate marker for tracing the formation of PGCs in M. lateralis. In addition, the expression profiles of Ml-prdm14 hinted that it may not be associated with PGCs of M. lateralis. The present study provides insights into the evolution of the PRDM family in mollusks and offers a better understanding of the formation of PGCs in mollusks.
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Affiliation(s)
- Feng Zhao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Xiaolin Guo
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Xixi Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Fang Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Yifan Fu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Xiaohan Sun
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Zujing Yang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Zhenkui Qin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
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12
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García de Oteyza G, Fernández Engroba J, Charoenrook V. New ZNF469 Mutations in Spanish Siblings With Brittle Cornea Syndrome. Cornea 2023:00003226-990000000-00280. [PMID: 37098112 DOI: 10.1097/ico.0000000000003280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/05/2023] [Indexed: 04/27/2023]
Abstract
PURPOSE The aim of this study was to describe the clinical, tomographic, and genetic findings of 2 Spanish siblings with brittle cornea syndrome and report a new mutation of gene ZNF469 implicated in the development of this disorder. METHODS In this study, 2 male siblings who had been diagnosed with brittle cornea syndrome underwent ophthalmologic and genetic assessment. RESULTS A novel homozygous deletion c.2972del, p.(Pro991Hisfs62) in the ZNF469 gene was identified in a Spanish family. CONCLUSIONS This is the first report of a ZNF469 mutation in a Spanish family causing brittle cornea syndrome. The discovery of this new mutation amplifies the spectrum of ZNF469 variants implicated in this syndrome.
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Affiliation(s)
- Gonzalo García de Oteyza
- Centro de Oftalmología Barraquer, Barcelona, Spain; and
- Institut Universitari Barraquer. Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jorge Fernández Engroba
- Centro de Oftalmología Barraquer, Barcelona, Spain; and
- Institut Universitari Barraquer. Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Victor Charoenrook
- Centro de Oftalmología Barraquer, Barcelona, Spain; and
- Institut Universitari Barraquer. Universitat Autònoma de Barcelona, Barcelona, Spain
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13
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Kumar A, Kos MZ, Roybal D, Carless MA. A pilot investigation of differential hydroxymethylation levels in patient-derived neural stem cells implicates altered cortical development in bipolar disorder. Front Psychiatry 2023; 14:1077415. [PMID: 37139321 PMCID: PMC10150707 DOI: 10.3389/fpsyt.2023.1077415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/24/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction Bipolar disorder (BD) is a chronic mental illness characterized by recurrent episodes of mania and depression and associated with social and cognitive disturbances. Environmental factors, such as maternal smoking and childhood trauma, are believed to modulate risk genotypes and contribute to the pathogenesis of BD, suggesting a key role in epigenetic regulation during neurodevelopment. 5-hydroxymethylcytosine (5hmC) is an epigenetic variant of particular interest, as it is highly expressed in the brain and is implicated in neurodevelopment, and psychiatric and neurological disorders. Methods Induced pluripotent stem cells (iPSCs) were generated from the white blood cells of two adolescent patients with bipolar disorder and their same-sex age-matched unaffected siblings (n = 4). Further, iPSCs were differentiated into neuronal stem cells (NSCs) and characterized for purity using immuno-fluorescence. We used reduced representation hydroxymethylation profiling (RRHP) to perform genome-wide 5hmC profiling of iPSCs and NSCs, to model 5hmC changes during neuronal differentiation and assess their impact on BD risk. Functional annotation and enrichment testing of genes harboring differentiated 5hmC loci were performed with the online tool DAVID. Results Approximately 2 million sites were mapped and quantified, with the majority (68.8%) located in genic regions, with elevated 5hmC levels per site observed for 3' UTRs, exons, and 2-kb shorelines of CpG islands. Paired t-tests of normalized 5hmC counts between iPSC and NSC cell lines revealed global hypo-hydroxymethylation in NSCs and enrichment of differentially hydroxymethylated sites within genes associated with plasma membrane (FDR = 9.1 × 10-12) and axon guidance (FDR = 2.1 × 10-6), among other neuronal processes. The most significant difference was observed for a transcription factor binding site for the KCNK9 gene (p = 8.8 × 10-6), encoding a potassium channel protein involved in neuronal activity and migration. Protein-protein-interaction (PPI) networking showed significant connectivity (p = 3.2 × 10-10) between proteins encoded by genes harboring highly differentiated 5hmC sites, with genes involved in axon guidance and ion transmembrane transport forming distinct sub-clusters. Comparison of NSCs of BD cases and unaffected siblings revealed additional patterns of differentiation in hydroxymethylation levels, including sites in genes with functions related to synapse formation and regulation, such as CUX2 (p = 2.4 × 10-5) and DOK-7 (p = 3.6 × 10-3), as well as an enrichment of genes involved in the extracellular matrix (FDR = 1.0 × 10-8). Discussion Together, these preliminary results lend evidence toward a potential role for 5hmC in both early neuronal differentiation and BD risk, with validation and more comprehensive characterization to be achieved through follow-up study.
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Affiliation(s)
- Ashish Kumar
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Mark Z. Kos
- South Texas Diabetes and Obesity Institute, Department of Human Genetics, The University of Texas Rio Grande Valley School of Medicine, San Antonio, TX, United States
| | - Donna Roybal
- Traditions Behavioral Health, Larkspur, CA, United States
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Melanie A. Carless
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- Brain Health Consortium, The University of Texas at San Antonio, San Antonio, TX, United States
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14
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Truong BT, Shull LC, Lencer E, Bend EG, Field M, Blue EE, Bamshad MJ, Skinner C, Everman D, Schwartz CE, Flanagan-Steet H, Artinger KB. PRDM1 DNA-binding zinc finger domain is required for normal limb development and is disrupted in split hand/foot malformation. Dis Model Mech 2023; 16:dmm049977. [PMID: 37083955 PMCID: PMC10151829 DOI: 10.1242/dmm.049977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/09/2023] [Indexed: 04/22/2023] Open
Abstract
Split hand/foot malformation (SHFM) is a rare limb abnormality with clefting of the fingers and/or toes. For many individuals, the genetic etiology is unknown. Through whole-exome and targeted sequencing, we detected three novel variants in a gene encoding a transcription factor, PRDM1, that arose de novo in families with SHFM or segregated with the phenotype. PRDM1 is required for limb development; however, its role is not well understood and it is unclear how the PRDM1 variants affect protein function. Using transient and stable overexpression rescue experiments in zebrafish, we show that the variants disrupt the proline/serine-rich and DNA-binding zinc finger domains, resulting in a dominant-negative effect. Through gene expression assays, RNA sequencing, and CUT&RUN in isolated pectoral fin cells, we demonstrate that Prdm1a directly binds to and regulates genes required for fin induction, outgrowth and anterior/posterior patterning, such as fgfr1a, dlx5a, dlx6a and smo. Taken together, these results improve our understanding of the role of PRDM1 in the limb gene regulatory network and identified novel PRDM1 variants that link to SHFM in humans.
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Affiliation(s)
- Brittany T. Truong
- Human Medical Genetics & Genomics Graduate Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lomeli C. Shull
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ezra Lencer
- Biology Department, Lafayette College, Easton, PA 18042, USA
| | - Eric G. Bend
- Greenwood Genetics Center, Greenwood, SC 29646, USA
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, AUS
| | - Elizabeth E. Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Michael J. Bamshad
- Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | | | | | | | | | - Kristin B. Artinger
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
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15
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Hanquier JN, Sanders K, Berryhill CA, Sahoo FK, Hudmon A, Vilseck JZ, Cornett EM. Identification of non-histone substrates of the lysine methyltransferase PRDM9. J Biol Chem 2023; 299:104651. [PMID: 36972790 PMCID: PMC10164904 DOI: 10.1016/j.jbc.2023.104651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Lysine methylation is a dynamic, post-translational mark that regulates the function of histone and non-histone proteins. Many of the enzymes that mediate lysine methylation, known as lysine methyltransferases (KMTs), were originally identified to modify histone proteins but have also been discovered to methylate non-histone proteins. In this work, we investigate the substrate selectivity of the lysine methyltransferase PRDM9 to identify both potential histone and non-histone substrates. Though normally expressed in germ cells, PRDM9 is significantly upregulated across many cancer types. The methyltransferase activity of PRDM9 is essential for double-strand break formation during meiotic recombination. PRDM9 has been reported to methylate histone H3 at lysine residues 4 and 36; however, PRDM9 KMT activity had not previously been evaluated on non-histone proteins. Using lysine-oriented peptide (K-OPL) libraries to screen potential substrates of PRDM9, we determined that PRDM9 preferentially methylates peptide sequences not found in any histone protein. We confirmed PRDM9 selectivity through in vitro KMT reactions using peptides with substitutions at critical positions. A multisite λ-dynamics computational analysis provided a structural rationale for the observed PRDM9 selectivity. The substrate selectivity profile was then used to identify putative non-histone substrates, which were tested by peptide spot array, and a subset were further validated at the protein level by in vitro KMT assays on recombinant proteins. Finally, one of the non-histone substrates, CTNNBL1, was found to be methylated by PRDM9 in cells.
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Affiliation(s)
- Jocelyne N Hanquier
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A; Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A
| | - Kenidi Sanders
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A; Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A
| | - Christine A Berryhill
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A
| | - Firoj K Sahoo
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, U.S.A
| | - Andy Hudmon
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, U.S.A
| | - Jonah Z Vilseck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A; Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A
| | - Evan M Cornett
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A; Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A; Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A.
