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Santasusagna S, Zhu S, Jawalagatti V, Carceles-Cordon M, Ertel A, Garcia-Longarte S, Song WM, Fujiwara N, Li P, Mendizabal I, Petrylak DP, Kelly WK, Reddy EP, Wang L, Schiewer MJ, Lujambio A, Karnes J, Knudsen KE, Cordon-Cardo C, Dong H, Huang H, Carracedo A, Hoshida Y, Rodriguez-Bravo V, Domingo-Domenech J. Master Transcription Factor Reprogramming Unleashes Selective Translation Promoting Castration Resistance and Immune Evasion in Lethal Prostate Cancer. Cancer Discov 2023; 13:2584-2609. [PMID: 37676710 PMCID: PMC10714140 DOI: 10.1158/2159-8290.cd-23-0306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/28/2023] [Accepted: 09/05/2023] [Indexed: 09/08/2023]
Abstract
Signaling rewiring allows tumors to survive therapy. Here we show that the decrease of the master regulator microphthalmia transcription factor (MITF) in lethal prostate cancer unleashes eukaryotic initiation factor 3B (eIF3B)-dependent translation reprogramming of key mRNAs conferring resistance to androgen deprivation therapy (ADT) and promoting immune evasion. Mechanistically, MITF represses through direct promoter binding eIF3B, which in turn regulates the translation of specific mRNAs. Genome-wide eIF3B enhanced cross-linking immunoprecipitation sequencing (eCLIP-seq) showed specialized binding to a UC-rich motif present in subsets of 5' untranslated regions. Indeed, translation of the androgen receptor and major histocompatibility complex I (MHC-I) through this motif is sensitive to eIF3B amount. Notably, pharmacologic targeting of eIF3B-dependent translation in preclinical models sensitizes prostate cancer to ADT and anti-PD-1 therapy. These findings uncover a hidden connection between transcriptional and translational rewiring promoting therapy-refractory lethal prostate cancer and provide a druggable mechanism that may transcend into effective combined therapeutic strategies. SIGNIFICANCE Our study shows that specialized eIF3B-dependent translation of specific mRNAs released upon downregulation of the master transcription factor MITF confers castration resistance and immune evasion in lethal prostate cancer. Pharmacologic targeting of this mechanism delays castration resistance and increases immune-checkpoint efficacy. This article is featured in Selected Articles from This Issue, p. 2489.
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Affiliation(s)
- Sandra Santasusagna
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Shijia Zhu
- Department of Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Vijayakumar Jawalagatti
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | | | - Adam Ertel
- Department of Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Saioa Garcia-Longarte
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Won-Min Song
- Department of Genetics and Genome Sciences, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Naoto Fujiwara
- Department of Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Peiyao Li
- Department of Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Isabel Mendizabal
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Daniel P. Petrylak
- Department of Oncology, Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - William Kevin Kelly
- Department of Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - E. Premkumar Reddy
- Department of Oncological Sciences, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Liguo Wang
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Matthew J. Schiewer
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Amaia Lujambio
- Department of Oncological Sciences, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jeffrey Karnes
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Karen E. Knudsen
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Carlos Cordon-Cardo
- Department of Pathology. Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Haidong Dong
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Immunology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Haojie Huang
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Arkaitz Carracedo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Traslational prostate cancer Research Lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
- CIBERONC, Madrid, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Yujin Hoshida
- Department of Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Veronica Rodriguez-Bravo
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Josep Domingo-Domenech
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
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Konstantinidis I, Sætrom P, Brieuc S, Jakobsen KS, Liedtke H, Pohlmann C, Tsoulia T, Fernandes JMO. DNA hydroxymethylation differences underlie phenotypic divergence of somatic growth in Nile tilapia reared in common garden. Epigenetics 2023; 18:2282323. [PMID: 38010265 PMCID: PMC10732659 DOI: 10.1080/15592294.2023.2282323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023] Open
Abstract
Phenotypic plasticity of metabolism and growth are essential for adaptation to new environmental conditions, such as those experienced during domestication. Epigenetic regulation plays a key role in this process but the underlying mechanisms are poorly understood, especially in the case of hydroxymethylation. Using reduced representation 5-hydroxymethylcytosine profiling, we compared the liver hydroxymethylomes in full-sib Nile tilapia with distinct growth rates (3.8-fold difference) and demonstrated that DNA hydroxymethylation is strongly associated with phenotypic divergence of somatic growth during the early stages of domestication. The 2677 differentially hydroxymethylated cytosines between fast- and slow-growing fish were enriched within gene bodies (79%), indicating a pertinent role in transcriptional regulation. Moreover, they were found in genes involved in biological processes related to skeletal system and muscle structure development, and there was a positive association between somatic growth and 5hmC levels in genes coding for growth factors, kinases and receptors linked to myogenesis. Single nucleotide polymorphism analysis revealed no genetic differentiation between fast- and slow-growing fish. In addition to unveiling a new link between DNA hydroxymethylation and epigenetic regulation of growth in fish during the initial stages of domestication, this study suggests that epimarkers may be applied in selective breeding programmes for superior phenotypes.
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Affiliation(s)
| | - Pål Sætrom
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Computer Science, Norwegian University of Science and Technology, Trondheim, Norway
- Bioinformatics core facility-BioCore, Norwegian University of Science and Technology, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - S.O. Brieuc
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S. Jakobsen
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Hannes Liedtke
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Caroline Pohlmann
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Thomais Tsoulia
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Deacon E, Li A, Boivin F, Dvorkin-Gheva A, Cunanan J, Bridgewater D. β-Catenin in the kidney stroma modulates pathways and genes to regulate kidney development. Dev Dyn 2023; 252:1224-1239. [PMID: 37227110 DOI: 10.1002/dvdy.603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Kidney development is regulated by cellular interactions between the ureteric epithelium, mesenchyme, and stroma. Previous studies demonstrate essential roles for stromal β-catenin in kidney development. However, how stromal β-catenin regulates kidney development is not known. We hypothesize that stromal β-catenin modulates pathways and genes that facilitate communications with neighboring cell populations to regulate kidney development. RESULTS We isolated purified stromal cells with wild type, deficient, and overexpressed β-catenin by fluorescence-activated cell sorting and conducted RNA Sequencing. A Gene Ontology network analysis demonstrated that stromal β-catenin modulates key kidney developmental processes, including branching morphogenesis, nephrogenesis and vascular formation. Specific stromal β-catenin candidate target genes that may mediate these effects included secreted, cell-surface and transcriptional factors that regulate branching morphogenesis and nephrogenesis (Wnts, Bmp, Fgfr, Tcf/Lef) and secreted vascular guidance cues (Angpt1, VEGF, Sema3a). We validated established β-catenin targets including Lef1 and novel candidate β-catenin targets including Sema3e which have unknown roles in kidney development. CONCLUSIONS These studies advance our understanding of gene and biological pathway dysregulation in the context of stromal β-catenin misexpression during kidney development. Our findings suggest that during normal kidney development, stromal β-catenin may regulate secreted and cell-surface proteins to communicate with adjacent cell populations.
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Affiliation(s)
- Erin Deacon
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Anna Li
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Felix Boivin
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Anna Dvorkin-Gheva
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Joanna Cunanan
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Darren Bridgewater
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
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Wang Q, Qi H, Wu Y, Yu L, Bouchareb R, Li S, Lassén E, Casalena G, Stadler K, Ebefors K, Yi Z, Shi S, Salem F, Gordon R, Lu L, Williams RW, Duffield J, Zhang W, Itan Y, Böttinger E, Daehn I. Genetic susceptibility to diabetic kidney disease is linked to promoter variants of XOR. Nat Metab 2023; 5:607-625. [PMID: 37024752 PMCID: PMC10821741 DOI: 10.1038/s42255-023-00776-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
The lifetime risk of kidney disease in people with diabetes is 10-30%, implicating genetic predisposition in the cause of diabetic kidney disease (DKD). Here we identify an expression quantitative trait loci (QTLs) in the cis-acting regulatory region of the xanthine dehydrogenase, or xanthine oxidoreductase (Xor), a binding site for C/EBPβ, to be associated with diabetes-induced podocyte loss in DKD in male mice. We examine mouse inbred strains that are susceptible (DBA/2J) and resistant (C57BL/6J) to DKD, as well as a panel of recombinant inbred BXD mice, to map QTLs. We also uncover promoter XOR orthologue variants in humans associated with high risk of DKD. We introduced the risk variant into the 5'-regulatory region of XOR in DKD-resistant mice, which resulted in increased Xor activity associated with podocyte depletion, albuminuria, oxidative stress and damage restricted to the glomerular endothelium, which increase further with type 1 diabetes, high-fat diet and ageing. Therefore, differential regulation of Xor contributes to phenotypic consequences with diabetes and ageing.
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Affiliation(s)
- Qin Wang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacy, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Haiying Qi
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yiming Wu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liping Yu
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rihab Bouchareb
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shuyu Li
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emelie Lassén
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gabriella Casalena
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Krisztian Stadler
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, USA
| | - Kerstin Ebefors
- Department of Neuroscience and Physiology, Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Zhengzi Yi
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shaolin Shi
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fadi Salem
- Pathology, Molecular and Cell based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ronald Gordon
- Pathology, Molecular and Cell based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Weijia Zhang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuval Itan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erwin Böttinger
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Heath at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Digital Health Center, Hasso Plattner Institut, University of Potsdam, Potsdam, Germany
| | - Ilse Daehn
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Benaouda S, Stöcker T, Schoof H, Léon J, Ballvora A. Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat. BMC PLANT BIOLOGY 2023; 23:25. [PMID: 36631761 PMCID: PMC9835304 DOI: 10.1186/s12870-022-03986-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The transition from vegetative to floral phase is the result of complex crosstalk of exogenous and endogenous floral integrators. This critical physiological event is the response to environmental interaction, which causes biochemical cascades of reactions at different internal tissues, organs, and releases signals that make the plant moves from vegetative status to a reproductive phase. This network controlling flowering time is not deciphered largely in bread wheat. In this study, a comparative transcriptome analysis at a transition time in combination with genetic mapping was used to identify responsible genes in a stage and tissue-specific manner. For this reason, two winter cultivars that have been bred in Germany showing contrasting and stable heading time in different environments were selected for the analysis. RESULTS In total, 670 and 1075 differentially expressed genes in the shoot apical meristem and leaf tissue, respectively, could be identified in 23 QTL intervals for the heading date. In the transition apex, Histone methylation H3-K36 and regulation of circadian rhythm are both controlled by the same homoeolog genes mapped in QTL TaHd112, TaHd124, and TaHd137. TaAGL14 gene that identifies the floral meristem was mapped in TaHd054 in the double ridge. In the same stage, the homoeolog located on chromosome 7D of FLOWERING TIME LOCUS T mapped on chr 7B, which evolved an antagonist function and acts as a flowering repressor was uncovered. The wheat orthologue of transcription factor ASYMMETRIC LEAVES 1 (AS1) was identified in the late reproductive stage and was mapped in TaHd102, which is strongly associated with heading date. Deletion of eight nucleotides in the AS1 promoter could be identified in the binding site of the SUPPRESSOR OF CONSTANS OVEREXPRESSION 1 (SOC1) gene in the late flowering cultivar. Both proteins AS1 and SOC1 are inducing flowering time in response to gibberellin biosynthesis. CONCLUSION The global transcriptomic at the transition phase uncovered stage and tissue-specific genes mapped in QTL of heading date in winter wheat. In response to Gibberellin signaling, wheat orthologous transcription factor AS1 is expressed in the late reproductive phase of the floral transition. The locus harboring this gene is the strongest QTL associated with the heading date trait in the German cultivars. Consequently, we conclude that this is another indication of the Gibberellin biosynthesis as the mechanism behind the heading variation in wheat.
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Affiliation(s)
- Salma Benaouda
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Tyll Stöcker
- Institute for Crop Science and Resource Conservation, Chair of Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Heiko Schoof
- Institute for Crop Science and Resource Conservation, Chair of Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Jens Léon
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
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Ruddle RA, Bernard J, Lucke-Tieke H, May T, Kohlhammer J. The Effect of Alignment on People's Ability to Judge Event Sequence Similarity. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2022; 28:3070-3081. [PMID: 33434130 DOI: 10.1109/tvcg.2021.3050497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Event sequences are central to the analysis of data in domains that range from biology and health, to logfile analysis and people's everyday behavior. Many visualization tools have been created for such data, but people are error-prone when asked to judge the similarity of event sequences with basic presentation methods. This article describes an experiment that investigates whether local and global alignment techniques improve people's performance when judging sequence similarity. Participants were divided into three groups (basic versus local versus global alignment), and each participant judged the similarity of 180 sets of pseudo-randomly generated sequences. Each set comprised a target, a correct choice and a wrong choice. After training, the global alignment group was more accurate than the local alignment group (98 versus 93 percent correct), with the basic group getting 95 percent correct. Participants' response times were primarily affected by the number of event types, the similarity of sequences (measured by the Levenshtein distance) and the edit types (nine combinations of deletion, insertion and substitution). In summary, global alignment is superior and people's performance could be further improved by choosing alignment parameters that explicitly penalize sequence mismatches.
