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Bai Y, Wang S, Wu K, Zhang M, Alatan S, Cang M, Cao G, Jin H, Li C, Tong B. The Impact of Novel BMPR1B Mutations on Litter Size in Short-Tailed Gobi Sheep and Larger-Tailed Ujimqin Sheep. Vet Sci 2024; 11:297. [PMID: 39057981 PMCID: PMC11281403 DOI: 10.3390/vetsci11070297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
The significant deposition of tail fat in sheep has a profound impact on the economic benefits of animal husbandry. Furthermore, increasing the litter size is a crucial means of enhancing economic benefits. The BMPR1B and T/Brachyury genes are considered major functional genes that could affect sheep litter size and tail bone number, respectively. In this study, we employed direct sequencing to identify specific mutations of the BMPR1B gene in Gobi short tail sheep and carried out genotyping using MassARRAY technology for each variant of both the BMPR1B and T genes. Significant associations were demonstrated between the c.687G>A mutation of BMPR1B and the litter size in both the Gobi short tail sheep and Ujimqin sheep breeds. Meanwhile, the g.30058882_30058873GCAGATTAAAIndel mutation was significantly associated with the litter size in Gobi short tail sheep. These findings may provide valuable genetic markers for expanding sheep litter size. In addition, we also confirmed that the frequency of tail-bone-number-related T alleles was significantly higher in Gobi short tail sheep than in longer-tailed Ujimqin sheep.
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Affiliation(s)
- Yanyu Bai
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010020, China; (Y.B.); (M.C.)
| | - Shenyuan Wang
- Inner Mongolia Key Laboratory of Biomanufacture, College of Life Sciences, Inner Mongolia Agriculture University, Hohhot 010020, China;
| | - Kaifeng Wu
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China;
| | - Ming Zhang
- Inner Mongolia Mengyuan Sheep Breeding Company, Baotou 014016, China;
| | - Suhe Alatan
- East Ujimqin Hexig Animal Husbandry Development Company, Xilingol 026399, China;
| | - Ming Cang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010020, China; (Y.B.); (M.C.)
| | - Guifang Cao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010011, China;
| | - Hai Jin
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China;
| | - Changqing Li
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China;
| | - Bin Tong
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010020, China; (Y.B.); (M.C.)
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2
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Steinhart MR, van der Valk WH, Osorio D, Serdy SA, Zhang J, Nist-Lund C, Kim J, Moncada-Reid C, Sun L, Lee J, Koehler KR. Mapping oto-pharyngeal development in a human inner ear organoid model. Development 2023; 150:dev201871. [PMID: 37796037 DOI: 10.1242/dev.201871] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023]
Abstract
Inner ear development requires the coordination of cell types from distinct epithelial, mesenchymal and neuronal lineages. Although we have learned much from animal models, many details about human inner ear development remain elusive. We recently developed an in vitro model of human inner ear organogenesis using pluripotent stem cells in a 3D culture, fostering the growth of a sensorineural circuit, including hair cells and neurons. Despite previously characterizing some cell types, many remain undefined. This study aimed to chart the in vitro development timeline of the inner ear organoid to understand the mechanisms at play. Using single-cell RNA sequencing at ten stages during the first 36 days of differentiation, we tracked the evolution from pluripotency to various ear cell types after exposure to specific signaling modulators. Our findings showcase gene expression that influences differentiation, identifying a plethora of ectodermal and mesenchymal cell types. We also discern aspects of the organoid model consistent with in vivo development, while highlighting potential discrepancies. Our study establishes the Inner Ear Organoid Developmental Atlas (IODA), offering deeper insights into human biology and improving inner ear tissue differentiation.
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Affiliation(s)
- Matthew R Steinhart
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Wouter H van der Valk
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA 02115, USA
- OtoBiology Leiden, Department of Otorhinolaryngology and Head & Neck Surgery; Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW); Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands
| | - Daniel Osorio
- Research Computing, Department of Information Technology; Boston Children's Hospital, Boston, MA 02115, USA
| | - Sara A Serdy
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jingyuan Zhang
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Carl Nist-Lund
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Jin Kim
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA 02115, USA
- Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Cynthia Moncada-Reid
- Speech and Hearing Bioscience and Technology (SHBT) Graduate Program, Harvard Medical School, Boston, MA 02115, USA
| | - Liang Sun
- Research Computing, Department of Information Technology; Boston Children's Hospital, Boston, MA 02115, USA
| | - Jiyoon Lee
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA 02115, USA
- Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Karl R Koehler
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA 02115, USA
- Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA 02115, USA
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3
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Huang C, Bi J. Expression Regulation and Function of T-Bet in NK Cells. Front Immunol 2021; 12:761920. [PMID: 34675939 PMCID: PMC8524037 DOI: 10.3389/fimmu.2021.761920] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/20/2021] [Indexed: 11/14/2022] Open
Abstract
Natural killer (NK) cells are cytotoxic innate lymphocytes that play an important role in immune surveillance. The development, maturation and effector functions of NK cells are orchestrated by the T-box transcription factor T-bet, whose expression is induced by cytokines such as IFN-γ, IL-12, IL-15 and IL-21 through the respective cytokine receptors and downstream JAK/STATs or PI3K-AKT-mTORC1 signaling pathways. In this review, we aim to discuss the expression and regulation of T-bet in NK cells, the role of T-bet in mouse NK cell development, maturation, and function, as well as the role of T-bet in acute, chronic infection, inflammation, autoimmune diseases and tumors.
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Affiliation(s)
- Chen Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiacheng Bi
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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4
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Kalds P, Luo Q, Sun K, Zhou S, Chen Y, Wang X. Trends towards revealing the genetic architecture of sheep tail patterning: Promising genes and investigatory pathways. Anim Genet 2021; 52:799-812. [PMID: 34472112 DOI: 10.1111/age.13133] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2021] [Indexed: 12/22/2022]
Abstract
Different sheep breeds have evolved after initial domestication, generating various tail phenotypic patterns. The phenotypic diversity of sheep tail patterns offers ideal materials for comparative analysis of its genetic basis. Evolutionary biologists, animal geneticists, breeders, and producers have been curious to clearly understand the underlying genetics behind phenotypic differences in sheep tails. Understanding the causal gene(s) and mutation(s) underlying these differences will help probe an evolutionary riddle, improve animal production performance, promote animal welfare, and provide lessons that help comprehend human diseases related to fat deposition (i.e., obesity). Historically, fat tails have served as an adaptive response to aridification and climate change. However, the fat tail is currently associated with compromised mating and animal locomotion, fat distribution in the animal body, increased raising costs, reduced consumer preference, and other animal welfare issues such as tail docking. The developing genomic approaches provide unprecedented opportunities to determine causal variants underlying phenotypic differences among populations. In the last decade, researchers have performed several genomic investigations to assess the genomic causality underlying phenotypic variations in sheep tails. Various genes have been suggested with the prominence of several potentially significant causatives, including the BMP2 and PDGFD genes associated with the fat tail phenotype and the TBXT gene linked with the caudal vertebrae number and tail length. Although the potential genes related to sheep tail characteristics have been revealed, the causal variant(s) and mutation(s) of these high-ranking candidate genes are still elusive and need further investigation. The review discusses the potential genes, sheds light on a knowledge gap, and provides possible investigative approaches that could help determine the specific genomic causatives of sheep tail patterns. Besides, characterizing and revealing the genetic determinism of sheep tails will help solve issues compromising sheep breeding and welfare in the future.