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16
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Di Zazzo E, Rienzo M, Casamassimi A, De Rosa C, Medici N, Gazzerro P, Bifulco M, Abbondanza C. Exploring the putative role of PRDM1 and PRDM2 transcripts as mediators of T lymphocyte activation. J Transl Med 2023; 21:217. [PMID: 36964555 PMCID: PMC10039509 DOI: 10.1186/s12967-023-04066-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/17/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND T cell activation and programming from their naïve/resting state, characterized by widespread modifications in chromatin accessibility triggering extensive changes in transcriptional programs, is orchestrated by several cytokines and transcription regulators. PRDM1 and PRDM2 encode for proteins with PR/SET and zinc finger domains that control several biological processes, including cell differentiation, through epigenetic regulation of gene expression. Different transcripts leading to main protein isoforms with (PR +) or without (PR-) the PR/SET domain have been described. Although many studies have established the critical PRDM1 role in hematopoietic cell differentiation, maintenance and/or function, the single transcript contribution has not been investigated before. Otherwise, very few evidence is currently available on PRDM2. Here, we aimed to analyze the role of PRDM1 and PRDM2 different transcripts as mediators of T lymphocyte activation. METHODS We analyzed the transcription signature of the main variants from PRDM1 (BLIMP1a and BLIMP1b) and PRDM2 (RIZ1 and RIZ2) genes, in human T lymphocytes and Jurkat cells overexpressing PRDM2 cDNAs following activation through different signals. RESULTS T lymphocyte activation induced an early increase of RIZ2 and RIZ1 followed by BLIMP1b increase and finally by BLIMP1a increase. The "first" and the "second" signals shifted the balance towards the PR- forms for both genes. Interestingly, the PI3K signaling pathway modulated the RIZ1/RIZ2 ratio in favor of RIZ1 while the balance versus RIZ2 was promoted by MAPK pathway. Cytokines mediating different Jak/Stat signaling pathways (third signal) early modulated the expression of PRDM1 and PRDM2 and the relationship of their different transcripts confirming the early increase of the PR- transcripts. Different responses of T cell subpopulations were also observed. Jurkat cells showed that the acute transient RIZ2 increase promoted the balancing of PRDM1 forms towards BLIMP1b. The stable forced expression of RIZ1 or RIZ2 induced a significant variation in the expression of key transcription factors involved in T lymphocyte differentiation. The BLIMP1a/b balance shifted in favor of BLIMP1a in RIZ1-overexpressing cells and of BLIMP1b in RIZ2-overexpressing cells. CONCLUSIONS This study provides the first characterization of PRDM2 in T-lymphocyte activation/differentiation and novel insights on PRDM1 and PRDM2 transcription regulation during initial activation phases.
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Affiliation(s)
- Erika Di Zazzo
- Department of Medicine and Health Sciences "V. Tiberio", University of Molise, 86100, Campobasso, Italy
| | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Caterina De Rosa
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Nicola Medici
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084, Salerno, Fisciano (SA), Italy
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131, Naples, Italy
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy.
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17
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PRDM16, Negatively Regulated by miR-372-3p, Suppresses Cell Proliferation and Invasion in Prostate Cancer. Andrologia 2023. [DOI: 10.1155/2023/9821829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent malignant tumors. The alternation of microRNA (miRNA) expression is associated with prostate cancer progression, whereas its way to influence progression of prostate cancer remains elusive. The expression levels of PRDM16 mRNA and miR-372-3p in PCa cell lines were analyzed using qRT-PCR. The protein expression of PRDM16 in PCa cell lines was also analyzed using western blot. CCK-8, wound healing, and Transwell assays were applied to examine cell proliferation, migration, and invasion in prostate cancer cells, respectively. Dual-luciferase reporter assay was utilized to validate the interaction between miR-372-3p and PRDM16. In the present study, markedly decreased PRDM16 mRNA and protein expression levels were observed in prostate cancer cells. PRDM16 overexpression hampered cellular proliferation, migration, and invasion, while silencing PRDM16 had the opposite effect. Moreover, miR-372-3p could target the regulation expression of PRDM16. Rescue experiments demonstrated that upregulating miR-372-3p conspicuously restored the inhibitory effect of increased PRDM16 on cell proliferation, migration, and invasion in PCa. Overall, our study clarifies the biological role of miR-372-3p/PRDM16 axis in prostate cancer progression, which may be effective biomarkers for clinical treatment of prostate cancer.
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18
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Zou M, Mangum KD, Magin JC, Cao HH, Yarboro MT, Shelton EL, Taylor JM, Reese J, Furey TS, Mack CP. Prdm6 drives ductus arteriosus closure by promoting ductus arteriosus smooth muscle cell identity and contractility. JCI Insight 2023; 8:e163454. [PMID: 36749647 PMCID: PMC10077476 DOI: 10.1172/jci.insight.163454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/23/2023] [Indexed: 02/08/2023] Open
Abstract
Based upon our demonstration that the smooth muscle cell-selective (SMC-selective) putative methyltransferase, Prdm6, interacts with myocardin-related transcription factor-A, we examined Prdm6's role in SMCs in vivo using cell type-specific knockout mouse models. Although SMC-specific depletion of Prdm6 in adult mice was well tolerated, Prdm6 depletion in Wnt1-expressing cells during development resulted in perinatal lethality and a completely penetrant patent ductus arteriosus (DA) phenotype. Lineage tracing experiments in Wnt1Cre2 Prdm6fl/fl ROSA26LacZ mice revealed normal neural crest-derived SMC investment of the outflow tract. In contrast, myography measurements on DA segments isolated from E18.5 embryos indicated that Prdm6 depletion significantly reduced DA tone and contractility. RNA-Seq analyses on DA and ascending aorta samples at E18.5 identified a DA-enriched gene program that included many SMC-selective contractile associated proteins that was downregulated by Prdm6 depletion. Chromatin immunoprecipitation-sequencing experiments in outflow tract SMCs demonstrated that 50% of the genes Prdm6 depletion altered contained Prdm6 binding sites. Finally, using several genome-wide data sets, we identified an SMC-selective enhancer within the Prdm6 third intron that exhibited allele-specific activity, providing evidence that rs17149944 may be the causal SNP for a cardiovascular disease GWAS locus identified within the human PRDM6 gene.
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Affiliation(s)
- Meng Zou
- Department of Pathology and McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kevin D. Mangum
- Department of Pathology and McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Justin C. Magin
- Department of Pathology and McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Heidi H. Cao
- Department of Pathology and McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michael T. Yarboro
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Elaine L. Shelton
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Joan M. Taylor
- Department of Pathology and McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeff Reese
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Terrence S. Furey
- Department of Pathology and McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christopher P. Mack
- Department of Pathology and McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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19
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Yao Z, van Velthoven CTJ, Kunst M, Zhang M, McMillen D, Lee C, Jung W, Goldy J, Abdelhak A, Baker P, Barkan E, Bertagnolli D, Campos J, Carey D, Casper T, Chakka AB, Chakrabarty R, Chavan S, Chen M, Clark M, Close J, Crichton K, Daniel S, Dolbeare T, Ellingwood L, Gee J, Glandon A, Gloe J, Gould J, Gray J, Guilford N, Guzman J, Hirschstein D, Ho W, Jin K, Kroll M, Lathia K, Leon A, Long B, Maltzer Z, Martin N, McCue R, Meyerdierks E, Nguyen TN, Pham T, Rimorin C, Ruiz A, Shapovalova N, Slaughterbeck C, Sulc J, Tieu M, Torkelson A, Tung H, Cuevas NV, Wadhwani K, Ward K, Levi B, Farrell C, Thompson CL, Mufti S, Pagan CM, Kruse L, Dee N, Sunkin SM, Esposito L, Hawrylycz MJ, Waters J, Ng L, Smith KA, Tasic B, Zhuang X, Zeng H. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531121. [PMID: 37034735 PMCID: PMC10081189 DOI: 10.1101/2023.03.06.531121] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The mammalian brain is composed of millions to billions of cells that are organized into numerous cell types with specific spatial distribution patterns and structural and functional properties. An essential step towards understanding brain function is to obtain a parts list, i.e., a catalog of cell types, of the brain. Here, we report a comprehensive and high-resolution transcriptomic and spatial cell type atlas for the whole adult mouse brain. The cell type atlas was created based on the combination of two single-cell-level, whole-brain-scale datasets: a single-cell RNA-sequencing (scRNA-seq) dataset of ~7 million cells profiled, and a spatially resolved transcriptomic dataset of ~4.3 million cells using MERFISH. The atlas is hierarchically organized into five nested levels of classification: 7 divisions, 32 classes, 306 subclasses, 1,045 supertypes and 5,200 clusters. We systematically analyzed the neuronal, non-neuronal, and immature neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell type organization in different brain regions, in particular, a dichotomy between the dorsal and ventral parts of the brain: the dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. We also systematically characterized cell-type specific expression of neurotransmitters, neuropeptides, and transcription factors. The study uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types across the brain, suggesting they mediate a myriad of modes of intercellular communications. Finally, we found that transcription factors are major determinants of cell type classification in the adult mouse brain and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole-mouse-brain transcriptomic and spatial cell type atlas establishes a benchmark reference atlas and a foundational resource for deep and integrative investigations of cell type and circuit function, development, and evolution of the mammalian brain.
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Affiliation(s)
- Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Meng Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Won Jung
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Pamela Baker
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Daniel Carey
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Min Chen
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Scott Daniel
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - James Gee
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jessica Gloe
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - James Gray
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Windy Ho
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kelly Jin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Arielle Leon
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zoe Maltzer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Naomi Martin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Rachel McCue
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
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20
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Whole-Genome Sequencing Reveals Mutational Signatures Related to Radiation-Induced Sarcomas and DNA-Damage-Repair Pathways. Mod Pathol 2023; 36:100004. [PMID: 36788076 DOI: 10.1016/j.modpat.2022.100004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/01/2022] [Accepted: 09/18/2022] [Indexed: 01/19/2023]
Abstract
Radiation-induced sarcoma (RIS) is a rare but serious late complication arising from radiotherapy. Despite unfavorable clinical outcomes, the genomic footprints of ionizing radiation in RIS development remain largely unknown. Hence, this study aimed to characterize RIS genomes and the genomic alterations in them. We analyzed whole-genome sequencing in 11 RIS genomes matched with normal genomes to identify somatic alterations potentially associated with RIS development. Furthermore, the abundance of mutations, mutation signatures, and structural variants in RIS were compared with those in radiation-naïve spontaneous sarcomas. The mutation abundance in RIS genomes, including one hypermutated genome, was variable. Cancer-related genes might show different types of genomic alterations. For instance, NF1, NF2, NOTCH1, NOTCH2, PIK3CA, RB1, and TP53 showed singleton somatic mutations; MYC, CDKN2A, RB1, and NF1 showed recurrent copy number alterations; and NF2, ARID1B, and RAD51B showed recurrent structural variations. The genomic footprints of nonhomologous end joining are prevalent at indels of RIS genomes compared with those in spontaneous sarcoma genomes, representing the genomic hallmark of RIS genomes. In addition, frequent chromothripsis was identified along with predisposing germline variants in the DNA-damage-repair pathways in RIS genomes. The characterization of RIS genomes on a whole-genome sequencing scale highlighted that the nonhomologous end joining pathway was associated with tumorigenesis, and it might pave the way for the development of advanced diagnostic and therapeutic strategies for RIS.
