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Turrero García M, Baizabal JM, Tran DN, Peixoto R, Wang W, Xie Y, Adam MA, English LA, Reid CM, Brito SI, Booker MA, Tolstorukov MY, Harwell CC. Transcriptional regulation of MGE progenitor proliferation by PRDM16 controls cortical GABAergic interneuron production. Development 2020; 147:dev187526. [PMID: 33060132 PMCID: PMC7687860 DOI: 10.1242/dev.187526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 10/05/2020] [Indexed: 11/20/2022]
Abstract
The mammalian cortex is populated by neurons derived from neural progenitors located throughout the embryonic telencephalon. Excitatory neurons are derived from the dorsal telencephalon, whereas inhibitory interneurons are generated in its ventral portion. The transcriptional regulator PRDM16 is expressed by radial glia, neural progenitors present in both regions; however, its mechanisms of action are still not fully understood. It is unclear whether PRDM16 plays a similar role in neurogenesis in both dorsal and ventral progenitor lineages and, if so, whether it regulates common or unique networks of genes. Here, we show that Prdm16 expression in mouse medial ganglionic eminence (MGE) progenitors is required for maintaining their proliferative capacity and for the production of proper numbers of forebrain GABAergic interneurons. PRDM16 binds to cis-regulatory elements and represses the expression of region-specific neuronal differentiation genes, thereby controlling the timing of neuronal maturation. PRDM16 regulates convergent developmental gene expression programs in the cortex and MGE, which utilize both common and region-specific sets of genes to control the proliferative capacity of neural progenitors, ensuring the generation of correct numbers of cortical neurons.
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Affiliation(s)
| | | | - Diana N Tran
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Rui Peixoto
- Howard Hughes Medical Institute, Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Wengang Wang
- Howard Hughes Medical Institute, Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Yajun Xie
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Manal A Adam
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Lauren A English
- Summer Honors Undergraduate Research Program, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher M Reid
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Salvador I Brito
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew A Booker
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Michael Y Tolstorukov
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Corey C Harwell
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
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Abstract
Primary nociceptors are a heterogeneous class of peripheral somatosensory neurons, responsible for detecting noxious, pruriceptive, and thermal stimuli. These neurons are further divided into several molecularly defined subtypes that correlate with their functional sensory modalities and morphological features. During development, all nociceptors arise from a common pool of embryonic precursors, and then segregate progressively into their mature specialized phenotypes. In this review, we summarize the intrinsic transcriptional programs and extrinsic trophic factor signaling mechanisms that interact to control nociceptor diversification. We also discuss how recent transcriptome profiling studies have significantly advanced the field of sensory neuron development.
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Affiliation(s)
- Suna L Cranfill
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Wenqin Luo
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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Wu B, Jiang S, Wang X, Zhong S, Bi Y, Yi D, Liu G, Hu F, Dou G, Chen Y, Wu Y, Dong J. Identification of driver genes and key pathways of non-functional pituitary adenomas predicts the therapeutic effect of STO-609. PLoS One 2020; 15:e0240230. [PMID: 33119597 PMCID: PMC7595405 DOI: 10.1371/journal.pone.0240230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 09/22/2020] [Indexed: 12/24/2022] Open
Abstract
Objective Our study is to identify DEGs (Differentially Expressed Genes), comprehensively investigate hub genes, annotate enrichment functions and key pathways of Non-functional pituitary adenomas (NFPAs), and also to verify STO-609 therapeutic effect. Methods The gene expression level of NFPA and normal tissues were compared to identify the DEGs (Differential expressed genes) based on gene expression profiles (GSE2175, GSE26966 and GSE51618). Enrichment functions, pathways and key genes were identified by carrying out GO (Gene Ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis and PPI (Protein-Protein Interation) network analysis. Moreover, experiments in vitro were conducted to verify the anti-NFPAs effects of STO-609. Results 169 over-expression genes and 182 low expression genes were identified among 3 datasets. Dopaminergic synapse and vibrio cholerae infection pathways have distinctly changed in NFPA tissues. The Ca2+/CaM pathway played important roles in NFPA. Four hub proteins encoded by genes CALM1, PRDM10, RIPK4 and MAD2L1 were recognized as hub proteins. In vitro, assays showed that STO-609 induced apoptosis of NFPA cells to inhibit the hypophysoma cellular viability, diffusion and migration. Conclusion Four hub proteins, encoded by gene CALM1, PRDM10, RIPK4 and MAD2L1, played important roles in NFPA development. The Ca2+/CaM signaling pathway had significant alternations during NFPA forming process, the STO-609, a selective CaM-KK inhibitor, inhibited NFPA cellular viability, proliferation and migration. Meanwhile, NFPA was closely related to parkinson’s disease (PD) in many aspects.
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Affiliation(s)
- Bo Wu
- Clinical College, Jilin University, Changchun, China
- Department of Orthopedics, Jilin University First Hospital, Changchun, China
| | - Shanshan Jiang
- Institute of Zoology, China Academy of Science, Beijing, China
| | - Xinhui Wang
- Clinical College, Jilin University, Changchun, China
- Department of Oncology, Jilin University First Hospital, Changchun, China
| | - Sheng Zhong
- Department of Neurosurgery, Cancer Hospital of Sun Yat sen University, Guangzhou, China
| | - Yiming Bi
- Department of Neurosurgery, The First Bethune Hospital of Jilin University, Changchun, China
| | - Dazhuang Yi
- Department of Neurosurgery, The First Bethune Hospital of Jilin University, Changchun, China
| | - Ge Liu
- College of Pharmacy, Jilin University, Changchun, China
| | - Fangfei Hu
- College of Pharmacy, Jilin University, Changchun, China
| | - Gaojing Dou
- Clinical College, Jilin University, Changchun, China
- Department of Breast Surgery, Jilin University First Hospital, Changchun, China
| | - Yong Chen
- Department of Neurosurgery, The First Bethune Hospital of Jilin University, Changchun, China
| | - Yi Wu
- Department of Neurosurgy, Jiangmen Central Hospital, Jiangmen, China
- * E-mail: (YW); (JD)
| | - Jiajun Dong
- Department of Neurosurgy, Jiangmen Central Hospital, Jiangmen, China
- * E-mail: (YW); (JD)
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Vermeiren S, Bellefroid EJ, Desiderio S. Vertebrate Sensory Ganglia: Common and Divergent Features of the Transcriptional Programs Generating Their Functional Specialization. Front Cell Dev Biol 2020; 8:587699. [PMID: 33195244 PMCID: PMC7649826 DOI: 10.3389/fcell.2020.587699] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/08/2020] [Indexed: 12/13/2022] Open
Abstract
Sensory fibers of the peripheral nervous system carry sensation from specific sense structures or use different tissues and organs as receptive fields, and convey this information to the central nervous system. In the head of vertebrates, each cranial sensory ganglia and associated nerves perform specific functions. Sensory ganglia are composed of different types of specialized neurons in which two broad categories can be distinguished, somatosensory neurons relaying all sensations that are felt and visceral sensory neurons sensing the internal milieu and controlling body homeostasis. While in the trunk somatosensory neurons composing the dorsal root ganglia are derived exclusively from neural crest cells, somato- and visceral sensory neurons of cranial sensory ganglia have a dual origin, with contributions from both neural crest and placodes. As most studies on sensory neurogenesis have focused on dorsal root ganglia, our understanding of the molecular mechanisms underlying the embryonic development of the different cranial sensory ganglia remains today rudimentary. However, using single-cell RNA sequencing, recent studies have made significant advances in the characterization of the neuronal diversity of most sensory ganglia. Here we summarize the general anatomy, function and neuronal diversity of cranial sensory ganglia. We then provide an overview of our current knowledge of the transcriptional networks controlling neurogenesis and neuronal diversification in the developing sensory system, focusing on cranial sensory ganglia, highlighting specific aspects of their development and comparing it to that of trunk sensory ganglia.
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Affiliation(s)
- Simon Vermeiren
- ULB Neuroscience Institute, Université Libre de Bruxelles, Gosselies, Belgium
| | - Eric J Bellefroid
- ULB Neuroscience Institute, Université Libre de Bruxelles, Gosselies, Belgium
| | - Simon Desiderio
- Institute for Neurosciences of Montpellier, INSERM U1051, University of Montpellier, Montpellier, France
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Differential epigenetic regulation between the alternative promoters, PRDM1α and PRDM1β, of the tumour suppressor gene PRDM1 in human multiple myeloma cells. Sci Rep 2020; 10:15899. [PMID: 32985591 PMCID: PMC7522722 DOI: 10.1038/s41598-020-72946-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 09/07/2020] [Indexed: 12/23/2022] Open
Abstract
Multiple myeloma (MM) is a B-cell neoplasm that is characterized by the accumulation of malignant plasma cells in the bone marrow. The transcription factor PRDM1 is a master regulator of plasma cell development and is considered to be an oncosuppressor in several lymphoid neoplasms. The PRDM1β isoform is an alternative promoter of the PRDM1 gene that may interfere with the normal role of the PRDM1α isoform. To explain the induction of the PRDM1β isoform in MM and to offer potential therapeutic strategies to modulate its expression, we characterized the cis regulatory elements and epigenetic status of its promoter. We observed unexpected patterns of hypermethylation and hypomethylation at the PRDM1α and PRDM1β promoters, respectively, and prominent H3K4me1 and H3K9me2 enrichment at the PRDM1β promoter in non-expressing cell lines compared to PRDM1β-expressing cell lines. After treatment with drugs that inhibit DNA methylation, we were able to modify the activity of the PRDM1β promoter but not that of the PRDM1α promoter. Epigenetic drugs may offer the ability to control the expression of the PRDM1α/PRDM1β promoters as components of novel therapeutic approaches.
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Rahman MM, Kim IS, Ahn D, Tae HJ, Park BY. PR domaincontaining protein 12 (prdm12) is a downstream target of the transcription factor zic1 during cellular differentiation in the central nervous system: PR domain containing protein is the right form. Int J Dev Neurosci 2020; 80:528-537. [PMID: 32640092 DOI: 10.1002/jdn.10048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 11/05/2022] Open
Abstract
Transcription factor zic1 is an important regulator of neural plate patterning, formation of neural crest and cerebellar development, where its main function is neuronal cell differentiation. Among the genes identified, PR domain-containing 12 (prdm12) is a member of the prdm family and is expressed in the placode domain in the neurula stage. prdm12 is distinctly expressed in the dorsal part of the midbrain, trigeminal ganglion, and the motor neuron in the spinal cord. prdm12 knockdown results in the ventralization of the neural tube. zic1 knockdown results in the reduction of prdm12 expression in the midbrain, motor neuron and trigeminal ganglion, and overexpression of zic1 results in the expansion of prdm12 expression in the midbrain. zic1-activated wnt signaling is also a regulator of prdm12 expression in the midbrain. We propose that prdm12 is the downstream of zic1 and a novel player in the gene regulatory network controlling brain cell differentiation, along with some ganglions in Xenopus.
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Affiliation(s)
- Md Mahfujur Rahman
- College of Veterinary Medicine and Biosafety Research Institute, Jeonbuk National University, Iksan, Republic of Korea.,Department of Medicine, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet, Bangladesh
| | - In-Shik Kim
- College of Veterinary Medicine and Biosafety Research Institute, Jeonbuk National University, Iksan, Republic of Korea
| | - Dongchoon Ahn
- College of Veterinary Medicine and Biosafety Research Institute, Jeonbuk National University, Iksan, Republic of Korea
| | - Hyun-Jin Tae
- College of Veterinary Medicine and Biosafety Research Institute, Jeonbuk National University, Iksan, Republic of Korea
| | - Byung-Yong Park
- College of Veterinary Medicine and Biosafety Research Institute, Jeonbuk National University, Iksan, Republic of Korea
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57
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Zhang B, Zhao N, Peng K, He X, Chen CX, Liu H, Liu K, Jia L, Bao B. A combination of genome-wide association study screening and SNaPshot for detecting sex-related SNPs and genes in Cynoglossus semilaevis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100711. [PMID: 32683285 DOI: 10.1016/j.cbd.2020.100711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 11/16/2022]
Abstract
Chinese tongue sole (Cynoglossus semilaevis) males and females exhibit great differences in growth rate and appearance. The species is heterogametic (ZW/ZZ) and has sex-reversed "pseudomales" that are genetically female and physiologically male. In this study, we identified eight sex-specific single nucleotide polymorphism (SNP) markers for the sex identification of C. semilaevis by using a combination of genome-wide association study (GWAS) screening and SnaPshot validation. Candidate SNPs were screened using genotyping by sequencing to perform GWAS of the differential SNPs between the sexes of C. semilaevis. The SNP loci were amplified using a multiplex PCR system and detected via SNaPshot, which enables multiplexing of up to 30-40 SNPs in a single assay and ensures high accuracy of the results. The molecular markers detected in our study were used to successfully identify normal males and pseudomales from 45 caught and 40 cultured C. semilaevis specimens. Linkage disequilibrium analysis showed that the eight SNP loci were related to each other, with a strong linkage. Moreover, we investigated the expression of prdm6 mRNA containing a missense SNP and confirmed that the gene is differentially expressed in the gonads of the different sexes of C. semilaevis; the expression of prdm6 mRNA was significantly higher in the males than in the females and pseudomales. This means prdm6 may be related to sex differentiation in C. semilaevis.