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Affiliation(s)
- P Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, Egypt
| | - Q Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - K Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - S Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Y Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - X Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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5
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Chen J. NF-Y is critical for the proper growth of zebrafish embryonic heart and its cardiomyocyte proliferation. Genesis 2021; 59:e23408. [PMID: 33417743 DOI: 10.1002/dvg.23408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 11/06/2022]
Abstract
The ubiquitous NF-Y gene regulates the expression of different genes in various signaling pathways. However, the function of NF-Y in zebrafish heart development is largely unknown. Previously we identified a same group of cell cycle related gene cluster (CCRG) was downregulated in the embryonic hearts with impeded growth due to various stresses. The promoter regions of these CCRG genes shared a most common motif for NF-Y. Chromatin immunoprecipitation experiment demonstrated that the binding of NF-Y to its motif was real on the CCRG candidate gene promoters. Knockdown of embryonic NF-Y by morpholinos led to a small heart, mimicking the abnormal heart phenotype caused by other stresses. In parallel the expression of certain CCRG candidate genes was reduced in the NF-Y A morphant hearts exposed to malignant environments. Absence of NF-Y A also led to undermine cardiomyocyte proliferation and hence less total number of caridomyocytes per heart. Trans-AM Elisa experiment also found that in the presence of the stresses such as TCDD and TNNT2 MO, the binding capacity of NF-Y A subunit to its core motif was reduced. We conclude that NF-Y sustains proper cardiomyocyte proliferation in the heart, thus it plays a positive role in promoting early zebrafish heart growth.
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Affiliation(s)
- Jing Chen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
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6
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Rajesh V, Deepan N, Anitha V, Kalaiselvan D, Jayaseelan S, Sivakumar P, Ganesan V. Heart malformation is an early response to valproic acid in developing zebrafish. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2020; 393:2387-2409. [PMID: 32699959 DOI: 10.1007/s00210-020-01949-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 07/13/2020] [Indexed: 10/23/2022]
Abstract
Valproic acid (VPA) is a branched short-chain fatty acid primarily used in epilepsy, but is also used in bipolar disorder, migraine, and psychotic disorders. Despite its wide range of use, it is a teratogen resulting in various congenital abnormalities. Although a large number of scientific studies evidenced the teratogenic effects, there are limited data on embryonic exposure to VPA at specific or different stages of early embryogenesis. Based on this, the present study was planned to investigate the embryonic exposure to VPA at specific and different hours post fertilization (hpf) in zebrafish embryonic model. In first set of experiments, embryos from spawning groups of adult zebrafish were exposed to different molar concentrations of VPA at 2.5 hpf, and in the second set of experiments, embryos were exposed to VPA 100 μM at 24 hpf, 36 hpf, 48 hpf, 72 hpf, and 96 hpf. The parameters examined were hatching rate, mortality, morphology, body length, pericardial sac size, heartrate, anatomical changes in heart, skeletal and notochord till 120 hpf. It was observed that the embryos exposed to VPA at 2.5 hpf suffered from cardiac abnormalities including heart malformation, bradycardia, circulatory failure, and pericardial sac enlargement which was more apparent in embryos exposed to 100 μM VPA. In the second set of experiments, embryos exposed to VPA 100 μM at 24 hpf and 36 hpf suffered from heart malformations, but there was no incidence of cardiac malformation in embryos exposed to VPA at 48 hpf, 72 hpf, and 96 hpf. From the results, it was evident that exposure to VPA at early developmental stage of embryogenesis produced congenital cardiac abnormalities. Since VPA is a selective HDAC inhibitor, histone acetylation with aberrant gene expression during cardiogenesis might be the underlying cause of cardiac malformation.
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Affiliation(s)
- Venugopalan Rajesh
- Department of Pharmacology, The Erode College of Pharmacy, Veppampalayam, Vallipurathampalayam (Po), Erode, Tamil Nadu, 638112, India.
| | - Natarajan Deepan
- Department of Pharmacology, The Erode College of Pharmacy, Veppampalayam, Vallipurathampalayam (Po), Erode, Tamil Nadu, 638112, India
| | - Vijayakumar Anitha
- Department of Pharmacology, The Erode College of Pharmacy, Veppampalayam, Vallipurathampalayam (Po), Erode, Tamil Nadu, 638112, India
| | - Duraisamy Kalaiselvan
- Department of Pharmacology, The Erode College of Pharmacy, Veppampalayam, Vallipurathampalayam (Po), Erode, Tamil Nadu, 638112, India
| | - Subramanian Jayaseelan
- Department of Pharmaceutical Analysis, The Erode College of Pharmacy, Veppampalayam, Vallipurathampalayam (Po), Erode, Tamil Nadu, 638112, India
| | - Palanivel Sivakumar
- Department of Pharmaceutical Chemistry, The Erode College of Pharmacy, Veppampalayam, Vallipurathampalayam (Po), Erode, Tamil Nadu, 638112, India
| | - Vellaiyachamy Ganesan
- Department of Pharmaceutics, The Erode College of Pharmacy, Veppampalayam, Vallipurathampalayam (Po), Erode, Tamil Nadu, 638112, India
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7
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Li M, Yamada S, Shi A, Singh RD, Rolland TJ, Jeon R, Lopez N, Shelerud L, Terzic A, Behfar A. Brachyury engineers cardiac repair competent stem cells. Stem Cells Transl Med 2020; 10:385-397. [PMID: 33098750 PMCID: PMC7900595 DOI: 10.1002/sctm.20-0193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
To optimize the regenerative proficiency of stem cells, a cardiopoietic protein-based cocktail consisting of multiple growth factors has been developed and advanced into clinical trials for treatment of ischemic heart failure. Streamlining the inductors of cardiopoiesis would address the resource intensive nature of the current stem cell enhancement protocol. To this end, the microencapsulated-modified-mRNA (M3 RNA) technique was here applied to introduce early cardiogenic genes into human adipose-derived mesenchymal stem cells (AMSCs). A single mesodermal transcription factor, Brachyury, was sufficient to trigger high expression of cardiopoietic markers, Nkx2.5 and Mef2c. Engineered cardiopoietic stem cells (eCP) featured a transcriptome profile distinct from pre-engineered AMSCs. In vitro, eCP demonstrated protective antioxidant capacity with enhanced superoxide dismutase expression and activity; a vasculogenic secretome driving angiogenic tube formation; and macrophage polarizing immunomodulatory properties. In vivo, in a murine model of myocardial infarction, intramyocardial delivery of eCP (600 000 cells per heart) improved cardiac performance and protected against decompensated heart failure. Thus, heart repair competent stem cells, armed with antioxidant, vasculogenic, and immunomodulatory traits, are here engineered through a protein-independent single gene manipulation, expanding the available regenerative toolkit.
