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Ferguson CA, Firulli BA, Zoia M, Osterwalder M, Firulli AB. Identification and characterization of Hand2 upstream genomic enhancers active in developing stomach and limbs. Dev Dyn 2024; 253:215-232. [PMID: 37551791 DOI: 10.1002/dvdy.646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND The bHLH transcription factor HAND2 plays important roles in the development of the embryonic heart, face, limbs, and sympathetic and enteric nervous systems. To define how and when HAND2 regulates these developmental systems, requires understanding the transcriptional regulation of Hand2. RESULTS Remarkably, Hand2 is flanked by an extensive upstream gene desert containing a potentially diverse enhancer landscape. Here, we screened the regulatory interval 200 kb proximal to Hand2 for putative enhancers using evolutionary conservation and histone marks in Hand2-expressing tissues. H3K27ac signatures across embryonic tissues pointed to only two putative enhancer regions showing deep sequence conservation. Assessment of the transcriptional enhancer potential of these elements using transgenic reporter lines uncovered distinct in vivo enhancer activities in embryonic stomach and limb mesenchyme, respectively. Activity of the identified stomach enhancer was restricted to the developing antrum and showed expression within the smooth muscle and enteric neurons. Surprisingly, the activity pattern of the limb enhancer did not overlap Hand2 mRNA but consistently yielded a defined subectodermal anterior expression pattern within multiple transgenic lines. CONCLUSIONS Together, these results start to uncover the diverse regulatory potential inherent to the Hand2 upstream regulatory interval.
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Affiliation(s)
- Chloe A Ferguson
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Beth A Firulli
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Matteo Zoia
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Marco Osterwalder
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Anthony B Firulli
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Datta S, Cao W, Skillman M, Wu M. Hypoplastic Left Heart Syndrome: Signaling & Molecular Perspectives, and the Road Ahead. Int J Mol Sci 2023; 24:15249. [PMID: 37894928 PMCID: PMC10607600 DOI: 10.3390/ijms242015249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/07/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Hypoplastic left heart syndrome (HLHS) is a lethal congenital heart disease (CHD) affecting 8-25 per 100,000 neonates globally. Clinical interventions, primarily surgical, have improved the life expectancy of the affected subjects substantially over the years. However, the etiological basis of HLHS remains fundamentally unclear to this day. Based upon the existing paradigm of studies, HLHS exhibits a multifactorial mode of etiology mediated by a complicated course of genetic and signaling cascade. This review presents a detailed outline of the HLHS phenotype, the prenatal and postnatal risks, and the signaling and molecular mechanisms driving HLHS pathogenesis. The review discusses the potential limitations and future perspectives of studies that can be undertaken to address the existing scientific gap. Mechanistic studies to explain HLHS etiology will potentially elucidate novel druggable targets and empower the development of therapeutic regimens against HLHS in the future.
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Affiliation(s)
| | | | | | - Mingfu Wu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, USA; (S.D.); (W.C.); (M.S.)
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Cooper RBV, Kim KB, Oliver DR, Armbrecht E, Behrents RG, Montaño AM. DLX6 and MSX1 from saliva samples as potential predictors of mandibular size: A cross-sectional study. Am J Orthod Dentofacial Orthop 2023; 163:368-377. [PMID: 36494218 DOI: 10.1016/j.ajodo.2021.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 12/01/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Morphologic features of the mandible are influenced by the genes of each individual. Mandible size is important to orthodontists because the mandible is the mechanism by which the lower face influences facial esthetics and dental function. To date, no biological marker has been identified that indicates eventual mandible size. This study aimed to correlate the expression of DLX5, DLX6, EDN1, HAND2, PRRX1, and MSX1 to mandible size. METHODS Fifty-nine orthodontic patients aged >6 years who had available cephalometric radiographs were studied. Patients were classified on the basis of condylion-to-gnathion measurements. Messenger RNA was isolated from saliva and subjected to real-time quantitative polymerase chain reaction. RESULTS Threshold cycle values for subjects with small mandibles (>1 standard deviation [SD] from the mean) had the least expression of DLX6 and MSX1. Threshold cycle values for subjects with large mandibles (>1 SD) had less expression of DLX6 and MSX1 than subjects within 1 SD but more than those with small mandibles. CONCLUSIONS DLX6 and MSX1 are related to mandible development and size. This finding could be used to improve treatment planning for medical and dental professionals seeking to understand the impact of genetics on bone growth.
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Affiliation(s)
- Rachel Bryn V Cooper
- Formerly, Department of Orthodontics, School of Medicine, Saint Louis University, St Louis, Mo currently, Private practice, Houston, Tex.
| | - Ki Beom Kim
- Department of Orthodontics, School of Medicine, Saint Louis University, St Louis, Mo
| | - Donald R Oliver
- Department of Orthodontics, School of Medicine, Saint Louis University, St Louis, Mo
| | - Eric Armbrecht
- Center for Health Outcomes Research, Saint Louis University, St Louis, Mo
| | - Rolf G Behrents
- Department of Orthodontics, School of Medicine, Saint Louis University, St Louis, Mo
| | - Adriana M Montaño
- Departments of Pediatrics and Biochemistry and Molecular Biology, School of Medicine, Saint Louis University, St Louis, Mo.
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Zheng M, Erhardt S, Ai D, Wang J. Bmp Signaling Regulates Hand1 in a Dose-Dependent Manner during Heart Development. Int J Mol Sci 2021; 22:ijms22189835. [PMID: 34576009 PMCID: PMC8465227 DOI: 10.3390/ijms22189835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 01/22/2023] Open
Abstract
The bone morphogenetic protein (Bmp) signaling pathway and the basic helix–loop–helix (bHLH) transcription factor Hand1 are known key regulators of cardiac development. In this study, we investigated the Bmp signaling regulation of Hand1 during cardiac outflow tract (OFT) development. In Bmp2 and Bmp4loss-of-function embryos with varying levels of Bmp in the heart, Hand1 is sensitively decreased in response to the dose of Bmp expression. In contrast, Hand1 in the heart is dramatically increased in Bmp4 gain-of-function embryos. We further identified and characterized the Bmp/Smad regulatory elements in Hand1. Combined transfection assays and chromatin immunoprecipitation (ChIP) experiments indicated that Hand1 is directly activated and bound by Smads. In addition, we found that upon the treatment of Bmp2 and Bmp4, P19 cells induced Hand1 expression and favored cardiac differentiation. Together, our data indicated that the Bmp signaling pathway directly regulates Hand1 expression in a dose-dependent manner during heart development.
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Affiliation(s)
- Mingjie Zheng
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (M.Z.); (S.E.)
| | - Shannon Erhardt
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (M.Z.); (S.E.)
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Di Ai
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA;
| | - Jun Wang
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (M.Z.); (S.E.)
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Correspondence:
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Mechanisms of Binding Specificity among bHLH Transcription Factors. Int J Mol Sci 2021; 22:ijms22179150. [PMID: 34502060 PMCID: PMC8431614 DOI: 10.3390/ijms22179150] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 12/25/2022] Open
Abstract
The transcriptome of every cell is orchestrated by the complex network of interaction between transcription factors (TFs) and their binding sites on DNA. Disruption of this network can result in many forms of organism malfunction but also can be the substrate of positive natural selection. However, understanding the specific determinants of each of these individual TF-DNA interactions is a challenging task as it requires integrating the multiple possible mechanisms by which a given TF ends up interacting with a specific genomic region. These mechanisms include DNA motif preferences, which can be determined by nucleotide sequence but also by DNA’s shape; post-translational modifications of the TF, such as phosphorylation; and dimerization partners and co-factors, which can mediate multiple forms of direct or indirect cooperative binding. Binding can also be affected by epigenetic modifications of putative target regions, including DNA methylation and nucleosome occupancy. In this review, we describe how all these mechanisms have a role and crosstalk in one specific family of TFs, the basic helix-loop-helix (bHLH), with a very conserved DNA binding domain and a similar DNA preferred motif, the E-box. Here, we compile and discuss a rich catalog of strategies used by bHLH to acquire TF-specific genome-wide landscapes of binding sites.
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Ye Z, Li Y, Xie J, Feng Z, Yang X, Wu Y, Pu Y, Gao J, Xu X, Zhu Z, Li W, Chen W, Xing C. Integrated bioinformatics identifies the dysregulation induced by aberrant gene methylation in colorectal carcinoma. Genes Dis 2021; 8:521-530. [PMID: 34179314 PMCID: PMC8209361 DOI: 10.1016/j.gendis.2020.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/31/2020] [Accepted: 04/09/2020] [Indexed: 02/06/2023] Open
Abstract
Colorectal carcinoma (CRC) is one of the most common cancers, and is associated with a poor clinical outcome. The key genes and potential prognostic markers in colorectal carcinoma remain to be identified and explored for clinical application. DNA expression/methylation profiles were downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed/methylated genes (DEGs and DEMs). A total of 255 genes and 372 genes were identified as being up-regulated and down-regulated, respectively, in GSE113513, GSE81558, and GSE89076. There were a total of 3350 hypermethylated genes and 443 hypomethylated genes identified in GSE48684. Twenty genes were found to be hypermethylated as well as down-regulated, and a functional enrichment analysis revealed that these genes were mainly involved in cancer-related pathways. Among these 20 genes, GPM6A, HAND2 and C2orf40 were related to poor outcomes in cancer patients based on a survival analysis. Concurrent decreases of GPM6A, HAND2 and C2orf40 protein expression were observed in highly-differentiated colorectal carcinoma tissues, and higher expression levels were found in undifferentiated or minimally-differentiated colorectal carcinoma tissues. In conclusion, 20 genes were found to be downregulated and hypermethylated in CRC, among which GPM6A, HAND2 and C2orf40 were explored for their potential prognostic value.
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Affiliation(s)
| | | | - Jiaming Xie
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215004, PR China
| | - Zhenyu Feng
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215004, PR China
| | - Xiaodong Yang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215004, PR China
| | - Yong Wu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215004, PR China
| | - Yuwei Pu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215004, PR China
| | - Jiawei Gao
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215004, PR China
| | - Xiangrong Xu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215004, PR China
| | - Zhaobi Zhu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215004, PR China
| | - Wei Li
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215004, PR China
| | - Wei Chen
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215004, PR China
| | - Chungen Xing
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215004, PR China
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Elliott KH, Chen X, Salomone J, Chaturvedi P, Schultz PA, Balchand SK, Servetas JD, Zuniga A, Zeller R, Gebelein B, Weirauch MT, Peterson KA, Brugmann SA. Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks. eLife 2020; 9:e56450. [PMID: 33006313 PMCID: PMC7556880 DOI: 10.7554/elife.56450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 10/01/2020] [Indexed: 12/17/2022] Open
Abstract
Despite a common understanding that Gli TFs are utilized to convey a Hh morphogen gradient, genetic analyses suggest craniofacial development does not completely fit this paradigm. Using the mouse model (Mus musculus), we demonstrated that rather than being driven by a Hh threshold, robust Gli3 transcriptional activity during skeletal and glossal development required interaction with the basic helix-loop-helix TF Hand2. Not only did genetic and expression data support a co-factorial relationship, but genomic analysis revealed that Gli3 and Hand2 were enriched at regulatory elements for genes essential for mandibular patterning and development. Interestingly, motif analysis at sites co-occupied by Gli3 and Hand2 uncovered mandibular-specific, low-affinity, 'divergent' Gli-binding motifs (dGBMs). Functional validation revealed these dGBMs conveyed synergistic activation of Gli targets essential for mandibular patterning and development. In summary, this work elucidates a novel, sequence-dependent mechanism for Gli transcriptional activity within the craniofacial complex that is independent of a graded Hh signal.