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Tianjin Fisheries Research Institute, Tianjin, China
| | - Na Zhao
- Tianjin Medicine Biotechnology Co, Ltd, Tianjin, China
| | - Kangkang Peng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaoxu He
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Chun Xiu Chen
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Hao Liu
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Kefeng Liu
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Lei Jia
- Tianjin Fisheries Research Institute, Tianjin, China.
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
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58
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Global translation during early development depends on the essential transcription factor PRDM10. Nat Commun 2020; 11:3603. [PMID: 32681107 PMCID: PMC7368010 DOI: 10.1038/s41467-020-17304-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 05/21/2020] [Indexed: 01/08/2023] Open
Abstract
Members of the PR/SET domain-containing (PRDM) family of zinc finger transcriptional regulators play diverse developmental roles. PRDM10 is a yet uncharacterized family member, and its function in vivo is unknown. Here, we report an essential requirement for PRDM10 in pre-implantation embryos and embryonic stem cells (mESCs), where loss of PRDM10 results in severe cell growth inhibition. Detailed genomic and biochemical analyses reveal that PRDM10 functions as a sequence-specific transcription factor. We identify Eif3b, which encodes a core component of the eukaryotic translation initiation factor 3 (eIF3) complex, as a key downstream target, and demonstrate that growth inhibition in PRDM10-deficient mESCs is in part mediated through EIF3B-dependent effects on global translation. Our work elucidates the molecular function of PRDM10 in maintaining global translation, establishes its essential role in early embryonic development and mESC homeostasis, and offers insights into the functional repertoire of PRDMs as well as the transcriptional mechanisms regulating translation.
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59
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Chokeshaiusaha K, Puthier D, Sananmuang T, Olanratmanee EO, Nguyen C, Kedkovid R. Differential DNA methylation analysis across the promoter regions using methylated DNA immunoprecipitation sequencing profiling of porcine loin muscle. Vet World 2020; 13:1113-1125. [PMID: 32801562 PMCID: PMC7396332 DOI: 10.14202/vetworld.2020.1113-1125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
Background and Aim: Pork leanness and marbling are among the essential traits of consumer preference. To acquire knowledge about universal epigenetic regulations for improving breed selection, a meta-analysis of methylated DNA immunoprecipitation sequencing (MeDIP-seq) profiling data of mixed loin muscle types was performed in this study. Materials and Methods: MeDIP-seq profiling datasets of longissimus dorsi muscle and psoas major muscles from male and female pigs of Landrace and Tibetan breeds were preprocessed and aligned to the porcine genome. Analysis of differential methylated DNA regions (DMRs) between the breeds was performed by focusing on transcription start sites (TSSs) of known genes (−20,000-3000 bases from TSS). All associated genes were further reviewed for their functions and predicted for transcription factors (TF) possibly associated with their TSSs. Results: When the methylation levels of DMRs in TSS regions of Landrace breed were compared to those of Tibetan breed, 10 DMRs were hypomethylated (Landrace < Tibetan), and 19 DMRs were hypermethylated (Landrace > Tibetan), accordingly (p≤0.001). According to the reviews about gene functions, all associated genes were pieces of evidence for their roles in a variety of muscle and lipid metabolisms. Prediction of the binding TFs revealed the six most abundant binding TFs to such DMRs-associated TSS (p≤0.0001) as follows: ZNF384, Foxd3, IRF1, KLF9, EWSR1-FLI1, HES5, and TFAP2A. Conclusion: Common DMRs-associated TSS between the lean-type and the marbled-type loin muscles were identified in this study. Interestingly, the genes associated with such regions were strongly evidenced for their possible roles on the muscle trait characteristics by which further novel research topics could be focused on them in the future.
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Affiliation(s)
- Kaj Chokeshaiusaha
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chon Buri, Thailand
| | - Denis Puthier
- Aix-Marseille University, INSERM UMR 1090, TAGC, Marseille, France
| | - Thanida Sananmuang
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chon Buri, Thailand
| | - Em-On Olanratmanee
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chon Buri, Thailand
| | - Catherine Nguyen
- Aix-Marseille University, INSERM UMR 1090, TAGC, Marseille, France
| | - Roongtham Kedkovid
- Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Swine Reproduction Research Unit, Chulalongkorn University, Bangkok, Thailand
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60
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Bartesaghi L, Wang Y, Fontanet P, Wanderoy S, Berger F, Wu H, Akkuratova N, Bouçanova F, Médard JJ, Petitpré C, Landy MA, Zhang MD, Harrer P, Stendel C, Stucka R, Dusl M, Kastriti ME, Croci L, Lai HC, Consalez GG, Pattyn A, Ernfors P, Senderek J, Adameyko I, Lallemend F, Hadjab S, Chrast R. PRDM12 Is Required for Initiation of the Nociceptive Neuron Lineage during Neurogenesis. Cell Rep 2020; 26:3484-3492.e4. [PMID: 30917305 PMCID: PMC7676307 DOI: 10.1016/j.celrep.2019.02.098] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/06/2018] [Accepted: 02/25/2019] [Indexed: 12/21/2022] Open
Abstract
The sensation of pain is essential for the preservation of the functional integrity of the body. However, the key molecular regulators necessary for the initiation of the development of pain-sensing neurons have remained largely unknown. Here, we report that, in mice, inactivation of the transcriptional regulator PRDM12, which is essential for pain perception in humans, results in a complete absence of the nociceptive lineage, while proprioceptive and touch-sensitive neurons remain. Mechanistically, our data reveal that PRDM12 is required for initiation of neurogenesis and activation of a cascade of downstream pro-neuronal transcription factors, including NEUROD1, BRN3A, and ISL1, in the nociceptive lineage while it represses alternative fates other than nociceptors in progenitor cells. Our results thus demonstrate that PRDM12 is necessary for the generation of the entire lineage of pain-initiating neurons. The sensation of pain, temperature, and itch by neurons of the nociceptive lineage is essential for animal survival. Bartesaghi et al. report that the transcriptional regulator PRDM12 is indispensable in neural crest cells (NCCs) for the initiation of the sensory neuronal differentiation program that generates the entire nociceptive lineage.
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Affiliation(s)
- Luca Bartesaghi
- Department of Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Yiqiao Wang
- Department of Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Paula Fontanet
- Department of Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Simone Wanderoy
- Department of Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Finja Berger
- Department of Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Haohao Wu
- Department of Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Natalia Akkuratova
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, 17165, Sweden; Institute of Translational Biomedicine, Saint Petersburg State University, St. Petersburg, 199034, Russia
| | - Filipa Bouçanova
- Department of Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Jean-Jacques Médard
- Department of Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Charles Petitpré
- Department of Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Mark A Landy
- Department of Neuroscience, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ming-Dong Zhang
- Department of Medical Biochemistry and Biophysics, Division of Molecular Neurobiology, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Philip Harrer
- Friedrich-Baur-Institute at the Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Claudia Stendel
- Friedrich-Baur-Institute at the Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Rolf Stucka
- Friedrich-Baur-Institute at the Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Marina Dusl
- Friedrich-Baur-Institute at the Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Maria Eleni Kastriti
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, 17165, Sweden; Center for Brain Research, Medical University Vienna, Vienna, Austria
| | - Laura Croci
- Center for Brain Research, Medical University Vienna, Vienna, Austria
| | - Helen C Lai
- Department of Neuroscience, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | | | - Alexandre Pattyn
- Institute for Neurosciences of Montpellier, INSERM, UMR1051, Hôpital Saint-Eloi, Montpellier, 34000, France
| | - Patrik Ernfors
- Department of Medical Biochemistry and Biophysics, Division of Molecular Neurobiology, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Jan Senderek
- Friedrich-Baur-Institute at the Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, 17165, Sweden; Center for Brain Research, Medical University Vienna, Vienna, Austria
| | - Francois Lallemend
- Department of Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden.
| | - Saida Hadjab
- Department of Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden.
| | - Roman Chrast
- Department of Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, 17165, Sweden.
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61
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McGlynn KA, Sun R, Vonica A, Rudzinskas S, Zhang Y, Perkins AS. Prdm3 and Prdm16 cooperatively maintain hematopoiesis and clonogenic potential. Exp Hematol 2020; 85:20-32.e3. [PMID: 32437910 DOI: 10.1016/j.exphem.2020.04.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/14/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022]
Abstract
Mds1-Evi1 (also known as Prdm3) and Prdm16 are two highly related zinc finger transcription factors that, within the hematopoietic system, are both expressed primarily in hematopoietic stem cells (HSCs). Our laboratory previously found that constitutive Mds1-Evi1 knockout mice are viable, but their HSCs are unable to withstand myeloablative chemotherapy or effectively transplant irradiated recipient mice. A similar phenotype has been observed for Prdm16, except that the Prdm16 constitutive knockout is lethal. Here, we created a novel double-knockout model of Mds1-Evi1 and Prdm16 in the bone marrow, in which double knockout occurs only in cells that endogenously express Mds1-Evi1 and only upon induction with tamoxifen. We show that combined Mds1-Evi1/Prdm16 deficiency causes bone marrow failure within 15 days, with rapid loss in all progenitor compartments, while the peripheral blood exhibits progressive reductions in peripheral monocytes and granulocytes. We found that surviving hematopoietic stem cells and granulocytic progenitors had elevated apoptosis and cell division, and were unable to form colonies in vitro; adding back wild-type Mds1-Evi1 or Prdm16 to double-knockout bone marrow restores colony formation, and for MDS1-EVI1, this activity depends on a functional PR domain. All of these phenotypic effects were exhibited at milder levels in Mds1-Evi1 and Prdm16 single-knockout controls. Overall, these results illustrate that Mds1-Evi1 and Prdm16 play additive roles in maintaining normal hematopoietic stem cell survival.
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Affiliation(s)
- Kelly A McGlynn
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY
| | - Rongli Sun
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY
| | - Alin Vonica
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY
| | - Sarah Rudzinskas
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY
| | - Yi Zhang
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY.
| | - Archibald S Perkins
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY.
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Zhao LN, Kaldis P. Cascading proton transfers are a hallmark of the catalytic mechanism of SAM-dependent methyltransferases. FEBS Lett 2020; 594:2128-2139. [PMID: 32353165 DOI: 10.1002/1873-3468.13799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 11/10/2022]
Abstract
The S-adenosyl methionine (SAM)-dependent methyltransferases attach a methyl group to the deprotonated methyl lysine using SAM as a donor. An intriguing, yet unanswered, question is how the deprotonation takes place. PRDM9 with well-defined enzyme activity is a good representative of the methyltransferase family to study the deprotonation and subsequently the methyl transfer. Our study has found that the pKa of Tyr357 is low enough to make it an ideal candidate for proton abstraction from the methyl lysine. The partially deprontonated Tyr357 is able to change its H-bond pattern thus bridging two proton tunneling states and providing a cascading proton transfer. We have uncovered a new catalytic mechanism for the deprotonation of the methyl lysine in methyltransferases.
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Affiliation(s)
- Li Na Zhao
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Clinical Sciences, Lund University, Clinical Research Center (CRC), Malmö, Sweden
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63
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Karjosukarso DW, Ali Z, Peters TA, Zhang JQC, Hoogendoorn ADM, Garanto A, van Wijk E, Jensen LD, Collin RWJ. Modeling ZNF408-Associated FEVR in Zebrafish Results in Abnormal Retinal Vasculature. Invest Ophthalmol Vis Sci 2020; 61:39. [PMID: 32097476 PMCID: PMC7329629 DOI: 10.1167/iovs.61.2.39] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Purpose Familial exudative vitreoretinopathy (FEVR) is an inherited retinal disease in which the retinal vasculature is affected. Patients with FEVR typically lack or have abnormal vasculature in the peripheral retina, the outcome of which can range from mild visual impairment to complete blindness. A missense mutation (p.His455Tyr) in ZNF408 was identified in an autosomal dominant FEVR family. Little, however, is known about the molecular role of ZNF408 and how its defect leads to the clinical features of FEVR. Methods Using CRISPR/Cas9 technology, two homozygous mutant zebrafish models with truncated znf408 were generated, as well as one heterozygous and one homozygous missense znf408 model in which the human p.His455Tyr mutation is mimicked. Results Intriguingly, all three znf408-mutant zebrafish strains demonstrated progressive retinal vascular pathology, initially characterized by a deficient hyaloid vessel development at 5 days postfertilization (dpf) leading to vascular insufficiency in the retina. The generation of stable mutant lines allowed long-term follow up studies, which showed ectopic retinal vascular hyper-sprouting at 90 dpf and extensive vascular leakage at 180 dpf. Conclusions Together, our data demonstrate an important role for znf408 in the development and maintenance of the vascular system within the retina.