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Rodríguez‐Barrueco R, Latorre J, Devis‐Jáuregui L, Lluch A, Bonifaci N, Llobet FJ, Olivan M, Coll‐Iglesias L, Gassner K, Davis ML, Moreno‐Navarrete JM, Castells‐Nobau A, Plata‐Peña L, Dalmau‐Pastor M, Höring M, Liebisch G, Olkkonen VM, Arnoriaga‐Rodríguez M, Ricart W, Fernández‐Real JM, Silva JM, Ortega FJ, Llobet‐Navas D. A microRNA Cluster Controls Fat Cell Differentiation and Adipose Tissue Expansion By Regulating SNCG. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104759. [PMID: 34898027 PMCID: PMC8811811 DOI: 10.1002/advs.202104759] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Indexed: 05/08/2023]
Abstract
The H19X-encoded miR-424(322)/503 cluster regulates multiple cellular functions. Here, it is reported for the first time that it is also a critical linchpin of fat mass expansion. Deletion of this miRNA cluster in mice results in obesity, while increasing the pool of early adipocyte progenitors and hypertrophied adipocytes. Complementary loss and gain of function experiments and RNA sequencing demonstrate that miR-424(322)/503 regulates a conserved genetic program involved in the differentiation and commitment of white adipocytes. Mechanistically, it is demonstrated that miR-424(322)/503 targets γ-Synuclein (SNCG), a factor that mediates this program rearrangement by controlling metabolic functions in fat cells, allowing adipocyte differentiation and adipose tissue enlargement. Accordingly, diminished miR-424(322) in mice and obese humans co-segregate with increased SNCG in fat and peripheral blood as mutually exclusive features of obesity, being normalized upon weight loss. The data unveil a previously unknown regulatory mechanism of fat mass expansion tightly controlled by the miR-424(322)/503 through SNCG.
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Affiliation(s)
- Ruth Rodríguez‐Barrueco
- Molecular Mechanisms and Experimental Therapy in Oncology‐Oncobell ProgramBellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de Llobregat08908Spain
- Anatomy UnitDepartment of Pathology and Experimental TherapySchool of MedicineUniversity of Barcelona (UB)L'Hospitalet de Llobregat08907Spain
| | - Jessica Latorre
- Department of DiabetesEndocrinology, and Nutrition (UDEN)Institut d'Investigació Biomèdica de Girona (IDIBGI)Salt17190Spain
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBEROBN)Instituto de Salud Carlos III (ISCIII)Madrid28029Spain
| | - Laura Devis‐Jáuregui
- Molecular Mechanisms and Experimental Therapy in Oncology‐Oncobell ProgramBellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de Llobregat08908Spain
| | - Aina Lluch
- Molecular Mechanisms and Experimental Therapy in Oncology‐Oncobell ProgramBellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de Llobregat08908Spain
- Department of DiabetesEndocrinology, and Nutrition (UDEN)Institut d'Investigació Biomèdica de Girona (IDIBGI)Salt17190Spain
| | - Nuria Bonifaci
- Molecular Mechanisms and Experimental Therapy in Oncology‐Oncobell ProgramBellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de Llobregat08908Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)Instituto de Salud Carlos III, (ISCIII)Madrid28029Spain
| | - Francisco J. Llobet
- Molecular Mechanisms and Experimental Therapy in Oncology‐Oncobell ProgramBellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de Llobregat08908Spain
| | - Mireia Olivan
- Molecular Mechanisms and Experimental Therapy in Oncology‐Oncobell ProgramBellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de Llobregat08908Spain
- Anatomy UnitDepartment of Pathology and Experimental TherapySchool of MedicineUniversity of Barcelona (UB)L'Hospitalet de Llobregat08907Spain
| | - Laura Coll‐Iglesias
- Molecular Mechanisms and Experimental Therapy in Oncology‐Oncobell ProgramBellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de Llobregat08908Spain
| | - Katja Gassner
- Molecular Mechanisms and Experimental Therapy in Oncology‐Oncobell ProgramBellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de Llobregat08908Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)Instituto de Salud Carlos III, (ISCIII)Madrid28029Spain
| | - Meredith L. Davis
- Molecular Mechanisms and Experimental Therapy in Oncology‐Oncobell ProgramBellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de Llobregat08908Spain
- Department of PathologyDuke University School of MedicineDurhamNC27710USA
| | - José M. Moreno‐Navarrete
- Department of DiabetesEndocrinology, and Nutrition (UDEN)Institut d'Investigació Biomèdica de Girona (IDIBGI)Salt17190Spain
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBEROBN)Instituto de Salud Carlos III (ISCIII)Madrid28029Spain
| | - Anna Castells‐Nobau
- Department of DiabetesEndocrinology, and Nutrition (UDEN)Institut d'Investigació Biomèdica de Girona (IDIBGI)Salt17190Spain
| | - Laura Plata‐Peña
- Molecular Mechanisms and Experimental Therapy in Oncology‐Oncobell ProgramBellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de Llobregat08908Spain
| | - Miki Dalmau‐Pastor
- Anatomy UnitDepartment of Pathology and Experimental TherapySchool of MedicineUniversity of Barcelona (UB)L'Hospitalet de Llobregat08907Spain
- MIFAS by GRECMIP (Minimally Invasive Foot and Ankle Society)Merignac33700France
| | - Marcus Höring
- Institute of Clinical Chemistry and Laboratory MedicineRegensburg University HospitalRegensburg93053Germany
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory MedicineRegensburg University HospitalRegensburg93053Germany
| | - Vesa M. Olkkonen
- Minerva Foundation Institute for Medical Research (Biomedicum 2U)and Department of AnatomyFaculty of MedicineUniversity of HelsinkiHelsinki00290Finland
| | - Maria Arnoriaga‐Rodríguez
- Department of DiabetesEndocrinology, and Nutrition (UDEN)Institut d'Investigació Biomèdica de Girona (IDIBGI)Salt17190Spain
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBEROBN)Instituto de Salud Carlos III (ISCIII)Madrid28029Spain
| | - Wifredo Ricart
- Department of DiabetesEndocrinology, and Nutrition (UDEN)Institut d'Investigació Biomèdica de Girona (IDIBGI)Salt17190Spain
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBEROBN)Instituto de Salud Carlos III (ISCIII)Madrid28029Spain
| | - José M. Fernández‐Real
- Department of DiabetesEndocrinology, and Nutrition (UDEN)Institut d'Investigació Biomèdica de Girona (IDIBGI)Salt17190Spain
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBEROBN)Instituto de Salud Carlos III (ISCIII)Madrid28029Spain
| | - José M. Silva
- Department of PathologyIcahn School of Medicine at Mount SinaiNew YorkNY10029USA
| | - Francisco J. Ortega
- Department of DiabetesEndocrinology, and Nutrition (UDEN)Institut d'Investigació Biomèdica de Girona (IDIBGI)Salt17190Spain
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBEROBN)Instituto de Salud Carlos III (ISCIII)Madrid28029Spain
| | - David Llobet‐Navas
- Molecular Mechanisms and Experimental Therapy in Oncology‐Oncobell ProgramBellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de Llobregat08908Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)Instituto de Salud Carlos III, (ISCIII)Madrid28029Spain
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8
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Raza H, Khan MR, Zafar SA, Kirch HH, Bartles D. Aldehyde dehydrogenase 3I1 gene is recruited in conferring multiple abiotic stress tolerance in plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:85-94. [PMID: 34670007 DOI: 10.1111/plb.13337] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Plant growth and productivity is restricted by a multitude of abiotic stresses. These stresses negatively affect physiological and metabolic pathways, leading to the production of many harmful substances like ROS, lipid peroxides and aldehydes. This study was conducted to investigate the role of Arabidopsis ALDH3I1 gene in multiple abiotic stress tolerance. Transgenic tobacco plants were generated that overexpress the ALDH3I1 gene driven by the CaMV35S promoter and evaluated under different abiotic stresses, namely salt, drought, cold and oxidative stress. Tolerance to stress was evaluated based on responses of various growth and physiological traits under stress condition. Transgenic plants displayed elevated ALDH3I1 transcript levels compared to WT plants. The constitutive ectopic expression of ALDH3I1 conferred increased tolerance to salt, drought, cold and oxidative stresses in transgenic plants, along with improved plant growth. Transgenic plants overexpressing ALDH3I1 had higher chlorophyll content, photosynthesis rate and proline, and less accumulation of ROS and malondialdehyde compared to the WT, which contributed to stress tolerance in transgenic plants. Our results further revealed that ALDH3I1 had a positive effect on CO2 assimilation rate in plants under abiotic stress conditions. Overall, this study revealed that ALDH3I1 positively regulates abiotic stress tolerance in plants, and has future implications in producing transgenic cereal and horticultural plants tolerant to abiotic stresses.
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Affiliation(s)
- H Raza
- Institute for Molecular Physiology & Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - M R Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - S A Zafar
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - H H Kirch
- Institute for Molecular Physiology & Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - D Bartles
- Institute for Molecular Physiology & Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
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9
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Wang J, Fu CN, Mo ZQ, Möller M, Yang JB, Zhang ZR, Li DZ, Gao LM. Testing the Complete Plastome for Species Discrimination, Cryptic Species Discovery and Phylogenetic Resolution in Cephalotaxus (Cephalotaxaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:768810. [PMID: 35599857 PMCID: PMC9116380 DOI: 10.3389/fpls.2022.768810] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/07/2022] [Indexed: 05/17/2023]
Abstract
Species of Cephalotaxus have great economic and ecological values. However, the taxonomy and interspecific phylogenetic relationships within the genus have been controversial and remained not fully resolved until now. To date, no study examined the efficiency of the complete plastome as super-barcode across Cephalotaxus species with multiple samples per taxon. In this study, we have evaluated the complete plastome in species discrimination and phylogenetic resolution in Cephalotaxus by including 32 individuals of all eight recognized species and five varieties following Farjon's classification (2010) with multiple samples per taxon. Our results indicated that not all species recognized in recent taxonomic revisions of Cephalotaxus could be distinguished and not all were monophyletic. Based on the plastome phylogeny, a new taxonomic classification for the genus comprising nine species and two varieties, including a cryptic species, was proposed. The phylogeny also resolved all interspecific relationships. Compared to the plastome based classification, standard DNA barcodes, alone or in combination, only recognized a maximum of seven out of the nine species. Moreover, two highly variable single loci, ycf1 and rps16, each alone achieved full species discrimination. With the moderate length of 1079 bp, rps16 is proposed as a specific barcode to discriminate Cephalotaxus species. The super-barcodes and specific barcode candidates will aid in the identification of endangered Cephalotaxus species, and to help focus conservation measures.
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Affiliation(s)
- Jie Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Michael Möller
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, China
- *Correspondence: Lian-Ming Gao,
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10
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Gomes G, do Amaral MJ, Bagri KM, Vasconcellos LM, Almeida MDS, Alvares LE, Mermelstein C. New Findings on LMO7 Transcripts, Proteins and Regulatory Regions in Human and Vertebrate Model Organisms and the Intracellular Distribution in Skeletal Muscle Cells. Int J Mol Sci 2021; 22:ijms222312885. [PMID: 34884689 PMCID: PMC8657913 DOI: 10.3390/ijms222312885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/04/2022] Open
Abstract
LMO7 is a multifunctional PDZ–LIM protein that can interact with different molecular partners and is found in several intracellular locations. The aim of this work was to shed light on LMO7 evolution, alternative transcripts, protein structure and gene regulation through multiple in silico analyses. We also explored the intracellular distribution of the LMO7 protein in chicken and zebrafish embryonic skeletal muscle cells by means of confocal fluorescence microscopy. Our results revealed a single LMO7 gene in mammals, sauropsids, Xenopus and in the holostean fish spotted gar while two lmo7 genes (lmo7a and lmo7b) were identified in teleost fishes. In addition, several different transcripts were predicted for LMO7 in human and in major vertebrate model organisms (mouse, chicken, Xenopus and zebrafish). Bioinformatics tools revealed several structural features of the LMO7 protein including intrinsically disordered regions. We found the LMO7 protein in multiple intracellular compartments in chicken and zebrafish skeletal muscle cells, such as membrane adhesion sites and the perinuclear region. Curiously, the LMO7 protein was detected within the nuclei of muscle cells in chicken but not in zebrafish. Our data showed that a conserved regulatory element may be related to muscle-specific LMO7 expression. Our findings uncover new and important information about LMO7 and open new challenges to understanding how the diverse regulation, structure and distribution of this protein are integrated into highly complex vertebrate cellular milieux, such as skeletal muscle cells.