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Affiliation(s)
- Kelsey H Elliott
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research FoundationCincinnatiUnited States
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Joseph Salomone
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research FoundationCincinnatiUnited States
- Medical-Scientist Training Program, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Praneet Chaturvedi
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Preston A Schultz
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Sai K Balchand
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | | | - Aimée Zuniga
- Developmental Genetics, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Rolf Zeller
- Developmental Genetics, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Matthew T Weirauch
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | | | - Samantha A Brugmann
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Shriners Children’s HospitalCincinnatiUnited States
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Partially Penetrant Cardiac Neural Crest Defects in Hand1 Phosphomutant Mice: Dimer Choice That Is Not So Critical. Pediatr Cardiol 2019; 40:1339-1344. [PMID: 31338559 PMCID: PMC6786956 DOI: 10.1007/s00246-019-02162-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 07/16/2019] [Indexed: 10/26/2022]
Abstract
Hand1 is a basic Helix-loop-Helix transcription factor that exhibits post-translationally regulated dimer partner choice that allows for a diverse set of Hand1 transcriptional complexes. Indeed, when Hand1 phosphoregulation is altered, conditionally activated hypophorylation (Hand1PO4-) and phosphorylation mimic (Hand1PO4+) Hand1 alleles disrupt both craniofacial and limb morphogenesis with 100% penetrance. Interestingly, activation of conditional Hand1 Phosphomutant alleles within post-migratory neural crest cells produce heart defects that include ventricular septal defects, double-outlet right ventricle, persistent truncus arteriosus with partial penetrance. Single versus double-lobed thymus is a distinguishing feature between Wnt1-Cre;Hand1PO4-/+ and Wnt1-Cre;Hand1PO4+/+ mice. These data show that although Hand1 dimer regulation plays critical and consistent roles in disrupting craniofacial and limb morphogenesis, Hand1 dimer regulation during cardiac outflow track formation is less critical for normal morphogenesis. This review will present the OFT phenotypes observed in Hand1 Phosphomutant mice, and discuss possible mechanisms of how penetrance differences within the same tissues within the same embryos could be variable.
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Toiyama Y, Okugawa Y, Kondo S, Okita Y, Araki T, Kusunoki K, Uchino M, Ikeuchi H, Hirota S, Mitsui A, Takehana K, Umezawa T, Kusunoki M. Comprehensive analysis identifying aberrant DNA methylation in rectal mucosa from ulcerative colitis patients with neoplasia. Oncotarget 2018; 9:33149-33159. [PMID: 30237858 PMCID: PMC6145694 DOI: 10.18632/oncotarget.26032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
Background There are no biomarkers to facilitate the identification of patients with ulcerative colitis (UC) who are at high risk for developing colorectal cancer (CRC). In our current study, we used rectal tissues from UC patients to identify aberrant DNA methylations and evaluated whether they could be used to identify UC patients with coexisting colorectal neoplasia. Results Using a training set, we identified 484 differentially methylated regions (DMRs) with absolute delta beta-values > 0.1 in rectal mucosa by using the ChAMP algorithm. Next, pathway enrichment analysis was performed using 484 DMRs to select coordinately methylated DMRs, resulting in the selection of 187 aberrant DMRs in rectal tissues from UC-CRC. Then, the Elastic Net classification algorithm was performed to narrow down optimal aberrant DMRs, and we finally selected 11 DMRs as biomarkers for identification of UC-CRC patients. The 11 chosen DMRs could discriminate UC patients with or without CRC in a training set (area under the curve, 0.96) and the validation set (area under the curve, 0.81). Conclusions In conclusion, we identified 11 DMRs that could identify UC patients with CRC complications. Prospective studies should further confirm the validity of these biomarkers. Methods We performed genome-wide DNA methylation profiles in rectal mucosal tissues (n = 48) from 24 UC-CRC and 24 UC patients in a training set. Next, we performed comprehensive DNA methylation analysis using rectal mucosal tissues (n = 16) from 8 UC-CRC and 8 UC patients for validation.
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Affiliation(s)
- Yuji Toiyama
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Graduate School of Medicine, Mie University, Mie, Japan
| | - Yoshinaga Okugawa
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Graduate School of Medicine, Mie University, Mie, Japan
| | - Satoru Kondo
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Graduate School of Medicine, Mie University, Mie, Japan
| | - Yoshiki Okita
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Graduate School of Medicine, Mie University, Mie, Japan
| | - Toshimitsu Araki
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Graduate School of Medicine, Mie University, Mie, Japan
| | - Kurando Kusunoki
- Department of Inflammatory Bowel Disease, Hyogo College of Medicine, Hyogo, Japan
| | - Motoi Uchino
- Department of Inflammatory Bowel Disease, Hyogo College of Medicine, Hyogo, Japan
| | - Hiroki Ikeuchi
- Department of Inflammatory Bowel Disease, Hyogo College of Medicine, Hyogo, Japan
| | - Seiichi Hirota
- Department of Surgical Pathology, Hyogo College of Medicine, Hyogo, Japan
| | - Akira Mitsui
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Kenji Takehana
- R&D Planning Department, EA Pharma Co., Ltd., Tokyo, Japan
| | | | - Masato Kusunoki
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Graduate School of Medicine, Mie University, Mie, Japan
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Majewska M, Lipka A, Paukszto L, Jastrzebski JP, Gowkielewicz M, Jozwik M, Majewski MK. Preliminary RNA-Seq Analysis of Long Non-Coding RNAs Expressed in Human Term Placenta. Int J Mol Sci 2018; 19:ijms19071894. [PMID: 29954144 PMCID: PMC6073670 DOI: 10.3390/ijms19071894] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 06/24/2018] [Indexed: 12/20/2022] Open
Abstract
Development of particular structures and proper functioning of the placenta are under the influence of sophisticated pathways, controlled by the expression of substantial genes that are additionally regulated by long non-coding RNAs (lncRNAs). To date, the expression profile of lncRNA in human term placenta has not been fully established. This study was conducted to characterize the lncRNA expression profile in human term placenta and to verify whether there are differences in the transcriptomic profile between the sex of the fetus and pregnancy multiplicity. RNA-Seq data were used to profile, quantify, and classify lncRNAs in human term placenta. The applied methodology enabled detection of the expression of 4463 isoforms from 2899 annotated lncRNA loci, plus 990 putative lncRNA transcripts from 607 intergenic regions. Those placentally expressed lncRNAs displayed features such as shorter transcript length, longer exon length, fewer exons, and lower expression levels compared to messenger RNAs (mRNAs). Among all placental transcripts, 175,268 were classified as mRNAs and 15,819 as lncRNAs, and 56,727 variants were discovered within unannotated regions. Five differentially expressed lncRNAs (HAND2-AS1, XIST, RP1-97J1.2, AC010084.1, TTTY15) were identified by a sex-bias comparison. Splicing events were detected within 37 genes and 4 lncRNA loci. Functional analysis of cis-related potential targets for lncRNAs identified 2021 enriched genes. It is presumed that the obtained data will expand the current knowledge of lncRNAs in placenta and human non-coding catalogs, making them more contemporary and specific.
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Affiliation(s)
- Marta Majewska
- Department of Human Physiology, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, 10-082 Olsztyn, Poland.
| | - Aleksandra Lipka
- Department of Gynecology and Obstetrics, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, 10-045 Olsztyn, Poland.
| | - Lukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland.
| | - Jan Pawel Jastrzebski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland.
| | - Marek Gowkielewicz
- Department of Gynecology and Obstetrics, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, 10-045 Olsztyn, Poland.
| | - Marcin Jozwik
- Department of Gynecology and Obstetrics, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, 10-045 Olsztyn, Poland.
| | - Mariusz Krzysztof Majewski
- Department of Human Physiology, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, 10-082 Olsztyn, Poland.
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Yang Y, Chu FH, Xu WR, Sun JQ, Sun X, Ma XM, Yu MW, Yang GW, Wang XM. Identification of regulatory role of DNA methylation in colon cancer gene expression via systematic bioinformatics analysis. Medicine (Baltimore) 2017; 96:e8487. [PMID: 29381923 PMCID: PMC5708922 DOI: 10.1097/md.0000000000008487] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Colon cancer arises from the accumulations of genetic and epigenetic changes. Currently, profiles of DNA methylation and gene expression of colon cancer have not been elucidated clearly. This articles aims to characterize the profile of DNA methylation and gene expression of colon cancer systemically, and acquire candidate genes potentially regulated by altered methylation for this disease.Data were downloaded from The Cancer Genome Atlas database. Differentially methylated CpG sites (DMCs) and differentially methylated regions (DMRs) were calculated via COHCAP. Differentially expressed genes (DEGs) were identified by DESeq2. Weighted gene co-expression network analysis (WGCNA) package in R was applied for WGCNA.Data of 275 solid tumor tissues and 19 adjacent tumor tissues of colon cancer were obtained. A total of 1828 DMCs, including 1390 hypermethylated and 438 hypomethylated CpG sites, were identified between tumor and normal groups. A total of 789 DEGs, containing 435 upregulated genes and 354 downregulated genes were observed. It revealed that 8 DMRs-DEGs and 95 DMCs-DEGs pairs were significantly correlated. Furthermore, genes of yellow and brown modules from WGCNA were significantly correlated with tumor/normal status, and significantly enriched in peroxisome proliferator activated receptor signaling pathway, glutamatergic synapse, and neuroactive ligand-receptor interaction. Genes in the above 2 modules were also significantly enriched in DMCs or DMRs-associated genes. Specifically, ADHFE1, HAND2, and GNAO1 were hypermethylated and downregulated in colon cancer, suggesting that the low expression levels of these genes may be regulated by DNA hypermethylation. In addition, the 3 genes were involved in brown module of WGCNA, indicating their important roles in colon cancer.The investigation of the relationship between DNA methylation and gene expression may help to understand the effect of DNA methylation alteration on genes expression, especially gene co-expression network in the development of colon cancer. Genes such as ADHFE1, HAND2, and GNAO1 may be served as potential candidates for diagnosis and therapy targets in colon cancer.