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Hael CE, Rojo D, Orquera DP, Low MJ, Rubinstein M. The transcriptional regulator PRDM12 is critical for Pomc expression in the mouse hypothalamus and controlling food intake, adiposity, and body weight. Mol Metab 2020; 34:43-53. [PMID: 32180559 PMCID: PMC7011018 DOI: 10.1016/j.molmet.2020.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/04/2020] [Accepted: 01/07/2020] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE Regulation of food intake and energy balance depends on a group of hypothalamic neurons that release anorexigenic melanocortins encoded by the Pomc gene. Although the physiological importance of central melanocortins is well appreciated, the genetic program that defines the functional identity of melanocortin neurons and assures high levels of hypothalamic Pomc expression is only beginning to be understood. This study assessed whether the transcriptional regulator PRDM12, identified as a highly expressed gene in adult mouse POMC neurons, plays an important role in the identity and function of melanocortin neurons. METHODS We first determined the cellular distribution of PRDM12 in the developing hypothalamus. Then we studied mutant mice with constitutively inactivated Prdm12 to evaluate possible changes in hypothalamic Pomc expression. In addition, we characterized conditional mutant mice specifically lacking Prdm12 in ISL1-positive or POMC neurons during development. Finally, we measured food intake, body weight progression up to 16 weeks of age, adiposity, and glucose tolerance in adult mice lacking Prdm12 selectively from POMC neurons. RESULTS PRDM12 co-expressed with POMC in mouse hypothalamic neurons from early development to adulthood. Mice lacking Prdm12 displayed greatly reduced Pomc expression in the developing hypothalamus. Selective ablation of Prdm12 from ISL1 neurons prevented hypothalamic Pomc expression. The conditional ablation of Prdm12 limited to POMC neurons greatly reduced Pomc expression in the developing hypothalamus and in adult mice led to increased food intake, adiposity, and obesity. CONCLUSIONS Altogether, our results demonstrate that PRDM12 plays an essential role in the early establishment of hypothalamic melanocortin neuron identity and the maintenance of high expression levels of Pomc. Its absence in adult mice greatly impairs Pomc expression and leads to increased food intake, adiposity, and obesity.
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Affiliation(s)
- Clara E Hael
- Institute of Investigations in Genetic Engineering and Molecular Biology, National Council of Scientific and Technological Research, 1428 Buenos Aires, Argentina
| | - Daniela Rojo
- Institute of Investigations in Genetic Engineering and Molecular Biology, National Council of Scientific and Technological Research, 1428 Buenos Aires, Argentina
| | - Daniela P Orquera
- Institute of Investigations in Genetic Engineering and Molecular Biology, National Council of Scientific and Technological Research, 1428 Buenos Aires, Argentina
| | - Malcolm J Low
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48105, USA.
| | - Marcelo Rubinstein
- Institute of Investigations in Genetic Engineering and Molecular Biology, National Council of Scientific and Technological Research, 1428 Buenos Aires, Argentina; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48105, USA; Department of Physiology, Molecular and Cellular Biology, School of Exact and Natural Sciences, University of Buenos Aires, 1428 Buenos Aires, Argentina.
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65
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Enikanolaiye A, Ruston J, Zeng R, Taylor C, Schrock M, Buchovecky CM, Shendure J, Acar E, Justice MJ. Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology. Genome Res 2020; 30:540-552. [PMID: 32317254 PMCID: PMC7197480 DOI: 10.1101/gr.258400.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/20/2020] [Indexed: 12/31/2022]
Abstract
Mutations in X-linked methyl-CpG-binding protein 2 (MECP2) cause Rett syndrome (RTT). To identify functional pathways that could inform therapeutic entry points, we carried out a genetic screen for secondary mutations that improved phenotypes in Mecp2/Y mice after mutagenesis with N-ethyl-N-nitrosourea (ENU). Here, we report the isolation of 106 founder animals that show suppression of Mecp2-null traits from screening 3177 Mecp2/Y genomes. Whole-exome sequencing, genetic crosses, and association analysis identified 22 candidate genes. Additional lesions in these candidate genes or pathway components associate variant alleles with phenotypic improvement in 30 lines. A network analysis shows that 63% of the genes cluster into the functional categories of transcriptional repression, chromatin modification, or DNA repair, delineating a pathway relationship with MECP2. Many mutations lie in genes that modulate synaptic signaling or lipid homeostasis. Mutations in genes that function in the DNA damage response (DDR) also improve phenotypes in Mecp2/Y mice. Association analysis was successful in resolving combinatorial effects of multiple loci. One line, which carries a suppressor mutation in a gene required for cholesterol synthesis, Sqle, carries a second mutation in retinoblastoma binding protein 8, endonuclease (Rbbp8, also known as CtIP), which regulates a DDR choice in double-stranded break (DSB) repair. Cells from Mecp2/Y mice have increased DSBs, so this finding suggests that the balance between homology-directed repair and nonhomologous end joining is important for neuronal cells. In this and other lines, two suppressor mutations confer greater improvement than one alone, suggesting that combination therapies could be effective in RTT.
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Affiliation(s)
- Adebola Enikanolaiye
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Julie Ruston
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Rong Zeng
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Christine Taylor
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Marijke Schrock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Christie M Buchovecky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, Washington 98195, USA
- Howard Hughes Medical Institute, Seattle, Washington 98195, USA
| | - Elif Acar
- The Centre for Phenogenomics, Toronto, Ontario, M5T 3H7, Canada
- Department of Statistics, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Monica J Justice
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- The Centre for Phenogenomics, Toronto, Ontario, M5T 3H7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
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Ye J, Huang A, Wang H, Zhang AMY, Huang X, Lan Q, Sato T, Goyama S, Kurokawa M, Deng C, Sander M, Schaeffer DF, Li W, Kopp JL, Xie R. PRDM3 attenuates pancreatitis and pancreatic tumorigenesis by regulating inflammatory response. Cell Death Dis 2020; 11:187. [PMID: 32179733 PMCID: PMC7075911 DOI: 10.1038/s41419-020-2371-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 12/21/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is associated with metaplastic changes in the pancreas but the transcriptional program underlying these changes is incompletely understood. The zinc finger transcription factor, PRDM3, is lowly expressed in normal pancreatic acini and its expression increases during tumorigenesis. Although PRDM3 promotes proliferation and migration of PDAC cell lines, the role of PRDM3 during tumor initiation from pancreatic acinar cells in vivo is unclear. In this study, we showed that high levels of PRDM3 expression in human pancreas was associated with pancreatitis, and well-differentiated but not poorly differentiated carcinoma. We examined PRDM3 function in pancreatic acinar cells during tumor formation and pancreatitis by inactivating Prdm3 using a conditional allele (Ptf1aCreER;Prdm3flox/flox mice) in the context of oncogenic Kras expression and supraphysiological cerulein injections, respectively. In Prdm3-deficient mice, KrasG12D-driven preneoplastic lesions were more abundant and progressed to high-grade precancerous lesions more rapidly. This is consistent with our observations that low levels of PRDM3 in human PDAC was correlated significantly with poorer survival in patient. Moreover, loss of Prdm3 in acinar cells elevated exocrine injury, enhanced immune cell activation and infiltration, and greatly increased acinar-to-ductal cell reprogramming upon cerulein-induced pancreatitis. Whole transcriptome analyses of Prdm3 knockout acini revealed that pathways involved in inflammatory response and Hif-1 signaling were significantly upregulated in Prdm3-depleted acinar cells. Taken together, our results suggest that Prdm3 favors the maintenance of acinar cell homeostasis through modulation of their response to inflammation and oncogenic Kras activation, and thus plays a previously unexpected suppressive role during PDAC initiation.
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Affiliation(s)
- Jie Ye
- Cancer Centre, Faculty of Health Sciences, University of Macau, 999078, Macau SAR, China
- Institute of Translational Medicine, Faculty of Health of Sciences, University of Macau, 999078, Macau SAR, China
| | - Anpei Huang
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, 510275, Guangzhou, China
| | - Haitao Wang
- Cancer Centre, Faculty of Health Sciences, University of Macau, 999078, Macau SAR, China
- Division of Medical Sciences, National Cancer Centre Singapore, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Anni M Y Zhang
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Xiaojun Huang
- Cancer Centre, Faculty of Health Sciences, University of Macau, 999078, Macau SAR, China
- Institute of Translational Medicine, Faculty of Health of Sciences, University of Macau, 999078, Macau SAR, China
| | - Qingping Lan
- Cancer Centre, Faculty of Health Sciences, University of Macau, 999078, Macau SAR, China
- Institute of Translational Medicine, Faculty of Health of Sciences, University of Macau, 999078, Macau SAR, China
| | - Tomohiko Sato
- Department of Hematology and Oncology, University of Tokyo, Tokyo, 113-8654, Japan
| | - Susumu Goyama
- Department of Hematology and Oncology, University of Tokyo, Tokyo, 113-8654, Japan
| | - Mineo Kurokawa
- Department of Hematology and Oncology, University of Tokyo, Tokyo, 113-8654, Japan
| | - Chuxia Deng
- Cancer Centre, Faculty of Health Sciences, University of Macau, 999078, Macau SAR, China
- Institute of Translational Medicine, Faculty of Health of Sciences, University of Macau, 999078, Macau SAR, China
| | - Maike Sander
- Department of Pediatrics and Cellular and Molecular Medicine, University of California-San Diego, La Jolla, CA, 92093, USA
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Wen Li
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, 510275, Guangzhou, China.
| | - Janel L Kopp
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Ruiyu Xie
- Cancer Centre, Faculty of Health Sciences, University of Macau, 999078, Macau SAR, China.
- Institute of Translational Medicine, Faculty of Health of Sciences, University of Macau, 999078, Macau SAR, China.
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Chui A, Zhang Q, Dai Q, Shi SH. Oxidative stress regulates progenitor behavior and cortical neurogenesis. Development 2020; 147:dev.184150. [PMID: 32041791 DOI: 10.1242/dev.184150] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/17/2020] [Indexed: 12/13/2022]
Abstract
Orderly division of radial glial progenitors (RGPs) in the developing mammalian cerebral cortex generates deep and superficial layer neurons progressively. However, the mechanisms that control RGP behavior and precise neuronal output remain elusive. Here, we show that the oxidative stress level progressively increases in the developing mouse cortex and regulates RGP behavior and neurogenesis. As development proceeds, numerous gene pathways linked to reactive oxygen species (ROS) and oxidative stress exhibit drastic changes in RGPs. Selective removal of PRDM16, a transcriptional regulator highly expressed in RGPs, elevates ROS level and induces expression of oxidative stress-responsive genes. Coinciding with an enhanced level of oxidative stress, RGP behavior was altered, leading to abnormal deep and superficial layer neuron generation. Simultaneous expression of mitochondrially targeted catalase to reduce cellular ROS levels significantly suppresses cortical defects caused by PRDM16 removal. Together, these findings suggest that oxidative stress actively regulates RGP behavior to ensure proper neurogenesis in the mammalian cortex.