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21
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Yao J, Ma F, Zhang L, Zhu C, Jumabay M, Yao Z, Wang L, Cai X, Zhang D, Qiao X, Shivkumar K, Pellegrini M, Yao Y, Wu X, Boström KI. Single-Cell RNA-Seq Identifies Dynamic Cardiac Transition Program from Adipose Derived Cells Induced by Leukemia Inhibitory Factor. Stem Cells 2022; 40:932-948. [PMID: 35896368 PMCID: PMC9585902 DOI: 10.1093/stmcls/sxac048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022]
Abstract
Adipose-derived cells (ADCs) from white adipose tissue (WAT) are promising stem cell candidates because of their large regenerative reserves and the potential for cardiac regeneration. However, given the heterogeneity of ADC and its unsolved mechanisms of cardiac acquisition, ADC-cardiac transition efficiency remains low. In this study, we explored the heterogeneity of ADCs and the cellular kinetics of 39,432 single-cell transcriptomes along the leukemia inhibitory factor (LIF) induced ADC-cardiac transition. We identified distinct ADC subpopulations that reacted differentially to LIF when entering the cardiomyogenic program, further demonstrating that ADC-myogenesis is time-dependent and initiates from transient changes in nuclear factor erythroid 2-related factor 2 (Nrf2) signaling. At later stages, pseudotime analysis of ADCs navigated a trajectory with two branches corresponding to activated myofibroblast or cardiomyocyte-like cells. Our findings offer a high-resolution dissection of ADC heterogeneity and cell fate during ADC-cardiac transition, thus providing new insights into potential cardiac stem cells.
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Affiliation(s)
- Jiayi Yao
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | - Feiyang Ma
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA.,Chongqing International Institute for Immunology, Chongqing 401338, China
| | - Li Zhang
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | - Ching Zhu
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | - Medet Jumabay
- Division of Allergy, Immunology Center for Immunity, Infection, and Inflammation Pediatrics, Dept of Medicine, University of California, San Diego, San Diego, CA
| | - Zehao Yao
- Peking Union Medical College, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Lumin Wang
- Institute of Precision Medicine, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xinjiang Cai
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | - Daoqin Zhang
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | - Xiaojing Qiao
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | | | - Matteo Pellegrini
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA.,Dept of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA
| | - Yucheng Yao
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | - Xiuju Wu
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | - Kristina I Boström
- Division of Cardiology, David Geffen School of Medicine at UCLA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA
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22
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Yin G, Yan C, Hao J, Zhang C, Wang P, Zhao C, Cai S, Meng B, Zhang A, Li L. PRDM16, negatively regulated by miR-372-3p, suppresses cell proliferation and invasion in prostate cancer. Andrologia 2022:e14529. [PMID: 35858224 DOI: 10.1111/and.14529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/27/2022] [Accepted: 06/26/2022] [Indexed: 11/26/2022] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent malignant tumours. The alternation of microRNAs (miRNAs) expression is associated with prostate cancer progression, whereas its way to influence progression of prostate cancer remains elusive. The expression levels of PRDM16 mRNA and miR-372-3p in PCa cell lines were analysed using qRT-PCR. The protein expression of PRDM16 in PCa cell lines was also analysed using Western blot. CCK-8, wound healing and Transwell assays were applied to examine cell proliferation, migration, and invasion in prostate cancer cells, respectively. Dual-luciferase reporter assay was utilised to validate the interaction between miR-372-3p and PRDM16. In the present study, markedly decreased PRDM16 mRNA and protein expression levels were observed in prostate cancer cells. PRDM16 overexpression hampered cellular proliferation, migration, and invasion, while silencing PRDM16 had the opposite effect. Moreover, miR-372-3p could target the regulation expression of PRDM16. Rescue experiments demonstrated that upregulating miR-372-3p conspicuously restored the inhibitory effect of increased PRDM16 on cell proliferation, migration, and invasion in PCa. Overall, our study clarifies the biological role of miR-372-3p/PRDM16 axis in prostate cancer progression, which may be effective biomarkers for clinical treatment of prostate cancer.
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Affiliation(s)
- Guangwei Yin
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Chengquan Yan
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Jing Hao
- Office of Academic Affairs, North China University of Science and Technology, Tangshan, Hebei Province, China
| | - Chunying Zhang
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Pengfei Wang
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Chaofei Zhao
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Shengyong Cai
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Bin Meng
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Aili Zhang
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Lin Li
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
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23
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El-Meligui YM, Hassan NM, Kassem AB, Gouda NA, Mohanad M, Hamouda MA, Salahuddin A. Impact of HOXB4 and PRDM16 Gene Expressions on Prognosis and Treatment Response in Acute Myeloid Leukemia Patients. Pharmgenomics Pers Med 2022; 15:663-674. [PMID: 35782688 PMCID: PMC9241994 DOI: 10.2147/pgpm.s368640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/14/2022] [Indexed: 12/08/2022] Open
Abstract
Introduction Acute myeloid leukemia (AML) is the most common type of leukemia among adults and is characterized by various genetic abnormalities. HOXB4 and PRDM16 are promising markers of AML. Our objective is to assess the potential roles of HOXB4 and PRDM16 as prognostic and predictive markers in newly diagnosed AML patients and determine the correlation between their expressions and other prognostic markers as FLT3-ITD, NPM1 exon 12 mutations, response to treatment, and patient’s survival. Methods This study included 83 de novo AML adult patients. All patients were subjected to clinical, morphological, cytochemical, and molecular analysis to detect HOXB4 and PRDM16 gene expressions and FLT3-ITD, NPM1 exon 12 mutations. Results The results showed that a low expression of HOXB4 was found in 31.3% of AML patients, whereas a high expression of PRDM16 was evident in 33.8% of AML patients. FLT3-ITD mutations were detected in 6 patients (7.2%), while NPM1 exon 12 mutations were detected in 7 patients (19.4%) out of 36 patients with intermediate genetic risk. Out of the 50 patients who achieved complete remission (CR), relapse occurred in 16% of the cases. Low expression of HOXB4 and high expression of PRDM16 were associated with CR of 32% and 28%, respectively, and a short overall survival (OS) and disease-free survival (DFS). Conclusion Further larger study should be conducted to verify that high PRDM16 and low HOXB4 gene expressions could be used as a poor prognostic predictor for AML. The correlation between PRDM16 and HOXB4 gene expressions and FLT3-ITD and NPM1 exon 12 mutations might have a role on CR, relapse, OS, and, however, this should be clarified in analysis with a larger number of samples.
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Affiliation(s)
- Yomna M El-Meligui
- Clinical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Naglaa M Hassan
- Clinical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Amira B Kassem
- Clinical Pharmacy and Pharmacy Practice Department, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
- Correspondence: Amira B Kassem, Email
| | - Nora A Gouda
- Cancer Epidemiology and Biostatistics Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Marwa Mohanad
- Biochemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Giza, Egypt
| | - Manal A Hamouda
- Clinical Pharmacy Department, Faculty of Pharmacy, Menoufia University, Shibin El Kom, Egypt
| | - Ahmad Salahuddin
- Biochemistry Department, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
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24
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Buontempo S, Laise P, Hughes JM, Trattaro S, Das V, Rencurel C, Testa G. EZH2-Mediated H3K27me3 Targets Transcriptional Circuits of Neuronal Differentiation. Front Neurosci 2022; 16:814144. [PMID: 35645710 PMCID: PMC9133892 DOI: 10.3389/fnins.2022.814144] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/11/2022] [Indexed: 12/27/2022] Open
Abstract
The Polycomb Repressive Complex 2 (PRC2) plays important roles in the epigenetic regulation of cellular development and differentiation through H3K27me3-dependent transcriptional repression. Aberrant PRC2 activity has been associated with cancer and neurodevelopmental disorders, particularly with respect to the malfunction of sits catalytic subunit EZH2. Here, we investigated the role of the EZH2-mediated H3K27me3 apposition in neuronal differentiation. We made use of a transgenic mouse model harboring Ezh2 conditional KO alleles to derive embryonic stem cells and differentiate them into glutamatergic neurons. Time course transcriptomics and epigenomic analyses of H3K27me3 in absence of EZH2 revealed a significant dysregulation of molecular networks affecting the glutamatergic differentiation trajectory that resulted in: (i) the deregulation of transcriptional circuitries related to neuronal differentiation and synaptic plasticity, in particular LTD, as a direct effect of EZH2 loss and (ii) the appearance of a GABAergic gene expression signature during glutamatergic neuron differentiation. These results expand the knowledge about the molecular pathways targeted by Polycomb during glutamatergic neuron differentiation.
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Affiliation(s)
- Serena Buontempo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Pasquale Laise
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - James M. Hughes
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Sebastiano Trattaro
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Human Technopole, Milan, Italy
| | - Vivek Das
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Chantal Rencurel
- Department of Structural Biology and Biophysics, Biozentrum of the University of Basel, Basel, Switzerland
| | - Giuseppe Testa
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Human Technopole, Milan, Italy
- *Correspondence: Giuseppe Testa,
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25
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Shull LC, Lencer ES, Kim HM, Goyama S, Kurokawa M, Costello JC, Jones K, Artinger KB. PRDM paralogs antagonistically balance Wnt/β-catenin activity during craniofacial chondrocyte differentiation. Development 2022; 149:274527. [PMID: 35132438 PMCID: PMC8918787 DOI: 10.1242/dev.200082] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/13/2022] [Indexed: 12/20/2022]
Abstract
Cranial neural crest cell (NCC)-derived chondrocyte precursors undergo a dynamic differentiation and maturation process to establish a scaffold for subsequent bone formation, alterations in which contribute to congenital birth defects. Here, we demonstrate that transcription factor and histone methyltransferase proteins Prdm3 and Prdm16 control the differentiation switch of cranial NCCs to craniofacial cartilage. Loss of either paralog results in hypoplastic and disorganized chondrocytes due to impaired cellular orientation and polarity. We show that these proteins regulate cartilage differentiation by controlling the timing of Wnt/β-catenin activity in strikingly different ways: Prdm3 represses whereas Prdm16 activates global gene expression, although both act by regulating Wnt enhanceosome activity and chromatin accessibility. Finally, we show that manipulating Wnt/β-catenin signaling pharmacologically or generating prdm3-/-;prdm16-/- double mutants rescues craniofacial cartilage defects. Our findings reveal upstream regulatory roles for Prdm3 and Prdm16 in cranial NCCs to control Wnt/β-catenin transcriptional activity during chondrocyte differentiation to ensure proper development of the craniofacial skeleton.