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Affiliation(s)
- Mark Li
- Center for Regenerative Medicine, Van Cleve Cardiac Regenerative Medicine Program, Marriott Heart Disease Research Program, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Satsuki Yamada
- Center for Regenerative Medicine, Van Cleve Cardiac Regenerative Medicine Program, Marriott Heart Disease Research Program, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Division of Geriatric Medicine and Gerontology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ao Shi
- Center for Regenerative Medicine, Van Cleve Cardiac Regenerative Medicine Program, Marriott Heart Disease Research Program, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Raman Deep Singh
- Center for Regenerative Medicine, Van Cleve Cardiac Regenerative Medicine Program, Marriott Heart Disease Research Program, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Tyler J Rolland
- Center for Regenerative Medicine, Van Cleve Cardiac Regenerative Medicine Program, Marriott Heart Disease Research Program, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ryounghoon Jeon
- Center for Regenerative Medicine, Van Cleve Cardiac Regenerative Medicine Program, Marriott Heart Disease Research Program, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Natalia Lopez
- Center for Regenerative Medicine, Van Cleve Cardiac Regenerative Medicine Program, Marriott Heart Disease Research Program, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Lukas Shelerud
- Center for Regenerative Medicine, Van Cleve Cardiac Regenerative Medicine Program, Marriott Heart Disease Research Program, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Andre Terzic
- Center for Regenerative Medicine, Van Cleve Cardiac Regenerative Medicine Program, Marriott Heart Disease Research Program, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Atta Behfar
- Center for Regenerative Medicine, Van Cleve Cardiac Regenerative Medicine Program, Marriott Heart Disease Research Program, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA.,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
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8
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Pan CM, Chan KH, Chen CH, Jan CI, Liu MC, Lin CM, Cho DY, Tsai WC, Chu YT, Cheng CH, Chuang HY, Chiu SC. MicroRNA-7 targets T-Box 2 to inhibit epithelial-mesenchymal transition and invasiveness in glioblastoma multiforme. Cancer Lett 2020; 493:133-142. [PMID: 32861705 DOI: 10.1016/j.canlet.2020.08.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 08/11/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022]
Abstract
The dysregulation of microRNA expression in cancer has been associated with the epithelial-mesenchymal transition (EMT) that triggers invasive ability and increases therapeutic resistance. Here, we determined the microRNA expression profile of seven tumor tissues from patients with glioblastoma multiforme (GBM) by use of microRNA array analysis. We discovered that microRNA-7 (miR-7) is consistently downregulated in all tumor samples. Using the microRNA.org algorithm, the T-box 2 gene (TBX2) was identified as a candidate gene targeted by miR-7. In contrast to miR-7, TBX2 had an increased expression in GBM tumors and was linked to poor prognosis. We confirmed that TBX2 mRNA and protein production are significantly repressed by overexpressing miR-7 in GBM cells in vitro. The reporter assay showed that miR-7 significantly represses the signal from luciferase with the 3' UTR of TBX2. Furthermore, TBX2 overexpression decreased E-cadherin expression and increased Vimentin expression, causing an increasing number of invaded cells in the invasion assay, as well as pulmonary metastasis in vivo. Our findings demonstrated that overexpression of TBX2 in GBM tumors via the downregulation of miR-7 leads to EMT induction and increased cell invasion.
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Affiliation(s)
- Chih-Ming Pan
- Translational Cell Therapy Center, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Kai-Hsiang Chan
- Cell Therapy Center, An Nan Hospital, China Medical University, Tainan, 70967, Taiwan; Department of Radiation Oncology, Tainan Municipal An-Nan Hospital-China Medical University, Tainan, 70967, Taiwan
| | - Chao-Hsuan Chen
- Department of Neurosurgery, Neuropsychiatric Center, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Chia-Ing Jan
- Translational Cell Therapy Center, China Medical University Hospital, Taichung, 40447, Taiwan; Division of Molecular Pathology, Department of Pathology, China Medical University and Hospital, Taichung, 40447, Taiwan; Department of Medicine, China Medical University, Taichung, 40447, Taiwan; Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Ming-Chao Liu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan
| | - Chien-Min Lin
- Taipei Neuroscience Institute, Taipei Medical University, Taipei, 11031, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, 11031, Taiwan; Department of Neurology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, 11031, Taiwan; Division of Neurosurgery, Department of Surgery, Taipei Medical University-Shuang Ho Hospital, New Taipei City, 23561, Taiwan
| | - Der-Yang Cho
- Translational Cell Therapy Center, China Medical University Hospital, Taichung, 40447, Taiwan; Department of Neurosurgery, Neuropsychiatric Center, China Medical University Hospital, Taichung, 40447, Taiwan; Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan; Drug Development Center, China Medical University, Taichung, 40402, Taiwan
| | - Wan-Chen Tsai
- Translational Cell Therapy Center, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Yen-Tse Chu
- Department of Neurosurgery, An Nan Hospital, China Medical University, Tainan, 70967, Taiwan
| | - Cheng-Hsin Cheng
- Department of Neurosurgery, An Nan Hospital, China Medical University, Tainan, 70967, Taiwan
| | - Hao-Yu Chuang
- Cell Therapy Center, An Nan Hospital, China Medical University, Tainan, 70967, Taiwan; Department of Neurosurgery, An Nan Hospital, China Medical University, Tainan, 70967, Taiwan; Department of Neurosurgery, China Medical University Beigang Hospital, Yunlin County, 65152, Taiwan.
| | - Shao-Chih Chiu
- Translational Cell Therapy Center, China Medical University Hospital, Taichung, 40447, Taiwan; Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan; Drug Development Center, China Medical University, Taichung, 40402, Taiwan.