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Affiliation(s)
- Angela Chui
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA .,Neuroscience Graduate Program, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Qiangqiang Zhang
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Qi Dai
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Song-Hai Shi
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA .,Neuroscience Graduate Program, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA.,IDG/McGovern Institute for Brain Research, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Center of Biological Molecules, School of Life Sciences, Tsinghua University, Beijing 100084, China
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68
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Nam JM, Lim JE, Ha TW, Oh B, Kang JO. Cardiac-specific inactivation of Prdm16 effects cardiac conduction abnormalities and cardiomyopathy-associated phenotypes. Am J Physiol Heart Circ Physiol 2020; 318:H764-H777. [PMID: 32083975 DOI: 10.1152/ajpheart.00647.2019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A variant in the PRDM16 locus has been correlated with QRS duration in an electrocardiogram genome-wide association study, and the deletion of PRDM16 has been implicated as a causal factor of the dilated cardiomyopathy that is linked to 1p36 deletion syndrome. We aimed to determine how a null mutation of Prdm16 affects cardiac function and study the underlying mechanism of the resulting phenotype in an appropriate mouse model. We used cardiac-specific Prdm16 conditional knockout mice to examine cardiac function by electrocardiography. QRS duration and QTc interval increased significantly in cardiac-specific Prdm16 knockout animals compared with wild-type mice. Further, we assessed cardiomyopathy-associated features by trichrome staining, densitometry, and hydroxyproline assay. Prdm16-null hearts showed greater fibrosis and cardiomyocyte hypertrophy. By quantitative real-time PCR, Prdm16-null hearts upregulated extracellular matrix-related genes (Ctgf, Timp1) and α-smooth muscle actin (Acta2), a myofibroblast marker. Moreover, TGF-β signaling was activated in Prdm16-null hearts, as evidenced by increased Tgfb1-3 transcript levels and phosphorylated Smad2. However, the inhibition of TGF-β receptor did not reverse the aberrations in conduction in cardiac-specific Prdm16 knockout mice. To determine the underlying mechanisms, we performed RNA-seq using mouse left ventricular tissue. By functional analysis, Prdm16-null hearts experienced dysregulated expression of ion channel genes, including Kcne1, Scn5a, Cacna1h, and Cacna2d2. Mice with Prdm16-null hearts develop abnormalities in cardiac conduction and cardiomyopathy-associated phenotypes, including fibrosis and cellular hypertrophy. Further, the RNA-seq findings suggest that impairments in ion homeostasis (Ca2+, K+, and Na+) may at least partially underlie the abnormal conduction in cardiac-specific Prdm16 knockout mice.NEW & NOTEWORTHY This is the first study that describes aberrant cardiac function and cardiomyopathy-associated phenotypes in an appropriate murine genetic model with cardiomyocyte-specific Prdm16-null mutation. It is noteworthy that the correlation of PRDM16 with QRS duration is replicated in a murine animal model and the potential underlying mechanism may be the impairment of ion homeostasis.
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Affiliation(s)
- Jeong Min Nam
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Ji Eun Lim
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Tae Woong Ha
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Bermseok Oh
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Ji-One Kang
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
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Shull LC, Sen R, Menzel J, Goyama S, Kurokawa M, Artinger KB. The conserved and divergent roles of Prdm3 and Prdm16 in zebrafish and mouse craniofacial development. Dev Biol 2020; 461:132-144. [PMID: 32044379 DOI: 10.1016/j.ydbio.2020.02.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 12/21/2022]
Abstract
The formation of the craniofacial skeleton is a highly dynamic process that requires proper orchestration of various cellular processes in cranial neural crest cell (cNCC) development, including cell migration, proliferation, differentiation, polarity and cell death. Alterations that occur during cNCC development result in congenital birth defects and craniofacial abnormalities such as cleft lip with or without cleft palate. While the gene regulatory networks facilitating neural crest development have been extensively studied, the epigenetic mechanisms by which these pathways are activated or repressed in a temporal and spatially regulated manner remain largely unknown. Chromatin modifiers can precisely modify gene expression through a variety of mechanisms including histone modifications such as methylation. Here, we investigated the role of two members of the PRDM (Positive regulatory domain) histone methyltransferase family, Prdm3 and Prdm16 in craniofacial development using genetic models in zebrafish and mice. Loss of prdm3 or prdm16 in zebrafish causes craniofacial defects including hypoplasia of the craniofacial cartilage elements, undefined posterior ceratobranchials, and decreased mineralization of the parasphenoid. In mice, while conditional loss of Prdm3 in the early embryo proper causes mid-gestation lethality, loss of Prdm16 caused craniofacial defects including anterior mandibular hypoplasia, clefting in the secondary palate and severe middle ear defects. In zebrafish, prdm3 and prdm16 compensate for each other as well as a third Prdm family member, prdm1a. Combinatorial loss of prdm1a, prdm3, and prdm16 alleles results in severe hypoplasia of the anterior cartilage elements, abnormal formation of the jaw joint, complete loss of the posterior ceratobranchials, and clefting of the ethmoid plate. We further determined that loss of prdm3 and prdm16 reduces methylation of histone 3 lysine 9 (repression) and histone 3 lysine 4 (activation) in zebrafish. In mice, loss of Prdm16 significantly decreased histone 3 lysine 9 methylation in the palatal shelves but surprisingly did not change histone 3 lysine 4 methylation. Taken together, Prdm3 and Prdm16 play an important role in craniofacial development by maintaining temporal and spatial regulation of gene regulatory networks necessary for proper cNCC development and these functions are both conserved and divergent across vertebrates.
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Affiliation(s)
- Lomeli Carpio Shull
- Department of Craniofacial Biology, School of Dental Medicine, Aurora, CO, USA
| | - Rwik Sen
- Department of Craniofacial Biology, School of Dental Medicine, Aurora, CO, USA
| | - Johannes Menzel
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Susumu Goyama
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Mineo Kurokawa
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Investigation of PRDM7 and PRDM12 expression pattern during mouse embryonic development by using a modified passive clearing technique. Biochem Biophys Res Commun 2020; 524:346-353. [PMID: 32000999 DOI: 10.1016/j.bbrc.2019.12.133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 12/18/2019] [Indexed: 12/28/2022]
Abstract
Recent developments in tissue clearing methods such as CLARITY (Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging/Immunostaining/In situ hybridization-compatible Tissue hYdrogel) have allowed for the three-dimensional analysis of biological structures in whole, intact tissue, providing greater understanding of spatial relationships and biological circuits. Nonetheless, studies have reported issues with maintaining structural integrity and preventing tissue disintegration, preventing the wide application of these techniques to fragile tissues such as developing embryos. Here, we present optimized passive clearing techniques, mPACT-A, that improve tissue rigidity without the expense of optical transparency. We also present a further modified mPACT-A protocol that is specifically optimized for handling mouse embryos, which are small and fragile, such that they easily dismantle when processed via established tissue clearing methods. We demonstrate proof-of-concept by investigating the expression of two relatively understudied PRDM proteins, PRDM7 and PRDM12, in intact cleared mouse embryos at various stages of development. We observed strong PRDM7 and PRDM12 expression in the developing mouse nervous system, suggestive of potential roles in neural development that will be tested in future functional studies.
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71
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Miller KN, Clark JP, Martin SA, Howell PR, Burhans MS, Haws SA, Johnson NB, Rhoads TW, Pavelec DM, Eliceiri KW, Roopra AS, Ntambi JM, Denu JM, Parks BW, Anderson RM. PGC-1a integrates a metabolism and growth network linked to caloric restriction. Aging Cell 2019; 18:e12999. [PMID: 31267675 PMCID: PMC6718593 DOI: 10.1111/acel.12999] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/07/2019] [Accepted: 06/13/2019] [Indexed: 12/25/2022] Open
Abstract
Deleterious changes in energy metabolism have been linked to aging and disease vulnerability, while activation of mitochondrial pathways has been linked to delayed aging by caloric restriction (CR). The basis for these associations is poorly understood, and the scope of impact of mitochondrial activation on cellular function has yet to be defined. Here, we show that mitochondrial regulator PGC-1a is induced by CR in multiple tissues, and at the cellular level, CR-like activation of PGC-1a impacts a network that integrates mitochondrial status with metabolism and growth parameters. Transcriptional profiling reveals that diverse functions, including immune pathways, growth, structure, and macromolecule homeostasis, are responsive to PGC-1a. Mechanistically, these changes in gene expression were linked to chromatin remodeling and RNA processing. Metabolic changes implicated in the transcriptional data were confirmed functionally including shifts in NAD metabolism, lipid metabolism, and membrane lipid composition. Delayed cellular proliferation, altered cytoskeleton, and attenuated growth signaling through post-transcriptional and post-translational mechanisms were also identified as outcomes of PGC-1a-directed mitochondrial activation. Furthermore, in vivo in tissues from a genetically heterogeneous mouse population, endogenous PGC-1a expression was correlated with this same metabolism and growth network. These data show that small changes in metabolism have broad consequences that arguably would profoundly alter cell function. We suggest that this PGC-1a sensitive network may be the basis for the association between mitochondrial function and aging where small deficiencies precipitate loss of function across a spectrum of cellular activities.
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Affiliation(s)
- Karl N. Miller
- Division of Geriatrics, Department of Medicine SMPH, University of Wisconsin Madison Wisconsin USA
| | - Josef P. Clark
- Division of Geriatrics, Department of Medicine SMPH, University of Wisconsin Madison Wisconsin USA
| | - Stephen A. Martin
- Division of Geriatrics, Department of Medicine SMPH, University of Wisconsin Madison Wisconsin USA
| | - Porsha R. Howell
- Division of Geriatrics, Department of Medicine SMPH, University of Wisconsin Madison Wisconsin USA
| | - Maggie S. Burhans
- Division of Geriatrics, Department of Medicine SMPH, University of Wisconsin Madison Wisconsin USA
| | - Spencer A. Haws
- Department of Biomolecular Chemistry University of Wisconsin Madison Wisconsin USA
- Wisconsin Institute for Discovery University of Wisconsin Madison Wisconsin USA
| | - Nathan B. Johnson
- Division of Geriatrics, Department of Medicine SMPH, University of Wisconsin Madison Wisconsin USA
| | - Timothy W Rhoads
- Division of Geriatrics, Department of Medicine SMPH, University of Wisconsin Madison Wisconsin USA
| | - Derek M. Pavelec
- Biotechnology Center University of Wisconsin Madison Wisconsin USA
| | - Kevin W. Eliceiri
- Laboratory for Optical and Computational Instrumentation University of Wisconsin Madison Wisconsin USA
| | - Avtar S. Roopra
- Department of Neuroscience University of Wisconsin Madison Wisconsin USA
| | - James M. Ntambi
- Department of Biochemistry University of Wisconsin Madison Wisconsin USA
- Department of Nutritional Sciences University of Wisconsin Madison Wisconsin USA
| | - John M. Denu
- Department of Biomolecular Chemistry University of Wisconsin Madison Wisconsin USA
- Wisconsin Institute for Discovery University of Wisconsin Madison Wisconsin USA
- Morgridge Institute for Research Madison Wisconsin USA
| | - Brian W. Parks
- Department of Nutritional Sciences University of Wisconsin Madison Wisconsin USA
| | - Rozalyn M. Anderson
- Division of Geriatrics, Department of Medicine SMPH, University of Wisconsin Madison Wisconsin USA
- Geriatric Research, Education, and Clinical Center William S. Middleton Memorial Veterans Hospital Madison Wisconsin USA
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[Chemical targeting of DNA and histone methylation in cancer: Novelties, hopes and promises]. Bull Cancer 2019; 106:823-833. [PMID: 31522746 DOI: 10.1016/j.bulcan.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 07/29/2019] [Indexed: 01/10/2023]
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73
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Ivanochko D, Halabelian L, Henderson E, Savitsky P, Jain H, Marcon E, Duan S, Hutchinson A, Seitova A, Barsyte-Lovejoy D, Filippakopoulos P, Greenblatt J, Lima-Fernandes E, Arrowsmith CH. Direct interaction between the PRDM3 and PRDM16 tumor suppressors and the NuRD chromatin remodeling complex. Nucleic Acids Res 2019; 47:1225-1238. [PMID: 30462309 PMCID: PMC6379669 DOI: 10.1093/nar/gky1192] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/31/2018] [Accepted: 11/15/2018] [Indexed: 01/01/2023] Open
Abstract
Aberrant isoform expression of chromatin-associated proteins can induce epigenetic programs related to disease. The MDS1 and EVI1 complex locus (MECOM) encodes PRDM3, a protein with an N-terminal PR-SET domain, as well as a shorter isoform, EVI1, lacking the N-terminus containing the PR-SET domain (ΔPR). Imbalanced expression of MECOM isoforms is observed in multiple malignancies, implicating EVI1 as an oncogene, while PRDM3 has been suggested to function as a tumor suppressor through an unknown mechanism. To elucidate functional characteristics of these N-terminal residues, we compared the protein interactomes of the full-length and ΔPR isoforms of PRDM3 and its closely related paralog, PRDM16. Unlike the ΔPR isoforms, both full-length isoforms exhibited a significantly enriched association with components of the NuRD chromatin remodeling complex, especially RBBP4. Typically, RBBP4 facilitates chromatin association of the NuRD complex by binding to histone H3 tails. We show that RBBP4 binds to the N-terminal amino acid residues of PRDM3 and PRDM16, with a dissociation constant of 3.0 μM, as measured by isothermal titration calorimetry. Furthermore, high-resolution X-ray crystal structures of PRDM3 and PRDM16 N-terminal peptides in complex with RBBP4 revealed binding to RBBP4 within the conserved histone H3-binding groove. These data support a mechanism of isoform-specific interaction of PRDM3 and PRDM16 with the NuRD chromatin remodeling complex.