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Affiliation(s)
- Geyse Gomes
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; (G.G.); (K.M.B.); (L.M.V.)
| | | | - Kayo Moreira Bagri
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; (G.G.); (K.M.B.); (L.M.V.)
| | - Larissa Melo Vasconcellos
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; (G.G.); (K.M.B.); (L.M.V.)
| | - Marcius da Silva Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil;
| | - Lúcia Elvira Alvares
- Departamento de Bioquímica e Biologia Tecidual, Universidade de Campinas (UNICAMP), Campinas, São Paulo 13083-872, Brazil;
| | - Claudia Mermelstein
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; (G.G.); (K.M.B.); (L.M.V.)
- Correspondence:
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11
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Matosinho CGR, Rosse IC, Fonseca PAS, de Oliveira FS, Dos Santos FG, Araújo FMG, de Matos Salim AC, Lopes BC, Arbex WA, Machado MA, Peixoto MGCD, da Silva Verneque R, Martins MF, da Silva MVGB, Oliveira G, Pires DEV, Carvalho MRS. Identification and in silico characterization of structural and functional impacts of genetic variants in milk protein genes in the Zebu breeds Guzerat and Gyr. Trop Anim Health Prod 2021; 53:524. [PMID: 34705124 DOI: 10.1007/s11250-021-02970-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/14/2021] [Indexed: 10/20/2022]
Abstract
Whole genome sequencing of bovine breeds has allowed identification of genetic variants in milk protein genes. However, functional repercussion of such variants at a molecular level has seldom been investigated. Here, the results of a multistep Bioinformatic analysis for functional characterization of recently identified genetic variants in Brazilian Gyr and Guzerat breeds is described, including predicted effects on the following: (i) evolutionary conserved nucleotide positions/regions; (ii) protein function, stability, and interactions; (iii) splicing, branching, and miRNA binding sites; (iv) promoters and transcription factor binding sites; and (v) collocation with QTL. Seventy-one genetic variants were identified in the caseins (CSN1S1, CSN2, CSN1S2, and CSN3), LALBA, LGB, and LTF genes. Eleven potentially regulatory variants and two missense mutations were identified. LALBA Ile60Val was predicted to affect protein stability and flexibility, by reducing the number the disulfide bonds established. LTF Thr546Asn is predicted to generate steric clashes, which could mildly affect iron coordination. In addition, LALBA Ile60Val and LTF Thr546Asn affect exonic splicing enhancers and silencers. Consequently, both mutations have the potential of affecting immune response at individual level, not only in the mammary gland. Although laborious, this multistep procedure for classifying variants allowed the identification of potentially functional variants for milk protein genes.
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Affiliation(s)
- Carolina Guimarães Ramos Matosinho
- Programa de Pós-Graduação Em GenéticaDepartamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31901-207, Brazil
| | - Izinara Cruz Rosse
- Programa de Pós-Graduação Em GenéticaDepartamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31901-207, Brazil
- Departamento de Farmácia, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Pablo Augusto Souza Fonseca
- Programa de Pós-Graduação Em GenéticaDepartamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31901-207, Brazil.
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G2W1, Canada.
| | - Francislon Silva de Oliveira
- Programa de Pós-Graduação Em GenéticaDepartamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31901-207, Brazil
- Grupo de Genômica E Biologia Computacional, Centro de Pesquisas René Rachou - Fiocruz Minas, Belo Horizonte, MG, 30190-00, Brazil
| | - Fausto Gonçalves Dos Santos
- Grupo de Genômica E Biologia Computacional, Centro de Pesquisas René Rachou - Fiocruz Minas, Belo Horizonte, MG, 30190-00, Brazil
| | - Flávio Marcos Gomes Araújo
- Grupo de Genômica E Biologia Computacional, Centro de Pesquisas René Rachou - Fiocruz Minas, Belo Horizonte, MG, 30190-00, Brazil
| | - Anna Christina de Matos Salim
- Grupo de Genômica E Biologia Computacional, Centro de Pesquisas René Rachou - Fiocruz Minas, Belo Horizonte, MG, 30190-00, Brazil
| | | | | | | | | | - Rui da Silva Verneque
- EPAMIG, Belo Horizonte, MG, 31170-495, Brazil
- Embrapa Gado de Leite, Juiz de Fora, MG, 36038-330, Brazil
| | | | | | - Guilherme Oliveira
- Grupo de Genômica E Biologia Computacional, Centro de Pesquisas René Rachou - Fiocruz Minas, Belo Horizonte, MG, 30190-00, Brazil
- Instituto Tecnológico Vale, Belém, PA, 66055-09, Brazil
| | - Douglas Eduardo Valente Pires
- School of Computing and Information Systems, University of Melbourne, Parkville, VIC, 3052, Australia
- Bio21 Institute, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Maria Raquel Santos Carvalho
- Programa de Pós-Graduação Em GenéticaDepartamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31901-207, Brazil
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12
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Role of macrophages in fetal development and perinatal disorders. Pediatr Res 2021; 90:513-523. [PMID: 33070164 DOI: 10.1038/s41390-020-01209-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/17/2020] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
In the fetus and the neonate, altered macrophage function has been implicated not only in inflammatory disorders but also in developmental abnormalities marked by altered onset, interruption, or imbalance of key structural changes. The developmental role of macrophages were first noted nearly a century ago, at about the same time when these cells were being identified as central effectors in phagocytosis and elimination of microbes. Since that time, we have made considerable progress in understanding the diverse roles that these cells play in both physiology and disease. Here, we review the role of fetal and neonatal macrophages in immune surveillance, innate immunity, homeostasis, tissue remodeling, angiogenesis, and repair of damaged tissues. We also discuss the possibility of therapeutic manipulation of the relative abundance and activation status of macrophage subsets in various diseases. This article combines peer-reviewed evidence from our own studies with results of an extensive literature search in the databases PubMed, EMBASE, and Scopus. IMPACT: We have reviewed the structure, differentiation, and classification of macrophages in the neonatal period. Neonatal macrophages are derived from embryonic, hepatic, and bone marrow precursors. Macrophages play major roles in tissue homeostasis, innate immunity, inflammation, tissue repair, angiogenesis, and apoptosis of various cellular lineages in various infectious and inflammatory disorders. Macrophages and related inflammatory mediators could be important therapeutic targets in several neonatal diseases.
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13
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Xu H, Ma G, Mu F, Ning B, Li H, Wang N. STAT3 Partly Inhibits Cell Proliferation via Direct Negative Regulation of FST Gene Expression. Front Genet 2021; 12:678667. [PMID: 34239543 PMCID: PMC8259742 DOI: 10.3389/fgene.2021.678667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Follistatin (FST) is a secretory glycoprotein and belongs to the TGF-β superfamily. Previously, we found that two single nucleotide polymorphisms (SNPs) of sheep FST gene were significantly associated with wool quality traits in Chinese Merino sheep (Junken type), indicating that FST is involved in the regulation of hair follicle development and hair trait formation. The transcription regulation of human and mouse FST genes has been widely investigated, and many transcription factors have been identified to regulate FST gene. However, to date, the transcriptional regulation of sheep FST is largely unknown. In the present study, genome walking was used to close the genomic gap upstream of the sheep genomic FST gene and to obtain the FST gene promoter sequence. Transcription factor binding site analysis showed sheep FST promoter region contained a conserved putative binding site for signal transducer and activator of transcription 3 (STAT3), located at nucleotides -423 to -416 relative to the first nucleotide (A, +1) of the initiation codon (ATG) of sheep FST gene. The dual-luciferase reporter assay demonstrated that STAT3 inhibited the FST promoter activity and that the mutation of the putative STAT3 binding site attenuated the inhibitory effect of STAT3 on the FST promoter activity. Additionally, chromatin immunoprecipitation assay (ChIP) exhibited that STAT3 is directly bound to the FST promoter. Cell proliferation assay displayed that FST and STAT3 played opposite roles in cell proliferation. Overexpression of sheep FST significantly promoted the proliferation of sheep fetal fibroblasts (SFFs) and human keratinocyte (HaCaT) cells, and overexpression of sheep STAT3 displayed opposite results, which was accompanied by a significantly reduced expression of FST gene (P < 0.05). Taken together, STAT3 directly negatively regulates sheep FST gene and depresses cell proliferation. Our findings may contribute to understanding molecular mechanisms that underlie hair follicle development and morphogenesis.
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Affiliation(s)
- Haidong Xu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Guangwei Ma
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Fang Mu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Bolin Ning
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Hui Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Ning Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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14
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Xu G, Xu W. Complete chloroplast genomes of Chinese wild-growing Vitis species: molecular structures and comparative and adaptive radiation analysis. PROTOPLASMA 2021; 258:559-571. [PMID: 33230625 DOI: 10.1007/s00709-020-01585-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
As a basalmost family of Vitaceae, Chinese wild Vitis species offer key insights into the demographic history of grapes. In this study, we obtained 10 complete chloroplast (cp) genomes from Chinese wild-growing Vitis species based on our whole genome re-sequencing data. These chloroplast genomes ranged from 160,838 to 232,020 bp in size and exhibited typical quadripartite structures. Comparative analyses revealed that inverted repeat (IR) regions are especially abundant and contribute to cp genome arrangements. Phylogenetic analysis of the whole Vitis cp genomes supported three clearly partitioned main origins, in keeping with their geographic distributions, among which East Asian species from China were found to be sister species with Eurasian Vitis species but exhibited significant divergence from the North American group. Two well-supported subgroups were observed within the Chinese wild-growing Vitis species. Among these species, Vitis piasezkii and Vitis betulifolia were closely related species, exhibiting a support rate of 100%. The molecular clock-based divergence time suggested that the earliest split subspecies was Vitis pseudoreticulata, which further indicated that the origin and initial gene pool are located in southern China (the habitat of V. pseudoreticulata is located in the region). Coincidentally, the divergence time was during the Pleistocene period (2.6-0.1 Ma). Due to glacial/interglacial temperature fluctuations, cold-adapted subspecies, e.g., Vitis amurensis, could re-colonize new habitats. Our results may help to elucidate the adaptive radiation of Chinese wild Vitis species in different environments.
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Affiliation(s)
- Guangya Xu
- School of Agronomy, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China
| | - Weirong Xu
- School of Food & Wine, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China.
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China.
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, 750021, China.
- Chinese Wine Industry Technology Institute, Yinchuan, 750021, China.
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15
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Raza S, Jokl E, Pritchett J, Martin K, Su K, Simpson K, Birchall L, Mullan AF, Athwal VS, Doherty DT, Zeef L, Henderson NC, Kalra PA, Hanley NA, Piper Hanley K. SOX9 is required for kidney fibrosis and activates NAV3 to drive renal myofibroblast function. Sci Signal 2021; 14:14/672/eabb4282. [PMID: 33653921 DOI: 10.1126/scisignal.abb4282] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Renal fibrosis is a common end point for kidney injury and many chronic kidney diseases. Fibrogenesis depends on the sustained activation of myofibroblasts, which deposit the extracellular matrix that causes progressive scarring and organ failure. Here, we showed that the transcription factor SOX9 was associated with kidney fibrosis in humans and required for experimentally induced kidney fibrosis in mice. From genome-wide analysis, we identified Neuron navigator 3 (NAV3) as acting downstream of SOX9 in kidney fibrosis. NAV3 increased in abundance and colocalized with SOX9 after renal injury in mice, and both SOX9 and NAV3 were present in diseased human kidneys. In an in vitro model of renal pericyte transdifferentiation into myofibroblasts, we demonstrated that NAV3 was required for multiple aspects of fibrogenesis, including actin polymerization linked to cell migration and sustained activation of the mechanosensitive transcription factor YAP1. In summary, our work identifies a SOX9-NAV3-YAP1 axis involved in the progression of kidney fibrosis and points to NAV3 as a potential target for pharmacological intervention.