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9
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Legitimo A, Bertini V, Costagliola G, Baroncelli GI, Morganti R, Valetto A, Consolini R. Vitamin D status and the immune assessment in 22q11.2 deletion syndrome. Clin Exp Immunol 2020; 200:272-286. [PMID: 32149392 PMCID: PMC7231997 DOI: 10.1111/cei.13429] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/19/2020] [Accepted: 03/05/2020] [Indexed: 02/06/2023] Open
Abstract
22q11.2 deletion syndrome (22q11.2DS) is characterized by a heterogeneous phenotype, including alterations in phospho-calcium metabolism and immunodeficiency. We analyzed vitamin D status and the immune assessment, focusing on T cell subpopulations and dendritic cells (DCs) in a cohort of 17 pediatric 22q11.2DS patients and 17 age-matched healthy subjects. As antigen-presenting cells, DCs are the main target of vitamin D, promoting a tolerogenic T cell response. Patients were subdivided into three groups according to the parameters of phospho-calcium metabolism and serum levels of 25OHD: normal values, vitamin D deficiency and hypoparathyroidism. Different degrees of T cell deficiency, ranging from normal to partial T cell numbers, were observed in the cohort of patients. The group with vitamin D deficiency showed a significant reduction of naive T cells and a significant increase of central memory T cells compared to controls. In this group the number of circulating DCs was significantly reduced. DC decrease affected both myeloid and plasmacytoid DC subsets (mDCs and pDCs), with the most relevant reduction involving pDCs. A direct correlation between 25OHD levels and recent thymic emigrant (RTE) and DC number was identified. Despite the limited cohort analyzed, our results show that deficiency of the pDC subset in patients with 22q11.2DS may be included among the causative factors of the progressive increase of risk of autoimmune diseases in these patients. As most patients suffer from increased susceptibility to infections and heightened prevalence of autoimmune disorders, we suggest a potential role of vitamin D supplementation in preventing autoimmune or proinflammatory diseases in 22q11.2DS.
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Affiliation(s)
- A. Legitimo
- Department of Clinical and Experimental Medicine, Section of PediatricsUniversity of PisaPisaItaly
| | - V. Bertini
- Department of Medicine of Laboratory, Section of CytogeneticsAzienda Ospedaliero Universitaria PisanaPisaItaly
| | - G. Costagliola
- Department of Clinical and Experimental Medicine, Section of PediatricsUniversity of PisaPisaItaly
| | - G. I. Baroncelli
- Department of Clinical and Experimental Medicine, Section of PediatricsAzienda Ospedaliero Universitaria PisanaPisaItaly
| | - R. Morganti
- Section of StatisticsAzienda Ospedaliero Universitaria PisanaPisaItaly
| | - A. Valetto
- Department of Medicine of Laboratory, Section of CytogeneticsAzienda Ospedaliero Universitaria PisanaPisaItaly
| | - R. Consolini
- Department of Clinical and Experimental Medicine, Section of PediatricsUniversity of PisaPisaItaly
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10
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Kariminejad A, Szenker-Ravi E, Lekszas C, Tajsharghi H, Moslemi AR, Naert T, Tran HT, Ahangari F, Rajaei M, Nasseri M, Haaf T, Azad A, Superti-Furga A, Maroofian R, Ghaderi-Sohi S, Najmabadi H, Abbaszadegan MR, Vleminckx K, Nikuei P, Reversade B. Homozygous Null TBX4 Mutations Lead to Posterior Amelia with Pelvic and Pulmonary Hypoplasia. Am J Hum Genet 2019; 105:1294-1301. [PMID: 31761294 DOI: 10.1016/j.ajhg.2019.10.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/25/2019] [Indexed: 12/16/2022] Open
Abstract
The development of hindlimbs in tetrapod species relies specifically on the transcription factor TBX4. In humans, heterozygous loss-of-function TBX4 mutations cause dominant small patella syndrome (SPS) due to haploinsufficiency. Here, we characterize a striking clinical entity in four fetuses with complete posterior amelia with pelvis and pulmonary hypoplasia (PAPPA). Through exome sequencing, we find that PAPPA syndrome is caused by homozygous TBX4 inactivating mutations during embryogenesis in humans. In two consanguineous couples, we uncover distinct germline TBX4 coding mutations, p.Tyr113∗ and p.Tyr127Asn, that segregated with SPS in heterozygous parents and with posterior amelia with pelvis and pulmonary hypoplasia syndrome (PAPPAS) in one available homozygous fetus. A complete absence of TBX4 transcripts in this proband with biallelic p.Tyr113∗ stop-gain mutations revealed nonsense-mediated decay of the endogenous mRNA. CRISPR/Cas9-mediated TBX4 deletion in Xenopus embryos confirmed its restricted role during leg development. We conclude that SPS and PAPPAS are allelic diseases of TBX4 deficiency and that TBX4 is an essential transcription factor for organogenesis of the lungs, pelvis, and hindlimbs in humans.
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Affiliation(s)
| | - Emmanuelle Szenker-Ravi
- Institute of Medical Biology, Agency for Science, Technology, and Research, 8A Biomedical Grove, Singapore 138648, Republic of Singapore
| | - Caroline Lekszas
- Institute of Human Genetics, Julius-Maximilians-Universität, 97074 Würzburg, Germany
| | - Homa Tajsharghi
- School of Health Sciences, Division Biomedicine, University of Skövde, 54128 Skövde, Sweden
| | - Ali-Reza Moslemi
- Institute of Biomedicine, Sahlgrenska University Hospital, Gothenburg University, 41390 Gothenburg, Sweden
| | - Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Hong Thi Tran
- Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Fatemeh Ahangari
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran 14665, Iran
| | - Minoo Rajaei
- Fertility and Infertility Research Center, Hormozgan University of Medical Sciences, Bandar Abbas 7919915519, Iran
| | - Mojila Nasseri
- Pardis Clinical and Genetics Laboratory, Mashhad 9177948974, Iran
| | - Thomas Haaf
- Institute of Human Genetics, Julius-Maximilians-Universität, 97074 Würzburg, Germany
| | - Afrooz Azad
- Fertility and Infertility Research Center, Hormozgan University of Medical Sciences, Bandar Abbas 7919915519, Iran
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), University of Lausanne, 1011 Lausanne, Switzerland
| | - Reza Maroofian
- Molecular and Clinical Sciences Institute, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | | | - Hossein Najmabadi
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran 14665, Iran; Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran 1985713834, Iran
| | - Mohammad Reza Abbaszadegan
- Pardis Clinical and Genetics Laboratory, Mashhad 9177948974, Iran; Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad 15731, Iran
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Pooneh Nikuei
- Fertility and Infertility Research Center, Hormozgan University of Medical Sciences, Bandar Abbas 7919915519, Iran.
| | - Bruno Reversade
- Institute of Medical Biology, Agency for Science, Technology, and Research, 8A Biomedical Grove, Singapore 138648, Republic of Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, 61 Biopolis Drive, Singapore 138673, Republic of Singapore; Department of Medical Genetics, Koç University, School of Medicine, 34010 Topkapı, Istanbul, Turkey.