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Affiliation(s)
- Danton Ivanochko
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Elizabeth Henderson
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Pavel Savitsky
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Harshika Jain
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Edyta Marcon
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Shili Duan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Evelyne Lima-Fernandes
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
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74
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Monaghan L, Massett ME, Bunschoten RP, Hoose A, Pirvan PA, Liskamp RMJ, Jørgensen HG, Huang X. The Emerging Role of H3K9me3 as a Potential Therapeutic Target in Acute Myeloid Leukemia. Front Oncol 2019; 9:705. [PMID: 31428579 PMCID: PMC6687838 DOI: 10.3389/fonc.2019.00705] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/16/2019] [Indexed: 12/23/2022] Open
Abstract
Growing evidence has demonstrated that epigenetic dysregulation is a common pathological feature in human cancer cells. Global alterations in the epigenetic landscape are prevalent in malignant cells across different solid tumors including, prostate cancer, non-small-cell lung cancer, renal cell carcinoma, and in haemopoietic malignancy. In particular, DNA hypomethylation and histone hypoacetylation have been observed in acute myeloid leukemia (AML) patient blasts, with histone methylation being an emerging area of study. Histone 3 lysine 9 trimethylation (H3K9me3) is a post-translational modification known to be involved in the regulation of a broad range of biological processes, including the formation of transcriptionally silent heterochromatin. Following the observation of its aberrant methylation status in hematological malignancy and several other cancer phenotypes, recent studies have associated H3K9me3 levels with patient outcome and highlighted key molecular mechanisms linking H3K9me3 profile with AML etiology in a number of large-scale meta-analysis. Consequently, the development and application of small molecule inhibitors which target the histone methyltransferases or demethylase enzymes known to participate in the oncogenic regulation of H3K9me3 in AML represents an advancing area of ongoing study. Here, we provide a comprehensive review on how this particular epigenetic mark is regulated within cells and its emerging role as a potential therapeutic target in AML, along with an update on the current research into advancing the generation of more potent and selective inhibitors against known H3K9 methyltransferases and demethylases.
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Affiliation(s)
- Laura Monaghan
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Matthew E. Massett
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Alex Hoose
- School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Heather G. Jørgensen
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Xu Huang
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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75
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Li M, Huang T, Li MJ, Zhang CX, Yu XC, Yin YY, Liu C, Wang X, Feng HW, Zhang T, Liu MF, Han CS, Lu G, Li W, Ma JL, Chen ZJ, Liu HB, Liu K. The histone modification reader ZCWPW1 is required for meiosis prophase I in male but not in female mice. SCIENCE ADVANCES 2019; 5:eaax1101. [PMID: 31453335 PMCID: PMC6693912 DOI: 10.1126/sciadv.aax1101] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/08/2019] [Indexed: 05/12/2023]
Abstract
Meiosis is a specialized type of cell division that creates haploid germ cells and ensures their genetic diversity through homologous recombination. We show that the H3K4me3 reader ZCWPW1 is specifically required for meiosis prophase I progression in male but not in female germ cells in mice. Loss of Zcwpw1 in male mice caused a complete failure of synapsis, resulting in meiotic arrest at the zygotene to pachytene stage, accompanied by incomplete DNA double-strand break repair and lack of crossover formation, leading to male infertility. In oocytes, deletion of Zcwpw1 only somewhat slowed down meiosis prophase I progression; Zcwpw1-/- oocytes were able to complete meiosis, and Zcwpw1-/- female mice had normal fertility until mid-adulthood. We conclude that the H3K4me3 reader ZCWPW1 is indispensable for meiosis synapsis in males but is dispensable for females. Our results suggest that ZCWPW1 may represent a previously unknown, sex-dependent epigenetic regulator of germ cell meiosis in mammals.
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Affiliation(s)
- Miao Li
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
| | - Tao Huang
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
| | - Meng-Jing Li
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
| | - Chuan-Xin Zhang
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
| | - Xiao-Chen Yu
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
| | - Ying-Ying Yin
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Hai-Wei Feng
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, Haiyuan First Road 1, Shenzhen, Guangdong 518053 China
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tuo Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Chun-Sheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Lu
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Long Ma
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University and Shanghai Key Laboratory of Assisted Reproduction and Reproductive Genetics, Shanghai 200031, China
| | - Hong-Bin Liu
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
- Corresponding author. (H.-B.L.); (K.L.)
| | - Kui Liu
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, Haiyuan First Road 1, Shenzhen, Guangdong 518053 China
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Corresponding author. (H.-B.L.); (K.L.)
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Abstract
PURPOSE Brittle cornea syndrome (BCS) is a rare recessive disorder affecting connective tissues, most prominently in the eye. Pathogenic mutations causing BCS have been identified in PRDM5 and ZNF469 genes. This study investigates the genetic cause of BCS in a large, consanguineous Pakistani family with 4 affected and 3 unaffected individuals. METHODS The coding region and exon-intron splice junctions of PRDM5 and ZNF469 genes were amplified by polymerase chain reaction, and bidirectional Sanger sequencing was performed to find the pathogenic change responsible for causing the disease in the family. RESULTS A novel homozygous duplication c.9831dupC (p.Arg3278GlnfsX197) in the ZNF469 gene was identified, which was found to be co-segregating with the disease in the family. CONCLUSIONS This is the first report of a ZNF469 homozygous mutation causing a BCS phenotype in a consanguineous Pakistani family. Our data extend the mutation spectrum of ZNF469 variants implicated in BCS.
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77
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Karjosukarso DW, van Gestel SHC, Qu J, Kouwenhoven EN, Duijkers L, Garanto A, Zhou H, Collin RWJ. An FEVR-associated mutation in ZNF408 alters the expression of genes involved in the development of vasculature. Hum Mol Genet 2019; 27:3519-3527. [PMID: 29982478 DOI: 10.1093/hmg/ddy244] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/26/2018] [Indexed: 11/13/2022] Open
Abstract
Familial exudative vitreoretinopathy (FEVR) is an inherited retinal disorder hallmarked by an abnormal development of retinal vasculature. A missense mutation in ZNF408 (p.H455Y) was reported to underlie autosomal dominant FEVR in a large Dutch family, and ZNF408 was shown to play a role in the development of vasculature. Nonetheless, little is known about the molecular mechanism of ZNF408-associated FEVR. To investigate this, an in vitro model of ZNF408-associated FEVR was generated by overexpressing wild-type and p.H455Y ZNF408 in human umbilical vein endothelial cells. Cells overexpressing mutant ZNF408 were unable to form a capillary-like network in an in vitro tube formation assay, thereby mimicking the clinical feature observed in patients with FEVR. Intriguingly, transcriptome analysis revealed that genes involved in the development of vasculature were deregulated by the p.H455Y mutation. Chromatin immunoprecipitation showed that p.H455Y ZNF408 has reduced DNA-binding ability, as compared to the wild-type protein. The fact that the p.H455Y mutation disrupts the expression of genes important for the development of vasculature sheds further light on the molecular mechanisms underlying ZNF408-associated FEVR.
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Affiliation(s)
- Dyah W Karjosukarso
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sebastianus H C van Gestel
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Jieqiong Qu
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Evelyn N Kouwenhoven
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lonneke Duijkers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alejandro Garanto
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Huiqing Zhou
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
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78
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Sybirna A, Wong FCK, Surani MA. Genetic basis for primordial germ cells specification in mouse and human: Conserved and divergent roles of PRDM and SOX transcription factors. Curr Top Dev Biol 2019; 135:35-89. [PMID: 31155363 DOI: 10.1016/bs.ctdb.2019.04.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Primordial germ cells (PGCs) are embryonic precursors of sperm and egg that pass on genetic and epigenetic information from one generation to the next. In mammals, they are induced from a subset of cells in peri-implantation epiblast by BMP signaling from the surrounding tissues. PGCs then initiate a unique developmental program that involves comprehensive epigenetic resetting and repression of somatic genes. This is orchestrated by a set of signaling molecules and transcription factors that promote germ cell identity. Here we review significant findings on mammalian PGC biology, in particular, the genetic basis for PGC specification in mice and human, which has revealed an evolutionary divergence between the two species. We discuss the importance and potential basis for these differences and focus on several examples to illustrate the conserved and divergent roles of critical transcription factors in mouse and human germline.
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Affiliation(s)
- Anastasiya Sybirna
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
| | - Frederick C K Wong
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, United Kingdom
| | - M Azim Surani
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
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79
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Neidhart M, Pajak A, Laskari K, Riksen NP, Joosten LAB, Netea MG, Lutgens E, Stroes ESG, Ciurea A, Distler O, Grigorian M, Karouzakis E. Oligomeric S100A4 Is Associated With Monocyte Innate Immune Memory and Bypass of Tolerance to Subsequent Stimulation With Lipopolysaccharides. Front Immunol 2019; 10:791. [PMID: 31037071 PMCID: PMC6476283 DOI: 10.3389/fimmu.2019.00791] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/26/2019] [Indexed: 11/24/2022] Open
Abstract
Objectives: Most DAMPs in inflammatory diseases are TLR2- and TLR4-ligands and according to the current concept, repeated stimuli would result in tolerance. Aims of the study were to verify this assumption, to investigate whether epigenetic effectors are involved and to explore the situation in rheumatoid arthritis (RA). Methods: A trained immunity (TI) and tolerance protocol was established using peripheral blood monocytes from healthy donors, β-glucan and lipopolysaccharide (LPS). The training or tolerance capacities of RA-relevant DAMPs were tested. Results: β-Glucan-, oS100A4-, HMBG1-, and HSP90-pretreated monocytes showed increased IL-6 responses to LPS re-stimulation. β-Glucan, oS100A and tenascin C induced training of monocytes to release more TNFα. In comparison to β-glucan, most DAMPs tested induced less TI, with exception of oS100A4. Monocytes exposed to oS100A4 showed increased IL-1β, IL-6, and TNFα in response to LPS, in spite that both stimulate TLR4. RNASEq upon β-glucan or oS100A4 revealed similar changes in chemokines/cytokines and epigenetic effectors; 17 epigenetic effectors correlated with chemokine/cytokine gene expression; PRDM8 was associated with more chemokine and cytokine transcripts. Knockdown of PRDM8 abolished TI induced by oS100A4. In RA, plasma S100A4 correlated with increased CSF2, and increased PRDM8 transcription in RA monocytes was associated with increased plasma CCL5 and IL-6, as well as therapy-resistance. Conclusion: Bypass of tolerance by DAMPs might be a phenomenon as important as TI, since it could explain how chronic inflammation can be maintained in spite of an environment with multiple TLR2/TLR4-ligands. In RA monocytes, a PRDM8-dependent TI mechanism could be responsible for sustained chemokine/cytokines levels.
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Affiliation(s)
- Michel Neidhart
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Agnieszka Pajak
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Katerina Laskari
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Niels P Riksen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, Romania.,Department for Immunology & Metabolism, Life and Medical Science Institute (LIMES), University of Bonn, Bonn, Germany
| | - Esther Lutgens
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-University, Munich, Germany.,Department of Medical Biochemistry, Amsterdam University Medical Centre, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Eric S G Stroes
- Department of Vascular Medicine, Academic Medical Center, Amsterdam, Netherlands
| | - Adrian Ciurea
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Oliver Distler
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mariam Grigorian
- Faculty of Health Sciences, Center of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Emmanuel Karouzakis
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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80
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Zha J, Ying M, Alexander-Floyd J, Gidalevitz T. HSP-4/BiP expression in secretory cells is regulated by a developmental program and not by the unfolded protein response. PLoS Biol 2019; 17:e3000196. [PMID: 30908491 PMCID: PMC6448932 DOI: 10.1371/journal.pbio.3000196] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 04/04/2019] [Accepted: 03/11/2019] [Indexed: 12/18/2022] Open
Abstract
Differentiation of secretory cells leads to sharp increases in protein synthesis, challenging endoplasmic reticulum (ER) proteostasis. Anticipatory activation of the unfolded protein response (UPR) prepares cells for the onset of secretory function by expanding the ER size and folding capacity. How cells ensure that the repertoire of induced chaperones matches their postdifferentiation folding needs is not well understood. We find that during differentiation of stem-like seam cells, a typical UPR target, the Caenorhabditis elegans immunoglobulin heavy chain-binding protein (BiP) homologue Heat-Shock Protein 4 (HSP-4), is selectively induced in alae-secreting daughter cells but is repressed in hypodermal daughter cells. Surprisingly, this lineage-dependent induction bypasses the requirement for UPR signaling. Instead, its induction in alae-secreting cells is controlled by a specific developmental program, while its repression in the hypodermal-fated cells requires a transcriptional regulator B-Lymphocyte–Induced Maturation Protein 1 (BLMP-1/BLIMP1), involved in differentiation of mammalian secretory cells. The HSP-4 induction is anticipatory and is required for the integrity of secreted alae. Thus, differentiation programs can directly control a broad-specificity chaperone that is normally stress dependent to ensure the integrity of secreted proteins. A study in the nematode Caenorhabditis elegans shows that dedicated developmental programs can bypass the requirements for the unfolded protein response during the differentiation of secretory cells, anticipating their future high folding needs. During differentiation, cells that specialize in secretion of proteins, such as antibody-secreting B cells, prepare for the onset of secretory function by expanding the size of the major secretory organelle, the endoplasmic reticulum (ER), and by increasing the expression of molecular chaperones and folding enzymes. This pre-emptive expansion of the ER depends on activation of the ER stress response pathways and is required for the secretory phenotype. In addition, cells may also need to up-regulate a selected subset of chaperones because different secreted proteins may require different chaperones for their folding and secretion. Except in specialized cases, how this selective up-regulation is achieved, and whether it depends on the ER stress pathways, is not well understood. Using Caenorhabditis elegans, we find that a chaperone BiP/HSP-4, which is usually induced in most cells by stress, is selectively induced during differentiation of stem cells into the alae-secreting cells while being repressed in their sister lineage, the hypodermal cells. We find that induction of this chaperone is independent of the known ER stress pathways, while its repression requires a known regulator of development in mammals, BLIMP1/BLMP-1. The pre-emptive induction of BiP/HSP-4 is important for the integrity of secreted alae and cuticle, suggesting that a general molecular chaperone that is a canonical target of ER stress pathways can be selectively regulated by development to ensure the quality of secreted proteome and functionality of the cells postdifferentiation.