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Affiliation(s)
- Lomeli C. Shull
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ezra S. Lencer
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Hyun Min Kim
- Department of Pharmacology and University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Susumu Goyama
- Division of Cellular Therapy, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Mineo Kurokawa
- Department of Hematology and Oncology, The University of Tokyo, Tokyo, 113-8655, Japan
| | - James C. Costello
- Department of Pharmacology and University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kenneth Jones
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristin B. Artinger
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA,Author for correspondence ()
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Wu T, Liang Z, Zhang Z, Liu C, Zhang L, Gu Y, Peterson KL, Evans SM, Fu XD, Chen J. PRDM16 Is a Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle. Circulation 2022; 145:586-602. [PMID: 34915728 PMCID: PMC8860879 DOI: 10.1161/circulationaha.121.056666] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/29/2021] [Indexed: 01/28/2023]
Abstract
BACKGROUND Left ventricular noncompaction cardiomyopathy (LVNC) was discovered half a century ago as a cardiomyopathy with excessive trabeculation and a thin ventricular wall. In the decades since, numerous studies have demonstrated that LVNC primarily has an effect on left ventricles (LVs) and is often associated with LV dilation and dysfunction. However, in part because of the lack of suitable mouse models that faithfully mirror the selective LV vulnerability in patients, mechanisms underlying the susceptibility of LVs to dilation and dysfunction in LVNC remain unknown. Genetic studies have revealed that deletions and mutations in PRDM16 (PR domain-containing 16) cause LVNC, but previous conditional Prdm16 knockout mouse models do not mirror the LVNC phenotype in patients, and the underlying molecular mechanisms by which PRDM16 deficiency causes LVNC are still unclear. METHODS Prdm16 cardiomyocyte-specific knockout (Prdm16cKO) mice were generated and analyzed for cardiac phenotypes. RNA sequencing and chromatin immunoprecipitation deep sequencing were performed to identify direct transcriptional targets of PRDM16 in cardiomyocytes. Single-cell RNA sequencing in combination with spatial transcriptomics was used to determine cardiomyocyte identity at the single-cell level. RESULTS Cardiomyocyte-specific ablation of Prdm16 in mice caused LV-specific dilation and dysfunction, as well as biventricular noncompaction, which fully recapitulated LVNC in patients. PRDM16 functioned mechanistically as a compact myocardium-enriched transcription factor that activated compact myocardial genes while repressing trabecular myocardial genes in LV compact myocardium. Consequently, Prdm16cKO LV compact myocardial cardiomyocytes shifted from their normal transcriptomic identity to a transcriptional signature resembling trabecular myocardial cardiomyocytes or neurons. Chamber-specific transcriptional regulation by PRDM16 was attributable in part to its cooperation with LV-enriched transcription factors Tbx5 and Hand1. CONCLUSIONS These results demonstrate that disruption of proper specification of compact cardiomyocytes may play a key role in the pathogenesis of LVNC. They also shed light on underlying mechanisms of the LV-restricted transcriptional program governing LV chamber growth and maturation, providing a tangible explanation for the susceptibility of LV in a subset of LVNC cardiomyopathies.
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Affiliation(s)
- Tongbin Wu
- Department of Medicine, University of California San Diego, La Jolla, CA
- These authors contributed equally
| | - Zhengyu Liang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
- These authors contributed equally
| | - Zengming Zhang
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Canzhao Liu
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Lunfeng Zhang
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Yusu Gu
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Kirk L. Peterson
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Sylvia M. Evans
- Department of Medicine, University of California San Diego, La Jolla, CA
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
- Institute of Genomic Medicine, University of California San Diego, La Jolla, CA
| | - Ju Chen
- Department of Medicine, University of California San Diego, La Jolla, CA
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Silva KCDP, Messias TS, Soares S. The Public Health Importance of Flaviviruses as an Etiological Environmental Factor in Nonsyndromic Cleft Lip and/or Palate: In silico Study. Cleft Palate Craniofac J 2022; 60:544-550. [PMID: 35164580 DOI: 10.1177/10556656221074206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This in silico study aims to investigate flaviviruses as an environmental factor in the etiology of nonsyndromic cleft lip and/or palate (CL/P). A scoring method with 7 topics—disease, transplacental passage, tropism, cellular damage, reported case, analysis of genome similarity, and transcriptome between virus and host, was created based on literature and in silico experimentation. Viral genomes of NCBI virus were obtained and BLAST 2.12.0 was applied for the similarity analysis, adjusted to search for only human sequences related to CL/P with the statistical threshold defined for E-value ≤1. Flaviviruses with high potential to cause CL/P were: serotypes 2, 3, and 4 of the Dengue virus and lineage 2 of the West Nile virus, while the Yellow Fever virus, Japanese encephalitis virus, Tick-borne encephalitis virus, and Saint Louis encephalitis virus presented with medium potential to cause CL/P. As for the Zika virus, even strains associated with microcephaly showed only medium potential. Dengue virus and West Nile virus presented with high potential to act as environmental factors in the etiology of CL/P.
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Affiliation(s)
| | - Thiago Silva Messias
- Hospital of Rehabilitation of Craniofacial Anomalies, University of São Paulo, USP, Bauru, SP, Brazil
| | - Simone Soares
- Bauru School of Dentistry, Hospital of Rehabilitation of Craniofacial Anomalies, University of São Paulo, USP, Bauru, SP, Brazil
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Prdm12 regulates inhibitory neuron differentiation in mouse embryonal carcinoma cells. Cytotechnology 2022; 74:329-339. [PMID: 35464160 PMCID: PMC8975904 DOI: 10.1007/s10616-022-00519-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/04/2022] [Indexed: 11/03/2022] Open
Abstract
The epigenetic regulatory system significant influences the fate determination of cells during developmental processes. Prdm12 is a transcriptional regulator that modulates gene expression epigenetically. The Prdm12 gene has been shown to be expressed in neural tissues, specifically during development, but its detailed function is not fully understood. This study investigated the function of the Prdm12 gene in P19 mouse embryonic tumor cells as a model for neural differentiation. A decrease in the expression of neuron-specific genes and the alterations of dendrites and axons morphology was confirmed in Prdm12-knockout P19 cells. In addition, almost no astrocytes were generated in Prdm12-knockout P19 cells. Comprehensive gene expression analysis revealed that there was a reduction in the expression of the inhibitory neuron-specific genes Gad1/2 and Glyt2, but not the excitatory neuron-specific gene VGLUT2, in Prdm12-knockout P19 cells. Furthermore, the expression of inhibitory neuron-related factors, Ptf1a, Dbx1, and Gsx1/2, decreased in Prdm12-knockout P19 cells. Gene expression analysis also revealed that the Ptf1a, Hic1, and Foxa1 genes were candidate targets of Prdm12 during neurogenesis. These results suggest that Prdm12 regulates the differentiation of inhibitory neurons and astrocytes by controlling the expression of these genes during the neural differentiation of P19 cells.
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29
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Bang ML, Bogomolovas J, Chen J. Understanding the molecular basis of cardiomyopathy. Am J Physiol Heart Circ Physiol 2022; 322:H181-H233. [PMID: 34797172 PMCID: PMC8759964 DOI: 10.1152/ajpheart.00562.2021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 02/03/2023]
Abstract
Inherited cardiomyopathies are a major cause of mortality and morbidity worldwide and can be caused by mutations in a wide range of proteins located in different cellular compartments. The present review is based on Dr. Ju Chen's 2021 Robert M. Berne Distinguished Lectureship of the American Physiological Society Cardiovascular Section, in which he provided an overview of the current knowledge on the cardiomyopathy-associated proteins that have been studied in his laboratory. The review provides a general summary of the proteins in different compartments of cardiomyocytes associated with cardiomyopathies, with specific focus on the proteins that have been studied in Dr. Chen's laboratory.
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Affiliation(s)
- Marie-Louise Bang
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Milan Unit, Milan, Italy
- IRCCS Humanitas Research Hospital, Rozzano (Milan), Italy
| | - Julius Bogomolovas
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
| | - Ju Chen
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
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30
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Li M, Ren H, Zhang Y, Liu N, Fan M, Wang K, Yang T, Chen M, Shi P. MECOM/PRDM3 and PRDM16 Serve as Prognostic-Related Biomarkers and Are Correlated With Immune Cell Infiltration in Lung Adenocarcinoma. Front Oncol 2022; 12:772686. [PMID: 35174083 PMCID: PMC8841357 DOI: 10.3389/fonc.2022.772686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/03/2022] [Indexed: 12/24/2022] Open
Abstract
Background The MDS1 and EVI1 complex locus (MECOM, also called PRDM3) and PR domain containing 16 (PRDM16) are two highly related zinc finger transcription factors associated with many malignancies. However, the mechanisms of MECOM and PRDM16 in prognosis and tumor immune infiltration in lung adenocarcinoma (LUAD) remain uncertain. Methods The Cancer Genome Atlas (TCGA), Oncomine, UALCAN, GEPIA, and TIMER databases were searched to determine the relationship between the expression of MECOM and PRDM16, clinicopathological features, immune infiltration, and prognosis in LUAD. Coexpressed genes of the two genes were investigated by CBioPortal, and the potential mechanism of MECOM- and PRDM16-related genes was elucidated by GO and KEGG analyses. STRING database was utilized to further construct the protein-protein interaction network of the coexpressed genes, and the hub genes were identified by Cytoscape. Finally, qRT-PCR was performed to identify the mRNA levels of the target genes in LUAD. Results mRNA levels of MECOM and PRDM16 were downregulated in LUAD (p < 0.05), and the low expression of the two genes was associated with the age, gender, smoking duration, tissue subtype, poor stage, nodal metastasis status, TP53 mutation, and prognosis in LUAD (p < 0.05). MECOM and PRDM16 were also found to be correlated with the expression of a variety of immune cell subsets and their markers. KEGG analysis showed that both of them were mainly enriched in the cell cycle, cellular senescence, DNA replication, and p53 signaling pathway. Importantly, the mRNA levels of the two genes were also found to be decreased in the clinical samples of LUAD by qRT-PCR. Conclusion MECOM and PRDM16 may serve as potential prognostic biomarkers which govern immune cell recruitment to LUAD.