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Affiliation(s)
- Yong Yang
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
| | - Fu-Hao Chu
- Department of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Wei-Ru Xu
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
| | - Jia-Qi Sun
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
| | - Xu Sun
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
| | - Xue-Man Ma
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
| | - Ming-Wei Yu
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
| | - Guo-Wang Yang
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
| | - Xiao-Min Wang
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
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12
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Square T, Jandzik D, Romášek M, Cerny R, Medeiros DM. The origin and diversification of the developmental mechanisms that pattern the vertebrate head skeleton. Dev Biol 2017; 427:219-229. [DOI: 10.1016/j.ydbio.2016.11.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/06/2016] [Accepted: 11/20/2016] [Indexed: 01/30/2023]
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Fortunato SAV, Vervoort M, Adamski M, Adamska M. Conservation and divergence of bHLH genes in the calcisponge Sycon ciliatum. EvoDevo 2016; 7:23. [PMID: 27757221 PMCID: PMC5064789 DOI: 10.1186/s13227-016-0060-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/27/2016] [Indexed: 12/18/2022] Open
Abstract
Background Basic Helix-Loop-Helix (bHLH) genes encode a large family of eukaryotic transcription factors, categorized into six high-order groups: pan-eukaryotic group B involved in regulation of cell cycle, metabolism, and development; holozoan-specific groups C and F involved in development and maintenance of homeostasis; and metazoan-specific groups A, D and E including well-studied genes, such as Atonal, Twist and Hairy, with diverse developmental roles including control of morphogenesis and specification of neurons. Current scenarios of bHLH evolution in animals are mainly based on the bHLH gene set found in the genome of demosponge Amphimedon queenslandica. In this species, the majority of the 21 identified bHLH genes belong to group B, and the single group A gene is orthologous to several neurogenic bilaterian subfamilies, including atonal and neurogenin. Results Given recently discovered differences in developmental toolkit components between siliceous and calcareous sponges, we have carried out genome-wide analysis of bHLH genes in Sycon ciliatum, an emerging calcisponge model. We identified 30 bHLH genes in this species, representing 12 individual families, including four group A families not found in Amphimedon, and two larger family groupings. Notably, the families represented in Sycon are only partially overlapping with those represented in Amphimedon. Developmental expression analysis of a subset of the identified genes revealed patterns consistent with deeply conserved roles, such as specification of sensory cells by Atona-related and stem cells by Myc genes. Conclusions Our results demonstrate independent gene loss events in demosponges and calcisponges, implying a complex bHLH toolkit in the last common metazoan ancestor. Electronic supplementary material The online version of this article (doi:10.1186/s13227-016-0060-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sofia A V Fortunato
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway.,ARC Centre for Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - Michel Vervoort
- Institut Jacques Monod - CNRS, Université Paris Diderot, 75005 Paris Cedex 13, France
| | - Marcin Adamski
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway.,Research School of Biology, Australian National University, Canberra, Australia
| | - Maja Adamska
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway.,Research School of Biology, Australian National University, Canberra, Australia
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Ulrich V, Gelber SE, Vukelic M, Sacharidou A, Herz J, Urbanus RT, de Groot PG, Natale DR, Harihara A, Redecha P, Abrahams VM, Shaul PW, Salmon JE, Mineo C. ApoE Receptor 2 Mediation of Trophoblast Dysfunction and Pregnancy Complications Induced by Antiphospholipid Antibodies in Mice. Arthritis Rheumatol 2016; 68:730-739. [PMID: 26474194 DOI: 10.1002/art.39453] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/24/2015] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Pregnancies in women with the antiphospholipid syndrome (APS) are frequently complicated by fetal loss and intrauterine growth restriction (IUGR). How circulating antiphospholipid antibodies (aPL) cause pregnancy complications in APS is poorly understood. We sought to determine whether the low-density lipoprotein receptor family member apolipoprotein E receptor 2 (ApoER2) mediates trophoblast dysfunction and pregnancy complications induced by aPL. METHODS Placental and trophoblast ApoER2 expression was evaluated by immunohistochemistry and immunoblotting. Normal human IgG and aPL were purified from healthy individuals and APS patients, respectively. The role of ApoER2 in aPL-induced changes in trophoblast proliferation and migration and in kinase activation was assessed using RNA interference in HTR-8/SVneo cells. The participation of ApoER2 in aPL-induced pregnancy loss and IUGR was evaluated in pregnant ApoER2(+/+) and ApoER2(-/-) mice injected with aPL or normal human IgG. RESULTS We found that ApoER2 is abundant in human and mouse placental trophoblasts and in multiple trophoblast-derived cell lines, including HTR-8/SVneo cells. ApoER2 and its interaction with the cell surface protein β2 -glycoprotein I were required for aPL-induced inhibition of cultured trophoblast proliferation and migration. In parallel, aPL antagonism of Akt kinase activation by epidermal growth factor in trophoblasts was mediated by ApoER2. Furthermore, in a murine passive-transfer model of pregnancy complications of APS, ApoER2(-/-) mice were protected from both aPL-induced fetal loss and aPL-induced IUGR. CONCLUSION ApoER2 plays a major role in the attenuation of trophoblast function by aPL, and the receptor mediates aPL-induced pregnancy complications in vivo in mice. ApoER2-directed interventions can now potentially be developed to combat the pregnancy complications associated with APS.
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Affiliation(s)
- Victoria Ulrich
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Shari E Gelber
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, New York
| | - Milena Vukelic
- Department of Medicine, Hospital for Special Surgery, Weill Cornell Medical College, New York, New York
| | - Anastasia Sacharidou
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Joachim Herz
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Rolf T Urbanus
- Clinical Chemistry and Hematology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Philip G de Groot
- Clinical Chemistry and Hematology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - David R Natale
- Department of Reproductive Medicine, University of California-San Diego, San Diego, California
| | - Anirudha Harihara
- Department of Reproductive Medicine, University of California-San Diego, San Diego, California
| | - Patricia Redecha
- Department of Medicine, Hospital for Special Surgery, Weill Cornell Medical College, New York, New York
| | - Vikki M Abrahams
- Department of Obstetrics, Gynecology & Reproductive Sciences, Divisions of Reproductive Sciences and Maternal-Fetal Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Philip W Shaul
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jane E Salmon
- Department of Medicine, Hospital for Special Surgery, Weill Cornell Medical College, New York, New York
| | - Chieko Mineo
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
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A Haplotype of Two Novel Polymorphisms in δ-Sarcoglycan Gene Increases Risk of Dilated Cardiomyopathy in Mongoloid Population. PLoS One 2015; 10:e0145602. [PMID: 26720722 PMCID: PMC4697846 DOI: 10.1371/journal.pone.0145602] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 12/07/2015] [Indexed: 11/21/2022] Open
Abstract
The role of genetic abnormality of δ-sarcoglycan (δ-SG) gene in dilated (DCM) and hypertrophied (HCM) cardiomyopathy patients is still unfolding. In this study we first defined the promoter region and then searched for polymorphisms/mutations among the promoter, 5'-untranslated region, and the encoding exons in δ-SG gene in 104 Chinese patients with DCM, 145 with HCM, and 790 normal controls. Two novel polymorphisms were found, an 11 base-pair (bp) deletion (c.-100~-110; -) in the promoter region and a missense polymorphism of A848G resulting in p.Q283R in the highly conserved C-terminus. The prevalence of homozygous genotype -/- of c.-100~-110 was slightly higher in DCM (14.42%) and HCM patients (14.48%), as compared with normal controls (11.01%). The prevalence of genotype of 848A/G was significantly higher in DCM (6.73%; OR = 9.43; p = 0.0002), but not in HCM patients (1.38%; OR = 1.37; p = 0.62), as compared with controls (0.76%). Haplotype -_G consisting c.-100~-110 and A848G was associated with increased risk of DCM (OR = 17.27; 95%CI = 3.19–93.56; p = 0.001) but not associated with HCM (OR = 1.90; 95%CI = 0.38–9.55; p = 0.44). Co-occurrence of the genotypes -/- of c.-100~-110 and 848A/G was found in 5 patients with DCM (4.81%; OR = 39.85; p = 0.0001), none of HCM patients, and only 1 of the controls (0.13%). Both polymorphisms were also found in the Japanese population, but not in the Africans and Caucasians. C.-100~-110 resulted in a decrease of δ-SG promoter activity to 64±3% of the control level (p<0.01). Both co-immunoprecipitation and in vitro protein pull-down assays demonstrated that δ-SG-283R interacts normally to β- and γ-SG, but significantly decreased localization of β/δ/γ-SG on the plasma membrane. In conclusion, haplotype -_G composed of c.-100~-110 and A848G confers higher susceptibility to DCM in the Mongoloid population.
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Fukuda T, Shirane A, Wada-Hiraike O, Oda K, Tanikawa M, Sakuabashi A, Hirano M, Fu H, Morita Y, Miyamoto Y, Inaba K, Kawana K, Osuga Y, Fujii T. HAND2-mediated proteolysis negatively regulates the function of estrogen receptor α. Mol Med Rep 2015; 12:5538-44. [PMID: 26166202 DOI: 10.3892/mmr.2015.4070] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 06/11/2015] [Indexed: 11/05/2022] Open
Abstract
A previous study demonstrated that the progesterone‑inducible HAND2 gene product is a basic helix‑loop‑helix transcription factor and prevents mitogenic effects of estrogen receptor α (ERα) by inhibiting fibroblast growth factor signalling in mouse uteri. However, whether HAND2 directly affects the transcriptional activation function of ERα remains to be elucidated. In the present study, the physical interaction between HAND2 and ERα was investigating by performing an immunoprecipitation assay and an in vitro pull‑down assay. The results demonstrated that HAND2 and ERα interacted in a ligand‑independent manner. The in vitro pull‑down assays revealed a direct interaction between HAND2 and the amino‑terminus of ERα, termed the activation function‑1 domain. To determine the physiological significance of this interaction, the role of HAND2 as a cofactor of ERα was investigated, which revealed that HAND2 inhibited the ligand‑dependent transcriptional activation function of ERα. This result was further confirmed and the mRNA expression of vascular endothelial growth factor, an ERα‑downstream factor, was decreased by the overexpression of HAND2. This inhibition of ligand‑dependent transcriptional activation function of ERα was possibly attributed to the proteasomic degradation of ERα by HAND2. These results indicate a novel anti‑tumorigenic function of HAND2 in regulating ERα‑dependent gene expression. Considering that HAND2 is commonly hypermethylated and silenced in endometrial cancer, it is hypothesized that HAND2 may serve as a possible tumor suppressor, particularly in uterine tissue.