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Affiliation(s)
- Sayyid Raza
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health and Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - Elliot Jokl
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health and Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - James Pritchett
- School of Healthcare Science, Manchester Metropolitan University, Manchester M1 5GD, UK
| | - Katherine Martin
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health and Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - Kim Su
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health and Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - Kara Simpson
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health and Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - Lindsay Birchall
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health and Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - Aoibheann F Mullan
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health and Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - Varinder S Athwal
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health and Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK.,Manchester University NHS Foundation Trust, Oxford Road, Manchester M13 9PT, UK
| | - Daniel T Doherty
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health and Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - Leo Zeef
- Bioinformatics Core Facility, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Neil C Henderson
- MRC Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Philip A Kalra
- Salford Royal NHS Foundation Trust, Stott Lane, Salford, UK
| | - Neil A Hanley
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health and Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK.,Manchester University NHS Foundation Trust, Oxford Road, Manchester M13 9PT, UK
| | - Karen Piper Hanley
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health and Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK. .,Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
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16
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Xu H, Leng Q, Zheng J, Adu-Asiamah P, Lin S, Li T, Wang Z, An L, Zhao Z, Zhang L. Effects of Circular RNA of Chicken Growth Hormone Receptor Gene on Cell Proliferation. Front Genet 2021; 12:598575. [PMID: 33643379 PMCID: PMC7905176 DOI: 10.3389/fgene.2021.598575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/11/2021] [Indexed: 11/25/2022] Open
Abstract
Animal growth and development are regulated by neural and endocrine growth axes, in which cell proliferation plays key roles. Recently, many research showed that circular RNAs were involved in hepatocyte and myoblast proliferation. Previously, we identified a circular RNA derived from the chicken GHR gene, named circGHR. However, the function of circGHR is unclear. The objective of this study was to investigate circGHR expression pattern and its roles in cell proliferation. Results indicated that circGHR was a closed-loop structure molecule, and it was richer in the nucleus of hepatocytes and myoblast. Real-time PCR showed that circGHR was increased from E13 to the 7th week in the liver but decreased in the thigh and breast muscle. The CCK-8 assay displayed that circGHR promoted cell proliferation. Simultaneously, the biomarker genes PCNA, CCND1, and CDK2 and the linear transcripts GHR and GHBP were upregulated when circGHR was overexpressed. Altogether, these data exhibited that circGHR could promote cell proliferation possibly by regulating GHR mRNA and GHBP expression.
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Affiliation(s)
- Haidong Xu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Qiying Leng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Jiahui Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Patricia Adu-Asiamah
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Shudai Lin
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
| | - Ting Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Zhang Wang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Lilong An
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Zhuihui Zhao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Li Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
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17
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Abstract
Aims:
Robust and more accurate method for identifying transcription factor binding sites
(TFBS) for gene expression.
Background:
Deep neural networks (DNNs) have shown promising growth in solving complex
machine learning problems. Conventional techniques are comfortably replaced by DNNs in
computer vision, signal processing, healthcare, and genomics. Understanding DNA sequences is
always a crucial task in healthcare and regulatory genomics. For DNA motif prediction, choosing the
right dataset with a sufficient number of input sequences is crucial in order to design an effective
model.
Objective:
Designing a new algorithm which works on different dataset while an improved
performance for TFBS prediction.
Methods:
With the help of Layerwise Relevance Propagation, the proposed algorithm identifies the
invariant features with adaptive noise patterns.
Results:
The performance is compared by calculating various metrics on standard as well as recent
methods and significant improvement is noted.
Conclusion:
By identifying the invariant and robust features in the DNA sequences, the
classification performance can be increased.
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Affiliation(s)
- Kanu Geete
- Department of Computer Science & Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Manish Pandey
- Department of Computer Science & Engineering, Maulana Azad National Institute of Technology, Bhopal, India
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18
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Sanmarco LM, Wheeler MA, Gutiérrez-Vázquez C, Polonio CM, Linnerbauer M, Pinho-Ribeiro FA, Li Z, Giovannoni F, Batterman KV, Scalisi G, Zandee SEJ, Heck ES, Alsuwailm M, Rosene DL, Becher B, Chiu IM, Prat A, Quintana FJ. Gut-licensed IFNγ + NK cells drive LAMP1 +TRAIL + anti-inflammatory astrocytes. Nature 2021; 590:473-479. [PMID: 33408417 PMCID: PMC8039910 DOI: 10.1038/s41586-020-03116-4] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023]
Abstract
Astrocytes are glial cells that are abundant in the central nervous system (CNS) and that have important homeostatic and disease-promoting functions1. However, little is known about the homeostatic anti-inflammatory activities of astrocytes and their regulation. Here, using high-throughput flow cytometry screening, single-cell RNA sequencing and CRISPR-Cas9-based cell-specific in vivo genetic perturbations in mice, we identify a subset of astrocytes that expresses the lysosomal protein LAMP12 and the death receptor ligand TRAIL3. LAMP1+TRAIL+ astrocytes limit inflammation in the CNS by inducing T cell apoptosis through TRAIL-DR5 signalling. In homeostatic conditions, the expression of TRAIL in astrocytes is driven by interferon-γ (IFNγ) produced by meningeal natural killer (NK) cells, in which IFNγ expression is modulated by the gut microbiome. TRAIL expression in astrocytes is repressed by molecules produced by T cells and microglia in the context of inflammation. Altogether, we show that LAMP1+TRAIL+ astrocytes limit CNS inflammation by inducing T cell apoptosis, and that this astrocyte subset is maintained by meningeal IFNγ+ NK cells that are licensed by the microbiome.
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Affiliation(s)
- Liliana M Sanmarco
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cristina Gutiérrez-Vázquez
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Carolina Manganeli Polonio
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mathias Linnerbauer
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Federico Giovannoni
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Katelyn V Batterman
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA, USA
| | - Giulia Scalisi
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephanie E J Zandee
- Neuroimmunology Unit, Centre de Recherche du CHUM, Montréal, Quebec, Canada
- Department of Neuroscience, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Evelyn S Heck
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Moneera Alsuwailm
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Douglas L Rosene
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA, USA
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Isaac M Chiu
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Alexandre Prat
- Neuroimmunology Unit, Centre de Recherche du CHUM, Montréal, Quebec, Canada
- Department of Neuroscience, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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19
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Idris AB, Idris EB, Ataelmanan AE, Mohamed AEA, Osman Arbab BM, Ibrahim EAM, Hassan MA. First insights into the molecular basis association between promoter polymorphisms of the IL1B gene and Helicobacter pylori infection in the Sudanese population: computational approach. BMC Microbiol 2021; 21:16. [PMID: 33413117 PMCID: PMC7792167 DOI: 10.1186/s12866-020-02072-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Helicobacter pylori (H. pylori) infects nearly half of the world's population with a variation in incidence among different geographic regions. Genetic variants in the promoter regions of the IL1B gene can affect cytokine expression and creates a condition of hypoacidity which favors the survival and colonization of H. pylori. Therefore, the aim of this study was to characterize the polymorphic sites in the 5'- region [-687_ + 297] of IL1B in H. pylori infection using in silico tools. RESULTS A total of five nucleotide variations were detected in the 5'-regulatory region [-687_ + 297] of IL1B which led to the addition or alteration of transcription factor binding sites (TFBSs) or composite regulatory elements (CEs). Genotyping of IL1B - 31 C > T revealed a significant association between -31 T and susceptibility to H. pylori infection in the studied population (P = 0.0363). Comparative analysis showed conservation rates of IL1B upstream [-368_ + 10] region above 70% in chimpanzee, rhesus monkey, a domesticated dog, cow and rat. CONCLUSIONS In H. pylori-infected patients, three detected SNPs (- 338, - 155 and - 31) located in the IL1B promoter were predicted to alter TFBSs and CE, which might affect the gene expression. These in silico predictions provide insight for further experimental in vitro and in vivo studies of the regulation of IL1B expression and its relationship to H. pylori infection. However, the recognition of regulatory motifs by computer algorithms is fundamental for understanding gene expression patterns.
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Affiliation(s)
- Abeer Babiker Idris
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan.
| | - Einas Babiker Idris
- Medical Laboratory Specialist, Department of Medical Microbiology, Rashid Medical Complex, Riyadh, Saudi Arabia
| | - Amany Eltayib Ataelmanan
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Al-Gazirah, Wad Madani, Sudan
| | | | | | - El-Amin Mohamed Ibrahim
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Mohamed A Hassan
- Department of Bioinformatics, Africa city of technology, Khartoum, Sudan.,Department of Bioinformatics, DETAGEN Genetic Diagnostics Center, Kayseri, Turkey.,Department of Translation Bioinformatics, Detavax Biotech, Kayseri, Turkey
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20
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Taefehshokr N, Miao T, Symonds ALJ, Wang P, Li S. Egr2 regulation in T cells is mediated through IFNγ/STAT1 and IL-6/STAT3 signalling pathway. Pathol Res Pract 2020; 216:153259. [PMID: 33099163 DOI: 10.1016/j.prp.2020.153259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 11/18/2022]
Abstract
The immune system is a host defence system to protect the body against foreign invaders. T cells are one of the major components of the immune cells and they are essential for immune responses. Early growth response gene (Egr2) in T cells is important for maintaining immune functions of T cells by promoting adaptive immune responses while controlling inflammation and preventing the development of autoimmune diseases. A study by our group demonstrated the function of Egr2 as a checkpoint regulator controlling the proliferation and differentiation of the T cells. In association, Egr2 and 3 play indispensable role in T cell immune response, but the mechanism regulating Egr2 expression in T cells is still unclear. In this study, we analysed the Egr2 expression mechanism in CD4 T cells under antigen stimulation. We found that Egr2 expression is regulated by different cytokines including IL-2 and IL-4, which increased Egr2 induction in activated T cells. However, inflammatory cytokines, including INFγ and IL-6, suppressed Egr2 expression through STAT1 and STAT3 signalling pathway respectively, highlighting a mechanism for tolergenic immune response on T cells.
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Affiliation(s)
- Nima Taefehshokr
- Division of Biosciences, Department of Life Sciences, Brunel University London, Kingston Lane, UB8 3PH, UK.
| | - Tizong Miao
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, LONDON E1 2AD, UK
| | - Alistair L J Symonds
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, LONDON E1 2AD, UK
| | - Ping Wang
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, LONDON E1 2AD, UK
| | - Suling Li
- Division of Biosciences, Department of Life Sciences, Brunel University London, Kingston Lane, UB8 3PH, UK
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21
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Wheeler MA, Clark IC, Tjon EC, Li Z, Zandee SEJ, Couturier CP, Watson BR, Scalisi G, Alkwai S, Rothhammer V, Rotem A, Heyman JA, Thaploo S, Sanmarco LM, Ragoussis J, Weitz DA, Petrecca K, Moffitt JR, Becher B, Antel JP, Prat A, Quintana FJ. MAFG-driven astrocytes promote CNS inflammation. Nature 2020; 578:593-599. [PMID: 32051591 PMCID: PMC8049843 DOI: 10.1038/s41586-020-1999-0] [Citation(s) in RCA: 256] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 12/16/2019] [Indexed: 01/14/2023]
Abstract
Multiple sclerosis is a chronic inflammatory disease of the CNS1. Astrocytes contribute to the pathogenesis of multiple sclerosis2, but little is known about the heterogeneity of astrocytes and its regulation. Here we report the analysis of astrocytes in multiple sclerosis and its preclinical model experimental autoimmune encephalomyelitis (EAE) by single-cell RNA sequencing in combination with cell-specific Ribotag RNA profiling, assay for transposase-accessible chromatin with sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing (ChIP-seq), genome-wide analysis of DNA methylation and in vivo CRISPR-Cas9-based genetic perturbations. We identified astrocytes in EAE and multiple sclerosis that were characterized by decreased expression of NRF2 and increased expression of MAFG, which cooperates with MAT2α to promote DNA methylation and represses antioxidant and anti-inflammatory transcriptional programs. Granulocyte-macrophage colony-stimulating factor (GM-CSF) signalling in astrocytes drives the expression of MAFG and MAT2α and pro-inflammatory transcriptional modules, contributing to CNS pathology in EAE and, potentially, multiple sclerosis. Our results identify candidate therapeutic targets in multiple sclerosis.
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Affiliation(s)
- Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Centre of Excellence for Biomedicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Iain C Clark
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily C Tjon
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephanie E J Zandee
- Neuroimmunology Unit, Centre de recherche du CHUM (CRCHUM), Montreal, Quebec, Canada
- Department of Neuroscience, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Charles P Couturier
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Brianna R Watson
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Giulia Scalisi
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sarah Alkwai
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Centre of Excellence for Biomedicine, Brigham and Women's Hospital, Boston, MA, USA
- Centre of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Veit Rothhammer
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Assaf Rotem
- Department of Physics, Harvard University, Cambridge, MA, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - John A Heyman
- Department of Physics, Harvard University, Cambridge, MA, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Shravan Thaploo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Liliana M Sanmarco
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jiannis Ragoussis
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - David A Weitz
- Department of Physics, Harvard University, Cambridge, MA, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Kevin Petrecca
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Jeffrey R Moffitt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Jack P Antel
- Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Alexandre Prat
- Neuroimmunology Unit, Centre de recherche du CHUM (CRCHUM), Montreal, Quebec, Canada
- Department of Neuroscience, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Centre of Excellence for Biomedicine, Brigham and Women's Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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22
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Grade CVC, Mantovani CS, Alvares LE. Myostatin gene promoter: structure, conservation and importance as a target for muscle modulation. J Anim Sci Biotechnol 2019; 10:32. [PMID: 31044074 PMCID: PMC6477727 DOI: 10.1186/s40104-019-0338-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/19/2019] [Indexed: 12/12/2022] Open
Abstract
Myostatin (MSTN) is one of the key factors regulating myogenesis. Because of its role as a negative regulator of muscle mass deposition, much interest has been given to its protein and, in recent years, several studies have analysed MSTN gene regulation. This review discusses the MSTN gene promoter, focusing on its structure in several animal species, both vertebrate and invertebrate. We report the important binding sites considering their degree of phylogenetic conservation and roles they play in the promoter activity. Finally, we discuss recent studies focusing on MSTN gene regulation via promoter manipulation and the potential applications they have both in medicine and agriculture.