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Affiliation(s)
- Meng Li
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Talent Highland, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Hui Ren
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Talent Highland, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yanpeng Zhang
- Department of Talent Highland, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Thoracic Surgery, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Na Liu
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Meng Fan
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Ke Wang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Tian Yang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Mingwei Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Puyu Shi, ; ; Mingwei Chen, ;
| | - Puyu Shi
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Puyu Shi, ; ; Mingwei Chen, ;
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Role of Mel1/Prdm16 in bone differentiation and morphology. Exp Cell Res 2022; 410:112969. [PMID: 34883111 DOI: 10.1016/j.yexcr.2021.112969] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/01/2021] [Accepted: 12/04/2021] [Indexed: 11/23/2022]
Abstract
MEL1 (MDS1/EVI1-like gene 1/PRDM16), a zinc finger protein, is located near the chromosomal breakpoint at 1p36 in human acute myeloid leukemia (AML) cells with the t (1; 3) (p36; q21) translocation. Mel1/Prdm16 is not only a causative gene of leukemia, but also has multiple regulatory functions, such as the regulation of fat metabolism. To investigate the function of Mel1/Prdm16, we generated Mel1/Prdm16-deficient mice, but homozygous deficiency (Mel1/Prdm16-/-) was embryonic lethal at E 11.5. Heterozygous mice showed abnormal cartilage and bone formation in the postnatal skull and long bones, suggesting that Mel1/Prdm16 expression plays an important role in bone development. In osteoblast and chondrocyte cell lines, Mel1/Prdm16 promotes the differentiation of chondrocytes and regulates the differentiation of osteoblasts. Transient repression of the master regulator Runx2 is required for chondrocyte differentiation at an early stage of differentiation. However, in Mel1/Prdm16-suppressed ATDC5 cells, the initial suppression of Runx2 was lacking and its expression was upregulated at the beginning of differentiation, suggesting that chondrogenic differentiation is suppressed in Mel1/Prdm16+/- mesenchymal progenitor cells because Runx2 expression is upregulated during the early stage of differentiation. Thus, the Mel1/Prdm16 gene may be involved in the early repression of Runx2 expression during osteochondral differentiation and promote chondrogenic differentiation.
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32
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Rasouli HR, Talebi S, Ahmadpour F. Evaluation of Associated Genes with Traumatic Pain: A Systematic Review. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2022; 21:830-840. [PMID: 34872485 DOI: 10.2174/1871527320666211206121645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/06/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVES The knowledge about the molecular pathway of traumatic pain relief is less documented. This systematic review study aimed to identify the genes and molecular pathways associated with various traumatic pains. METHODS The online databases such as EMBASE, MEDLINE, PubMed, Cochrane Library, International Clinical Trials Registry Platform, Clinical Trials, Google Scholar, Wiley, ISI Web of Knowledge, and Scopus were searched. Two review authors searched and screened all records' titles and abstracts, and the third expert reviewer author resolved their disagreement. The study's design, various trauma injuries, types of genes, and molecular pathways were recorded. The genes and molecular pathways data were obtained via GeneCards®: The Human Gene Database (https://www.genecards.org). RESULTS Studies on a variety of trauma injuries regarding nerve and Spinal Cord Injuries (SCIs) (12 records), Hypertrophic scar with Severe Pain (one record), severe post-traumatic musculoskeletal pain (MSP) (one record), and orthopedic trauma (one record) were included. The main molecular pathways such as the immune system, apoptosis, and death receptor signaling, T-cell antigen receptor (TCR) signaling pathway, oxidative stress, interleukin(s) mediated signaling pathway, biological oxidations, metabolic pathways (especially amino acid metabolism and amino group), focal adhesion, the proliferation of vascular, epithelial, and connective tissue cells, angiogenesis and neural development were identified. CONCLUSION The immune system, apoptosis, and metabolic pathways are crucial for understanding the roles of genes in traumatic pain. It is recommended that these identified pathways and related genes be considered therapeutical targets for pain management in patients with trauma injuries. In addition, different forms of trauma injuries require different pathways and related genes to be considered.
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Affiliation(s)
- Hamid Reza Rasouli
- Trauma Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Samira Talebi
- National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Fathollah Ahmadpour
- Trauma Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Whittaker DE, Oleari R, Gregory LC, Le Quesne-Stabej P, Williams HJ, Torpiano JG, Formosa N, Cachia MJ, Field D, Lettieri A, Ocaka LA, Paganoni AJ, Rajabali SH, Riegman KL, De Martini LB, Chaya T, Robinson IC, Furukawa T, Cariboni A, Basson MA, Dattani MT. A recessive PRDM13 mutation results in congenital hypogonadotropic hypogonadism and cerebellar hypoplasia. J Clin Invest 2021; 131:e141587. [PMID: 34730112 PMCID: PMC8670848 DOI: 10.1172/jci141587] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/27/2021] [Indexed: 11/17/2022] Open
Abstract
The positive regulatory (PR) domain containing 13 (PRDM13) putative chromatin modifier and transcriptional regulator functions downstream of the transcription factor PTF1A, which controls GABAergic fate in the spinal cord and neurogenesis in the hypothalamus. Here, we report a recessive syndrome associated with PRDM13 mutation. Patients exhibited intellectual disability, ataxia with cerebellar hypoplasia, scoliosis, and delayed puberty with congenital hypogonadotropic hypogonadism (CHH). Expression studies revealed Prdm13/PRDM13 transcripts in the developing hypothalamus and cerebellum in mouse and human. An analysis of hypothalamus and cerebellum development in mice homozygous for a Prdm13 mutant allele revealed a significant reduction in the number of Kisspeptin (Kiss1) neurons in the hypothalamus and PAX2+ progenitors emerging from the cerebellar ventricular zone. The latter was accompanied by ectopic expression of the glutamatergic lineage marker TLX3. Prdm13-deficient mice displayed cerebellar hypoplasia and normal gonadal structure, but delayed pubertal onset. Together, these findings identify PRDM13 as a critical regulator of GABAergic cell fate in the cerebellum and of hypothalamic kisspeptin neuron development, providing a mechanistic explanation for the cooccurrence of CHH and cerebellar hypoplasia in this syndrome. To our knowledge, this is the first evidence linking disrupted PRDM13-mediated regulation of Kiss1 neurons to CHH in humans.
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Affiliation(s)
- Danielle E. Whittaker
- Centre for Craniofacial and Regenerative Biology, King’s College London, London, United Kingdom
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, United Kingdom
| | - Roberto Oleari
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Louise C. Gregory
- Section of Molecular Basis of Rare Disease, Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Polona Le Quesne-Stabej
- Section of Molecular Basis of Rare Disease, Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Hywel J. Williams
- Section of Molecular Basis of Rare Disease, Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - GOSgene
- Section of Molecular Basis of Rare Disease, Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- GOSgene is detailed in Supplemental Acknowledgments
| | - John G. Torpiano
- Department of Paediatrics and
- Adult Endocrinology Service, Mater Dei Hospital, Msida, Malta
| | | | - Mario J. Cachia
- Adult Endocrinology Service, Mater Dei Hospital, Msida, Malta
| | - Daniel Field
- Centre for Craniofacial and Regenerative Biology, King’s College London, London, United Kingdom
| | - Antonella Lettieri
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Louise A. Ocaka
- Section of Molecular Basis of Rare Disease, Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Alyssa J.J. Paganoni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Sakina H. Rajabali
- Centre for Craniofacial and Regenerative Biology, King’s College London, London, United Kingdom
| | - Kimberley L.H. Riegman
- Centre for Craniofacial and Regenerative Biology, King’s College London, London, United Kingdom
| | - Lisa B. De Martini
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Taro Chaya
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | | | - Takahisa Furukawa
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Anna Cariboni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - M. Albert Basson
- Centre for Craniofacial and Regenerative Biology, King’s College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom
| | - Mehul T. Dattani
- Section of Molecular Basis of Rare Disease, Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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Rienzo M, Di Zazzo E, Casamassimi A, Gazzerro P, Perini G, Bifulco M, Abbondanza C. PRDM12 in Health and Diseases. Int J Mol Sci 2021; 22:ijms222112030. [PMID: 34769459 PMCID: PMC8585061 DOI: 10.3390/ijms222112030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 11/18/2022] Open
Abstract
PRDM12 is a member of the PRDI-BF1 (positive regulatory domain I-binding factor 1) homologous domain (PRDM)-containing protein family, a subfamily of Kruppel-like zinc finger proteins, controlling key processes in the development of cancer. PRDM12 is expressed in a spatio-temporal manner in neuronal systems where it exerts multiple functions. PRDM12 is essential for the neurogenesis initiation and activation of a cascade of downstream pro-neuronal transcription factors in the nociceptive lineage. PRDM12 inactivation, indeed, results in a complete absence of the nociceptive lineage, which is essential for pain perception. Additionally, PRDM12 contributes to the early establishment of anorexigenic neuron identity and the maintenance of high expression levels of pro-opiomelanocortin, which impacts on the program bodyweight homeostasis. PRDMs are commonly involved in cancer, where they act as oncogenes/tumor suppressors in a “Yin and Yang” manner. PRDM12 is not usually expressed in adult normal tissues but its expression is re-activated in several cancer types. However, little information is currently available on PRDM12 expression in cancers and its mechanism of action has not been thoroughly described. In this review, we summarize the recent findings regarding PRDM12 by focusing on four main biological processes: neurogenesis, pain perception, oncogenesis and cell metabolism. Moreover, we wish to highlight the importance of future studies focusing on the PRDM12 signaling pathway(s) and its role in cancer onset and progression.
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Affiliation(s)
- Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Erika Di Zazzo
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy;
- Correspondence:
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Salerno, Italy;
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy;
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy;
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MECOM promotes supporting cell proliferation and differentiation in cochlea. J Otol 2021; 17:59-66. [PMID: 35949554 PMCID: PMC9349018 DOI: 10.1016/j.joto.2021.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022] Open
Abstract
Permanent damage to hair cells (HCs) is the leading cause of sensory deafness. Supporting cells (SCs) are essential in the restoration of hearing in mammals because they can proliferate and differentiate to HCs. MDS1 and EVI1 complex locus (MECOM) is vital in early development and cell differentiation and regulates the TGF-β signaling pathway to adapt to pathophysiological events, such as hematopoietic proliferation, differentiation and cells death. In addition, MECOM plays an essential role in neurogenesis and craniofacial development. However, the role of MECOM in the development of cochlea and its way to regulate related signaling are not fully understood. To address this problem, this study examined the expression of MECOM during the development of cochlea and observed a significant increase of MECOM at the key point of auditory epithelial morphogenesis, indicating that MECOM may have a vital function in the formation of cochlea and regeneration of HCs. Meanwhile, we tried to explore the possible effect and potential mechanism of MECOM in SC proliferation and HC regeneration. Findings from this study indicate that overexpression of MECOM markedly increases the proliferation of SCs in the inner ear, and the expression of Smad3 and Cdkn2b related to TGF signaling is significantly down-regulated, corresponding to the overexpression of MECOM. Collectively, these data may provide an explanation of the vital function of MECOM in SC proliferation and trans-differentiation into HCs, as well as its regulation. The interaction between MECOM, Wnt, Notch and the TGF-β signaling may provide a feasible approach to induce the regeneration of HCs.