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Affiliation(s)
- Tomohiko Fukuda
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113‑8655, Japan
| | - Akira Shirane
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113‑8655, Japan
| | - Osamu Wada-Hiraike
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113‑8655, Japan
| | - Katsutoshi Oda
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113‑8655, Japan
| | - Michihiro Tanikawa
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113‑8655, Japan
| | - Ayako Sakuabashi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113‑8655, Japan
| | - Mana Hirano
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113‑8655, Japan
| | - Houju Fu
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113‑8655, Japan
| | - Yoshihiro Morita
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113‑8655, Japan
| | - Yuichiro Miyamoto
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113‑8655, Japan
| | - Kanako Inaba
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113‑8655, Japan
| | - Kei Kawana
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113‑8655, Japan
| | - Yutaka Osuga
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113‑8655, Japan
| | - Tomoyuki Fujii
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113‑8655, Japan
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Square T, Jandzik D, Cattell M, Coe A, Doherty J, Medeiros DM. A gene expression map of the larval Xenopus laevis head reveals developmental changes underlying the evolution of new skeletal elements. Dev Biol 2014; 397:293-304. [PMID: 25446275 DOI: 10.1016/j.ydbio.2014.10.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 10/02/2014] [Accepted: 10/20/2014] [Indexed: 11/29/2022]
Abstract
The morphology of the vertebrate head skeleton is highly plastic, with the number, size, shape, and position of its components varying dramatically between groups. While this evolutionary flexibility has been key to vertebrate success, its developmental and genetic bases are poorly understood. The larval head skeleton of the frog Xenopus laevis possesses a unique combination of ancestral tetrapod features and anuran-specific novelties. We built a detailed gene expression map of the head mesenchyme in X. laevis during early larval development, focusing on transcription factor families with known functions in vertebrate head skeleton development. This map was then compared to homologous gene expression in zebrafish, mouse, and shark embryos to identify conserved and evolutionarily flexible aspects of vertebrate head skeleton development. While we observed broad conservation of gene expression between X. laevis and other gnathostomes, we also identified several divergent features that correlate to lineage-specific novelties. We noted a conspicuous change in dlx1/2 and emx2 expression in the second pharyngeal arch, presaging the differentiation of the reduced dorsal hyoid arch skeletal element typical of modern anamniote tetrapods. In the first pharyngeal arch we observed a shift in the expression of the joint inhibitor barx1, and new expression of the joint marker gdf5, shortly before skeletal differentiation. This suggests that the anuran-specific infrarostral cartilage evolved by partitioning of Meckel's cartilage with a new paired joint. Taken together, these comparisons support a model in which early patterning mechanisms divide the vertebrate head mesenchyme into a highly conserved set of skeletal precursor populations. While subtle changes in this early patterning system can affect skeletal element size, they do not appear to underlie the evolution of new joints or cartilages. In contrast, later expression of the genes that regulate skeletal element differentiation can be clearly linked to the evolution of novel skeletal elements. We posit that changes in the expression of downstream regulators of skeletal differentiation, like barx1 and gdf5, is one mechanism by which head skeletal element number and articulation are altered during evolution.
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Affiliation(s)
- Tyler Square
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
| | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 84215, Slovakia
| | - Maria Cattell
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Alex Coe
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Jacob Doherty
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
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Tamura M, Amano T, Shiroishi T. The Hand2 Gene Dosage Effect in Developmental Defects and Human Congenital Disorders. Curr Top Dev Biol 2014; 110:129-52. [DOI: 10.1016/b978-0-12-405943-6.00003-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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19
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Prat-Vidal C, Gálvez-Montón C, Nonell L, Puigdecanet E, Astier L, Solé F, Bayes-Genis A. Identification of temporal and region-specific myocardial gene expression patterns in response to infarction in swine. PLoS One 2013; 8:e54785. [PMID: 23372767 PMCID: PMC3556027 DOI: 10.1371/journal.pone.0054785] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 12/14/2012] [Indexed: 11/19/2022] Open
Abstract
Molecular mechanisms associated with pathophysiological changes in ventricular remodelling due to myocardial infarction (MI) remain poorly understood. We analyzed changes in gene expression by microarray technology in porcine myocardial tissue at 1, 4, and 6 weeks post-MI.MI was induced by coronary artery ligation in 9 female pigs (30-40 kg). Animals were randomly sacrificed at 1, 4, or 6 weeks post-MI (n = 3 per group) and 3 healthy animals were also included as control group. Total RNA from myocardial samples was hybridized to GeneChip® Porcine Genome Arrays. Functional analysis was obtained with the Ingenuity Pathway Analysis (IPA) online tool. Validation of microarray data was performed by quantitative real-time PCR (qRT-PCR).More than 8,000 different probe sets showed altered expression in the remodelling myocardium at 1, 4, or 6 weeks post-MI. Ninety-seven percent of altered transcripts were detected in the infarct core and 255 probe sets were differentially expressed in the remote myocardium. Functional analysis revealed 28 genes de-regulated in the remote myocardial region in at least one of the three temporal analyzed stages, including genes associated with heart failure (HF), systemic sclerosis and coronary artery disease. In the infarct core tissue, eight major time-dependent gene expression patterns were recognized among 4,221 probe sets commonly altered over time. Altered gene expression of ACVR2B, BID, BMP2, BMPR1A, LMNA, NFKBIA, SMAD1, TGFB3, TNFRSF1A, and TP53 were further validated.The clustering of similar expression patterns for gene products with related function revealed molecular footprints, some of them described for the first time, which elucidate changes in biological processes at different stages after MI.
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Affiliation(s)
- Cristina Prat-Vidal
- Imperial College Research Ethics Committee (Heart Failure and Cardiac Regeneration) Research Program, Health Sciences Research Institute Germans Trias i Pujol. Cardiology Service, Hospital Universitari Germans Trias i Pujol, Badalona (Barcelona), Spain
| | - Carolina Gálvez-Montón
- Imperial College Research Ethics Committee (Heart Failure and Cardiac Regeneration) Research Program, Health Sciences Research Institute Germans Trias i Pujol. Cardiology Service, Hospital Universitari Germans Trias i Pujol, Badalona (Barcelona), Spain
| | - Lara Nonell
- Servei d'Anàlisi de Microarrays, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Eulàlia Puigdecanet
- Servei d'Anàlisi de Microarrays, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Laura Astier
- Imperial College Research Ethics Committee (Heart Failure and Cardiac Regeneration) Research Program, Health Sciences Research Institute Germans Trias i Pujol. Cardiology Service, Hospital Universitari Germans Trias i Pujol, Badalona (Barcelona), Spain
| | - Francesc Solé
- Servei d'Anàlisi de Microarrays, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
- Laboratori de Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | - Antoni Bayes-Genis
- Imperial College Research Ethics Committee (Heart Failure and Cardiac Regeneration) Research Program, Health Sciences Research Institute Germans Trias i Pujol. Cardiology Service, Hospital Universitari Germans Trias i Pujol, Badalona (Barcelona), Spain
- Department of Medicine, University Autonomous of Barcelona, Barcelona, Spain
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Taubenschmid J, Weitzer G. Mechanisms of cardiogenesis in cardiovascular progenitor cells. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2012; 293:195-267. [PMID: 22251563 PMCID: PMC7615846 DOI: 10.1016/b978-0-12-394304-0.00012-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Self-renewing cells of the vertebrate heart have become a major subject of interest in the past decade. However, many researchers had a hard time to argue against the orthodox textbook view that defines the heart as a postmitotic organ. Once the scientific community agreed on the existence of self-renewing cells in the vertebrate heart, their origin was again put on trial when transdifferentiation, dedifferentiation, and reprogramming could no longer be excluded as potential sources of self-renewal in the adult organ. Additionally, the presence of self-renewing pluripotent cells in the peripheral blood challenges the concept of tissue-specific stem and progenitor cells. Leaving these unsolved problems aside, it seems very desirable to learn about the basic biology of this unique cell type. Thus, we shall here paint a picture of cardiovascular progenitor cells including the current knowledge about their origin, basic nature, and the molecular mechanisms guiding proliferation and differentiation into somatic cells of the heart.
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Affiliation(s)
- Jasmin Taubenschmid
- Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
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Takagaki Y, Yamagishi H, Matsuoka R. Factors Involved in Signal Transduction During Vertebrate Myogenesis. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2012; 296:187-272. [DOI: 10.1016/b978-0-12-394307-1.00004-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Krause M, Liu J. Somatic muscle specification during embryonic and post-embryonic development in the nematode C. elegans. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2011; 1:203-14. [PMID: 23801436 DOI: 10.1002/wdev.15] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Myogenesis has proved to be a powerful paradigm for understanding cell fate specification and differentiation in many model organisms. Studies of somatic bodywall muscle (BWM) development in Caenorhabditis elegans allow us to define, with single cell resolution, the distinct hierarchies of transcriptional regulators needed for myogenesis throughout development. Although all 95 BWM cells appear uniform after differentiation, there are several different regulatory cascades employed embryonically and post-embryonically. These, in turn, are integrated into multiple extrinsic cell signaling events. The convergence of these different pathways on the key nodal point, that is the activation of the core muscle module, commits individual cells to myogenesis. Comparisons of myogenesis between C. elegans and other model systems provide insights into the evolution of contractile cell types, demonstrating the conservation of regulatory schemes for muscles throughout the animal kingdom.
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Affiliation(s)
- Michael Krause
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
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He D, Liu ZP, Chen L. Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach. BMC Genomics 2011; 12:592. [PMID: 22136190 PMCID: PMC3256240 DOI: 10.1186/1471-2164-12-592] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 12/02/2011] [Indexed: 12/16/2022] Open
Abstract
Background The incidence of congenital heart disease (CHD) is continuously increasing among infants born alive nowadays, making it one of the leading causes of infant morbidity worldwide. Various studies suggest that both genetic and environmental factors lead to CHD, and therefore identifying its candidate genes and disease-markers has been one of the central topics in CHD research. By using the high-throughput genomic data of CHD which are available recently, network-based methods provide powerful alternatives of systematic analysis of complex diseases and identification of dysfunctional modules and candidate disease genes. Results In this paper, by modeling the information flow from source disease genes to targets of differentially expressed genes via a context-specific protein-protein interaction network, we extracted dysfunctional modules which were then validated by various types of measurements and independent datasets. Network topology analysis of these modules revealed major and auxiliary pathways and cellular processes in CHD, demonstrating the biological usefulness of the identified modules. We also prioritized a list of candidate CHD genes from these modules using a guilt-by-association approach, which are well supported by various kinds of literature and experimental evidence. Conclusions We provided a network-based analysis to detect dysfunctional modules and disease genes of CHD by modeling the information transmission from source disease genes to targets of differentially expressed genes. Our method resulted in 12 modules from the constructed CHD subnetwork. We further identified and prioritized candidate disease genes of CHD from these dysfunctional modules. In conclusion, module analysis not only revealed several important findings with regard to the underlying molecular mechanisms of CHD, but also suggested the distinct network properties of causal disease genes which lead to identification of candidate CHD genes.