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Affiliation(s)
- Carla Vermeulen Carvalho Grade
- 1Universidade Federal da Integração Latino-Americana, UNILA, Instituto Latino-Americano de Ciências da Vida e da Natureza, Avenida Tarquínio Joslin dos Santos, 1000, Foz do Iguaçu, PR CEP 85870-901 Brazil
| | - Carolina Stefano Mantovani
- 2Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas - UNICAMP, Rua Monteiro Lobato, 255, Campinas, SP CEP 13083-862 Brazil
| | - Lúcia Elvira Alvares
- 2Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas - UNICAMP, Rua Monteiro Lobato, 255, Campinas, SP CEP 13083-862 Brazil
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23
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Wheeler MA, Jaronen M, Covacu R, Zandee SEJ, Scalisi G, Rothhammer V, Tjon EC, Chao CC, Kenison JE, Blain M, Rao VTS, Hewson P, Barroso A, Gutiérrez-Vázquez C, Prat A, Antel JP, Hauser R, Quintana FJ. Environmental Control of Astrocyte Pathogenic Activities in CNS Inflammation. Cell 2019; 176:581-596.e18. [PMID: 30661753 PMCID: PMC6440749 DOI: 10.1016/j.cell.2018.12.012] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/01/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022]
Abstract
Genome-wide studies have identified genetic variants linked to neurologic diseases. Environmental factors also play important roles, but no methods are available for their comprehensive investigation. We developed an approach that combines genomic data, screens in a novel zebrafish model, computational modeling, perturbation studies, and multiple sclerosis (MS) patient samples to evaluate the effects of environmental exposure on CNS inflammation. We found that the herbicide linuron amplifies astrocyte pro-inflammatory activities by activating signaling via sigma receptor 1, inositol-requiring enzyme-1α (IRE1α), and X-box binding protein 1 (XBP1). Indeed, astrocyte-specific shRNA- and CRISPR/Cas9-driven gene inactivation combined with RNA-seq, ATAC-seq, ChIP-seq, and study of patient samples suggest that IRE1α-XBP1 signaling promotes CNS inflammation in experimental autoimmune encephalomyelitis (EAE) and, potentially, MS. In summary, these studies define environmental mechanisms that control astrocyte pathogenic activities and establish a multidisciplinary approach for the systematic investigation of the effects of environmental exposure in neurologic disorders.
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Affiliation(s)
- Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Merja Jaronen
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ruxandra Covacu
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stephanie E J Zandee
- Neuroimmunology Research Lab, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Giulia Scalisi
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Veit Rothhammer
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Emily C Tjon
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chun-Cheih Chao
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jessica E Kenison
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Manon Blain
- Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Vijayaraghava T S Rao
- Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Patrick Hewson
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andreia Barroso
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Cristina Gutiérrez-Vázquez
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alexandre Prat
- Neuroimmunology Research Lab, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Jack P Antel
- Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Russ Hauser
- Department of Epidemiology and Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Vincent Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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24
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Finch KN, Jones FA, Cronn RC. Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives. BMC Genomics 2019; 20:58. [PMID: 30658593 PMCID: PMC6339301 DOI: 10.1186/s12864-018-5382-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 12/16/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tree species in the genus Cedrela P. Browne are threatened by timber overexploitation across the Neotropics. Genetic identification of processed timber can be used to supplement wood anatomy to assist in the taxonomic and source validation of protected species and populations of Cedrela. However, few genetic resources exist that enable both species and source identification of Cedrela timber products. We developed several 'omic resources including a leaf transcriptome, organelle genome (cpDNA), and diagnostic single nucleotide polymorphisms (SNPs) that may assist the classification of Cedrela specimens to species and geographic origin and enable future research on this widespread Neotropical tree genus. RESULTS We designed hybridization capture probes to enrich for thousands of genes from both freshly preserved leaf tissue and from herbarium specimens across eight Meliaceae species. We first assembled a draft de novo transcriptome for C. odorata, and then identified putatively low-copy genes. Hybridization probes for 10,001 transcript models successfully enriched 9795 (98%) of these targets, and analysis of target capture efficiency showed that probes worked effectively for five Cedrela species, with each species showing similar mean on-target sequence yield and depth. The probes showed greater enrichment efficiency for Cedrela species relative to the other three distantly related Meliaceae species. We provide a set of candidate SNPs for species identification of four of the Cedrela species included in this analysis, and present draft chloroplast genomes for multiple individuals of eight species from four genera in the Meliaceae. CONCLUSIONS Deforestation and illegal logging threaten forest biodiversity globally, and wood screening tools offer enforcement agencies new approaches to identify illegally harvested timber. The genomic resources described here provide the foundation required to develop genetic screening methods for Cedrela species identification and source validation. Due to their transferability across the genus and family as well as demonstrated applicability for both fresh leaves and herbarium specimens, the genomic resources described here provide additional tools for studies examining the ecology and evolutionary history of Cedrela and related species in the Meliaceae.
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Affiliation(s)
- Kristen N. Finch
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
| | - F. Andrew Jones
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Richard C. Cronn
- USDA Forest Service Pacific Northwest Research Station, Corvallis, Oregon 97331 USA
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25
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Muzammil S, Shrestha A, Dadshani S, Pillen K, Siddique S, Léon J, Naz AA. An Ancestral Allele of Pyrroline-5-carboxylate synthase1 Promotes Proline Accumulation and Drought Adaptation in Cultivated Barley. PLANT PHYSIOLOGY 2018; 178:771-782. [PMID: 30131422 PMCID: PMC6181029 DOI: 10.1104/pp.18.00169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/08/2018] [Indexed: 05/20/2023]
Abstract
Water scarcity is a critical threat to global crop production. Here, we used the natural diversity of barley (Hordeum vulgare) to dissect the genetic control of proline (Pro) mediated drought stress adaptation. Genetic mapping and positional cloning of a major drought-inducible quantitative trait locus (QPro.S42-1H) revealed unique allelic variation in pyrroline-5-carboxylate synthase (P5cs1) between the cultivated cultivar Scarlett (ssp. vulgare) and the wild barley accession ISR42-8 (ssp. spontaneum). The putative causative mutations were located in the promoter of P5cs1 across the DNA binding motifs for abscisic acid-responsive element binding transcription factors. Introgression line (IL) S42IL-143 carrying the wild allele of P5cs1 showed significant up-regulation of P5cs1 expression compared to Scarlett, which was consistent with variation in Pro accumulation under drought. Next, we transiently expressed promoter::reporter constructs of ISR42-8 and Scarlett alleles in Arabidopsis (Arabidopsis thaliana) mesophyll protoplasts. GUS expression analysis showed a significantly higher activation of the ISR42-8 promoter compared to Scarlett upon abscisic acid treatment. Notably, the ISR42-8 promoter activity was impaired in protoplasts isolated from the loss-of-function abf1abf2abf3abf4 quadruple mutant. A series of phenotypic evaluations demonstrated that S42IL-143 maintained leaf water content and photosynthetic activity longer than Scarlett under drought. These findings suggest that the ancestral variant of P5cs1 has the potential for drought tolerance and understanding drought physiology of barley and related crops.
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Affiliation(s)
- Shumaila Muzammil
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany
| | - Asis Shrestha
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany
| | - Said Dadshani
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany
| | - Klaus Pillen
- Department of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Shahid Siddique
- Molecular Phytomedicine, Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany
| | - Jens Léon
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany
| | - Ali Ahmad Naz
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany
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26
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Curtale G, Renzi TA, Mirolo M, Drufuca L, Albanese M, De Luca M, Rossato M, Bazzoni F, Locati M. Multi-Step Regulation of the TLR4 Pathway by the miR-125a~99b~let-7e Cluster. Front Immunol 2018; 9:2037. [PMID: 30245693 PMCID: PMC6137199 DOI: 10.3389/fimmu.2018.02037] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 08/17/2018] [Indexed: 11/13/2022] Open
Abstract
An appropriate immune response requires a tight balance between pro- and anti-inflammatory mechanisms. IL-10 is induced at late time-points during acute inflammatory conditions triggered by TLR-dependent recognition of infectious agents and is involved in setting this balance, operating as a negative regulator of the TLR-dependent signaling pathway. We identified miR-125a~99b~let-7e as an evolutionary conserved microRNA cluster late-induced in human monocytes exposed to the TLR4 agonist LPS as an effect of this IL-10-dependent regulatory loop. We demonstrated that microRNAs generated by this cluster perform a pervasive regulation of the TLR signaling pathway by direct targeting receptors (TLR4, CD14), signaling molecules (IRAK1), and effector cytokines (TNFα, IL-6, CCL3, CCL7, CXCL8). Modulation of miR-125a~99b~let-7e cluster influenced the production of proinflammatory cytokines in response to LPS and the IL-10-mediated tolerance to LPS, thus identifying this gene as a previously unrecognized major regulatory element of the inflammatory response and endotoxin tolerance.
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Affiliation(s)
- Graziella Curtale
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Tiziana A Renzi
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Massimiliano Mirolo
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Lorenzo Drufuca
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Manuel Albanese
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Mariacristina De Luca
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Marzia Rossato
- Department of Medicine, Division of General Pathology, University of Verona, Verona, Italy
| | - Flavia Bazzoni
- Department of Medicine, Division of General Pathology, University of Verona, Verona, Italy
| | - Massimo Locati
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
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27
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Lee NK, Azizan FL, Wong YS, Omar N. DeepFinder: An integration of feature-based and deep learning approach for DNA motif discovery. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1438209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Nung Kion Lee
- Department of Cognitive Sciences, Faculty of Cognitive Sciences and Human Development, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Farah Liyana Azizan
- Centre For Pre-University Studies, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Yu Shiong Wong
- Department of Cognitive Sciences, Faculty of Cognitive Sciences and Human Development, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Norshafarina Omar
- Department of Cognitive Sciences, Faculty of Cognitive Sciences and Human Development, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
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28
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Alessio VM, Cavaçana N, Dantas LLDB, Lee N, Hotta CT, Imaizumi T, Menossi M. The FBH family of bHLH transcription factors controls ACC synthase expression in sugarcane. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2511-2525. [PMID: 29514290 PMCID: PMC5920332 DOI: 10.1093/jxb/ery083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 02/27/2018] [Indexed: 05/21/2023]
Abstract
Ethylene is a phytohormone involved in the regulation of several aspects of plant development and in responses to biotic and abiotic stress. The effects of exogenous application of ethylene to sugarcane plants are well characterized as growth inhibition of immature internodes and stimulation of sucrose accumulation. However, the molecular network underlying the control of ethylene biosynthesis in sugarcane remains largely unknown. The chemical reaction catalyzed by 1-aminocyclopropane-1-carboxylic acid synthase (ACS) is an important rate-limiting step that regulates ethylene production in plants. In this work, using a yeast one-hybrid approach, we identified three basic helix-loop-helix (bHLH) transcription factors, homologs of Arabidopsis FBH (FLOWERING BHLH), that bind to the promoter of ScACS2 (Sugarcane ACS2), a sugarcane type 3 ACS isozyme gene. Protein-protein interaction assays showed that sugarcane FBH1 (ScFBH1), ScFBH2, and ScFBH3 form homo- and heterodimers in the nucleus. Gene expression analysis revealed that ScFBHs and ScACS2 transcripts are more abundant in maturing internodes during afternoon and night. In addition, Arabidopsis functional analysis demonstrated that FBH controls ethylene production by regulating transcript levels of ACS7, a homolog of ScACS2. These results indicate that ScFBHs transcriptionally regulate ethylene biosynthesis in maturing internodes of sugarcane.