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11
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Chi H, Sørmo KG, Diao J, Dalmo RA. T-box transcription factor eomesodermin/Tbr2 in Atlantic cod (Gadus morhua L.): Molecular characterization, promoter structure and function analysis. FISH & SHELLFISH IMMUNOLOGY 2019; 93:28-38. [PMID: 31302288 DOI: 10.1016/j.fsi.2019.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 07/01/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
Eomesodermin (Eomes) is a member of T-box transcription factor family and plays an important role in the regulation of a wide variety of developmental processes and immune response in animals. Here we report cloning and characterization of the full-length cDNA of Atlantic cod Eomes (GmEomes), which possesses a TBOX_3 domain similar to its counterpart in mammals. The regulated expression was observed in head kidney and spleen in response to live Vibrio anguillarum infection in vivo, and spleen leukocytes in vitro after PMA and poly I:C stimulation. Furthermore, we determined a 694 bp sequence, upstream of the transcriptional start site (TSS), to contain a number of sequence motifs that matched known transcription factor-binding sites. Activities of the presumptive regulatory gene were assessed by transfecting different 5'-deletion constructs in CHSE-214 cells. The results showed that the basal promoters and positive transcriptional regulator activities of GmEomes were dependent by sequences located from -694 to -376 bp upstream of TSS. Furthermore, we found that some Eomes binding sites were present in the 5'-flanking regions of the cod IFNγ gene predicted by bioinformatics. However, Co-transfection of eomesodermin overexpression plasmids with INFγ reporter vector into CHSE-214 cells determined that Atlantic cod eomesodermin played a minor role in activation of the INFγ promoter.
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Affiliation(s)
- Heng Chi
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, N-9037, Tromsø, Norway; Shandong Key Laboratory of Disease Control in Mariculture, Marine Biology Institute of Shandong Province, 266104, Qingdao, China; Key Laboratory of Experimental Marine Biology, Chinese Academy of Sciences, Institute of Oceanology, 266071, Qingdao, China.
| | - Kristian Gillebo Sørmo
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, N-9037, Tromsø, Norway
| | - Jing Diao
- Shandong Key Laboratory of Disease Control in Mariculture, Marine Biology Institute of Shandong Province, 266104, Qingdao, China
| | - Roy Ambli Dalmo
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, N-9037, Tromsø, Norway.
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12
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Bhambri A, Dhaunta N, Patel SS, Hardikar M, Bhatt A, Srikakulam N, Shridhar S, Vellarikkal S, Pandey R, Jayarajan R, Verma A, Kumar V, Gautam P, Khanna Y, Khan JA, Fromm B, Peterson KJ, Scaria V, Sivasubbu S, Pillai B. Large scale changes in the transcriptome of Eisenia fetida during regeneration. PLoS One 2018; 13:e0204234. [PMID: 30260966 PMCID: PMC6160089 DOI: 10.1371/journal.pone.0204234] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 09/05/2018] [Indexed: 12/16/2022] Open
Abstract
Earthworms show a wide spectrum of regenerative potential with certain species like Eisenia fetida capable of regenerating more than two-thirds of their body while other closely related species, such as Paranais litoralis seem to have lost this ability. Earthworms belong to the phylum Annelida, in which the genomes of the marine oligochaete Capitella telata and the freshwater leech Helobdella robusta have been sequenced and studied. Herein, we report the transcriptomic changes in Eisenia fetida (Indian isolate) during regeneration. Following injury, E. fetida regenerates the posterior segments in a time spanning several weeks. We analyzed gene expression changes both in the newly regenerating cells and in the adjacent tissue, at early (15days post amputation), intermediate (20days post amputation) and late (30 days post amputation) by RNAseq based de novo assembly and comparison of transcriptomes. We also generated a draft genome sequence of this terrestrial red worm using short reads and mate-pair reads. An in-depth analysis of the miRNome of the worm showed that many miRNA gene families have undergone extensive duplications. Sox4, a master regulator of TGF-beta mediated epithelial-mesenchymal transition was induced in the newly regenerated tissue. Genes for several proteins such as sialidases and neurotrophins were identified amongst the differentially expressed transcripts. The regeneration of the ventral nerve cord was also accompanied by the induction of nerve growth factor and neurofilament genes. We identified 315 novel differentially expressed transcripts in the transcriptome, that have no homolog in any other species. Surprisingly, 82% of these novel differentially expressed transcripts showed poor potential for coding proteins, suggesting that novel ncRNAs may play a critical role in regeneration of earthworm.
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Affiliation(s)
- Aksheev Bhambri
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Mathura Road, Delhi, India
| | - Neeraj Dhaunta
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Surendra Singh Patel
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Mathura Road, Delhi, India
| | - Mitali Hardikar
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Abhishek Bhatt
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Nagesh Srikakulam
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Shruti Shridhar
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Shamsudheen Vellarikkal
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Mathura Road, Delhi, India
| | - Rajesh Pandey
- CSIR Ayurgenomics Unit - TRISUTRA, CSIR-IGIB, New Delhi, India
| | - Rijith Jayarajan
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Ankit Verma
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Vikram Kumar
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Pradeep Gautam
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Yukti Khanna
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | | | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Vinod Scaria
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Mathura Road, Delhi, India
| | - Sridhar Sivasubbu
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Mathura Road, Delhi, India
| | - Beena Pillai
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Mathura Road, Delhi, India
- * E-mail:
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13
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Hu Q, Meng Y, Wang D, Tian H, Xiao H. Characterization and function of the T-box 1 gene in Chinese giant salamander Andrias davidianus. Genomics 2018; 111:1351-1359. [PMID: 30244141 DOI: 10.1016/j.ygeno.2018.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/07/2018] [Accepted: 09/14/2018] [Indexed: 11/25/2022]
Abstract
We characterized the Andrias davidianus T-box 1 (Tbx1) gene. Tbx1 expression was high in testis and low in other examined tissues. Immunohistochemistry detected tbx1 expression in somatic and germ cells 62 days post-hatching (dph), prior to gonad differentiation. At 210 dph, after gonad differentiation, tbx1 was expressed in spermatogonia and testis somatic cells and in granulosa cells in ovary. Tbx1 expression was up-regulated in ovary after high temperature treatment. In the neomale, tbx1 expression showed a similar profile to normal males, and vice-versa for genetic male. Over-expression of tbx1 in females after injection of TBX1 protein down-regulated the female-biased genes cyp19a and foxl2 and up-regulated the male-biased amh gene. When tbx1 was knocked down by tbx1/siRNA, cyp19a and foxl2 expression was up-regulated, and expression of amh, cyp26a, dmrt1, and wt1 was down-regulated. Results suggest that tbx1 influenced sex-related gene expression and participates in regulation of A. davidianus testis development.
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Affiliation(s)
- Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.
| | - Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Dan Wang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Hanbing Xiao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.
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14
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Zhi D, Da L, Liu M, Cheng C, Zhang Y, Wang X, Li X, Tian Z, Yang Y, He T, Long X, Wei W, Cao G. Whole Genome Sequencing of Hulunbuir Short-Tailed Sheep for Identifying Candidate Genes Related to the Short-Tail Phenotype. G3 (BETHESDA, MD.) 2018; 8:377-383. [PMID: 29208649 PMCID: PMC5919745 DOI: 10.1534/g3.117.300307] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/27/2017] [Indexed: 01/03/2023]
Abstract
The Hulunbuir short-tailed sheep (Ovis aries) is a breed native to China, in which the short-tail phenotype is the result of artificial and natural selection favoring a specific set of genetic mutations. Here, we analyzed the genetic differences between short-tail and normal-tail phenotypes at the genomic level. Selection signals were identified in genome-wide sequences. From 16 sheep, we identified 72,101,346 single nucleotide polymorphisms. Selection signals were detected based on the fixation index and heterozygosity. Seven genomic regions under putative selection were identified, and these regions contained nine genes. Among these genes, T was the strongest candidate as T is related to vertebral development. In T, a nonsynonymous mutation at c.G334T resulted in p.G112W substitution. We inferred that the c.G334T mutation in T leads to functional changes in Brachyury-encoded by this gene-resulting in the short-tail phenotype. Our findings provide a valuable insight into the development of the short-tail phenotype in sheep and other short-tailed animals.