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Affiliation(s)
- Danning He
- Key Laboratory of Systems Biology, SIBS-Novo Nordisk Translational Research Centre for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Two novel HAND1 mutations in Chinese patients with ventricular septal defect. Clin Chim Acta 2011; 413:675-7. [PMID: 22032825 DOI: 10.1016/j.cca.2011.10.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 09/22/2011] [Accepted: 10/11/2011] [Indexed: 11/20/2022]
Abstract
BACKGROUND The HAND1 gene encodes a basic helix-loop-helix (bHLH) transcription factor which plays an essential role in the development of heart. Mutations in HAND1 have been identified in congenital heart disease (CHD) patients with hypoplastic hearts and septal defects. The spectrum of CHD relating to HAND1 mutations needs further study. METHODS AND RESULTS We screened HAND1 coding regions for mutations in 498 Chinese patients with CHD and 250 control subjects. We identified two novel non-synonymous mutations, c.217G>A (p.Gly73Ser) and c.456G>T (p.Lys152Asn), in the patients with ventricular septal defect (VSD). The two mutations were located in HAND1 evolutionarily conserved residues and enhanced the capability of HAND1 to form homodimers. CONCLUSIONS This is the first report of mutations in the HAND1 gene in Chinese patients with VSD and provides new insight into the etiology of VSD.
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Qin Q, Xu Y, He T, Qin C, Xu J. Normal and disease-related biological functions of Twist1 and underlying molecular mechanisms. Cell Res 2011; 22:90-106. [PMID: 21876555 DOI: 10.1038/cr.2011.144] [Citation(s) in RCA: 320] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
This article reviews the molecular structure, expression pattern, physiological function, pathological roles and molecular mechanisms of Twist1 in development, genetic disease and cancer. Twist1 is a basic helix-loop-helix domain-containing transcription factor. It forms homo- or hetero-dimers in order to bind the Nde1 E-box element and activate or repress its target genes. During development, Twist1 is essential for mesoderm specification and differentiation. Heterozygous loss-of-function mutations of the human Twist1 gene cause several diseases including the Saethre-Chotzen syndrome. The Twist1-null mouse embryos die with unclosed cranial neural tubes and defective head mesenchyme, somites and limb buds. Twist1 is expressed in breast, liver, prostate, gastric and other types of cancers, and its expression is usually associated with invasive and metastatic cancer phenotypes. In cancer cells, Twist1 is upregulated by multiple factors including SRC-1, STAT3, MSX2, HIF-1α, integrin-linked kinase and NF-κB. Twist1 significantly enhances epithelial-mesenchymal transition (EMT) and cancer cell migration and invasion, hence promoting cancer metastasis. Twist1 promotes EMT in part by directly repressing E-cadherin expression by recruiting the nucleosome remodeling and deacetylase complex for gene repression and by upregulating Bmi1, AKT2, YB-1, etc. Emerging evidence also suggests that Twist1 plays a role in expansion and chemotherapeutic resistance of cancer stem cells. Further understanding of the mechanisms by which Twist1 promotes metastasis and identification of Twist1 functional modulators may hold promise for developing new strategies to inhibit EMT and cancer metastasis.
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Affiliation(s)
- Qian Qin
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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D’Autréaux F, Margolis KG, Roberts J, Stevanovic K, Mawe G, Li Z, Karamooz N, Ahuja A, Morikawa Y, Cserjesi P, Setlick W, Gershon MD. Expression level of Hand2 affects specification of enteric neurons and gastrointestinal function in mice. Gastroenterology 2011; 141:576-87, 587.e1-6. [PMID: 21669203 PMCID: PMC3152642 DOI: 10.1053/j.gastro.2011.04.059] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 03/20/2011] [Accepted: 04/12/2011] [Indexed: 01/08/2023]
Abstract
BACKGROUND & AIMS Hand2 is a basic helix-loop-helix transcription factor required for terminal differentiation of enteric neurons. We studied Hand2 haploinsufficient mice, to determine whether reduced expression of Hand2 allows sufficient enteric neurogenesis for survival, but not for development of a normal enteric nervous system (ENS). METHODS Enteric transcripts that encode Hand2 and the neuron-specific embryonic lethal abnormal vision proteins HuB, HuC, and HuD were quantified. Immunocytochemistry was used to identify and quantify neurons. Apoptosis was analyzed with the terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick-end labeling procedure. Intracellular microelectrodes were used to record inhibitory junction potentials. Gastrointestinal transit and colonic motility were measured in vivo. RESULTS Levels of of enteric Hand2 transcripts were associated with genotypes of mice, in the following order: Hand2(+/+) > Hand2(LoxP/+) > Hand2(+/-) > Hand2(LoxP/-). Parallel reductions were found in expression of HuD and in regional and phenotypic manners. Numbers of neurons, numbers of neuronal nitric oxide synthase(+) and calretinin(+), but not substance P(+) or vasoactive intestinal peptide(+) neurons, decreased. No effects were observed in stomach or cecum. Apoptosis was not detected, consistent with the concept that Hand2 inhibits neuronal differentiation, rather than regulates survival. The amplitude of inhibitory junction potentials in colonic circular muscle was similar in Hand2 wild-type and haploinsufficient mice, although in haploinsufficient mice, the purinergic component was reduced and a nitrergic component appeared. The abnormal ENS of haploinsufficient mice slowed gastrointestinal motility but protected mice against colitis. CONCLUSIONS Reduced expression of factors required for development of the ENS can cause defects in the ENS that are subtle enough to escape detection yet cause significant abnormalities in bowel function.
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Affiliation(s)
- Fabien D’Autréaux
- Département de Biologie - Dévelopement et évolution du système nerveux, CNRS - Ecole Normale Supérieure, Paris, France
| | - Kara G. Margolis
- Department of Pediatrics, Columbia University, College of P&S, New York, NY, U.S.A
| | - Jane Roberts
- Department of Anatomy and Neurobiology, University of Vermont, Burlington, VT, U.S.A
| | - Korey Stevanovic
- Department of Pediatrics, Columbia University, College of P&S, New York, NY, U.S.A
| | - Gary Mawe
- Department of Anatomy and Neurobiology, University of Vermont, Burlington, VT, U.S.A
| | - Zhishan Li
- Pathology and Cell Biology, Columbia University, College of P&S, New York, NY, U.S.A
| | - Nima Karamooz
- Pathology and Cell Biology, Columbia University, College of P&S, New York, NY, U.S.A
| | - Ankur Ahuja
- Pathology and Cell Biology, Columbia University, College of P&S, New York, NY, U.S.A
| | - Yuka Morikawa
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, U.S.A
| | - Peter Cserjesi
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, U.S.A
| | - Wanda Setlick
- Pathology and Cell Biology, Columbia University, College of P&S, New York, NY, U.S.A
| | - Michael D. Gershon
- Pathology and Cell Biology, Columbia University, College of P&S, New York, NY, U.S.A
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Margolis KG, Stevanovic K, Karamooz N, Li ZS, Ahuja A, D'Autréaux F, Saurman V, Chalazonitis A, Gershon MD. Enteric neuronal density contributes to the severity of intestinal inflammation. Gastroenterology 2011; 141:588-98, 598.e1-2. [PMID: 21635893 PMCID: PMC4459707 DOI: 10.1053/j.gastro.2011.04.047] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 01/31/2011] [Accepted: 04/12/2011] [Indexed: 12/31/2022]
Abstract
BACKGROUND & AIMS Enteric neurons have been reported to be increased in inflamed regions of the bowel in patients with inflammatory bowel disease or intestinal neurogangliomatosis. It is impossible to determine whether this hyperinnervation predates intestinal inflammation, results from it, or contributes to its severity in humans, so we studied this process in mice. METHODS To determine whether the density of enteric neurons determines the severity of inflammation, we studied transgenic mice that have greater than normal (NSE-noggin mice, which overexpress noggin under the control of the neuron-specific enolase promoter) or fewer than normal (Hand2(+/-) mice) numbers of neurons in the enteric nervous system. Colitis was induced with trinitrobenzene sulfonic acid or dextran sulfate sodium, and the intensity of the resulting inflammation in Hand2(+/-) and NSE-noggin mice was compared with that of wild-type littermates. RESULTS Severity of each form of colitis (based on survival, symptom, and histologic scores; intestinal expression of genes that encode proinflammatory molecules; and levels of neutrophil elastase and p50 nuclear factor κB) were significantly reduced in Hand2(+/-) mice and significantly increased in NSE-noggin animals. Neither mouse differed from wild-type in the severity of delayed-type hypersensitivity (edema, T-cell and neutrophil infiltration, or expression of interleukin-1β, interferon-γ, or tumor necrosis factor-α) induced in the ears using 2,4-dinitro-1-fluorobenzene. Transgene effects on inflammation were therefore restricted to the gastrointestinal tract. CONCLUSIONS The severity of intestinal inflammation is associated with the density of the enteric innervation in mice. Abnormalities in development of the enteric nervous system might therefore contribute to the pathogenesis of inflammatory bowel disease.
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Affiliation(s)
- Kara Gross Margolis
- Department of Pediatrics, Morgan Stanley Children's Hospital, New York, New York 10032, USA.
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Barron F, Woods C, Kuhn K, Bishop J, Howard MJ, Clouthier DE. Downregulation of Dlx5 and Dlx6 expression by Hand2 is essential for initiation of tongue morphogenesis. Development 2011; 138:2249-59. [PMID: 21558373 DOI: 10.1242/dev.056929] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Lower jaw development is a complex process in which multiple signaling cascades establish a proximal-distal organization. These cascades are regulated both spatially and temporally and are constantly refined through both induction of normal signals and inhibition of inappropriate signals. The connective tissue of the tongue arises from cranial neural crest cell-derived ectomesenchyme within the mandibular portion of the first pharyngeal arch and is likely to be impacted by this signaling. Although the developmental mechanisms behind later aspects of tongue development, including innervation and taste acquisition, have been elucidated, the early patterning signals driving ectomesenchyme into a tongue lineage are largely unknown. We show here that the basic helix-loop-helix transcription factor Hand2 plays key roles in establishing the proximal-distal patterning of the mouse lower jaw, in part through establishing a negative-feedback loop in which Hand2 represses Dlx5 and Dlx6 expression in the distal arch ectomesenchyme following Dlx5- and Dlx6-mediated induction of Hand2 expression in the same region. Failure to repress distal Dlx5 and Dlx6 expression results in upregulation of Runx2 expression in the mandibular arch and the subsequent formation of aberrant bone in the lower jaw along with proximal-distal duplications. In addition, there is an absence of lateral lingual swelling expansion, from which the tongue arises, resulting in aglossia. Hand2 thus appears to establish a distal mandibular arch domain that is conducive for lower jaw development, including the initiation of tongue mesenchyme morphogenesis.