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Affiliation(s)
- Valter Miotto Alessio
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, CP, Campinas, SP, Brazil
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Natale Cavaçana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Nayoung Lee
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Carlos Takeshi Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Marcelo Menossi
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, CP, Campinas, SP, Brazil
- Correspondence:
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29
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O'Sullivan L, Lucid A, Neve H, Franz CMAP, Bolton D, McAuliffe O, Paul Ross R, Coffey A. Comparative genomics of Cp8viruses with special reference to Campylobacter phage vB_CjeM_los1, isolated from a slaughterhouse in Ireland. Arch Virol 2018; 163:2139-2154. [PMID: 29687158 DOI: 10.1007/s00705-018-3845-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 03/10/2018] [Indexed: 01/08/2023]
Abstract
Campylobacter phage vB_CjeM_Los1 was recently isolated from a slaughterhouse in the Republic of Ireland using the host Campylobacter jejuni subsp. jejuni PT14, and full-genome sequencing and annotation were performed. The genome was found to be 134,073 bp in length and to contain 169 predicted open reading frames. Transmission electron microscopy images of vB_CjeM_Los1 revealed that it belongs to the family Myoviridae, with tail fibres observed in both extended and folded conformations, as seen in T4. The genome size and morphology of vB_CjeM_Los1 suggest that it belongs to the genus Cp8virus, and seven other Campylobacter phages with similar size characteristics have also been fully sequenced. In this work, comparative studies were performed in relation to genomic rearrangements and conservation within each of the eight genomes. None of the eight genomes were found to have undergone internal rearrangements, and their sequences retained more than 98% identity with one another despite the widespread geographical distribution of each phage. Whole-genome phylogenetics were also performed, and clades were shown to be representative of the differing number of tRNAs present in each phage. This may be an indication of lineages within the genus, despite their striking homology.
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Affiliation(s)
- Lisa O'Sullivan
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
- Teagasc, Food Research Centre, Ashtown, Co. Dublin, Ireland
| | - Alan Lucid
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Declan Bolton
- Teagasc, Food Research Centre, Ashtown, Co. Dublin, Ireland
| | - Olivia McAuliffe
- Teagasc, Moorepark Food Research Centre, Fermoy, Co. Cork, Ireland
| | - R Paul Ross
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland.
- APC Microbiome Institute, University College Cork, Cork, Ireland.
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30
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Bakshi A, Bretz CL, Cain TL, Kim J. Intergenic and intronic DNA hypomethylated regions as putative regulators of imprinted domains. Epigenomics 2018; 10:445-461. [PMID: 29569934 DOI: 10.2217/epi-2017-0125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AIM To investigate the regulatory potential of intergenic/intronic hypomethylated regions (iHMRs) within imprinted domains. MATERIALS & METHODS Based on the preliminary results of the histone modification and conservation profiles, we conducted reporter assays on the Peg3 and H19 domain iHMRs. The in vitro results were confirmed by the in vivo deletion of Peg3-iHMR designed to test its function in the Peg3 imprinted domain. RESULTS & CONCLUSION Initial bioinformatic analyses suggested that some iHMRs may be noncanonical enhancers for imprinted genes. Consistent with this, Peg3- and H19-iHMRs showed context-dependent promoter and enhancer activity. Further, deletion of Peg3-iHMR resulted in allele- and sex-specific misregulation of several imprinted genes within the domain. Taken together, these results suggest that some iHMRs may function as domain-wide regulators for the associated imprinted domains.
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Affiliation(s)
- Arundhati Bakshi
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Corey L Bretz
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Terri L Cain
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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31
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Adurthi S, Kumar MM, Vinodkumar HS, Mukherjee G, Krishnamurthy H, Acharya KK, Bafna UD, Uma DK, Abhishekh B, Krishna S, Parchure A, Alka M, Jayshree RS. Oestrogen Receptor-α binds the FOXP3 promoter and modulates regulatory T-cell function in human cervical cancer. Sci Rep 2017; 7:17289. [PMID: 29229929 PMCID: PMC5725534 DOI: 10.1038/s41598-017-17102-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 11/14/2017] [Indexed: 01/07/2023] Open
Abstract
Oestrogen controls Foxp3 expression in regulatory T cells (Treg cells) via a mechanism thought to involve oestrogen receptor alpha (ERα), but the molecular basis and functional impact of ERα signalling in Treg cells remain unclear. We report that ERα ligand oestradiol (E2) is significantly increased in human cervical cancer (CxCa) tissues and tumour-infiltrating Treg cells (CD4+CD25hiCD127low), whereas blocking ERα with the antagonist ICI 182,780 abolishes FOXP3 expression and impairs the function of CxCa infiltrating Treg cells. Using a novel approach of co-immunoprecipitation with antibodies to E2 for capture, we identified binding of E2:ERα complexes to FOXP3 protein in CxCa-derived Treg cells. Chromatin immunoprecipitation analyses of male blood Treg cells revealed ERα occupancy at the FOXP3 promoter and conserved non-coding DNA elements 2 and 3. Accordingly, computational analyses of the enriched regions uncovered eight putative oestrogen response elements predicted to form a loop that can activate the FOXP3 promoter. Together, these data suggest that E2-mediated ERα signalling is critical for the sustenance of FOXP3 expression and Treg cell function in human CxCa via direct interaction of ERα with FOXP3 promoter. Overall, our work gives a molecular insight into ERα signalling and highlights a fundamental role of E2 in controlling human Treg cell physiology.
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Affiliation(s)
- Sreenivas Adurthi
- Department of Microbiology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Mahesh M Kumar
- Department of Microbiology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - H S Vinodkumar
- Shodhaka Life Sciences Private Limited, Bangalore, India
- Structural Biology Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Geetashree Mukherjee
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, India
- Department of Histopathology, Tata Medical Center, Kolkata, India
| | - H Krishnamurthy
- National Center for Biological Sciences, TIFR, Bangalore, India
| | - K Kshitish Acharya
- Shodhaka Life Sciences Private Limited, Bangalore, India
- Institute of Bioinformatics And Applied Biotechnology, Bangalore, India
| | - U D Bafna
- Department of Gynecology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Devi K Uma
- Department of Gynecology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - B Abhishekh
- Department of Immunohematology, Kidwai Memorial Institute of Oncology, Bangalore, India
- Department of Transfusion Medicine, JIPMER, Puducherry, India
| | - Sudhir Krishna
- National Center for Biological Sciences, TIFR, Bangalore, India
| | - A Parchure
- Department of Microbiology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Murali Alka
- Department of Microbiology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - R S Jayshree
- Department of Microbiology, Kidwai Memorial Institute of Oncology, Bangalore, India.
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32
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Zhuang H, Meng X, Li Y, Wang X, Huang S, Liu K, Hehir M, Fang R, Jiang L, Zhou JX, Wang P, Ren Y. Cyclic AMP responsive element-binding protein promotes renal cell carcinoma proliferation probably via the expression of spindle and kinetochore-associated protein 2. Oncotarget 2017; 7:16325-37. [PMID: 26824422 PMCID: PMC4941317 DOI: 10.18632/oncotarget.7017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 01/01/2016] [Indexed: 12/24/2022] Open
Abstract
Emerging evidence shows that the aberrantly expressed cyclic AMP responsive element-binding protein (CREB) is associated with tumor development and progression in several cancers. Spindle and kinetochore-associated protein 2 (SKA2) is essential for regulating the progress of mitosis. In this study, we evaluate in vitro and in vivo the functional relationship between CREB and SKA2 in renal cell carcinoma (RCC). Suppressing and replenishing CREB levels were used to manipulate SKA2 expression, observing the effects on RCC cell lines. Computational prediction and ChIP assay identified that CREB targeted ska2 by binding its CRE sequence in the human genome. Overexpression of CREB reversed the inhibited cell growth following siSKA2 treatment, and reduced the number of cells holding in mitosis. Decreased expression of CREB suppressed RCC cell growth and xenograft tumor formation, accompanied by reduced expression of SKA2. In RCC tumor samples from patients, mRNA for SKA2 were plotted near those of CREB in each sample, with significantly increased immunohistochemical staining of higher SKA2 and CREB in the higher TNM stages. The study adds evidence that CREB, a tumor oncogene, promotes RCC proliferation. It probably achieves this by increasing SKA2 expression.
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Affiliation(s)
- Haihui Zhuang
- Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China.,Laboratory of Kidney Carcinoma, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo 315000, China
| | - Xiangyu Meng
- Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China.,Laboratory of Kidney Carcinoma, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo 315000, China
| | - Yanyuan Li
- Department of Pathology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310031, China
| | - Xue Wang
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Ningbo 315000, China.,Laboratory of Kidney Carcinoma, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo 315000, China
| | - Shuaishuai Huang
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Ningbo 315000, China.,Laboratory of Kidney Carcinoma, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo 315000, China
| | - Kaitai Liu
- Ningbo Medical Center, LiHuiLi Hospital, Medical School, Ningbo University, Ningbo 315041, China
| | - Michael Hehir
- Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China.,Laboratory of Kidney Carcinoma, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo 315000, China
| | - Rong Fang
- Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Lei Jiang
- Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Jeff X Zhou
- Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Ping Wang
- Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China.,Laboratory of Kidney Carcinoma, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo 315000, China
| | - Yu Ren
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Ningbo 315000, China.,Laboratory of Kidney Carcinoma, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo 315000, China
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33
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Jiang L, Han Z, Chen Y, Zhao W, Sun J, Zhao Y, Liu S. Characterization of the complete genome, antigenicity, pathogenicity, tissue tropism, and shedding of a recombinant avian infectious bronchitis virus with a ck/CH/LJL/140901-like backbone and an S2 fragment from a 4/91-like virus. Virus Res 2017; 244:99-109. [PMID: 29141204 PMCID: PMC7114561 DOI: 10.1016/j.virusres.2017.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/24/2017] [Accepted: 11/07/2017] [Indexed: 01/09/2023]
Abstract
In this study, we isolated an infectious bronchitis virus, designated I1101/16, from broiler breeders in China. Analysis of the S1 gene showed that isolate I1101/16 was genetically close to strain ck/CH/LJL/140901, which belongs to the TW I genotype (also known as lineage GI-7 based on the recent IBV classification), however the S2 gene showed genetic diversity comparing to that of S1 gene. Comparison of the genomic sequences showed that the genome of isolate I1101/16 was similar to that of strain ck/CH/LJL/140901 from the 5' end of the genome to the 5' end of the S2 gene and from the 5' end of the 3a gene to the end of the genome, whereas the remaining parts of the genome sequences were more closely related to those of strain 4/91 than those of ck/CH/LJL/140901, thereby suggesting that recombination might have occurred during the origin of the virus. SimPlot and Bootscan analysis of the complete genomic sequence confirmed this hypothesis, where it showed that isolate I1101/16 arose through recombination events between ck/CH/LJL/140901- and 4/91-like viruses. Isolate I1101/16 and strain ck/CH/LJL/140901 shared identical amino acids in almost all five of their B cell epitopes, but the two viruses had a serotype relatedness value of 65, which is well below 80, i.e., the lower cutoff value for viruses of the same serotype. In addition, pathogenicity tests demonstrated that isolate I1101/16 was more pathogenic to 1-day-old specific-pathogen-free chickens than strain ck/CH/LJL/140901, according to analysis of the clinical signs, whereas strain ck/CH/LJL/140901 exhibited prolonged replication and shedding after challenge compared with isolate I1101/16. This study did not provide evidence that recombination can directly alter the antigenicity, virulence, replication, shedding, and tissue tropism of a virus, but it did show that recombination events are likely to be major determinants of viral evolution.
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Affiliation(s)
- Lei Jiang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Zongxi Han
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Yuqiu Chen
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Wenjun Zhao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Junfeng Sun
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Yan Zhao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Shengwang Liu
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China.
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34
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Complete chloroplast genome of Anemoclema glaucifolium (Ranunculaceae), a vulnerable and threatened species endemic to the Hengduan Mountains. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0874-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Hooker LN, Smoczer C, Abbott S, Fakhereddin M, Hudson JW, Crawford MJ. Xenopus pitx3 target genes lhx1 and xnr5 are identified using a novel three-fluor flow cytometry-based analysis of promoter activation and repression. Dev Dyn 2017; 246:657-669. [PMID: 28598520 DOI: 10.1002/dvdy.24532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/28/2017] [Accepted: 05/25/2017] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Pitx3 plays a well understood role in directing development of lens, muscle fiber, and dopaminergic neurons; however, in Xenopus laevis, it may also play a role in early gastrulation and somitogenesis. Potential downstream targets of pitx3 possess multiple binding motifs that would not be readily accessible by conventional promoter analysis. RESULTS We isolated and characterized pitx3 target genes lhx1 and xnr5 using a novel three-fluor flow cytometry tool that was designed to dissect promoters with multiple binding sites for the same transcription factor. This approach was calibrated using a known pitx3 target gene, Tyrosine hydroxylase. CONCLUSIONS We demonstrate how flow cytometry can be used to detect gene regulatory changes with exquisite precision on a cell-by-cell basis, and establish that in HEK293 cells, pitx3 directly activates lhx1 and represses xnr5. Developmental Dynamics 246:657-669, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Cristine Smoczer
- Biochemistry and Genetics, University of Detroit Mercy School of Dentistry, Detroit, Michigan
| | - Samuel Abbott
- Biological Sciences, University of Windsor, Windsor, Ontario, Canada
| | | | - John W Hudson
- Biological Sciences, University of Windsor, Windsor, Ontario, Canada
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36
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Miao T, Symonds ALJ, Singh R, Symonds JD, Ogbe A, Omodho B, Zhu B, Li S, Wang P. Egr2 and 3 control adaptive immune responses by temporally uncoupling expansion from T cell differentiation. J Exp Med 2017; 214:1787-1808. [PMID: 28487311 PMCID: PMC5460991 DOI: 10.1084/jem.20160553] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 11/23/2016] [Accepted: 03/24/2017] [Indexed: 12/30/2022] Open
Abstract
Miao et al. report a checkpoint mediated by Egr2 and 3 that controls the transition between T cell clonal expansion and differentiation by regulating genes involved in proliferation and differentiation, which is essential for optimal immune responses with limited immunopathology. Egr2 and 3 are important for maintaining immune homeostasis. Here we define a fundamental function of Egr2 and 3 operating as a checkpoint that controls the transition between clonal expansion and differentiation of effector T cells. Egr2 and 3 deficiency resulted in defective clonal expansion but hyperactivation and excessive differentiation of T cells in response to viral infection. Conversely, sustained Egr2 expression enhanced expansion but severely impaired effector differentiation. Egr2 bound to and controlled the expression of genes regulating proliferation (Myc and Myb) and differentiation repressors (Bcl6, Id3), while repressing transcription factors required for effector function (Zeb2, RORa, RORc, and Bhlhe40). Egr2 and 3 expression in T cells was regulated reciprocally by antigen and IFNγ, providing a mechanism for adjusting proliferation and differentiation of individual T cells. Thus, Egr2 and 3 are upstream regulators of effector CD4 and CD8 T cells that are essential for optimal responses with limited immunopathology.