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Kokotović T, Langeslag M, Lenartowicz EM, Manion J, Fell CW, Alehabib E, Tafakhori A, Darvish H, Bellefroid EJ, Neely GG, Kress M, Penninger JM, Nagy V. PRDM12 Is Transcriptionally Active and Required for Nociceptor Function Throughout Life. Front Mol Neurosci 2021; 14:720973. [PMID: 34646120 PMCID: PMC8502974 DOI: 10.3389/fnmol.2021.720973] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/20/2021] [Indexed: 12/21/2022] Open
Abstract
PR domain-containing member 12 (PRDM12) is a key developmental transcription factor in sensory neuronal specification and survival. Patients with rare deleterious variants in PRDM12 are born with congenital insensitivity to pain (CIP) due to the complete absence of a subtype of peripheral neurons that detect pain. In this paper, we report two additional CIP cases with a novel homozygous PRDM12 variant. To elucidate the function of PRDM12 during mammalian development and adulthood, we generated temporal and spatial conditional mouse models. We find that PRDM12 is expressed throughout the adult nervous system. We observed that loss of PRDM12 during mid-sensory neurogenesis but not in the adult leads to reduced survival. Comparing cellular biophysical nociceptive properties in developmental and adult-onset PRDM12 deletion mouse models, we find that PRDM12 is necessary for proper nociceptive responses throughout life. However, we find that PRDM12 regulates distinct age-dependent transcriptional programs. Together, our results implicate PRDM12 as a viable therapeutic target for specific pain therapies even in adults.
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Affiliation(s)
- Tomislav Kokotović
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Michiel Langeslag
- Department of Physiology and Medical Physics, Institute of Physiology, Medical University of Innsbruck, Innsbruck, Austria.,Institute of Pharmacy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria.,Department of Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ewelina M Lenartowicz
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - John Manion
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Christopher W Fell
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Elham Alehabib
- Student Research Committee, Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Tafakhori
- Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Darvish
- Neuroscience Research Center, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Eric J Bellefroid
- ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - G Gregory Neely
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Michaela Kress
- Department of Physiology and Medical Physics, Institute of Physiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, VBC - Vienna BioCenter, Vienna, Austria.,Department of Medical Genetics, Life Science Institute, University of British Columbia, Vancouver, BC, Canada
| | - Vanja Nagy
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Neurology, Medical University of Vienna, Vienna, Austria
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37
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Han J, Ke C, Jiang B, Zhou H, Xu H, Xie X. Down-regulation of PR/SET domain 10 underlies natural killer cell dysfunction in hepatocellular carcinoma. Clin Exp Immunol 2021; 206:366-377. [PMID: 34562314 DOI: 10.1111/cei.13666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/07/2021] [Accepted: 09/21/2021] [Indexed: 01/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the world's leading cause of tumor-related mortalities. Natural killer (NK) cells play a critical role at the first immunological defense line against HCC initiation and progression. NK cell dysfunction is therefore an important mechanism for immune evasion of HCC cells. In the present study using a murine HCC model, we revealed the down-regulation of PR/SET Domain 10 (PRDM10) in hepatic NK cells that were phenotypically and functionally exhausted. PRDM10 silencing diminished the expression of natural killer group 2 member D (NKG2D) and tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL), augmented T cell immunoglobulin and ITIM domain (TIGIT) expression, and decreased the expression of interferon (IFN)-γ, perforin and granzyme B in normal hepatic NK cells in vitro. Consistently, PRDM10-deficient NK cells exhibited impaired cytotoxicity on target cells. In contrast, PRDM10 over-expression promoted NKG2D and Fas ligand (FasL) expression, reduced CD96 expression and enhanced transcripts of IFN-γ, perforin and granzyme B in NK cells in vivo. Moreover, PRDM10 silencing and PRDM10 over-expression down-regulated and up-regulated Eomesodermin (Eomes) expression, respectively. In summary, this study reveals PRDM10 down-regulation as a novel mechanism underlying NK cell dysfunction and identifies PRDM10 as a supporting factor of NK cell function.
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Affiliation(s)
- Jiantao Han
- The Department of Hepatobiliary and Pancreatic Surgery, Tongren Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Chao Ke
- The Department of Gastrointestinal, Hernia and Abdominal Wall Surgery, Tongren Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Bin Jiang
- The Department of Gastrointestinal, Hernia and Abdominal Wall Surgery, Tongren Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Hongjian Zhou
- The Department of Gastrointestinal, Hernia and Abdominal Wall Surgery, Tongren Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Hanbin Xu
- The Department of Gastrointestinal, Hernia and Abdominal Wall Surgery, Tongren Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Xingwang Xie
- The Department of Hepatobiliary and Pancreatic Surgery, Tongren Hospital of Wuhan University, Wuhan, Hubei Province, China
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38
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In Silico Analysis to Explore Lineage-Independent and -Dependent Transcriptional Programs Associated with the Process of Endothelial and Neural Differentiation of Human Induced Pluripotent Stem Cells. J Clin Med 2021; 10:jcm10184161. [PMID: 34575270 PMCID: PMC8471316 DOI: 10.3390/jcm10184161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Despite a major interest in understanding how the endothelial cell phenotype is established, the underlying molecular basis of this process is not yet fully understood. We have previously reported the generation of induced pluripotent stem cells (iPS) from human umbilical vein endothelial cells and differentiation of the resulting HiPS back to endothelial cells (Ec-Diff), as well as neural (Nn-Diff) cell lineage that contained both neurons and astrocytes. Furthermore, the identities of these cell lineages were established by gene array analysis. Here, we explored the same arrays to gain insight into the gene alteration processes that accompany the establishment of endothelial vs. non-endothelial neural cell phenotypes. We compared the expression of genes that code for transcription factors and epigenetic regulators when HiPS is differentiated into these endothelial and non-endothelial lineages. Our in silico analyses have identified cohorts of genes that are similarly up- or downregulated in both lineages, as well as those that exhibit lineage-specific alterations. Based on these results, we propose that genes that are similarly altered in both lineages participate in priming the stem cell for differentiation in a lineage-independent manner, whereas those that are differentially altered in endothelial compared to neural cells participate in a lineage-specific differentiation process. Specific GATA family members and their cofactors and epigenetic regulators (DNMT3B, PRDM14, HELLS) with a major role in regulating DNA methylation were among participants in priming HiPS for lineage-independent differentiation. In addition, we identified distinct cohorts of transcription factors and epigenetic regulators whose alterations correlated specifically with the establishment of endothelial vs. non-endothelial neural lineages.
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39
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Zhang Y, McGrath KE, Ayoub E, Kingsley PD, Yu H, Fegan K, McGlynn KA, Rudzinskas S, Palis J, Perkins AS. Mds1 CreERT2, an inducible Cre allele specific to adult-repopulating hematopoietic stem cells. Cell Rep 2021; 36:109562. [PMID: 34407416 PMCID: PMC8428393 DOI: 10.1016/j.celrep.2021.109562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/24/2021] [Accepted: 07/28/2021] [Indexed: 12/16/2022] Open
Abstract
Hematopoietic ontogeny consists of two broad programs: an initial hematopoietic stem cell (HSC)-independent program followed by HSC-dependent hematopoiesis that sequentially seed the fetal liver and generate blood cells. However, the transition from HSC-independent to HSC-derived hematopoiesis remains poorly characterized. To help resolve this question, we developed Mds1CreERT2 mice, which inducibly express Cre-recombinase in emerging HSCs in the aorta and label long-term adult HSCs, but not HSC-independent yolk-sac-derived primitive or definitive erythromyeloid (EMP) hematopoiesis. Our lineage-tracing studies indicate that HSC-derived erythroid, myeloid, and lymphoid progeny significantly expand in the liver and blood stream between E14.5 and E16.5. Additionally, we find that HSCs contribute the majority of F4/80+ macrophages in adult spleen and marrow, in contrast to their limited contribution to macrophage populations in brain, liver, and lungs. The Mds1CreERT2 mouse model will be useful to deconvolute the complexity of hematopoiesis as it unfolds in the embryo and functions postnatally.
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Affiliation(s)
- Yi Zhang
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Kathleen E McGrath
- Center for Pediatric Biomedical Research and Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Edward Ayoub
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA; Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Paul D Kingsley
- Center for Pediatric Biomedical Research and Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Hongbo Yu
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Kate Fegan
- Center for Pediatric Biomedical Research and Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Kelly A McGlynn
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA; Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Sarah Rudzinskas
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - James Palis
- Center for Pediatric Biomedical Research and Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Archibald S Perkins
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA.
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40
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Fli1 + cells transcriptional analysis reveals an Lmo2-Prdm16 axis in angiogenesis. Proc Natl Acad Sci U S A 2021; 118:2008559118. [PMID: 34330825 DOI: 10.1073/pnas.2008559118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A network of molecular factors drives the development, differentiation, and maintenance of endothelial cells. Friend leukemia integration 1 transcription factor (FLI1) is a bona fide marker of endothelial cells during early development. In zebrafish Tg( f li1:EGFP) y1 , we identified two endothelial cell populations, high-fli1 + and low-fli1 +, by the intensity of green fluorescent protein signal. By comparing RNA-sequencing analysis of non-fli1 expressing cells (fli1 -) with these two (fli1 +) cell populations, we identified several up-regulated genes, not previously recognized as important, during endothelial development. Compared with fli1 - and low-fli1 + cells, high-fli1 + cells showed up-regulated expression of the zinc finger transcription factor PRDI-BF1 and RIZ homology domain containing 16 (prdm16). Prdm16 knockdown (KD) by morpholino in the zebrafish larva was associated with impaired angiogenesis and increased number of low-fli1 + cells at the expense of high-fli1 + cells. In addition, PRDM16 KD in endothelial cells derived from human-induced pluripotent stem cells impaired their differentiation and migration in vitro. Moreover, zebrafish mutants (mut) with loss of function for the oncogene LIM domain only 2 (lmo2) also showed reduced prdm16 gene expression combined with impaired angiogenesis. Prdm16 expression was reduced further in endothelial (CD31+) cells compared with CD31- cells isolated from l mo2-mutants (l mo2-mut) embryos. Chromatin immunoprecipitation-PCR demonstrated that Lmo2 binds to the promoter and directly regulates the transcription of prdm16 This work unveils a mechanism by which prdm16 expression is activated in endothelial cells by Lmo2 and highlights a possible therapeutic pathway by which to modulate endothelial cell growth and repair.