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Affiliation(s)
- Dafu Zhi
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhhot 010018, People's Republic of China
| | - Lai Da
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Huhhot 010018, People's Republic of China
| | - Moning Liu
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhhot 010018, People's Republic of China
| | - Chen Cheng
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhhot 010018, People's Republic of China
| | - Yukun Zhang
- College of Life Sciences, Inner Mongolia Agricultural University, Huhhot 010018, People's Republic of China
| | - Xin Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhhot 010018, People's Republic of China
| | - Xiunan Li
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhhot 010018, People's Republic of China
| | - Zhipeng Tian
- College of Life Sciences, Inner Mongolia Agricultural University, Huhhot 010018, People's Republic of China
| | - Yanyan Yang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Huhhot 010018, People's Republic of China
| | - Tingyi He
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Huhhot 010018, People's Republic of China
| | - Xin Long
- College of Life Sciences, Inner Mongolia Agricultural University, Huhhot 010018, People's Republic of China
| | - Wei Wei
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhhot 010018, People's Republic of China
| | - Guifang Cao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhhot 010018, People's Republic of China
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15
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Maguire JE, Pandey A, Wu Y, Di Gregorio A. Investigating Evolutionarily Conserved Molecular Mechanisms Controlling Gene Expression in the Notochord. TRANSGENIC ASCIDIANS 2018. [DOI: 10.1007/978-981-10-7545-2_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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16
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Wound healing, calcium signaling, and other novel pathways are associated with the formation of butterfly eyespots. BMC Genomics 2017; 18:788. [PMID: 29037153 PMCID: PMC5644175 DOI: 10.1186/s12864-017-4175-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/05/2017] [Indexed: 01/21/2023] Open
Abstract
Background One hypothesis surrounding the origin of novel traits is that they originate from the co-option of pre-existing genes or larger gene regulatory networks into novel developmental contexts. Insights into a trait’s evolutionary origins can, thus, be gained via identification of the genes underlying trait development, and exploring whether those genes also function in other developmental contexts. Here we investigate the set of genes associated with the development of eyespot color patterns, a trait that originated once within the Nymphalid family of butterflies. Although several genes associated with eyespot development have been identified, the eyespot gene regulatory network remains largely unknown. Results In this study, next-generation sequencing and transcriptome analyses were used to identify a large set of genes associated with eyespot development of Bicyclus anynana butterflies, at 3-6 h after pupation, prior to the differentiation of the color rings. Eyespot-associated genes were identified by comparing the transcriptomes of homologous micro-dissected wing tissues that either develop or do not develop eyespots in wild-type and a mutant line of butterflies, Spotty, with extra eyespots. Overall, 186 genes were significantly up and down-regulated in wing tissues that develop eyespots compared to wing tissues that do not. Many of the differentially expressed genes have yet to be annotated. New signaling pathways, including the Toll, Fibroblast Growth Factor (FGF), extracellular signal–regulated kinase (ERK) and/or Jun N-terminal kinase (JNK) signaling pathways are associated for the first time with eyespot development. In addition, several genes involved in wound healing and calcium signaling were also found to be associated with eyespots. Conclusions Overall, this study provides the identity of many new genes and signaling pathways associated with eyespots, and suggests that the ancient wound healing gene regulatory network may have been co-opted to cells at the center of the pattern to aid in eyespot origins. New transcription factors that may be providing different identities to distinct wing sectors, and genes with sexually dimorphic expression in the eyespots were also identified. Electronic supplementary material The online version of this article (10.1186/s12864-017-4175-7) contains supplementary material, which is available to authorized users.
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17
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The Genetic Origin of Short Tail in Endangered Korean Dog, DongGyeongi. Sci Rep 2017; 7:10048. [PMID: 28855671 PMCID: PMC5577146 DOI: 10.1038/s41598-017-10106-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/04/2017] [Indexed: 01/06/2023] Open
Abstract
The tail of many animal species is responsible for various physiological functions. The functional importance of tail may have brought tail-loss to attention in many evolutionary and developmental studies. To provide a better explanation for the loss of tail, the current study aims to identify the evolutionary history and putative causal variants for the short tail in DongGyeongi (DG), an endangered dog breed, which is also the only dog in Korea that possesses a short tail. Whole genome sequencing was conducted on 22 samples of DG, followed by an investigation of population stratification with 10 other dog breeds. The genotypes, selective sweep and demography of DG were also investigated. As a result, we discovered the unique genetic structure of DG and suggested two possible ways in which the short tail phenotype developed. Moreover, this study suggested that selective sweep genes, ANKRD11 and ACVR2B may contribute to the reduction in tail length, and non-synonymous variant in the coding sequence of T gene and the CpG island variant of SFRP2 gene are the candidate causal variants for the tail-loss.
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18
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Watanabe M, Yasuoka Y, Mawaribuchi S, Kuretani A, Ito M, Kondo M, Ochi H, Ogino H, Fukui A, Taira M, Kinoshita T. Conservatism and variability of gene expression profiles among homeologous transcription factors in Xenopus laevis. Dev Biol 2017; 426:301-324. [DOI: 10.1016/j.ydbio.2016.09.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 07/27/2016] [Accepted: 09/19/2016] [Indexed: 12/11/2022]
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19
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Takahashi T, Friedmacher F, Zimmer J, Puri P. Expression of T-box transcription factors 2, 4 and 5 is decreased in the branching airway mesenchyme of nitrofen-induced hypoplastic lungs. Pediatr Surg Int 2017; 33:139-143. [PMID: 27833996 DOI: 10.1007/s00383-016-4005-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2016] [Indexed: 11/29/2022]
Abstract
PURPOSE Pulmonary hypoplasia (PH), characterized by smaller lung size and reduced airway branching, remains a major therapeutic challenge in newborns with congenital diaphragmatic hernia (CDH). T-box transcription factors (Tbx) have been identified as key components of the gene network that regulates fetal lung development. Tbx2, Tbx4 and Tbx5 are expressed throughout the mesenchyme of the developing lung, regulating the process of lung branching morphogenesis. Furthermore, lungs of Tbx2-, Tbx4- and Tbx5-deficient mice are hypoplastic and exhibit decreased lung branching, similar to PH in human CDH. We hypothesized that the expression of Tbx2, Tbx4 and Tbx5 is decreased in the branching airway mesenchyme of hypoplastic rat lungs with nitrofen-induced CDH. METHODS Time-mated rats received either nitrofen or vehicle on gestational day 9 (D9). Fetuses were killed on D15, D18 and D21, and dissected lungs were divided into control and nitrofen-exposed specimens. Pulmonary gene expression of Tbx2, Tbx4 and Tbx5 was investigated by quantitative real-time polymerase chain reaction. Immunofluorescence double staining for Tbx2, Tbx4 and Tbx5 was combined with the mesenchymal marker Fgf10 to assess protein expression and localization in branching airway tissue. RESULTS Relative mRNA levels of Tbx2, Tbx4 and Tbx5 were significantly reduced in lungs of nitrofen-exposed fetuses on D15, D18 and D21 compared to controls. Confocal laser scanning microscopy showed markedly diminished immunofluorescence of Tbx2, Tbx4 and Tbx5 in mesenchymal cells surrounding branching airways of nitrofen-exposed fetuses on D15, D18 and D21 compared to controls. CONCLUSION Decreased expression of Tbx2, Tbx4 and Tbx5 in the pulmonary mesenchyme during fetal lung development may lead to a decrease or arrest of airway branching, thus contributing to PH in the nitrofen-induced CDH model.