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Affiliation(s)
- Francie Barron
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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Vincentz JW, Barnes RM, Firulli AB. Hand factors as regulators of cardiac morphogenesis and implications for congenital heart defects. BIRTH DEFECTS RESEARCH. PART A, CLINICAL AND MOLECULAR TERATOLOGY 2011; 91:485-94. [PMID: 21462297 PMCID: PMC3119928 DOI: 10.1002/bdra.20796] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 01/06/2011] [Accepted: 02/02/2011] [Indexed: 11/08/2022]
Abstract
Almost 15 years of careful study have established the related basic Helix-Loop-Helix (bHLH) transcription factors Hand1 and Hand2 as critical for heart development across evolution. Hand factors make broad contributions, revealed through animal models, to the development of multiple cellular lineages that ultimately contribute to the heart. They perform critical roles in ventricular cardiomyocyte growth, differentiation, morphogenesis, and conduction. They are also important for the proper development of the cardiac outflow tract, epicardium, and endocardium. Molecularly, they function both through DNA binding and through protein-protein interactions, which are regulated transcriptionally, posttranscriptionally by microRNAs, and posttranslationally through phosphoregulation. Although direct Hand factor transcriptional targets are progressively being identified, confirmed direct targets of Hand factor transcriptional activity in the heart are limited. Identification of these targets will be critical to model the mechanisms by which Hand factor bHLH interactions affect developmental pathways. Improved understanding of Hand factor-mediated transcriptional cascades will be necessary to determine how Hand factor dysregulation translates to human disease phenotypes. This review summarizes the insight that animal models have provided into the regulation and function of these factors during heart development, in addition to the recent findings that suggest roles for HAND1 and HAND2 in human congenital heart disease.
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Affiliation(s)
- Joshua W. Vincentz
- Riley Heart Research Center, Wells Center for Pediatric Research, Division of Pediatric Cardiology, Departments of Anatomy, Biochemistry and Medical and Molecular Genetics, Indiana Medical School, 1044 W. Walnut St., Indianapolis, IN 46202-5225, USA
| | - Ralston M. Barnes
- Riley Heart Research Center, Wells Center for Pediatric Research, Division of Pediatric Cardiology, Departments of Anatomy, Biochemistry and Medical and Molecular Genetics, Indiana Medical School, 1044 W. Walnut St., Indianapolis, IN 46202-5225, USA
| | - Anthony B. Firulli
- Riley Heart Research Center, Wells Center for Pediatric Research, Division of Pediatric Cardiology, Departments of Anatomy, Biochemistry and Medical and Molecular Genetics, Indiana Medical School, 1044 W. Walnut St., Indianapolis, IN 46202-5225, USA
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Lu S, Nie J, Luan Q, Feng Q, Xiao Q, Chang Z, Shan C, Hess D, Hemmings BA, Yang Z. Phosphorylation of the Twist1-family basic helix-loop-helix transcription factors is involved in pathological cardiac remodeling. PLoS One 2011; 6:e19251. [PMID: 21559426 PMCID: PMC3084786 DOI: 10.1371/journal.pone.0019251] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 03/24/2011] [Indexed: 01/12/2023] Open
Abstract
Background The Twist1-family basic helix-loop-helix (bHLH) transcription factors including Twist1, Hand1 and Hand2, play an essential role in heart development and are implicated in pathological heart remodeling. Previously, it was reported that these bHLH transcription factors can be regulated by phosphorylation within the basic-helix I domain, which is involved in developmental processes such as limb formation and trophoblast differentiation. However, how phosphorylation of Twist1 family functions in post-natal heart is elusive. Principal Findings Here, we generated transgenic mice with over-expression of Hand1 and Twist1 mutants (to mimic or to abolish phosphorylation) in cardiomyocytes and found pathological cardiac remodeling leading to heart failure and sudden death. Gene expression profile analysis revealed up-regulation of growth-promoting genes and down-regulation of metabolic genes. It is well known that aberrant activation of Akt signaling causes pathological cardiac remodeling and results in heart failure. The basic-helix I domain of Twist1 family members contain Akt substrate consensus motif and may be downstream targets of Akt signaling. Using biochemical analysis, we demonstrated that Hand1 and Twist1 were phosphorylated by Akt in the basic-helix I domain. Phosphorylation of Hand1 regulated its transcriptional activation of luciferase reporter genes and DNA binding ability. Conclusions This study provides novel insights into the regulation of Twist1 family in cardiac remodeling and suggests that the Twist1 family can be regulated by Akt signaling.
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Affiliation(s)
- Shuangshuang Lu
- The Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Junwei Nie
- The Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Qing Luan
- The Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Qiuting Feng
- The Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Qi Xiao
- The Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Zai Chang
- The Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Congjia Shan
- The Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Daniel Hess
- The Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Brian A. Hemmings
- The Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Zhongzhou Yang
- The Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
- * E-mail:
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Firulli BA, McConville DP, Byers JS, Vincentz JW, Barnes RM, Firulli AB. Analysis of a Hand1 hypomorphic allele reveals a critical threshold for embryonic viability. Dev Dyn 2011; 239:2748-60. [PMID: 20737509 DOI: 10.1002/dvdy.22402] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Loss-of-function analysis of the basic helix-loop-helix (bHLH) transcription factor Hand1 indicates critical roles in development. In an effort to generate a Hand1 cDNA knock-in reporter mouse, we generated two hypomorphic alleles, which extend embryonic survival to between embryonic day (E) 10.5 and E12.5. Heart morphogenesis appears largely normal; however, hypomorphic mice display thin left ventricular myocardium and reduction in pharyngeal mesoderm. Caudal defects, large allantois, and thickened yolk sac are observed and consistent with systemic Hand1 gene deletion. Hand1 mRNA is expressed at 30% of wild-type littermates and known Hand1-dependent genes show intermediate expression compared with wild-type and Hand1 null mice. Interestingly, putative bHLH partners, Hand2 and Twist1, show altered expression in both Hand1 null and hypomorphic backgrounds and intercrossing the Hand1 hypomorphic mice onto the Hand2 systemic null background exacerbates the cardiac and lateral mesoderm phenotypes. Together, these data define a critical threshold of Hand1 expression that is necessary for embryonic survival.
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Affiliation(s)
- Beth A Firulli
- Riley Heart Research Center, Herman B. Wells Center for Pediatric Research Division of Pediatrics Cardiology, Departments of Anatomy and Medical and Molecular Genetics, Indiana Medical School, Indianapolis, Indiana 46202-5225, USA
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Wang L, Bresee CS, Jiang H, He W, Ren T, Schweitzer R, Brigande JV. Scleraxis is required for differentiation of the stapedius and tensor tympani tendons of the middle ear. J Assoc Res Otolaryngol 2011; 12:407-21. [PMID: 21399989 DOI: 10.1007/s10162-011-0264-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 02/22/2011] [Indexed: 12/20/2022] Open
Abstract
Scleraxis (Scx) is a basic helix-loop-helix transcription factor expressed in tendon and ligament progenitor cells and the differentiated cells within these connective tissues in the axial and appendicular skeleton. Unexpectedly, we found expression of the Scx transgenic reporter mouse, Scx-GFP, in interdental cells, sensory hair cells, and cochlear supporting cells at embryonic day 18.5 (E18.5). We evaluated Scx-null mice to gain insight into the function of Scx in the inner ear. Paradoxical hearing loss was detected in Scx-nulls, with ~50% of the mutants presenting elevated auditory thresholds. However, Scx-null mice have no obvious, gross alterations in cochlear morphology or cellular patterning. Moreover, we show that the elevated auditory thresholds correlate with middle ear infection. Laser interferometric measurement of sound-induced malleal movements in the infected Scx-nulls demonstrates increased impedance of the middle ear that accounts for the hearing loss observed. The vertebrate middle ear transmits vibrations of the tympanic membrane to the cochlea. The tensor tympani and stapedius muscles insert into the malleus and stapes via distinct tendons and mediate the middle ear muscle reflex that in part protects the inner ear from noise-induced damage. Nothing, however, is known about the development and function of these tendons. Scx is expressed in tendon progenitors at E14.5 and differentiated tenocytes of the stapedius and tensor tympani tendons at E16.5-18.5. Scx-nulls have dramatically shorter stapedius and tensor tympani tendons with altered extracellular matrix consistent with abnormal differentiation in which condensed tendon progenitors are inefficiently incorporated into the elongating tendons. Scx-GFP is the first transgenic reporter that identifies middle ear tendon lineages from the time of their formation through complete tendon maturation. Scx-null is the first genetically defined mouse model for abnormal middle ear tendon differentiation. Scx mouse models will facilitate studies of tendon and muscle formation and function in the middle ear.
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Affiliation(s)
- Lingyan Wang
- Oregon Hearing Research Center, Oregon Health & Science University, Portland, USA.
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Kim TM, Huang W, Park R, Park PJ, Johnson MD. A developmental taxonomy of glioblastoma defined and maintained by MicroRNAs. Cancer Res 2011; 71:3387-99. [PMID: 21385897 DOI: 10.1158/0008-5472.can-10-4117] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
mRNA expression profiling has suggested the existence of multiple glioblastoma subclasses, but their number and characteristics vary among studies and the etiology underlying their development is unclear. In this study, we analyzed 261 microRNA expression profiles from The Cancer Genome Atlas (TCGA), identifying five clinically and genetically distinct subclasses of glioblastoma that each related to a different neural precursor cell type. These microRNA-based glioblastoma subclasses displayed microRNA and mRNA expression signatures resembling those of radial glia, oligoneuronal precursors, neuronal precursors, neuroepithelial/neural crest precursors, or astrocyte precursors. Each subclass was determined to be genetically distinct, based on the significant differences they displayed in terms of patient race, age, treatment response, and survival. We also identified several microRNAs as potent regulators of subclass-specific gene expression networks in glioblastoma. Foremost among these is miR-9, which suppresses mesenchymal differentiation in glioblastoma by downregulating expression of JAK kinases and inhibiting activation of STAT3. Our findings suggest that microRNAs are important determinants of glioblastoma subclasses through their ability to regulate developmental growth and differentiation programs in several transformed neural precursor cell types. Taken together, our results define developmental microRNA expression signatures that both characterize and contribute to the phenotypic diversity of glioblastoma subclasses, thereby providing an expanded framework for understanding the pathogenesis of glioblastoma in a human neurodevelopmental context.
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Affiliation(s)
- Tae-Min Kim
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Li Q, Kannan A, DeMayo FJ, Lydon JP, Cooke PS, Yamagishi H, Srivastava D, Bagchi MK, Bagchi IC. The antiproliferative action of progesterone in uterine epithelium is mediated by Hand2. Science 2011; 331:912-6. [PMID: 21330545 DOI: 10.1126/science.1197454] [Citation(s) in RCA: 278] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
During pregnancy, progesterone inhibits the growth-promoting actions of estrogen in the uterus. However, the mechanism for this is not clear. The attenuation of estrogen-mediated proliferation of the uterine epithelium by progesterone is a prerequisite for successful implantation. Our study reveals that progesterone-induced expression of the basic helix-loop-helix transcription factor Hand2 in the uterine stroma suppresses the production of several fibroblast growth factors (FGFs) that act as paracrine mediators of mitogenic effects of estrogen on the epithelium. In mouse uteri lacking Hand2, continued induction of these FGFs in the stroma maintains epithelial proliferation and stimulates estrogen-induced pathways, resulting in impaired implantation. Thus, Hand2 is a critical regulator of the uterine stromal-epithelial communication that directs proper steroid regulation conducive for the establishment of pregnancy.