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41
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de Barros Sene L, Lamana GL, Schwambach Vieira A, Scarano WR, Gontijo JAR, Boer PA. Gestational Low Protein Diet Modulation on miRNA Transcriptome and Its Target During Fetal and Breastfeeding Nephrogenesis. Front Physiol 2021; 12:648056. [PMID: 34239447 PMCID: PMC8258388 DOI: 10.3389/fphys.2021.648056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/22/2021] [Indexed: 12/03/2022] Open
Abstract
Background The kidney ontogenesis is the most structurally affected by gestational protein restriction, reducing 28% of their functional units. The reduced nephron number is predictive of hypertension and cardiovascular dysfunctions that are generally observed in the adult age of most fetal programming models. We demonstrate miRNAs and predict molecular pathway changes associated with reduced reciprocal interaction between metanephros cap (CM) and ureter bud (UB) and a 28% decreased nephron stem cells in the 17 gestational days (17GD) low protein (LP) intake male fetal kidney. Here, we evaluated the same miRNAs and predicted targets in the kidneys of 21GD and at 7 days of life (7DL) LP offspring to elucidate the molecular modulations during nephrogenesis. Methods Pregnant Wistar rats were allocated into two groups: NP (regular protein diet- 17%) or LP (diet-6%). miRNA transcriptome sequencing (miRNA-Seq) was performed on the MiSeq platform from 21GD and 7DL male offspring kidneys using previously described methods. Among the top 10 dysfunctional regulated miRNAs, we validated 7 related to proliferation, differentiation, and apoptosis processes and investigated predicted target genes and proteins by RT-qPCR and immunohistochemistry. Results In 21GD, LP fetuses were identified alongside 21 differently expressed miRNAs, of which 12 were upregulated and 9 downregulated compared to age-matched NP offspring. In 7-DL LP offspring, the differentially expressed miRNAs were counted to be 74, of which 46 were upregulated and 28 downregulated. The curve from 17-GD to 7-DL shows that mTOR was fundamental in reducing the number of nephrons in fetal kidneys where the mothers were subjected to a protein restriction. IGF1 and TGFβ curves also seemed to present the same mTOR pattern and were modulated by miRNAs 181a-5p, 181a-3p, and 199a-5p. The miRNA 181c-3p modulated SIX2 and Notch1 reduction in 7-DL but not in terms of the enhanced expression of both in the 21-GD, suggesting the participation of an additional regulator. We found enhanced Bax in 21-GD; it was regulated by miRNA 298-5p, and Bcl2 and Caspase-3 were controlled by miRNA (by 7a-5p and not by the predicted 181a-5p). The miRNA 144-3p regulated BCL6, which was enhanced, as well as Zeb 1 and 2 induced by BCL6. These results revealed that in 21GD, the compensatory mechanisms in LP kidneys led to the activation of UB ramification. Besides, an increase of 32% in the CM stem cells and a possible cell cycle halt of renal progenitor cells, which remaining undifferentiated, were observed. In the 7DL, much more altered miRNA expression was found in LP kidneys, and this was probably due to an increased maternal diet content. Additionally, we verified the activation of pathways related to differentiation and consumption of progenitor cells.
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Affiliation(s)
- Letícia de Barros Sene
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Gabriela Leme Lamana
- Fetal Programming and Hydroelectrolyte Metabolism Laboratory, Nucleus of Medicine and Experimental Surgery, Department of Internal Medicine, FCM, Campinas, Brazil
| | - Andre Schwambach Vieira
- Department of Structural and Functional Biology, Biology Institute, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Wellerson Rodrigo Scarano
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - José Antônio Rocha Gontijo
- Fetal Programming and Hydroelectrolyte Metabolism Laboratory, Nucleus of Medicine and Experimental Surgery, Department of Internal Medicine, FCM, Campinas, Brazil
| | - Patrícia Aline Boer
- Fetal Programming and Hydroelectrolyte Metabolism Laboratory, Nucleus of Medicine and Experimental Surgery, Department of Internal Medicine, FCM, Campinas, Brazil
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42
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Landy MA, Goyal M, Casey KM, Liu C, Lai HC. Loss of Prdm12 during development, but not in mature nociceptors, causes defects in pain sensation. Cell Rep 2021; 34:108913. [PMID: 33789102 PMCID: PMC8048104 DOI: 10.1016/j.celrep.2021.108913] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/11/2021] [Accepted: 03/05/2021] [Indexed: 12/30/2022] Open
Abstract
Prdm12 is a key transcription factor in nociceptor neurogenesis. Mutations of Prdm12 cause congenital insensitivity to pain (CIP) from failure of nociceptor development. However, precisely how deletion of Prdm12 during development or adulthood affects nociception is unknown. Here, we employ tissue- and temporal-specific knockout mouse models to test the function of Prdm12 during development and in adulthood. We find that constitutive loss of Prdm12 causes deficiencies in proliferation during sensory neurogenesis. We also demonstrate that conditional knockout from dorsal root ganglia (DRGs) during embryogenesis causes defects in nociception. In contrast, we find that, in adult DRGs, Prdm12 is dispensable for most pain-sensation and injury-induced hypersensitivity. Using transcriptomic analysis, we find mostly unique changes in adult Prdm12 knockout DRGs compared with embryonic knockout and that PRDM12 is likely a transcriptional activator in the adult. Overall, we find that the function of PRDM12 changes over developmental time.
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Affiliation(s)
- Mark A Landy
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Megan Goyal
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Katherine M Casey
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chen Liu
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Hypothalamic Research Center, Dallas, TX 75390, USA
| | - Helen C Lai
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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43
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Investigation of PRDM10 and PRDM13 Expression in Developing Mouse Embryos by an Optimized PACT-Based Embryo Clearing Method. Int J Mol Sci 2021; 22:ijms22062892. [PMID: 33809237 PMCID: PMC8000312 DOI: 10.3390/ijms22062892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/25/2021] [Accepted: 03/08/2021] [Indexed: 12/21/2022] Open
Abstract
Recent developments in tissue clearing methods have significantly advanced the three-dimensional analysis of biological structures in whole, intact tissue, providing a greater understanding of spatial relationships and biological circuits. Nonetheless, studies have reported issues with maintaining structural integrity and preventing tissue disintegration, limiting the wide application of these techniques to fragile tissues such as developing embryos. Here, we present an optimized passive tissue clearing technique (PACT)-based embryo clearing method, initial embedding PACT (IMPACT)-Basic, that improves tissue rigidity without compromising optical transparency. We also present IMPACT-Advance, which is specifically optimized for thin slices of mouse embryos past E13.5. We demonstrate proof-of-concept by investigating the expression of two relatively understudied PR domain (PRDM) proteins, PRDM10 and PRDM13, in intact cleared mouse embryos at various stages of development. We observed strong PRDM10 and PRDM13 expression in the developing nervous system and skeletal cartilage, suggesting a functional role for these proteins in these tissues throughout embryogenesis.
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44
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Rienzo M, Sorrentino A, Di Zazzo E, Di Donato M, Carafa V, Marino MM, De Rosa C, Gazzerro P, Castoria G, Altucci L, Casamassimi A, Abbondanza C. Searching for a Putative Mechanism of RIZ2 Tumor-Promoting Function in Cancer Models. Front Oncol 2021; 10:583533. [PMID: 33585202 PMCID: PMC7880127 DOI: 10.3389/fonc.2020.583533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/08/2020] [Indexed: 12/16/2022] Open
Abstract
Positive Regulatory Domain (PRDM) gene family members commonly express two main molecular variants, the PR-plus isoform usually acting as tumor suppressor and the PR-minus one functioning as oncogene. Accordingly, PRDM2/RIZ encodes for RIZ1 (PR-plus) and RIZ2 (PR-minus). In human cancers, genetic or epigenetic modifications induce RIZ1 silencing with an expression level imbalance in favor of RIZ2 that could be relevant for tumorigenesis. Additionally, in estrogen target cells and tissues, estradiol increases RIZ2 expression level with concurrent increase of cell proliferation and survival. Several attempts to study RIZ2 function in HeLa or MCF-7 cells by its over-expression were unsuccessful. Thus, we over-expressed RIZ2 in HEK-293 cells, which are both RIZ1 and RIZ2 positive but unresponsive to estrogens. The forced RIZ2 expression increased cell viability and growth, prompted the G2-to-M phase transition and organoids formation. Accordingly, microarray analysis revealed that RIZ2 regulates several genes involved in mitosis. Consistently, RIZ silencing in both estrogen-responsive MCF-7 and -unresponsive MDA-MB-231 cells induced a reduction of cell proliferation and an increase of apoptosis rate. Our findings add novel insights on the putative RIZ2 tumor-promoting functions, although additional attempts are warranted to depict the underlying molecular mechanism.
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Affiliation(s)
- Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Anna Sorrentino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Erika Di Zazzo
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.,Department of Medicine and Health Sciences "V. Tiberio", University of Molise, Campobasso, Italy
| | - Marzia Di Donato
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Vincenzo Carafa
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Maria Michela Marino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Caterina De Rosa
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | | | - Gabriella Castoria
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
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45
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Yang WT, Chen M, Xu R, Zheng PS. PRDM4 inhibits cell proliferation and tumorigenesis by inactivating the PI3K/AKT signaling pathway through targeting of PTEN in cervical carcinoma. Oncogene 2021; 40:3318-3330. [PMID: 33846573 PMCID: PMC8102194 DOI: 10.1038/s41388-021-01765-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 02/27/2021] [Accepted: 03/22/2021] [Indexed: 02/01/2023]
Abstract
PR domain zinc finger protein 4 (PRDM4) is a transcription factor that plays key roles in stem cell self-renewal and tumorigenesis. However, its biological role and exact mechanism in cervical cancer remain unknown. Here, both immunohistochemistry (IHC) and Western blot assays demonstrated that the expression of PRDM4 in cervical cancer tissues was much lower than that in the normal cervix. A xenograft assay showed that PRDM4 overexpression in the cervical cancer cell lines SiHa and HeLa dramatically inhibited cell proliferation and tumorigenic potential in vivo. Conversely, the silencing of PRDM4 promoted cervical cancer cell proliferation and tumorigenic potential. Mechanistically, PRDM4 induced cell cycle arrest at the transition from G0/G1 phase to S phase by upregulating p27 and p21 expression and downregulating Cyclin D1 and CDK4 expression. Furthermore, the PI3K/AKT signaling pathway was inactivated in PRDM4-overexpressing cells, which decreased the levels of p-AKT and upregulated the expression of PTEN, an inhibitor of the PI3K/AKT signaling pathway, at both the transcriptional and translational levels. Dual-luciferase reporter assays and qChIP assays confirmed that PRDM4 transactivated the expression of PTEN by binding to two specific regions in the PTEN promoter. Furthermore, PTEN silencing or a PTEN inhibitor rescued the cell defects induced by PRDM4 overexpression. Therefore, our data suggest that PRDM4 inhibits cell proliferation and tumorigenesis by downregulating the activity of the PI3K/AKT signaling pathway by directly transactivating PTEN expression in cervical cancer.