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Affiliation(s)
- Toshiaki Takahashi
- National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, 12, Ireland
| | - Florian Friedmacher
- National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, 12, Ireland
| | - Julia Zimmer
- National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, 12, Ireland
| | - Prem Puri
- National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, 12, Ireland. .,Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.
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Sebé-Pedrós A, Ruiz-Trillo I. Evolution and Classification of the T-Box Transcription Factor Family. Curr Top Dev Biol 2017; 122:1-26. [DOI: 10.1016/bs.ctdb.2016.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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Abstract
Ascidians are invertebrate chordates with a biphasic life cycle characterized by a dual body plan that displays simplified versions of chordate structures, such as a premetamorphic 40-cell notochord topped by a dorsal nerve cord and postmetamorphic pharyngeal slits. These relatively simple chordates are characterized by rapid development, compact genomes and ease of transgenesis, and thus provide the opportunity to rapidly characterize the genomic organization, developmental function, and transcriptional regulation of evolutionarily conserved gene families. This review summarizes the current knowledge on members of the T-box family of transcription factors in Ciona and other ascidians. In both chordate and nonchordate animals, these genes control a variety of morphogenetic processes, and their mutations are responsible for malformations and developmental defects in organisms ranging from flies to humans. In ascidians, T-box transcription factors are required for the formation and specialization of essential structures, including notochord, muscle, heart, and differentiated neurons. In recent years, the experimental advantages offered by ascidian embryos have allowed the rapid accumulation of a wealth of information on the molecular mechanisms that regulate the expression of T-box genes. These studies have also elucidated the strategies employed by these transcription factors to orchestrate the appropriate spatial and temporal deployment of the numerous target genes that they control.
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Affiliation(s)
- A Di Gregorio
- New York University College of Dentistry, New York, NY, United States.
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22
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Willmer T, Peres J, Mowla S, Abrahams A, Prince S. The T-Box factor TBX3 is important in S-phase and is regulated by c-Myc and cyclin A-CDK2. Cell Cycle 2016; 14:3173-83. [PMID: 26266831 DOI: 10.1080/15384101.2015.1080398] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The transcription factor, TBX3, is critical for the formation of, among other structures, the heart, limbs and mammary glands and haploinsufficiency of the human TBX3 gene result in ulnar-mammary syndrome which is characterized by hypoplasia of these structures. On the other hand, the overexpression of TBX3 is a feature of a wide range of cancers and it has been implicated in several aspects of the oncogenic process. This includes its ability to function as an immortalizing gene and to promote proliferation through actively repressing negative cell cycle regulators. Together this suggests that TBX3 levels may need to be tightly regulated during the cell cycle. Here we demonstrate that this is indeed the case and that TBX3 mRNA and protein levels peak at S-phase and that the TBX3 protein is predominantly localized to the nucleus of S-phase cells. The increased levels of TBX3 in S-phase are shown to occur transcriptionally through activation by c-Myc at E-box motifs located at -1210 and -701 bps and post-translationally by cyclin A-CDK2 phosphorylation. Importantly, when TBX3 is depleted by shRNA the cells accumulate in S-phase. These results suggest that TBX3 is required for cells to transit through S-phase and that this function may be linked to its role as a pro-proliferative factor.
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Affiliation(s)
- Tarryn Willmer
- a Department of Human Biology ; Faculty of Health Sciences; University of Cape Town ; Cape Town , South Africa
| | - Jade Peres
- a Department of Human Biology ; Faculty of Health Sciences; University of Cape Town ; Cape Town , South Africa
| | - Shaheen Mowla
- a Department of Human Biology ; Faculty of Health Sciences; University of Cape Town ; Cape Town , South Africa
| | - Amaal Abrahams
- a Department of Human Biology ; Faculty of Health Sciences; University of Cape Town ; Cape Town , South Africa
| | - Sharon Prince
- a Department of Human Biology ; Faculty of Health Sciences; University of Cape Town ; Cape Town , South Africa
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Dreßen M, Lahm H, Lahm A, Wolf K, Doppler S, Deutsch MA, Cleuziou J, Pabst von Ohain J, Schön P, Ewert P, Malcic I, Lange R, Krane M. A novel de novo TBX5 mutation in a patient with Holt-Oram syndrome leading to a dramatically reduced biological function. Mol Genet Genomic Med 2016; 4:557-67. [PMID: 27652283 PMCID: PMC5023941 DOI: 10.1002/mgg3.234] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 04/29/2016] [Accepted: 05/03/2016] [Indexed: 01/26/2023] Open
Abstract
Background The Holt–Oram syndrome (HOS) is an autosomal dominant disorder affecting 1/100.000 live births. It is defined by upper limb anomalies and congenital heart defects with variable severity. We describe a dramatic phenotype of a male, 15‐month‐old patient being investigated for strict diagnostic criteria of HOS. Methods and results Genetic analysis revealed a so far unpublished TBX5 mutation, which occurs de novo in the patient with healthy parents. TBX5 belongs to the large family of T‐box transcription factors playing major roles in morphogenesis and cell‐type specification. The mutation located in the DNA‐binding domain at position 920 (C→A) leads to an amino acid change at position 85 (proline → threonine). Three‐dimensional analysis of the protein structure predicted a cis to trans change in the respective peptide bond, thereby probably provoking major conformational and functional alterations of the protein. The p.Pro85Thr mutation showed a dramatically reduced activation (97%) of the NPPA promoter in luciferase assays and failed to induce NPPA expression in HEK 293 cells compared to wild‐type TBX5 protein. The mutation did not interfere with the nuclear localization of the protein. Conclusion These results suggest that the dramatic functional alteration of the p.Pro85Thr mutation leads to the distinctive phenotype of the patient.