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Affiliation(s)
- Ji Zha
- Biology Department, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Mingjie Ying
- Biology Department, Drexel University, Philadelphia, Pennsylvania, United States of America
| | | | - Tali Gidalevitz
- Biology Department, Drexel University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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81
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Wu K, Yin X, Jin Y, Liu F, Gao J. Identification of aberrantly methylated differentially expressed genes in prostate carcinoma using integrated bioinformatics. Cancer Cell Int 2019; 19:51. [PMID: 30872976 PMCID: PMC6402097 DOI: 10.1186/s12935-019-0763-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 02/21/2019] [Indexed: 12/19/2022] Open
Abstract
Background Methylation plays a key role in the aetiology and pathogenesis of prostate cancer (PCa). This study aimed to identify aberrantly methylated differentially expressed genes (DEGs) and pathways in PCa and explore the underlying mechanisms of tumourigenesis. Methods Expression profile (GSE29079) and methylation profile (GSE76938) datasets were obtained from the Gene Expression Omnibus (GEO). We used R 3.4.4 software to assess aberrantly methylated DEGs. The Cancer Genome Atlas (TCGA) RNA sequencing and Illumina HumanMethylation450 DNA methylation data were utilized to validate screened genes. Functional enrichment analysis of the screened genes was performed, and a protein–protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Gens (STRING). The results were visualized in Cytoscape. After confirmation using TCGA, cBioPortal was used to examine alterations in genes of interest. Then, protein localization in PCa cells was observed using immunohistochemistry. Results Overall, 536 hypomethylated upregulated genes were identified that were enriched in biological processes such as negative regulation of transcription, osteoblast differentiation, intracellular signal transduction, and the Wnt signalling pathway. Pathway enrichment showed significant changes in factors involved in AMPK signalling, cancer, and adherens junction pathways. The hub oncogenes were AKT1, PRDM10, and FASN. Additionally, 322 hypermethylated downregulated genes were identified that demonstrated enrichment in biological processes including positive regulation of the MAPK cascade, muscle contraction, ageing, and signal transduction. Pathway analysis indicated enrichment in arrhythmogenic right ventricular cardiomyopathy (ARVC), focal adhesion, dilated cardiomyopathy, and PI3K-AKT signalling. The hub tumour suppressor gene was FLNA. Immunohistochemistry showed that AKT1, FASN, and FLNA were mainly expressed in PCa cell cytoplasm, while PRDM10 was mainly expressed in nuclei. Conclusions Our results identify numerous novel genetic and epigenetic regulatory networks and offer molecular evidence crucial to understanding the pathogenesis of PCa. Aberrantly methylated hub genes, including AKT1, PRDM10, FASN, and FLNA, can be used as biomarkers for accurate PCa diagnosis and treatment. In conclusion, our study suggests that AKT1, PRDM10, and FASN may be tumour promoters and that FLNA may be a tumour suppressor in PCa. We hope these findings will draw more attention to these hub genes in future cancer studies.
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Affiliation(s)
- Kai Wu
- 1Department of Urology, Chinese PLA General Hospital, Beijing, China
| | - Xiaotao Yin
- 2Department of Urology, First Affiliated Hospital of Chinese PLA General Hospital, Beijing, China
| | - Yipeng Jin
- 1Department of Urology, Chinese PLA General Hospital, Beijing, China
| | - Fangfang Liu
- Hebei General Hospital of Civil Affairs, Xingtai, Hebei Province China
| | - Jiangping Gao
- 1Department of Urology, Chinese PLA General Hospital, Beijing, China
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Fellous A, Earley RL, Silvestre F. The Kdm/Kmt gene families in the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus, suggest involvement of histone methylation machinery in development and reproduction. Gene 2019; 687:173-187. [DOI: 10.1016/j.gene.2018.11.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/06/2018] [Accepted: 11/15/2018] [Indexed: 12/16/2022]
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Prdm12 Directs Nociceptive Sensory Neuron Development by Regulating the Expression of the NGF Receptor TrkA. Cell Rep 2019; 26:3522-3536.e5. [DOI: 10.1016/j.celrep.2019.02.097] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/21/2019] [Accepted: 02/25/2019] [Indexed: 12/13/2022] Open
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84
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Yildiz O, Downes GB, Sagerström CG. Zebrafish prdm12b acts independently of nkx6.1 repression to promote eng1b expression in the neural tube p1 domain. Neural Dev 2019; 14:5. [PMID: 30813944 PMCID: PMC6391800 DOI: 10.1186/s13064-019-0129-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 02/14/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Functioning of the adult nervous system depends on the establishment of neural circuits during embryogenesis. In vertebrates, neurons that make up motor circuits form in distinct domains along the dorsoventral axis of the neural tube. Each domain is characterized by a unique combination of transcription factors (TFs) that promote a specific fate, while repressing fates of adjacent domains. The prdm12 TF is required for the expression of eng1b and the generation of V1 interneurons in the p1 domain, but the details of its function remain unclear. METHODS We used CRISPR/Cas9 to generate the first germline mutants for prdm12 and employed this resource, together with classical luciferase reporter assays and co-immunoprecipitation experiments, to study prdm12b function in zebrafish. We also generated germline mutants for bhlhe22 and nkx6.1 to examine how these TFs act with prdm12b to control p1 formation. RESULTS We find that prdm12b mutants lack eng1b expression in the p1 domain and also possess an abnormal touch-evoked escape response. Using luciferase reporter assays, we demonstrate that Prdm12b acts as a transcriptional repressor. We also show that the Bhlhe22 TF binds via the Prdm12b zinc finger domain to form a complex. However, bhlhe22 mutants display normal eng1b expression in the p1 domain. While prdm12 has been proposed to promote p1 fates by repressing expression of the nkx6.1 TF, we do not observe an expansion of the nkx6.1 domain upon loss of prdm12b function, nor is eng1b expression restored upon simultaneous loss of prdm12b and nkx6.1. CONCLUSIONS We conclude that prdm12b germline mutations produce a phenotype that is indistinguishable from that of morpholino-mediated loss of prdm12 function. In terms of prdm12b function, our results indicate that Prdm12b acts as transcriptional repressor and interacts with both EHMT2/G9a and Bhlhe22. However, bhlhe22 function is not required for eng1b expression in vivo, perhaps indicating that other bhlh genes can compensate during embryogenesis. Lastly, we do not find evidence for nkx6.1 and prdm12b acting as a repressive pair in formation of the p1 domain - suggesting that prdm12b is not solely required to repress non-p1 fates, but is specifically needed to promote p1 fates.
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Affiliation(s)
- Ozge Yildiz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, 364 Plantation St/LRB815, Worcester, MA 01605 USA
| | - Gerald B. Downes
- Department of Biology, University of Massachusetts, Amherst, MA 01003 USA
| | - Charles G. Sagerström
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, 364 Plantation St/LRB815, Worcester, MA 01605 USA
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85
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Silva RS, Arno G, Cipriani V, Pontikos N, Defoort-Dhellemmes S, Kalhoro A, Carss KJ, Raymond FL, Dhaenens CM, Jensen H, Rosenberg T, van Heyningen V, Moore AT, Puech B, Webster AR. Unique noncoding variants upstream of PRDM13 are associated with a spectrum of developmental retinal dystrophies including progressive bifocal chorioretinal atrophy. Hum Mutat 2019; 40:578-587. [PMID: 30710461 DOI: 10.1002/humu.23715] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 12/20/2022]
Abstract
The autosomal dominant progressive bifocal chorioretinal atrophy (PBCRA) disease locus has been mapped to chromosome 6q14-16.2 that overlaps the North Carolina macular dystrophy (NCMD) locus MCDR1. NCMD is a nonprogressive developmental macular dystrophy, in which variants upstream of PRDM13 have been implicated. Whole genome sequencing was performed to interrogate structural variants (SVs) and single nucleotide variants (SNVs) in eight individuals, six affected individuals from two families with PBCRA, and two individuals from an additional family with a related developmental macular dystrophy. A SNV (chr6:100,046,804T>C), located 7.8 kb upstream of the PRDM13 gene, was shared by all PBCRA-affected individuals in the disease locus. Haplotype analysis suggested that the variant arose independently in the two families. The two affected individuals from Family 3 were screened for rare variants in the PBCRA and NCMD loci. This revealed a de novo variant in the proband, 21 bp from the first SNV (chr6:100,046,783A>C). This study expands the noncoding variant spectrum upstream of PRDM13 and suggests altered spatio-temporal expression of PRDM13 as a candidate disease mechanism in the phenotypically distinct but related conditions, NCMD and PBCRA.
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Affiliation(s)
- Raquel S Silva
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,Department of Genetics, Moorfields Eye Hospital, London, United Kingdom
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,Department of Genetics, Moorfields Eye Hospital, London, United Kingdom
| | - Valentina Cipriani
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,Department of Genetics, Moorfields Eye Hospital, London, United Kingdom.,Department of Clinical Pharmacology, William Harvey Research Institute, Queen Mary University of London, United Kingdom.,Department of Genetics, UCL Genetics Institute, Evolution and Environment, London, United Kingdom
| | - Nikolas Pontikos
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,Department of Genetics, Moorfields Eye Hospital, London, United Kingdom.,Department of Genetics, UCL Genetics Institute, Evolution and Environment, London, United Kingdom
| | | | - Ambreen Kalhoro
- Department of Genetics, Moorfields Eye Hospital, London, United Kingdom
| | - Keren J Carss
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom.,NIHR BioResource-Rare Diseases, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - F Lucy Raymond
- NIHR BioResource-Rare Diseases, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Claire Marie Dhaenens
- Biochemistry and Molecular Biology Department-UF Génopathies, CHU Lille, Univ Lille, Inserm UMR-S 1172, F-59000, Lille, France
| | - Hanne Jensen
- Department of Ophthalmology, The Kennedy Eye Clinic, Rigshospitalet Glostrup, Glostrup, Denmark
| | - Thomas Rosenberg
- Department of Ophthalmology, The Kennedy Eye Clinic, Rigshospitalet Glostrup, Glostrup, Denmark
| | - Veronica van Heyningen
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,Department of Genetics, Moorfields Eye Hospital, London, United Kingdom
| | - Anthony T Moore
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,Department of Genetics, Moorfields Eye Hospital, London, United Kingdom.,Department of Ophthalmology, UCSF School of Medicine, San Francisco, CA
| | - Bernard Puech
- Exploration de la Vision et Neuro-Ophtalmologie, Centre Hospitalier Universitaire, Lille, France
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,Department of Genetics, Moorfields Eye Hospital, London, United Kingdom
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PRDM16 functions as a suppressor of lung adenocarcinoma metastasis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:35. [PMID: 30683132 PMCID: PMC6347838 DOI: 10.1186/s13046-019-1042-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 01/15/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND The transcription factor PR domain containing 16 (PRDM16) is known to play a significant role in the determination and function of brown and beige fat. However, the role of PRDM16 in tumor biology has not been well addressed. Here we investigated the impact of PRDM16 on tumor growth and metastasis in lung cancer. METHODS UALCAN database, immunoblotting and immunohistochemistry analysis were used to assess PRDM16 expression in lung cancer patients. Kaplan-Meier plotter database was used to analyze the overall survival of patients with lung cancer stratified by PRDM16 expression. PRDM16 overexpression and knockdown experiments were conducted to assess the effects of PRDM16 on growth and metastasis in vitro and in vivo, and its molecular mechanism was investigated in lung adenocarcinoma cells by chromatin immunoprecipitation-sequencing (ChIP-Seq), real time-quantitative PCR (RT-qPCR), luciferase assay, xenograft models and rescue experiments. RESULTS PRDM16 was downregulated in lung adenocarcinomas, and its expression level correlated with key pathological characteristics and prognoses of lung adenocarcinoma patients. Overexpressing PRDM16 inhibited the epithelial-to-mesenchymal transition (EMT) of cancer cells both in vivo and in vitro by repressing the transcription of Mucin-4 (MUC4), one of the regulators of EMT in lung adenocarcinomas. Furthermore, deleting the PR domain from PRDM16 increased the transcriptional repression of MUC4 by exhibiting significant differences in histone modifications on its promoter. CONCLUSIONS Our findings demonstrate a critical interplay between transcriptional and epigenetic modifications during lung adenocarcinoma progression involving EMT of cancer cells and suggest that PRDM16 is a metastasis suppressor and potential therapeutic target for lung adenocarcinomas.