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Affiliation(s)
- Quanxi Li
- Department of Comparative Biosciences, University of Illinois Urbana/Champaign, Urbana, IL 61820, USA
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Barnes RM, Firulli BA, VanDusen NJ, Morikawa Y, Conway SJ, Cserjesi P, Vincentz JW, Firulli AB. Hand2 loss-of-function in Hand1-expressing cells reveals distinct roles in epicardial and coronary vessel development. Circ Res 2011; 108:940-9. [PMID: 21350214 DOI: 10.1161/circresaha.110.233171] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
RATIONALE The basic helix-loop-helix (bHLH) transcription factors Hand1 and Hand2 are essential for embryonic development. Given their requirement for cardiogenesis, it is imperative to determine their impact on cardiovascular function. OBJECTIVE To deduce the role of Hand2 within the epicardium. METHOD AND RESULTS We engineered a Hand1 allele expressing Cre recombinase. Cardiac Hand1 expression is largely limited to cells of the primary heart field, overlapping little with Hand2 expression. Hand1 is expressed within the septum transversum, and the Hand1 lineage marks the proepicardial organ and epicardium. To examine Hand factor functional overlap, we conditionally deleted Hand2 from Hand1-expressing cells. Hand2 mutants display defective epicardialization and fail to form coronary arteries, coincident with altered extracellular matrix deposition and Pdgfr expression. CONCLUSIONS These data demonstrate a hierarchal relationship whereby transient Hand1 septum transversum expression defines epicardial precursors that are subsequently dependent on Hand2 function.
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Affiliation(s)
- Ralston M Barnes
- Riley Heart Research Center, Wells Center for Pediatric Research, Division of Pediatric Cardiology, Departments of Anatomy and Medical and Molecular Genetics, Indiana Medical School, Indianapolis, 46202-5225, USA
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De Masi F, Grove CA, Vedenko A, Alibés A, Gisselbrecht SS, Serrano L, Bulyk ML, Walhout AJM. Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants. Nucleic Acids Res 2011; 39:4553-63. [PMID: 21335608 PMCID: PMC3113581 DOI: 10.1093/nar/gkr070] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Numerous efforts are underway to determine gene regulatory networks that describe physical relationships between transcription factors (TFs) and their target DNA sequences. Members of paralogous TF families typically recognize similar DNA sequences. Knowledge of the molecular determinants of protein–DNA recognition by paralogous TFs is of central importance for understanding how small differences in DNA specificities can dictate target gene selection. Previously, we determined the in vitro DNA binding specificities of 19 Caenorhabditis elegans basic helix-loop-helix (bHLH) dimers using protein binding microarrays. These TFs bind E-box (CANNTG) and E-box-like sequences. Here, we combine these data with logics, bHLH–DNA co-crystal structures and computational modeling to infer which bHLH monomer can interact with which CAN E-box half-site and we identify a critical residue in the protein that dictates this specificity. Validation experiments using mutant bHLH proteins provide support for our inferences. Our study provides insights into the mechanisms of DNA recognition by bHLH dimers as well as a blueprint for system-level studies of the DNA binding determinants of other TF families in different model organisms and humans.
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Affiliation(s)
- Federico De Masi
- Department of Medicine, Division of Genetics, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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Barnes RM, Firulli BA, Conway SJ, Vincentz JW, Firulli AB. Analysis of the Hand1 cell lineage reveals novel contributions to cardiovascular, neural crest, extra-embryonic, and lateral mesoderm derivatives. Dev Dyn 2011; 239:3086-97. [PMID: 20882677 DOI: 10.1002/dvdy.22428] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The basic Helix-Loop-Helix (bHLH) transcription factors Hand1 and Hand2 play critical roles in the development of multiple organ systems during embryogenesis. The dynamic expression patterns of these two factors within developing tissues obfuscate their respective unique and redundant organogenic functions. To define cell lineages potentially dependent upon Hand gene expression, we generated a mutant allele in which the coding region of Hand1 is replaced by Cre recombinase. Subsequent Cre-mediated activation of β-galactosidase or eYFP reporter alleles enabled lineage trace analyses that clearly define the fate of Hand1-expressing cells. Hand1-driven Cre marks specific lineages within the extra embryonic tissues, placenta, sympathetic nervous system, limbs, jaw, and several cell types within the cardiovascular system. Comparisons between Hand1 expression and Hand1-lineage greatly refine our understanding of its dynamic spatial-temporal expression domains and raise the possibility of novel Hand1 functions in structures not thought to be Hand1-dependent.
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Affiliation(s)
- Ralston M Barnes
- Riley Heart Research Center, Wells Center for Pediatric Research, Division of Pediatric Cardiology, Department of Anatomy, Indiana Medical School, Indianapolis, Indiana 46202-5225, USA
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Yin C, Kikuchi K, Hochgreb T, Poss KD, Stainier DYR. Hand2 regulates extracellular matrix remodeling essential for gut-looping morphogenesis in zebrafish. Dev Cell 2010; 18:973-84. [PMID: 20627079 DOI: 10.1016/j.devcel.2010.05.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Revised: 02/19/2010] [Accepted: 03/24/2010] [Indexed: 12/19/2022]
Abstract
Extracellular matrix (ECM) remodeling is critical for organogenesis, yet its molecular regulation is poorly understood. In zebrafish, asymmetric migration of the epithelial lateral plate mesoderm (LPM) displaces the gut leftward, allowing correct placement of the liver and pancreas. To observe LPM migration at cellular resolution, we transgenically expressed EGFP under the control of the regulatory sequences of the bHLH transcription factor gene hand2. We found that laminin is distributed along the LPM/gut boundary during gut looping, and that it appears to become diminished by the migrating hand2-expressing cells. Laminin diminishment is necessary for LPM migration and is dependent on matrix metalloproteinase (MMP) activity. Loss of Hand2 function causes reduced MMP activity and prolonged laminin deposition at the LPM/gut boundary, leading to failed asymmetric LPM migration and gut looping. Our study reveals an unexpected role for Hand2, a key regulator of cell specification and differentiation, in modulating ECM remodeling during organogenesis.
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Affiliation(s)
- Chunyue Yin
- Department of Biochemistry and Biophysics, Programs in Developmental Biology, Genetics, and Human Genetics, Cardiovascular Research Institute, Liver Center, University of California, San Francisco, San Francisco, CA 94158, USA
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Antonella Cecchetto, Alessandra Rampazzo, Annalisa Angelini,. From molecular mechanisms of cardiac development to genetic substrate of congenital heart diseases. Future Cardiol 2010; 6:373-93. [DOI: 10.2217/fca.10.10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Congenital heart disease is one of the most important chapters in medicine because its incidence is increasing and nowadays it is close to 1.2%. Most congenital heart disorders are the result of defects during embryogenesis, which implies that they are due to alterations in genes involved in cardiac development. This review summarizes current knowledge regarding the molecular mechanisms involved in cardiac development in order to clarify the genetic basis of congenital heart disease.
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Chooniedass-Kothari S, Hamedani MK, Auge C, Wang X, Carascossa S, Yan Y, Cooper C, Vincett D, Myal Y, Jalaguier S, Cavailles V, Leygue E. The steroid receptor RNA activator protein is recruited to promoter regions and acts as a transcriptional repressor. FEBS Lett 2010; 584:2218-24. [PMID: 20398657 DOI: 10.1016/j.febslet.2010.04.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 03/31/2010] [Accepted: 04/08/2010] [Indexed: 01/23/2023]
Abstract
Products of the steroid receptor RNA activator (SRA1) gene have the unusual property to function both at the RNA and the protein levels. SRA-RNA has long been known to increase the activity of multiple nuclear receptors. It has more recently been proposed than steroid receptor RNA activator protein (SRAP) also modulates steroid receptors activity. Herein, we show for the first time that SRAP physically interacts with multiple transcription factors and is recruited to specific promoter regions. Artificially recruiting SRAP to the promoter of a luciferase reporter gene under the control of the strong transcriptional activator VP16 leads to a decrease in transcription. Altogether we propose that SRAP could be a new transcriptional regulator, able to function as a repressor through direct association with promoters.
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Firulli AB, Firulli BA, Wang J, Rogers RH, Conway SJ. Gene replacement strategies to test the functional redundancy of basic helix-loop-helix transcription factor. Pediatr Cardiol 2010; 31:438-48. [PMID: 20155416 PMCID: PMC3581321 DOI: 10.1007/s00246-010-9669-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 01/26/2010] [Indexed: 02/02/2023]
Abstract
Basic helix-loop-helix (bHLH) transcription factors control developmental decisions for a wide range of embryonic cell types. Hand1 and Hand2 are closely related bHLH proteins that control cardiac, craniofacial, and limb development. Within the developing heart, Hand1 expression becomes restricted predominantly to the left ventricle, whereas Hand2 becomes restricted predominantly to the left ventricle, for which findings have shown each Hand factor to be necessary for normal chamber formation. Forced overexpression of Hand1 throughout the early developing heart induces abnormal interventricular septal development, with resulting pathogenesis of congenital heart defects. To investigate the potential transcriptional mechanisms involved in heart morphogenesis by Hand2, this study used a replacement targeting approach to knock Hand2 into the Hand1 locus and ectopically express one copy of Hand2 within the endogenous Hand1 expression domain in the developing hearts of transgenic mice. The findings show that high-percentage Hand1 ( Hand2 ) chimeras die at birth and exhibit a range of congenital heart defects. These findings suggest that Hand factors may act via unique transcriptional mechanisms mediated by bHLH factor partner choice, supporting the notion that alterations of Hand factor stoichiometry may be as deleterious to normal heart morphogenesis as Hand factor loss of function.
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Affiliation(s)
- Anthony B. Firulli
- Riley Heart Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 West Walnut Street, Room R4 W379, Indianapolis, IN 46202, USA
| | - Beth A. Firulli
- Riley Heart Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 West Walnut Street, Room R4 W379, Indianapolis, IN 46202, USA
| | - Jian Wang
- Riley Heart Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 West Walnut Street, Room R4 W379, Indianapolis, IN 46202, USA
| | - Rhonda H. Rogers
- Riley Heart Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 West Walnut Street, Room R4 W379, Indianapolis, IN 46202, USA
| | - Simon J. Conway
- Riley Heart Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 West Walnut Street, Room R4 W379, Indianapolis, IN 46202, USA
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Abstract
Cell specification and differentiation of cardiomyocytes from mesodermal precursors is orchestrated by epigenetic and transcriptional inputs throughout heart formation. Of the many transcription factor super families that play a role in this process, the basic Helix-loop Helix (bHLH) family of proteins is well represented. The bHLH protein by design allows for dimerization-both as homodimers and heterodimers with other proteins within the family. Although DNA binding is mediated via a short variable cis-element termed an E-box, it is clear that DNA-affinity for these elements as well as the transcriptional input conveyed is dictated largely by the transcriptional partners within the dimer complex. Dimer partner choice has a number of inputs requiring co-expression within a given cell nucleus and dimerization modulation by the level of protein present, and post-translational modifications that can both enhance or reduce protein-protein interactions. Due to these complex interrelationships, it has been difficult to identity bona-fide downstream transcriptional targets and define the molecular pathways regulated of bHLH factors within cardiogenesis, despite the clear roles suggested via loss-of-function animals models. This review focuses on the Hand bHLH proteins-key members of the Twist-family of bHLH factors. Despite over a decade of investigation, questions regarding functional redundancy, downstream targets, and biological role during heart specification and differentiation have still not been fully addressed. Our goal is to review what is currently known and address strategies for gaining further understanding of Hand/Twist gene dosage and functional redundancy relationships within the developing heart that may underlie congenital heart defect pathogenesis.