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Affiliation(s)
- Wen-Ting Yang
- grid.452438.cDepartment of Reproductive Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi People’s Republic of China ,grid.419897.a0000 0004 0369 313XKey Laboratory of Environment and Genes Related to Diseases, Ministry of Education of the People’s Republic of China, Xi’an, Shaanxi People’s Republic of China
| | - Mei Chen
- grid.452438.cDepartment of Reproductive Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi People’s Republic of China
| | - Rui Xu
- grid.43169.390000 0001 0599 1243Department of Internal Medicine One, Shaanxi Cancer Hospital, College of Medicine, Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Peng-Sheng Zheng
- grid.452438.cDepartment of Reproductive Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi People’s Republic of China ,grid.419897.a0000 0004 0369 313XKey Laboratory of Environment and Genes Related to Diseases, Ministry of Education of the People’s Republic of China, Xi’an, Shaanxi People’s Republic of China
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46
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Begeman IJ, Shin K, Osorio-Méndez D, Kurth A, Lee N, Chamberlain TJ, Pelegri FJ, Kang J. Decoding an organ regeneration switch by dissecting cardiac regeneration enhancers. Development 2020; 147:226055. [PMID: 33246928 DOI: 10.1242/dev.194019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022]
Abstract
Heart regeneration in regeneration-competent organisms can be accomplished through the remodeling of gene expression in response to cardiac injury. This dynamic transcriptional response relies on the activities of tissue regeneration enhancer elements (TREEs); however, the mechanisms underlying TREEs are poorly understood. We dissected a cardiac regeneration enhancer in zebrafish to elucidate the mechanisms governing spatiotemporal gene expression during heart regeneration. Cardiac lepb regeneration enhancer (cLEN) exhibits dynamic, regeneration-dependent activity in the heart. We found that multiple injury-activated regulatory elements are distributed throughout the enhancer region. This analysis also revealed that cardiac regeneration enhancers are not only activated by injury, but surprisingly, they are also actively repressed in the absence of injury. Our data identified a short (22 bp) DNA element containing a key repressive element. Comparative analysis across Danio species indicated that the repressive element is conserved in closely related species. The repression mechanism is not operational during embryogenesis and emerges when the heart begins to mature. Incorporating both activation and repression components into the mechanism of tissue regeneration constitutes a new paradigm that might be extrapolated to other regeneration scenarios.
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Affiliation(s)
- Ian J Begeman
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kwangdeok Shin
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Daniel Osorio-Méndez
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Andrew Kurth
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Nutishia Lee
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Francisco J Pelegri
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.,UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
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He S, Ma X, Zheng N, Wang G, Wang M, Xia W, Yu D. PRDM14 mediates chemosensitivity and glycolysis in drug‑resistant A549/cisplatin cells and their progenitor A549 human lung adenocarcinoma cells. Mol Med Rep 2020; 23:149. [PMID: 33355367 PMCID: PMC7789100 DOI: 10.3892/mmr.2020.11788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022] Open
Abstract
Recent studies have reported that aberrant PR domain zinc finger protein 14 (PRDM14) expression is associated with the therapeutic sensitivity of cancer cells to drugs. However, its role in lung adenocarcinoma (LUAD) remains unclear. The present study aimed to determine the functions of knockdown or overexpression of PRDM14 in the chemosensitivity and glycolysis of LUAD cells. PRDM14 expression was analyzed in lung cancer tissues from patients resistant and sensitive to cisplatin (DDP), as well as in LUAD cell lines A549 and DDP-resistant A549 (A549/DDP) using reverse transcription quantitative-PCR and western blotting. Additionally, apoptosis was analyzed by flow cytometry, and flow cytometry and biochemical analysis was used to analyze glycolysis, indicated by glucose uptake and lactate release. The results of the present study demonstrated that PRDM14 expression was upregulated in patients with DDP-resistant LUAD and DDP-resistant cell lines. Overexpression of PRDM14 suppressed the sensitivity of A549 cells to DDP and silencing of PRDM14 using shRNA targeting PRDM14 promoted the sensitivity of A549/DDP cells to DDP, compared with that in the respective control groups. In mice with xenograft tumors, knockdown of PRDM14 using shRNA targeting PRDM14 inhibited the A549/DDP cell-derived tumor growth compared with scramble shRNA. The results of the glycolysis assays demonstrated that PRDM14 silencing inhibited glucose uptake, lactate release and glucose transporter 1 expression in A549/DDP cells compared with those in the control cells. PRDM14 overexpression relieved the inhibitory effects of 3-bromopyruvate, a potent glycolytic inhibitor for glycolysis, on glucose uptake and lactate release in A549 cells compared with those in the control cells. Therefore, the results of the present study suggested that PRDM14 may inhibit the chemosensitivity and promote glycolysis in human LUAD cells.
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Affiliation(s)
- Saifei He
- Department of Science and Research, The Seventh People's Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Xiaokun Ma
- Department of Nuclear Medicine, The Seventh People's Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Ni Zheng
- Department of Nuclear Medicine, The Seventh People's Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Guoyu Wang
- Department of Nuclear Medicine, The Seventh People's Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Menghan Wang
- Department of Nuclear Medicine, The Seventh People's Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Wei Xia
- Department of Nuclear Medicine, The Seventh People's Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Donghai Yu
- Department of Science and Education, The Municipal Health Commission, Shanghai 200125, P.R. China
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48
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Emerging Roles of PRDM Factors in Stem Cells and Neuronal System: Cofactor Dependent Regulation of PRDM3/16 and FOG1/2 (Novel PRDM Factors). Cells 2020; 9:cells9122603. [PMID: 33291744 PMCID: PMC7761934 DOI: 10.3390/cells9122603] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/13/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022] Open
Abstract
PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1) (PR) homologous domain containing (PRDM) transcription factors are expressed in neuronal and stem cell systems, and they exert multiple functions in a spatiotemporal manner. Therefore, it is believed that PRDM factors cooperate with a number of protein partners to regulate a critical set of genes required for maintenance of stem cell self-renewal and differentiation through genetic and epigenetic mechanisms. In this review, we summarize recent findings about the expression of PRDM factors and function in stem cell and neuronal systems with a focus on cofactor-dependent regulation of PRDM3/16 and FOG1/2. We put special attention on summarizing the effects of the PRDM proteins interaction with chromatin modulators (NuRD complex and CtBPs) on the stem cell characteristic and neuronal differentiation. Although PRDM factors are known to possess intrinsic enzyme activity, our literature analysis suggests that cofactor-dependent regulation of PRDM3/16 and FOG1/2 is also one of the important mechanisms to orchestrate bidirectional target gene regulation. Therefore, determining stem cell and neuronal-specific cofactors will help better understanding of PRDM3/16 and FOG1/2-controlled stem cell maintenance and neuronal differentiation. Finally, we discuss the clinical aspect of these PRDM factors in different diseases including cancer. Overall, this review will help further sharpen our knowledge of the function of the PRDM3/16 and FOG1/2 with hopes to open new research fields related to these factors in stem cell biology and neuroscience.
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49
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Brandies PA, Wright BR, Hogg CJ, Grueber CE, Belov K. Characterization of reproductive gene diversity in the endangered Tasmanian devil. Mol Ecol Resour 2020; 21:721-732. [PMID: 33188658 DOI: 10.1111/1755-0998.13295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/25/2020] [Accepted: 11/05/2020] [Indexed: 01/11/2023]
Abstract
Interindividual variation at genes known to play a role in reproduction may impact reproductive fitness. The Tasmanian devil is an endangered Australian marsupial with low genetic diversity. Recent work has shown concerning declines in productivity in both wild and captive populations over time. Understanding whether functional diversity exists at reproductive genes in the Tasmanian devil is a key first step in identifying genes that may influence productivity. We characterized single nucleotide polymorphisms (SNPs) at 214 genes involved in reproduction in 37 Tasmanian devils. Twenty genes contained nonsynonymous substitutions, with genes involved in embryogenesis, fertilization and hormonal regulation of reproduction displaying greater numbers of nonsynonymous SNPs than synonymous SNPs. Two genes, ADAMTS9 and NANOG, showed putative signatures of balancing selection indicating that natural selection is maintaining diversity at these genes despite the species exhibiting low overall levels of genetic diversity. We will use this information in future to examine the interplay between reproductive gene variation and reproductive fitness in Tasmanian devil populations.
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Affiliation(s)
- Parice A Brandies
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Belinda R Wright
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW, Australia.,San Diego Zoo Global, San Diego, CA, USA
| | - Katherine Belov
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW, Australia
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50
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Xu W, Li H, Wang L, Zhang J, Liu C, Wan X, Liu X, Hu Y, Fang Q, Xiao Y, Bu Q, Wang H, Tian J, Zhao Y, Cen X. Endocannabinoid signaling regulates the reinforcing and psychostimulant effects of ketamine in mice. Nat Commun 2020; 11:5962. [PMID: 33235205 PMCID: PMC7686380 DOI: 10.1038/s41467-020-19780-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/27/2020] [Indexed: 02/05/2023] Open
Abstract
The abuse potential of ketamine limits its clinical application, but the precise mechanism remains largely unclear. Here we discovered that ketamine significantly remodels the endocannabinoid-related lipidome and activates 2-arachidonoylglycerol (2-AG) signaling in the dorsal striatum (caudate nucleus and putamen, CPu) of mice. Elevated 2-AG in the CPu is essential for the psychostimulant and reinforcing effects of ketamine, whereas blockade of the cannabinoid CB1 receptor, a predominant 2-AG receptor, attenuates ketamine-induced remodeling of neuronal dendrite structure and neurobehaviors. Ketamine represses the transcription of the monoacylglycerol lipase (MAGL) gene by promoting the expression of PRDM5, a negative transcription factor of the MAGL gene, leading to increased 2-AG production. Genetic overexpression of MAGL or silencing of PRDM5 expression in the CPu robustly reduces 2-AG production and ketamine effects. Collectively, endocannabinoid signaling plays a critical role in mediating the psychostimulant and reinforcing properties of ketamine.
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Affiliation(s)
- Wei Xu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, People's Republic of China
| | - Hongchun Li
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, People's Republic of China
| | - Liang Wang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, People's Republic of China
| | - Jiamei Zhang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, People's Republic of China
| | - Chunqi Liu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, People's Republic of China
| | - Xuemei Wan
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, People's Republic of China
| | - Xiaochong Liu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, People's Republic of China
| | - Yiming Hu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, People's Republic of China
| | - Qiyao Fang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, People's Republic of China
| | - Yuanyuan Xiao
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, People's Republic of China
| | - Qian Bu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, People's Republic of China
| | - Hongbo Wang
- Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, 264005, Yantai, People's Republic of China
| | - Jingwei Tian
- Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, 264005, Yantai, People's Republic of China
| | - Yinglan Zhao
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, People's Republic of China
| | - Xiaobo Cen
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, People's Republic of China.
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