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87
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Padalino G, Ferla S, Brancale A, Chalmers IW, Hoffmann KF. Combining bioinformatics, cheminformatics, functional genomics and whole organism approaches for identifying epigenetic drug targets in Schistosoma mansoni. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2018; 8:559-570. [PMID: 30455056 PMCID: PMC6288008 DOI: 10.1016/j.ijpddr.2018.10.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023]
Abstract
Schistosomiasis endangers the lives of greater than 200 million people every year and is predominantly controlled by a single class chemotherapy, praziquantel (PZQ). Development of PZQ replacement (to combat the threat of PZQ insensitivity/resistance arising) or combinatorial (to facilitate the killing of PZQ-insensitive juvenile schistosomes) chemotherapies would help sustain this control strategy into the future. Here, we re-categorise two families of druggable epigenetic targets in Schistosoma mansoni, the histone methyltransferases (HMTs) and the histone demethylases (HDMs). Amongst these, a S. mansoni Lysine Specific Demethylase 1 (SmLSD1, Smp_150560) homolog was selected for further analyses. Homology modelling of SmLSD1 and in silico docking of greater than four thousand putative inhibitors identified seven (L1 – L7) showing more favourable binding to the target pocket of SmLSD1 vs Homo sapiens HsLSD1; six of these seven (L1 – L6) plus three structural analogues of L7 (L8 – L10) were subsequently screened against schistosomula using the Roboworm anthelmintic discovery platform. The most active compounds (L10 - pirarubicin > L8 – danunorubicin hydrochloride) were subsequently tested against juvenile (3 wk old) and mature (7 wk old) schistosome stages and found to impede motility, suppress egg production and affect tegumental surfaces. When compared to a surrogate human cell line (HepG2), a moderate window of selectivity was observed for the most active compound L10 (selectivity indices - 11 for schistosomula, 9 for juveniles, 1.5 for adults). Finally, RNA interference of SmLSD1 recapitulated the egg-laying defect of schistosomes co-cultivated in the presence of L10 and L8. These preliminary results suggest that SmLSD1 represents an attractive new target for schistosomiasis; identification of more potent and selective SmLSD1 compounds, however, is essential. Nevertheless, the approaches described herein highlight an interdisciplinary strategy for selecting and screening novel/repositioned anti-schistosomals, which can be applied to any druggable (epigenetic) target encoded by the parasite's genome. Schistosoma mansoni contains 27 histone methyltransferases (HMTs) and 14 histone demethylases (HDMs). S. mansoni lysine specific demethylase 1 (SmLSD1) is a druggable target. Schistosomes treated with the putative SmLSD1 inhibitor pirarubicin or siRNAs targeting SmLSD1 are less fecund.
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Affiliation(s)
- Gilda Padalino
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, SY23 3DA, Wales, UK.
| | - Salvatore Ferla
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, United Kingdom.
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, United Kingdom.
| | - Iain W Chalmers
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, SY23 3DA, Wales, UK.
| | - Karl F Hoffmann
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, SY23 3DA, Wales, UK.
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Sorrentino A, Federico A, Rienzo M, Gazzerro P, Bifulco M, Ciccodicola A, Casamassimi A, Abbondanza C. PR/SET Domain Family and Cancer: Novel Insights from the Cancer Genome Atlas. Int J Mol Sci 2018; 19:ijms19103250. [PMID: 30347759 PMCID: PMC6214140 DOI: 10.3390/ijms19103250] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/12/2018] [Accepted: 10/17/2018] [Indexed: 12/17/2022] Open
Abstract
The PR/SET domain gene family (PRDM) encodes 19 different transcription factors that share a subtype of the SET domain [Su(var)3-9, enhancer-of-zeste and trithorax] known as the PRDF1-RIZ (PR) homology domain. This domain, with its potential methyltransferase activity, is followed by a variable number of zinc-finger motifs, which likely mediate protein⁻protein, protein⁻RNA, or protein⁻DNA interactions. Intriguingly, almost all PRDM family members express different isoforms, which likely play opposite roles in oncogenesis. Remarkably, several studies have described alterations in most of the family members in malignancies. Here, to obtain a pan-cancer overview of the genomic and transcriptomic alterations of PRDM genes, we reanalyzed the Exome- and RNA-Seq public datasets available at The Cancer Genome Atlas portal. Overall, PRDM2, PRDM3/MECOM, PRDM9, PRDM16 and ZFPM2/FOG2 were the most mutated genes with pan-cancer frequencies of protein-affecting mutations higher than 1%. Moreover, we observed heterogeneity in the mutation frequencies of these genes across tumors, with cancer types also reaching a value of about 20% of mutated samples for a specific PRDM gene. Of note, ZFPM1/FOG1 mutations occurred in 50% of adrenocortical carcinoma patients and were localized in a hotspot region. These findings, together with OncodriveCLUST results, suggest it could be putatively considered a cancer driver gene in this malignancy. Finally, transcriptome analysis from RNA-Seq data of paired samples revealed that transcription of PRDMs was significantly altered in several tumors. Specifically, PRDM12 and PRDM13 were largely overexpressed in many cancers whereas PRDM16 and ZFPM2/FOG2 were often downregulated. Some of these findings were also confirmed by real-time-PCR on primary tumors.
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Affiliation(s)
- Anna Sorrentino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 80138 Naples, Italy.
- Department of Science and Technology, University of Naples "Parthenope", 80143 Naples, Italy.
| | - Antonio Federico
- Department of Science and Technology, University of Naples "Parthenope", 80143 Naples, Italy.
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, 80131 Naples, Italy.
| | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084 Salerno, Italy.
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131 Naples, Italy.
| | - Alfredo Ciccodicola
- Department of Science and Technology, University of Naples "Parthenope", 80143 Naples, Italy.
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, 80131 Naples, Italy.
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 80138 Naples, Italy.
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 80138 Naples, Italy.
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PI3Ka-Akt1-mediated Prdm4 induction in adipose tissue increases energy expenditure, inhibits weight gain, and improves insulin resistance in diet-induced obese mice. Cell Death Dis 2018; 9:876. [PMID: 30158592 PMCID: PMC6115456 DOI: 10.1038/s41419-018-0904-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/20/2018] [Accepted: 07/20/2018] [Indexed: 12/23/2022]
Abstract
Stimulation of white adipose tissue (WAT) browning is considered as a potential approach to treat obesity and metabolic diseases. Our previous studies have shown that phytochemical butein can stimulate WAT browning through induction of Prdm4 in adipocytes. Here, we investigated the effects of butein on diet-induced obesity and its underlying molecular mechanism. Treatment with butein prevented weight gains and improved metabolic profiles in diet-induced obese mice. Butein treatment groups also displayed higher body temperature, increased energy expenditure, and enhanced expression of thermogenic genes in adipose tissue. Butein also suppressed body weight gains and improved glucose and insulin tolerance in mice housed at thermoneutrality (30 °C). These effects were associated with adipose-selective induction of Prdm4, suggesting the role of Prdm4 in butein-mediated anti-obese effects. To directly assess the in vivo role of Prdm4, we generated aP2-Prdm4 transgenic mouse lines overexpressing Prdm4 in adipose tissues. Adipose-specific transgenic expression of Prdm4 recapitulated the butein’s actions in stimulating energy expenditure, cold tolerance, and thermogenic gene expression, resulting in prevention of obesity and improvement of metabolism. Mechanistically, direct inhibition of PI3Kα activity followed by selective suppression of its downstream Akt1 mirrored butein’s effect on Ucp1 expression and oxygen consumption. In addition, effects of butein were completely abolished in Akt1 KO mouse embryonic fibroblasts. Together, these studies demonstrate the role of butein in obesity and metabolic diseases, further highlighting that adipose PI3Kα–Akt1–Prdm4 axis is a regulator of energy expenditure.
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90
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Blimp-1 Mediates Tracheal Lumen Maturation in Drosophila melanogaster. Genetics 2018; 210:653-663. [PMID: 30082278 DOI: 10.1534/genetics.118.301444] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/01/2018] [Indexed: 12/15/2022] Open
Abstract
The specification of tissue identity during embryonic development requires precise spatio-temporal coordination of gene expression. Many transcription factors required for the development of organs have been identified and their expression patterns are known; however, the mechanisms through which they coordinate gene expression in time remain poorly understood. Here, we show that hormone-induced transcription factor Blimp-1 participates in the temporal coordination of tubulogenesis in Drosophila melanogaster by regulating the expression of many genes involved in tube maturation. In particular, we demonstrate that Blimp-1 regulates the expression of genes involved in chitin deposition and F-actin organization. We show that Blimp-1 is involved in the temporal control of lumen maturation by regulating the beginning of chitin deposition. We also report that Blimp-1 represses a variety of genes involved in tracheal maturation. Finally, we reveal that the kinase Btk29A serves as a link between Blimp-1 transcriptional repression and apical extracellular matrix organization.
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Abstract
During meiosis, maternal and paternal chromosomes undergo exchanges by homologous recombination. This is essential for fertility and contributes to genome evolution. In many eukaryotes, sites of meiotic recombination, also called hotspots, are regions of accessible chromatin, but in many vertebrates, their location follows a distinct pattern and is specified by PR domain-containing protein 9 (PRDM9). The specification of meiotic recombination hotspots is achieved by the different activities of PRDM9: DNA binding, histone methyltransferase, and interaction with other proteins. Remarkably, PRDM9 activity leads to the erosion of its own binding sites and the rapid evolution of its DNA-binding domain. PRDM9 may also contribute to reproductive isolation, as it is involved in hybrid sterility potentially due to a reduction of its activity in specific heterozygous contexts.
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Affiliation(s)
- Corinne Grey
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Frédéric Baudat
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Bernard de Massy
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
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PRDM Histone Methyltransferase mRNA Levels Increase in Response to Curative Hormone Treatment for Cryptorchidism-Dependent Male Infertility. Genes (Basel) 2018; 9:genes9080391. [PMID: 30071651 PMCID: PMC6116052 DOI: 10.3390/genes9080391] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/16/2018] [Accepted: 07/24/2018] [Indexed: 12/17/2022] Open
Abstract
There is a correlation between cryptorchidism and an increased risk of testicular cancer and infertility. During orchidopexy, testicular biopsies are performed to confirm the presence of type A dark (Ad) spermatogonia, which are a marker for low infertility risk (LIR). The Ad spermatogonia are absent in high infertility risk (HIR) patients, who are treated with a gonadotropin-releasing hormone agonist (GnRHa) to significantly lower the risk of infertility. Despite its prevalence, little is known about the molecular events involved in cryptorchidism. Previously, we compared the transcriptomes of LIR versus HIR patients treated with and without hormones. Here, we interpreted data regarding members of the positive regulatory domain-containing (PRDM) family; some of which encoded histone methyltransferases that are important for reproduction. We found there were lower levels of PRDM1, PRDM6, PRDM9, PRDM13, and PRDM14 mRNA in the testes of HIR patients compared with LIR patients, and that PRDM7, PRDM9, PRDM12, and PRDM16 were significantly induced after GnRHa treatment. Furthermore, we observed PRDM9 protein staining in the cytoplasm of germ cells in the testes from LIR and HIR patients, indicating that the mRNA and protein levels corresponded. This result indicated that the curative hormonal therapy for cryptorchidism involved conserved chromatin modification enzymes.