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Affiliation(s)
- Simon J Conway
- Division of Pediatric Cardiology, Department Anatomy, Riley Heart Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 W. Walnut St, Indianapolis, IN 46202-5225, USA
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Du Puy L, Beqqali A, Monshouwer-Kloots J, Haagsman HP, Roelen BAJ, Passier R. CAZIP, a novel protein expressed in the developing heart and nervous system. Dev Dyn 2010; 238:2903-11. [PMID: 19806667 DOI: 10.1002/dvdy.22107] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recently, we have performed a whole genome micro-array analysis on human embryonic stem cells differentiating toward cardiomyocytes, which resulted in the identification of novel genes that were highly up-regulated during differentiation. Here, we describe one of these novel genes annotated as KIAA0774. The predicted protein contains a leucine-zipper domain at the C-terminus and has at least two isoforms (358 and 1354 amino acids). Whole-mount in situ hybridization confirmed that the mRNA of both the mouse and chicken orthologs of KIAA0774 is expressed during early cardiac development. Hence, we named this protein CAZIP (cardiac zipper protein). Later during embryonic development, Cazip was also expressed in parts of the nervous system. Northern blot and real-time polymerase chain reaction analysis showed that Cazip is expressed in heart and brain in adult mice. These results suggest a role for CAZIP in development and function of the heart and nervous system in vertebrates.
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Affiliation(s)
- Leonie Du Puy
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Holler KL, Hendershot TJ, Troy SE, Vincentz JW, Firulli AB, Howard MJ. Targeted deletion of Hand2 in cardiac neural crest-derived cells influences cardiac gene expression and outflow tract development. Dev Biol 2010; 341:291-304. [PMID: 20144608 DOI: 10.1016/j.ydbio.2010.02.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 01/29/2010] [Accepted: 02/01/2010] [Indexed: 11/29/2022]
Abstract
The basic helix-loop-helix DNA binding protein Hand2 has critical functions in cardiac development both in neural crest-derived and mesoderm-derived structures. Targeted deletion of Hand2 in the neural crest has allowed us to genetically dissect Hand2-dependent defects specifically in outflow tract and cardiac cushion independent of Hand2 functions in mesoderm-derived structures. Targeted deletion of Hand2 in the neural crest results in misalignment of the aortic arch arteries and outflow tract, contributing to development of double outlet right ventricle (DORV) and ventricular septal defects (VSD). These neural crest-derived developmental anomalies are associated with altered expression of Hand2-target genes we have identified by gene profiling. A number of Hand2 direct target genes have been identified using ChIP and ChIP-on-chip analyses. We have identified and validated a number of genes related to cell migration, proliferation/cell cycle and intracellular signaling whose expression is affected by Hand2 deletion in the neural crest and which are associated with development of VSD and DORV. Our data suggest that Hand2 is a multifunctional DNA binding protein affecting expression of target genes associated with a number of functional interactions in neural crest-derived cells required for proper patterning of the outflow tract, generation of the appropriate number of neural crest-derived cells for elongation of the conotruncus and cardiac cushion organization. Our genetic model has made it possible to investigate the molecular genetics of neural crest contributions to outflow tract morphogenesis and cell differentiation.
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Affiliation(s)
- Kristen L Holler
- Department of Neurosciences and Program in Neurosciences and Degenerative Disease, Health Sciences Campus, University of Toledo, 3000 Arlington Ave., Toledo, OH 43614-1007, USA
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Balic A, Adams D, Mina M. Prx1 and Prx2 cooperatively regulate the morphogenesis of the medial region of the mandibular process. Dev Dyn 2010; 238:2599-613. [PMID: 19777594 DOI: 10.1002/dvdy.22092] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mice lacking both Prx1 and Prx2 display severe abnormalities in the mandible. Our analysis showed that complete loss of Prx gene products leads to growth abnormalities in the mandibular processes evident as early as embryonic day (E) 10.5 associated with changes in the survival of the mesenchyme in the medial region. Changes in the gene expression in the medial and lateral regions were related to gradual loss of a subpopulation of mesenchyme in the medial region expressing eHand. Our analysis also showed that Prx gene products are required for the initiation and maintenance of chondrogenesis and terminal differentiation of the chondrocytes in the caudal and rostral ends of Meckel's cartilage. The fusion of the mandibular processes in the Prx1/Prx2 double mutants is caused by accelerated ossification. These observations together show that, during mandibular morphogenesis, Prx gene products play multiple roles including the cell survival, the region-specific terminal differentiation of Meckelian chondrocytes and osteogenesis.
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Affiliation(s)
- Anamaria Balic
- Department of Craniofacial Sciences, Division of Pediatric Dentistry, School of Dental Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
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Apostolova G, Dechant G. Development of neurotransmitter phenotypes in sympathetic neurons. Auton Neurosci 2009; 151:30-8. [DOI: 10.1016/j.autneu.2009.08.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Jin B, Yao B, Li JL, Fields CR, Delmas AL, Liu C, Robertson KD. DNMT1 and DNMT3B modulate distinct polycomb-mediated histone modifications in colon cancer. Cancer Res 2009; 69:7412-21. [PMID: 19723660 PMCID: PMC2745494 DOI: 10.1158/0008-5472.can-09-0116] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA methylation patterns are established and maintained by three DNA methyltransferases (DNMT): DNMT1, DNMT3A, and DNMT3B. Although essential for development, methylation patterns are frequently disrupted in cancer and contribute directly to carcinogenesis. Recent studies linking polycomb group repression complexes (PRC1 and PRC2) to the DNMTs have begun to shed light on how methylation is targeted. We identified previously a panel of genes regulated by DNMT3B. Here, we compare these with known polycomb group targets to show that approximately 47% of DNMT3B regulated genes are also bound by PRC1 or PRC2. We chose 44 genes coregulated by DNMT3B and PRC1/PRC2 to test whether these criteria would accurately identify novel targets of epigenetic silencing in colon cancer. Using reverse transcription-PCR, bisulfite genomic sequencing, and pyrosequencing, we show that the majority of these genes are frequently silenced in colorectal cancer cell lines and primary tumors. Some of these, including HAND1, HMX2, and SIX3, repressed cell growth. Finally, we analyzed the histone code, DNMT1, DNMT3B, and PRC2 binding by chromatin immunoprecipitation at epigenetically silenced genes to reveal a novel link between DNMT3B and the mark mediated by PRC1. Taken together, these studies suggest that patterns of epigenetic modifiers and the histone code influence the propensity of a gene to become hypermethylated in cancer and that DNMT3B plays an important role in regulating PRC1 function.
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Affiliation(s)
- Bilian Jin
- Department of Biochemistry and Molecular Biology and Cancer Research Center, Medical College of Georgia, Augusta, GA 30912
| | - Bing Yao
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610
| | - Jian-Liang Li
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610
| | - C. Robert Fields
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610
| | - Amber L. Delmas
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610
| | - Chen Liu
- Department of Pathology, University of Florida, Gainesville, FL 32610
| | - Keith D. Robertson
- Department of Biochemistry and Molecular Biology and Cancer Research Center, Medical College of Georgia, Augusta, GA 30912
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Gupta A, Hou R, Liu L, Hiroyasu S, Hadix JA, Huggins GS, Sibinga NES. Daxx inhibits muscle differentiation by repressing E2A-mediated transcription. J Cell Biochem 2009; 107:438-47. [PMID: 19308989 DOI: 10.1002/jcb.22140] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The basic helix-loop-helix (HLH) E2A transcription factors bind to DNA as homodimers or as heterodimers formed with other basic HLH factors, activate gene expression, and promote differentiation of muscle, lymphoid, neuronal, and other cell types. These E2A functions can be inhibited by the Id proteins, HLH factors that sequester E2A in non-DNA binding dimers. Here we describe the direct interaction of E2A with Daxx, a broadly expressed non-HLH protein previously associated with apoptosis and transcriptional repression. Daxx inhibits E2A function, but not via an Id-like mechanism; rather, it recruits histone deacetylase activity to E2A-dependent promoters. Increased Daxx expression during muscle differentiation inhibits E2A-dependent expression of key myogenic genes and reduces myotube formation, while decreased Daxx expression promotes myotube formation. These results identify a new mechanism for limiting E2A activity and establish a link between Daxx-mediated gene regulation and control of cellular differentiation.
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Affiliation(s)
- Amitabh Gupta
- Department of Neurology, Johns Hopkins Hospital, Baltimore, Maryland 21287, USA
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Maves L, Tyler A, Moens CB, Tapscott SJ. Pbx acts with Hand2 in early myocardial differentiation. Dev Biol 2009; 333:409-18. [PMID: 19607825 DOI: 10.1016/j.ydbio.2009.07.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 06/09/2009] [Accepted: 07/06/2009] [Indexed: 12/30/2022]
Abstract
Transcription factors of the basic helix-loop-helix (bHLH) family are critical regulators of muscle cell differentiation. For example, Myod drives skeletal muscle differentiation, and Hand2 potentiates cardiac muscle differentiation. Understanding how these bHLH factors regulate distinct transcriptional targets in a temporally and spatially controlled manner is critical for understanding their activity in cellular differentiation. We previously showed that Pbx homeodomain proteins modulate the activity of Myod to promote the differentiation of fast-twitch skeletal muscle. Here, we test the hypothesis that Pbx proteins are also necessary for cardiac muscle differentiation through interacting with Hand2. We show that Pbx proteins are required for the activation of cardiac muscle differentiation in zebrafish embryos. Loss of Pbx activity leads to delay of myocardial differentiation and subsequent defective cardiac morphogenesis, similar to reduced Hand2 activity. Genetic interaction experiments support the hypothesis that Pbx proteins modulate the activity of Hand2 in myocardial differentiation. Furthermore, we show that Pbx proteins directly bind the promoter of the myocardial differentiation gene myl7 in vitro, supporting a direct role for Pbx proteins in promoting cardiac muscle differentiation. Our findings demonstrate new roles for Pbx proteins in vertebrate cardiac development and also provide new insight into connections between the transcriptional regulation of skeletal and cardiac muscle differentiation programs.
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Affiliation(s)
- Lisa Maves
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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Reamon-Buettner SM, Ciribilli Y, Traverso I, Kuhls B, Inga A, Borlak J. A functional genetic study identifies HAND1 mutations in septation defects of the human heart. Hum Mol Genet 2009; 18:3567-78. [DOI: 10.1093/hmg/ddp305] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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