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Affiliation(s)
- Tizong Miao
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, England, UK
| | - Alistair L J Symonds
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, England, UK
| | - Randeep Singh
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, England, UK.,Bioscience, Brunel University, Uxbridge UB8 3PH, England, UK
| | - Janine D Symonds
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London WC1E 6BT, England, UK
| | - Ane Ogbe
- Bioscience, Brunel University, Uxbridge UB8 3PH, England, UK
| | - Becky Omodho
- Bioscience, Brunel University, Uxbridge UB8 3PH, England, UK
| | - Bo Zhu
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, England, UK.,Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, People's Republic of China
| | - Suling Li
- Bioscience, Brunel University, Uxbridge UB8 3PH, England, UK
| | - Ping Wang
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, England, UK
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Feng CZ, Yin JB, Yang JJ, Cao L. Regulatory factor X1 depresses ApoE-dependent Aβ uptake by miRNA-124 in microglial response to oxidative stress. Neuroscience 2017; 344:217-228. [DOI: 10.1016/j.neuroscience.2016.12.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 12/04/2016] [Accepted: 12/09/2016] [Indexed: 01/12/2023]
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Quinteros JA, Lee SW, Markham PF, Noormohammadi AH, Hartley CA, Legione AR, Coppo MJC, Vaz PK, Browning GF. Full genome analysis of Australian infectious bronchitis viruses suggests frequent recombination events between vaccine strains and multiple phylogenetically distant avian coronaviruses of unknown origin. Vet Microbiol 2016; 197:27-38. [PMID: 27938680 PMCID: PMC7117259 DOI: 10.1016/j.vetmic.2016.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/03/2016] [Accepted: 11/04/2016] [Indexed: 01/30/2023]
Abstract
Australian strains of infectious bronchitis virus (IBV) have been evolving independently for many years, with control achieved by vaccination with local attenuated strains. Previous studies have documented the emergence of recombinants over the last 20 years, with the most recent one, Ck/Aus/N1/08, detected in 2008. These recombinants did not appear to be controlled by the vaccines currently in use. In this study we sequenced the complete genomes of three emergent Australian strains of IBV (IBV/Ck/Aus/N1/88, IBV/Ck/Aus/N1/03 and IBV/Ck/Aus/N1/08) and a previously incompletely characterised vaccine strain, IBV/Ck/Aus/Armidale, and compared them to the genome of the vaccine strain VicS. We detected multiple recombination events throughout the genome between wild type viruses and the vaccine strains in all three emergent isolates. Moreover, we found that strain N1/88 was not entirely exogenous, as was previously hypothesised. Rather, it originated from a recombination event involving the VicS vaccine strain. The S glycoprotein genes of N1/88 and N1/03 were known to be genetically distinct from previously characterised circulating strains and from each other, and the original donors of these genes remains unknown. The S1 glycoprotein gene of N1/88, a subgroup 2 strain, shares a high nucleotide identity with the sequence of the S1 gene of the recent isolate N1/08. As the subgroup 2 strains have not been isolated for at least 20 years, it appears likely that an unknown avian coronavirus that was the donor of the S1 glycoprotein sequence of N1/88 in the 1980s is still recombining with IBV strains in the field.
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Affiliation(s)
- José A Quinteros
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia.
| | - Sang-Won Lee
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia; College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 143-701, Republic of Korea, Republic of Korea
| | - Philip F Markham
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Amir H Noormohammadi
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, 3030, Victoria, Australia
| | - Carol A Hartley
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Alistair R Legione
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Mauricio J C Coppo
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Paola K Vaz
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia
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Carmona-Antoñanzas G, Zheng X, Tocher DR, Leaver MJ. Regulatory divergence of homeologous Atlantic salmon elovl5 genes following the salmonid-specific whole-genome duplication. Gene 2016; 591:34-42. [DOI: 10.1016/j.gene.2016.06.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 06/28/2016] [Indexed: 12/30/2022]
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Fair JV, Voronova A, Bosiljcic N, Rajgara R, Blais A, Skerjanc IS. BRG1 interacts with GLI2 and binds Mef2c gene in a hedgehog signalling dependent manner during in vitro cardiomyogenesis. BMC DEVELOPMENTAL BIOLOGY 2016; 16:27. [PMID: 27484899 PMCID: PMC4970297 DOI: 10.1186/s12861-016-0127-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/28/2016] [Indexed: 12/22/2022]
Abstract
Background The Hedgehog (HH) signalling pathway regulates cardiomyogenesis in vivo and in differentiating P19 embryonal carcinoma (EC) cells, a mouse embryonic stem (mES) cell model. To further assess the transcriptional role of HH signalling during cardiomyogenesis in stem cells, we studied the effects of overexpressing GLI2, a primary transducer of the HH signalling pathway, in mES cells. Results Stable GLI2 overexpression resulted in an enhancement of cardiac progenitor-enriched genes, Mef2c, Nkx2-5, and Tbx5 during mES cell differentiation. In contrast, pharmacological blockade of the HH pathway in mES cells resulted in lower expression of these genes. Mass spectrometric analysis identified the chromatin remodelling factor BRG1 as a protein which co-immunoprecipitates with GLI2 in differentiating mES cells. We then determined that BRG1 is recruited to a GLI2-specific Mef2c gene element in a HH signalling-dependent manner during cardiomyogenesis in P19 EC cells, a mES cell model. Conclusions Thus, we propose a mechanism where HH/GLI2 regulates the expression of Mef2c by recruiting BRG1 to the Mef2c gene, most probably via chromatin remodelling, to ultimately regulate in vitro cardiomyogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12861-016-0127-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joel Vincent Fair
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Rd, K1H 8M5, Ottawa, Canada
| | - Anastassia Voronova
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Rd, K1H 8M5, Ottawa, Canada
| | - Neven Bosiljcic
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Rd, K1H 8M5, Ottawa, Canada
| | - Rashida Rajgara
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Rd, K1H 8M5, Ottawa, Canada
| | - Alexandre Blais
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Rd, K1H 8M5, Ottawa, Canada. .,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Rd, K1H 8M5, Ottawa, Canada.
| | - Ilona Sylvia Skerjanc
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Rd, K1H 8M5, Ottawa, Canada.
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Wang B, Qi T, Chen SQ, Ye L, Huang ZS, Li H. RFX1 maintains testis cord integrity by regulating the expression of Itga6 in male mouse embryos. Mol Reprod Dev 2016; 83:606-14. [PMID: 27228460 DOI: 10.1002/mrd.22660] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/21/2016] [Indexed: 01/13/2023]
Abstract
Formation and maintenance of testis cords during embryogenesis are essential for establishing testicular structure and function in adults. At least five genes (Wt1, Dhh, Sox8/Sox9, and Dax1) appear to be required for the maintenance of testis cord integrity in mice. Here, we report that RFX1 is specifically expressed in fetal Sertoli cells. Mouse embryos conditionally deficient in Rfx1 (Rfx1(flox/flox) , Amh-Cre) possessed disrupted testis cords, as the basal lamina lining was fragmented or completely absent in some areas of the testes. Spermatogenesis was blocked, leading to complete infertility. Expression of integrin alpha-6 was significantly decreased in Rfx1-deficient testes compared to control testes; indeed, luciferase and chromatin immunoprecipitation assays indicated that RFX1 directly activates transcription of Itga6 (the gene coding for integrin alpha-6). Taken together, RFX1 transcriptionally targets Itga6 in Sertoli cells, thereby, helping maintain the integrity of the basal lamina during testis cord development. Mol. Reprod. Dev. 83: 606-614, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Bo Wang
- Department of Infertility and Sexual Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guang Zhou, China
| | - Tao Qi
- Department of Infertility and Sexual Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guang Zhou, China
| | - Shi-Qin Chen
- Assisted Reproductive Center, General Hospital of Guangzhou Military Command, Guangzhou, China
| | - Lei Ye
- Department of Infertility and Sexual Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guang Zhou, China
| | - Zhan-Sen Huang
- Department of Infertility and Sexual Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guang Zhou, China
| | - Hao Li
- Department of Infertility and Sexual Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guang Zhou, China
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MohanKumar K, Namachivayam K, Chapalamadugu K, Garzon SA, Premkumar MH, Tipparaju S, Maheshwari A. Smad7 interrupts TGF-β signaling in intestinal macrophages and promotes inflammatory activation of these cells during necrotizing enterocolitis. Pediatr Res 2016; 79:951-61. [PMID: 26859364 PMCID: PMC4899224 DOI: 10.1038/pr.2016.18] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/18/2015] [Indexed: 12/31/2022]
Abstract
BACKGROUND Necrotizing enterocolitis (NEC) is an inflammatory bowel necrosis of premature infants. Based on our recent findings of increased Smad7 expression in surgically resected bowel affected by NEC, we hypothesized that NEC macrophages undergo inflammatory activation because increased Smad7 expression renders these cells resistant to normal, gut-specific, transforming growth factor (TGF)-β-mediated suppression of inflammatory pathways. METHODS We used surgically resected human NEC tissue, murine models of NEC-like injury, bone marrow-derived and intestinal macrophages, and RAW264.7 cells. Smad7 and IκB kinase-beta (IKK-β) were measured by quantitative PCR, western blots, and immunohistochemistry. Promoter activation was confirmed in luciferase reporter and chromatin immunoprecipitation assays. RESULTS NEC macrophages showed increased Smad7 expression, particularly in areas with severe tissue damage and high bacterial load. Lipopolysaccharide-induced Smad7 expression suppressed TGF-β signaling and augmented nuclear factor-kappa B (NF-κB) activation and cytokine production in macrophages. Smad7-mediated NF-κB activation was likely mediated via increased expression of IKK-β, which, further increased Smad7 expression in a feed-forward loop. We show that Smad7 induced IKK-β expression through direct binding to the IKK-β promoter and its transcriptional activation. CONCLUSION Smad7 expression in NEC macrophages interrupts TGF-β signaling and promotes NF-κB-mediated inflammatory signaling in these cells through increased expression of IKK-β.
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Affiliation(s)
- Krishnan MohanKumar
- Department of Pediatrics, University of Illinois at Chicago, Chicago, Illinois, USA, Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Kopperuncholan Namachivayam
- Department of Pediatrics, University of Illinois at Chicago, Chicago, Illinois, USA, Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Kalyan Chapalamadugu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, Florida, USA
| | - Steven A. Garzon
- Department of Pathology, University of Illinois at Chicago, Chicago, Illinois, USA
| | | | - Srinivas Tipparaju
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, Florida, USA
| | - Akhil Maheshwari
- Department of Pediatrics, University of Illinois at Chicago, Chicago, Illinois, USA, Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA, Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA, Department of Community and Family Health, College of Public Health, University of South Florida, Tampa, Florida, USA,Address for correspondence: Akhil Maheshwari, 1 Tampa General Circle, Suite F170, Tampa, FL 33606, USA; Phone: 813-844-3437; Fax: 813-844-1671;
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Differential expression and accumulation of 14-3-3 paralogs in 3T3-L1 preadipocytes and differentiated cells. Biochem Biophys Rep 2016; 7:106-112. [PMID: 28955896 PMCID: PMC5613295 DOI: 10.1016/j.bbrep.2016.05.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 05/16/2016] [Accepted: 05/27/2016] [Indexed: 11/22/2022] Open
Abstract
The 14-3-3 protein family interacts with more than 2000 different proteins in mammals, as a result of its specific phospho-serine/phospho-threonine binding activity. Seven paralogs are strictly conserved in mammalian species. Here, we show that during adipogenic differentiation of 3T3-L1 preadipocytes, the level of each 14-3-3 protein paralog is regulated independently. For instance 14-3-3β, γ, and η protein levels are increased compared to untreated cells. In contrast, 14-3-3ε protein levels decreased after differentiation while others remained constant. In silico analysis of the promoter region of each gene showed differences that explain the results obtained at mRNA and protein levels. 14-3-3 paralogs are regulated independently during 3T3-L1 adipogenesis. 14-3-3β, γ, and η are specifically accumulated during adipogenesis. Promoter sequence differences may explain this specific regulation.