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93
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Guarnieri V, Muscarella LA, Verdelli C, Corbetta S. Alterations of DNA methylation in parathyroid tumors. Mol Cell Endocrinol 2018; 469:60-69. [PMID: 28501573 DOI: 10.1016/j.mce.2017.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 05/01/2017] [Accepted: 05/07/2017] [Indexed: 12/11/2022]
Abstract
Parathyroid tumors are common endocrine neoplasias associated with primary hyperparathyroidism, a metabolic disorder characterized by parathormone hypersecretion. Parathyroid neoplasia are frequently benign adenomas or multiple glands hyperplasia, while malignancies are rare. The epigenetic scenario in parathyroid tumors has just begun to be decoded: DNA methylation, histones and chromatin modifiers expression have been investigated so far. The main findings suggest that DNA methylation and chromatin remodeling are active and deregulated in parathyroid tumors, cooperating with genetic alterations to drive the tumor phenotype: the tumor suppressors menin and parafibromin, involved in parathyroid tumorigenesis, interact with chromatin modifiers, defining distinct epigenetic derangements. Many epigenetic alterations identified in parathyroid tumors are common to those in human cancers; moreover, some aspects of the epigenetic profile resemble epigenetic features of embryonic stem cells. Epigenetic profile may contribute to define the heterogeneity of parathyroid tumors and to provide targets for new therapeutic approaches.
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Affiliation(s)
- Vito Guarnieri
- Genetic Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Chiara Verdelli
- Laboratory of Experimental Endocrinology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Sabrina Corbetta
- Endocrinology Service, Department of Biomedical Sciences for Health, University of Milan, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy.
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94
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Sorrentino A, Rienzo M, Ciccodicola A, Casamassimi A, Abbondanza C. Human PRDM2: Structure, function and pathophysiology. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:S1874-9399(18)30071-3. [PMID: 29883756 DOI: 10.1016/j.bbagrm.2018.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 12/22/2022]
Abstract
PRDM2/RIZ is a member of a superfamily of histone/protein methyltransferases (PRDMs), which are characterized by the conserved N-terminal PR domain, with methyltransferase activity and zinc finger arrays at the C-terminus. Similar to other family members, two main protein types, known as RIZ1 and RIZ2, are produced from the PRDM2 locus differing by the presence or absence of the PR domain. The imbalance in their respective amounts may be an important cause of malignancy, with the PR-positive isoform commonly lost or downregulated and the PR-negative isoform always being present at higher levels in cancer cells. Interestingly, the RIZ1 isoform also represents an important target of estradiol action downstream of the interaction with hormone receptor. Furthermore, the imbalance between the two products could also be a molecular basis for other human diseases. Thus, understanding the molecular mechanisms underlying PRDM2 function could be useful in the pathophysiological context, with a potential to exploit this information in clinical practice.
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Affiliation(s)
- A Sorrentino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy; Department of Science and Technology, University of Naples "Parthenope", Naples, Italy
| | - M Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - A Ciccodicola
- Department of Science and Technology, University of Naples "Parthenope", Naples, Italy; Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy
| | - A Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - C Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
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95
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Baizabal JM, Mistry M, García MT, Gómez N, Olukoya O, Tran D, Johnson MB, Walsh CA, Harwell CC. The Epigenetic State of PRDM16-Regulated Enhancers in Radial Glia Controls Cortical Neuron Position. Neuron 2018; 98:945-962.e8. [PMID: 29779941 PMCID: PMC6667181 DOI: 10.1016/j.neuron.2018.04.033] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 03/14/2018] [Accepted: 04/24/2018] [Indexed: 01/09/2023]
Abstract
The epigenetic landscape is dynamically remodeled during neurogenesis. However, it is not understood how chromatin modifications in neural stem cells instruct the formation of complex structures in the brain. We report that the histone methyltransferase PRDM16 is required in radial glia to regulate lineage-autonomous and stage-specific gene expression programs that control number and position of upper layer cortical projection neurons. PRDM16 regulates the epigenetic state of transcriptional enhancers to activate genes involved in intermediate progenitor cell production and repress genes involved in cell migration. The histone methyltransferase domain of PRDM16 is necessary in radial glia to promote cortical neuron migration through transcriptional silencing. We show that repression of the gene encoding the E3 ubiquitin ligase PDZRN3 by PRDM16 determines the position of upper layer neurons. These findings provide insights into how epigenetic control of transcriptional enhancers in radial glial determines the organization of the mammalian cerebral cortex.
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Affiliation(s)
| | - Meeta Mistry
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard Medical School, Boston, MA 02115, USA
| | | | - Nicolás Gómez
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Olubusola Olukoya
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Diana Tran
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew B Johnson
- Division of Genetics and Genomics, Manton Center for Orphan Disease and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Corey C Harwell
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
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96
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Tan SX, Hu RC, Xia Q, Tan YL, Liu JJ, Gan GX, Wang LL. The methylation profiles of PRDM promoters in non-small cell lung cancer. Onco Targets Ther 2018; 11:2991-3002. [PMID: 29872311 PMCID: PMC5973400 DOI: 10.2147/ott.s156775] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Non–small cell lung cancer (NSCLC) is one of the leading malignant tumors worldwide. Aberrant gene promoter methylation contributes to NSCLC, and PRDM is a tumor suppressor gene family that possesses histone methyltransferase activity. This study aimed to investigate whether aberrant methylation of PRDM promoter is involved in NSCLC. Materials and methods Primary tumor tissues, adjacent nontumorous tissues, and distant lung tissues were collected from 75 NSCLC patients including 52 lung squamous cell carcinoma (LSCC) patients and 23 lung adenocarcinoma patients. The expression of PRDMs was detected by polymerase chain reaction (PCR), Western blot, and immunohistochemical analysis. The methylation of PRDM promoters was detected by methylation-specific PCR. The correlation of methylation and expression of PRDMs with clinicopathological characteristics of patients were analyzed. Results mRNA expression of PRDM2, PRDM5, and PRDM16 was low or absent in tumor tissues compared to distant lung tissues. The methylation frequencies of PRDM2, PRDM5, and PRDM16 in tumor tissues were significantly higher than those in distal lung tissues. In LSCC patients, methylation of PRDM2 and PRDM16 was correlated with smoking status and methylation of PRDM5 was correlated with tumor differentiation. Conclusion The expression of PRDM2, PRDM5, and PRDM16 is low or absent in NSCLC, and this is mainly due to gene promoter methylation. Smoking may be an important cause of PRDM2 and PRDM16 methylation in NSCLC.
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Affiliation(s)
- Shuang-Xiang Tan
- Hunan Province Institute of Gerontology, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, China.,Department of Respiratory Medicine, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Rui-Cheng Hu
- Hunan Province Institute of Gerontology, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, China.,Department of Respiratory Medicine, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Qian Xia
- Department of Respiratory Medicine, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Yong-Li Tan
- Hunan Province Institute of Gerontology, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Jing-Jing Liu
- Hunan Province Institute of Gerontology, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Gui-Xiang Gan
- Hunan Province Institute of Gerontology, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Li-le Wang
- Hunan Province Institute of Gerontology, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, China
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97
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Zhang L, Cao H, He T, Yang J, Tao H, Wang Y, Hu Q. Overexpression of PRDM13 inhibits glioma cells via Rho and GTP enzyme activation protein. Int J Mol Med 2018; 42:966-974. [PMID: 29767251 PMCID: PMC6034930 DOI: 10.3892/ijmm.2018.3679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 05/10/2018] [Indexed: 11/17/2022] Open
Abstract
PR (PRDI-BFI and RIZ) domain containing (PRDM) proteins have been shown to be important in several types of human cancer. PRDM13, a member of the PRDM family, contains transcriptional regulators involved in modulating several cellular processes. However, the function of PRDM13 in glioma remains to be elucidated. The purpose of the present study was to evaluate the expression and effect of PRDM13 on glioma cells. It was found that the expression of PRDM13 was reduced in glioma cells, and the overexpression of PRDM13 significantly decreased the proliferation, migration and invasion of U87 glioma cells. Through validation of RNA-sequencing analysis, genes regulating cell proliferation and migration were classified from Gene Ontology sources. In addition, PRDM13 was shown to be associated with Rho protein and GTP enzyme activation protein. The over expression of PRDM13 upregulated deleted in liver cancer 1 (DLC1) to inhibit the proliferation and invasion of U87 cells. In conclusion, PRDM13 decreased the proliferation and invasion of U87 cells, and may be of potential value for glioma therapy.
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Affiliation(s)
- Linna Zhang
- Department of Physiology, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Huimei Cao
- Department of Physiology, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Tao He
- Department of Spinal Surgery, Dongfeng General Hospital of Chinese Medicine Affiliated to Hubei Medical University, Shiyan, Hubei 442000, P.R. China
| | - Jijuan Yang
- Department of Physiology, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Hong Tao
- Department of Physiology, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Yin Wang
- Ningxia Key Laboratory of Cerebrocranial Diseases, Basic Medical School of Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Qikuan Hu
- Department of Physiology, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
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98
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Abstract
Homologous recombination is required for proper segregation of homologous chromosomes during meiosis. It occurs predominantly at recombination hotspots that are defined by the DNA binding specificity of the PRDM9 protein. PRDM9 contains three conserved domains typically involved in regulation of transcription; yet, the role of PRDM9 in gene expression control is not clear. Here, we analyze the germline transcriptome of Prdm9−/− male mice in comparison to Prdm9+/+ males and find no apparent differences in the mRNA and miRNA profiles. We further explore the role of PRDM9 in meiosis by analyzing the effect of the KRAB, SSXRD, and post-SET zinc finger deletions in a cell culture expression system and the KRAB domain deletion in mice. We found that although the post-SET zinc finger and the KRAB domains are not essential for the methyltransferase activity of PRDM9 in cell culture, the KRAB domain mutant mice show only residual PRDM9 methyltransferase activity and undergo meiotic arrest. In aggregate, our data indicate that domains typically involved in regulation of gene expression do not serve that role in PRDM9, but are likely involved in setting the proper chromatin environment for initiation and completion of homologous recombination.
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99
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Liu H, Dai X, Cao X, Yan H, Ji X, Zhang H, Shen S, Si Y, Zhang H, Chen J, Li L, Zhao JC, Yu J, Feng XH, Zhao B. PRDM4 mediates YAP-induced cell invasion by activating leukocyte-specific integrin β2 expression. EMBO Rep 2018; 19:embr.201745180. [PMID: 29669796 DOI: 10.15252/embr.201745180] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 03/17/2018] [Accepted: 03/23/2018] [Indexed: 12/12/2022] Open
Abstract
Yes-associated protein (YAP) is a transcriptional co-activator and a major effector of the Hippo pathway that promotes cell proliferation and stemness, while inhibiting apoptosis. YAP plays a central role in organ size control, and its deregulation strongly promotes cancer initiation and progression. However, the mechanisms by which YAP promotes cell invasion and metastasis are not fully understood. Here, we report that YAP induces leukocyte-specific integrin β2 (ITGB2) expression in cancer cells, thereby promoting cell invasion through the endothelium in a manner mimicking leukocytes. Through independent biochemical purification and a functional screen, we further identified PR/SET domain 4 (PRDM4) as a transcription factor interacting with the WW domains of YAP to mediate ITGB2 expression and cell invasion. Consistently, ITGB2 and PRDM4 mRNA levels are significantly increased in metastatic prostate cancer. In addition, PRDM4 contributes to YAP-induced tumorigenesis possibly via mediating the expression of other YAP target genes. Our results demonstrate that YAP promotes cell invasion by inducing leukocyte-specific integrin expression, and identify PRDM4 as a novel transcription factor for YAP targets.
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Affiliation(s)
- Huan Liu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoming Dai
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaolei Cao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Huan Yan
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xinyan Ji
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haitao Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shuying Shen
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuan Si
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hailong Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jianfeng Chen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li Li
- Institute of Aging Research, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jonathan C Zhao
- Department of Medicine-Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jindan Yu
- Department of Medicine-Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xin-Hua Feng
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bin Zhao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
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100
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Draime A, Bridoux L, Belpaire M, Pringels T, Tys J, Rezsohazy R. PRDM14, a putative histone methyl-transferase, interacts with and decreases the stability and activity of the HOXA1 transcription factor. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:534-542. [PMID: 29471045 DOI: 10.1016/j.bbagrm.2018.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 11/18/2022]
Abstract
Understanding how the activity of transcription factors like HOX proteins is regulated remains a widely open question. In a recent screen for proteins interacting with HOXA1, we identified a PRDM protein family member, PRDM14, which is known to be transiently co-expressed with HOXA1 in epiblast cells before their specification towards somatic versus germ cell fate. Here, we confirm PRDM14 is an interactor of HOXA1 and we identify the homeodomain of HOXA1 as well as the PR domain and Zinc fingers of PRDM14 to be required for the interaction. An 11-His repeat of HOXA1 previously highlighted to contribute to HOXA1-mediated protein-protein interactions is also involved. At a functional level, we provide evidence that HOXA1 displays an unexpectedly long half-life and demonstrate that PRDM14 can reduce the stability and affect the transcriptional activity of HOXA1.
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Affiliation(s)
- Amandine Draime
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - Laure Bridoux
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - Magali Belpaire
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - Tamara Pringels
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - Janne Tys
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - René Rezsohazy
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium.
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