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Mehlem A, Palombo I, Wang X, Hagberg CE, Eriksson U, Falkevall A. PGC-1α Coordinates Mitochondrial Respiratory Capacity and Muscular Fatty Acid Uptake via Regulation of VEGF-B. Diabetes 2016; 65:861-73. [PMID: 26822083 DOI: 10.2337/db15-1231] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/04/2016] [Indexed: 11/13/2022]
Abstract
Vascular endothelial growth factor (VEGF) B belongs to the VEGF family, but in contrast to VEGF-A, VEGF-B does not regulate blood vessel growth. Instead, VEGF-B controls endothelial fatty acid (FA) uptake and was identified as a target for the treatment of type 2 diabetes. The regulatory mechanisms controlling Vegfb expression have remained unidentified. We show that peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) together with estrogen-related receptor α (ERR-α) regulates expression of Vegfb Mice overexpressing PGC-1α under the muscle creatine kinase promoter (MPGC-1αTG mice) displayed increased Vegfb expression, and this was accompanied by increased muscular lipid accumulation. Ablation of Vegfb in MPGC-1αTG mice fed a high-fat diet (HFD) normalized glucose intolerance, insulin resistance, and dyslipidemia. We suggest that VEGF-B is the missing link between PGC-1α overexpression and the development of the diabetes-like phenotype in HFD-fed MPGC-1αTG mice. The findings identify Vegfb as a novel gene regulated by the PGC-1α/ERR-α signaling pathway. Furthermore, the study highlights the role of PGC-1α as a master metabolic sensor that by regulating the expression levels of Vegfa and Vegfb coordinates blood vessel growth and FA uptake with mitochondrial FA oxidation.
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Affiliation(s)
- Annika Mehlem
- Department of Medical Biochemistry and Biophysics, Division of Vascular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Isolde Palombo
- Department of Medical Biochemistry and Biophysics, Division of Vascular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Xun Wang
- Department of Medical Biochemistry and Biophysics, Division of Vascular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Carolina E Hagberg
- Department of Medical Biochemistry and Biophysics, Division of Vascular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ulf Eriksson
- Department of Medical Biochemistry and Biophysics, Division of Vascular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Annelie Falkevall
- Department of Medical Biochemistry and Biophysics, Division of Vascular Biology, Karolinska Institutet, Stockholm, Sweden
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Garstang MG, Osborne PW, Ferrier DEK. TCF/Lef regulates the Gsx ParaHox gene in central nervous system development in chordates. BMC Evol Biol 2016; 16:57. [PMID: 26940763 PMCID: PMC4776371 DOI: 10.1186/s12862-016-0614-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/11/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ParaHox genes play an integral role in the anterior-posterior (A-P) patterning of the nervous system and gut of most animals. The ParaHox cluster is an ideal system in which to study the evolution and regulation of developmental genes and gene clusters, as it displays similar regulatory phenomena to its sister cluster, the Hox cluster, but offers a much simpler system with only three genes. RESULTS Using Ciona intestinalis transgenics, we isolated a regulatory element upstream of Branchiostoma floridae Gsx that drives expression within the central nervous system of Ciona embryos. The minimal amphioxus enhancer region required to drive CNS expression has been identified, along with surrounding sequence that increases the efficiency of reporter expression throughout the Ciona CNS. TCF/Lef binding sites were identified and mutagenized and found to be required to drive the CNS expression. Also, individual contributions of TCF/Lef sites varied across the regulatory region, revealing a partial division of function across the Bf-Gsx-Up regulatory element. Finally, when all TCF/Lef binding sites are mutated CNS expression is not only abolished, but a latent repressive function is also unmasked. CONCLUSIONS We have identified a B. floridae Gsx upstream regulatory element that drives CNS expression within transgenic Ciona intestinalis, and have shown that this CNS expression is dependent upon TCF/Lef binding sites. We examine the evolutionary and developmental implications of these results, and discuss the possibility of TCF/Lef not only as a regulator of chordate Gsx, but as a deeply conserved regulatory factor controlling all three ParaHox genes across the Metazoa.
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Affiliation(s)
- Myles G Garstang
- The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.
| | - Peter W Osborne
- The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.
| | - David E K Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.
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Moore BD, Jin RU, Lo H, Jung M, Wang H, Battle MA, Wollheim CB, Urano F, Mills JC. Transcriptional Regulation of X-Box-binding Protein One (XBP1) by Hepatocyte Nuclear Factor 4α (HNF4Α) Is Vital to Beta-cell Function. J Biol Chem 2016; 291:6146-57. [PMID: 26792861 DOI: 10.1074/jbc.m115.685750] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 12/20/2022] Open
Abstract
The transcription factor, X-box-binding protein-1 (XBP1), controls the development and maintenance of the endoplasmic reticulum (ER) in multiple secretory cell lineages. We show here that Hepatocyte Nuclear Factor 4α (HNF4α) directly induces XBP1 expression. Mutations in HNF4α cause Mature-Onset Diabetes of the Young I (MODYI), a subset of diabetes characterized by diminished GSIS. In mouse models, cell lines, and ex vivo islets, using dominant negative and human- disease-allele point mutants or knock-out and knockdown models, we show that disruption of HNF4α caused decreased expression of XBP1 and reduced cellular ER networks. GSIS depends on ER Ca(2+) signaling; we show that diminished XBP1 and/or HNF4α in β-cells led to impaired ER Ca(2+) homeostasis. Restoring XBP1 expression was sufficient to completely rescue GSIS in HNF4α-deficient β-cells. Our findings uncover a transcriptional relationship between HNF4α and Xbp1 with potentially broader implications about MODYI and the importance of transcription factor signaling in the regulation of secretion.
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Affiliation(s)
- Benjamin D Moore
- From the Division of Gastroenterology, Departments of Medicine, Pathology & Immunology, and Developmental Biology, Washington University, St. Louis, Missouri 63110
| | - Ramon U Jin
- From the Division of Gastroenterology, Departments of Medicine, Pathology & Immunology, and Developmental Biology, Washington University, St. Louis, Missouri 63110
| | - Heiyong Lo
- From the Division of Gastroenterology, Departments of Medicine, Pathology & Immunology, and Developmental Biology, Washington University, St. Louis, Missouri 63110
| | - Min Jung
- From the Division of Gastroenterology, Departments of Medicine, Pathology & Immunology, and Developmental Biology, Washington University, St. Louis, Missouri 63110
| | - Haiyan Wang
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Michele A Battle
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Claes B Wollheim
- Lund University Diabetes Center, Department of Clinical Sciences, Diabetes & Endocrinology, Skåne University Hospital, Lund University, Malmö 20502, Sweden, Department of Cell Physiology and Metabolism, Université de Genève, University Medical Centre, 1 rue Michel-Servet, Geneva 4 1211, Switzerland, and
| | - Fumihiko Urano
- Division of Endocrinology, Departments of Medicine, Metabolism, and Lipid Research, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Jason C Mills
- From the Division of Gastroenterology, Departments of Medicine, Pathology & Immunology, and Developmental Biology, Washington University, St. Louis, Missouri 63110,
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Schmickl R, Liston A, Zeisek V, Oberlander K, Weitemier K, Straub SCK, Cronn RC, Dreyer LL, Suda J. Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern AfricanOxalis(Oxalidaceae). Mol Ecol Resour 2015; 16:1124-35. [DOI: 10.1111/1755-0998.12487] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/06/2015] [Accepted: 11/05/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Roswitha Schmickl
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
| | - Aaron Liston
- Department of Botany and Plant Pathology; Oregon State University; 2082 Cordley Hall Corvallis OR 97331 USA
| | - Vojtěch Zeisek
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 128 01 Prague Czech Republic
| | - Kenneth Oberlander
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Conservation Ecology and Entomology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Kevin Weitemier
- Department of Botany and Plant Pathology; Oregon State University; 2082 Cordley Hall Corvallis OR 97331 USA
| | - Shannon C. K. Straub
- Department of Biology; Hobart and William Smith Colleges; 213 Eaton Hall Geneva NY 14456 USA
| | - Richard C. Cronn
- USDA Forest Service; Pacific Northwest Research Station; 3200 SW Jefferson Way Corvallis OR 97331 USA
| | - Léanne L. Dreyer
- Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Jan Suda
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 128 01 Prague Czech Republic
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Biressi S, Miyabara EH, Gopinath SD, Carlig PMM, Rando TA. A Wnt-TGFβ2 axis induces a fibrogenic program in muscle stem cells from dystrophic mice. Sci Transl Med 2015; 6:267ra176. [PMID: 25520397 DOI: 10.1126/scitranslmed.3008411] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have previously observed that Wnt signaling activates a fibrogenic program in adult muscle stem cells, called satellite cells, during aging. We genetically labeled satellite cells in a mouse model of Duchenne muscular dystrophy to follow their fate during the progression of the disease. We observed that a fraction of satellite cells had a reduced myogenic potential and showed enhanced expression of profibrotic genes compared to age-matched controls. By combining in vitro and in vivo results, we found that expression of transforming growth factor-β2 (TGFβ2) was induced in response to elevated canonical Wnt signaling in dystrophic muscles and that the resulting increase in TGFβ activity affected the behavior of satellite cells in an autocrine or paracrine fashion. Indeed, pharmacological inhibition of the TGFβ pathway in vivo reduced the fibrogenic characteristics of satellite cells. These studies shed new light on the cellular and molecular mechanisms responsible for stem cell dysfunction in dystrophic muscle and may contribute to the development of more effective and specific therapeutic approaches for the prevention of muscle fibrosis.
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Affiliation(s)
- Stefano Biressi
- Paul F. Glenn Laboratories for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elen H Miyabara
- Paul F. Glenn Laboratories for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA. Anatomy Department, Institute of Biomedical Sciences, University of São Paulo, 2415 Lineu Prestes Avenue, São Paulo, São Paulo 05508-000, Brazil
| | - Suchitra D Gopinath
- Paul F. Glenn Laboratories for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Poppy M M Carlig
- Paul F. Glenn Laboratories for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas A Rando
- Paul F. Glenn Laboratories for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA. Neurology Service, VA Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA.
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Rossi E, Radi O, De Lorenzi L, Iannuzzi A, Camerino G, Zuffardi O, Parma P. A Revised Genome Assembly of the Region 5′ to Canine SOX9 Includes the RevSex Orthologous Region. Sex Dev 2015; 9:155-61. [DOI: 10.1159/000435871] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2015] [Indexed: 11/19/2022] Open
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Faber-Hammond JJ, Phillips RB, Brown KH. Comparative Analysis of the Shared Sex-Determination Region (SDR) among Salmonid Fishes. Genome Biol Evol 2015; 7:1972-87. [PMID: 26112966 PMCID: PMC4524489 DOI: 10.1093/gbe/evv123] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Salmonids present an excellent model for studying evolution of young sex-chromosomes. Within the genus, Oncorhynchus, at least six independent sex-chromosome pairs have evolved, many unique to individual species. This variation results from the movement of the sex-determining gene, sdY, throughout the salmonid genome. While sdY is known to define sexual differentiation in salmonids, the mechanism of its movement throughout the genome has remained elusive due to high frequencies of repetitive elements, rDNA sequences, and transposons surrounding the sex-determining regions (SDR). Despite these difficulties, bacterial artificial chromosome (BAC) library clones from both rainbow trout and Atlantic salmon containing the sdY region have been reported. Here, we report the sequences for these BACs as well as the extended sequence for the known SDR in Chinook gained through genome walking methods. Comparative analysis allowed us to study the overlapping SDRs from three unique salmonid Y chromosomes to define the specific content, size, and variation present between the species. We found approximately 4.1 kb of orthologous sequence common to all three species, which contains the genetic content necessary for masculinization. The regions contain transposable elements that may be responsible for the translocations of the SDR throughout salmonid genomes and we examine potential mechanistic roles of each one.
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Affiliation(s)
- Joshua J Faber-Hammond
- Department of Biology, Portland State University School of Biological Sciences, Washington State University Vancouver
| | - Ruth B Phillips
- School of Biological Sciences, Washington State University Vancouver Center for Reproductive Biology, Washington State University, Pullman
| | - Kim H Brown
- Department of Biology, Portland State University
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