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Affiliation(s)
- Martina Dreßen
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Harald Lahm
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Armin Lahm
- Bioinformatics Project Support Rome Italy
| | - Klaudia Wolf
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Stefanie Doppler
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Marcus-André Deutsch
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Julie Cleuziou
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Jelena Pabst von Ohain
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Patric Schön
- Department of Paediatric Cardiology and Congenital Heart Defects German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Peter Ewert
- Department of Paediatric Cardiology and Congenital Heart Defects German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Ivan Malcic
- Department of Pediatrics Division of Cardiology and Intensive Care Unit University Hospital Zagreb Zagreb Croatia
| | - Rüdiger Lange
- Department of Cardiovascular SurgeryDivision of Experimental SurgeryGerman Heart Center Munich at the Technical University of MunichMunichGermany; DZHK (German Center for Cardiovascular Research) - partner site Munich Heart AllianceMunichGermany
| | - Markus Krane
- Department of Cardiovascular SurgeryDivision of Experimental SurgeryGerman Heart Center Munich at the Technical University of MunichMunichGermany; DZHK (German Center for Cardiovascular Research) - partner site Munich Heart AllianceMunichGermany
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24
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Szafranski P, Coban-Akdemir ZH, Rupps R, Grazioli S, Wensley D, Jhangiani SN, Popek E, Lee AF, Lupski JR, Boerkoel CF, Stankiewicz P. Phenotypic expansion ofTBX4mutations to include acinar dysplasia of the lungs. Am J Med Genet A 2016; 170:2440-4. [DOI: 10.1002/ajmg.a.37822] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/17/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
| | | | - Rosemarie Rupps
- Department of Medical Genetics; University of British Columbia; Vancouver Canada
| | - Serge Grazioli
- Department of Pediatrics; University of British Columbia; Vancouver Canada
| | - David Wensley
- Department of Pediatrics; University of British Columbia; Vancouver Canada
| | - Shalini N. Jhangiani
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
| | - Edwina Popek
- Department of Pathology and Immunology; Baylor College of Medicine; Houston Texas
| | - Anna F. Lee
- Department of Pathology and Laboratory Medicine; University of British Columbia; Vancouver Canada
| | - James R. Lupski
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
- Department of Pediatrics; Baylor College of Medicine; Houston Texas
- Human Genome Sequencing Center; Baylor College of Medicine; Houston Texas
- Texas Children's Hospital; Houston Texas
| | | | - Paweł Stankiewicz
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
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25
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Deng H, Zheng W, Jankovic J. Genetics and molecular biology of brain calcification. Ageing Res Rev 2015; 22:20-38. [PMID: 25906927 DOI: 10.1016/j.arr.2015.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 04/14/2015] [Accepted: 04/15/2015] [Indexed: 01/01/2023]
Abstract
Brain calcification is a common neuroimaging finding in patients with neurological, metabolic, or developmental disorders, mitochondrial diseases, infectious diseases, traumatic or toxic history, as well as in otherwise normal older people. Patients with brain calcification may exhibit movement disorders, seizures, cognitive impairment, and a variety of other neurologic and psychiatric symptoms. Brain calcification may also present as a single, isolated neuroimaging finding. When no specific cause is evident, a genetic etiology should be considered. The aim of the review is to highlight clinical disorders associated with brain calcification and provide summary of current knowledge of diagnosis, genetics, and pathogenesis of brain calcification.
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Affiliation(s)
- Hao Deng
- Department of Neurology, Third Xiangya Hospital, Central South University, Changsha, China; Center for Experimental Medicine, Third Xiangya Hospital, Central South University, Changsha, China.
| | - Wen Zheng
- Department of Neurology, Third Xiangya Hospital, Central South University, Changsha, China; Center for Experimental Medicine, Third Xiangya Hospital, Central South University, Changsha, China
| | - Joseph Jankovic
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA
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26
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Liu JJ, Fan LL, Chen JL, Tan ZP, Yang YF. A novel variant in TBX20 (p.D176N) identified by whole-exome sequencing in combination with a congenital heart disease related gene filter is associated with familial atrial septal defect. J Zhejiang Univ Sci B 2015; 15:830-7. [PMID: 25183037 DOI: 10.1631/jzus.b1400062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Congenital heart disease (CHD) is the leading cause of birth defects, and its etiology is not completely understood. Atrial septal defect (ASD) is one of the most common defects of CHD. Previous studies have demonstrated that mutations in the transcription factor T-box 20 (TBX20) contribute to congenital ASD. Whole-exome sequencing in combination with a CHD-related gene filter was used to detect a family of three generations with ASD. A novel TBX20 mutation, c.526G>A (p.D176N), was identified and co-segregated in all affected members in this family. This mutation was predicted to be deleterious by bioinformatics programs (SIFT, Polyphen2, and MutationTaster). This mutation was also not presented in the current Single Nucleotide Polymorphism Database (dbSNP) or National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project (ESP). In conclusion, our finding expands the spectrum of TBX20 mutations and provides additional support that TBX20 plays important roles in cardiac development. Our study also provided a new and cost-effective analysis strategy for the genetic study in small CHD pedigree.
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Affiliation(s)
- Ji-jia Liu
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital, Central South University, Changsha 410011, China; Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China; Center of Clinical Gene Diagnosis and Therapy, the State Key Laboratory of Medical Genetics, the Second Xiangya Hospital, Central South University, Changsha 410011, China
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27
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Stratification based on methylation of TBX2 and TBX3 into three molecular grades predicts progression in patients with pTa-bladder cancer. Mod Pathol 2015; 28:515-22. [PMID: 25394776 DOI: 10.1038/modpathol.2014.145] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 09/04/2014] [Accepted: 09/06/2014] [Indexed: 01/15/2023]
Abstract
The potential risk of recurrence and progression in patients with non-muscle-invasive bladder cancer necessitates followup by cystoscopy. The risk of progression to muscle-invasive bladder cancer is estimated based on the European Organisation of Research and Treatment of Cancer score, a combination of several clinicopathological variables. However, pathological assessment is not objective and reproducibility is insufficient. The use of molecular markers could contribute to the estimation of tumor aggressiveness. We recently demonstrated that methylation of GATA2, TBX2, TBX3, and ZIC4 genes could predict progression in Ta tumors. In this study, we aimed to validate the markers in a large patient set using DNA from formalin-fixed and paraffin-embedded tissue. PALGA: the Dutch Pathology Registry was used for patient selection. We included 192 patients with pTaG1/2 bladder cancer of whom 77 experienced progression. Methylation analysis was performed and log-rank analysis was used to calculate the predictive value of each methylation marker for developing progression over time. This analysis showed better progression-free survival in patients with low methylation rates compared with the patients with high methylation rates for all markers (P<0.001) during a followup of ten-years. The combined predictive effect of the methylation markers was analyzed with the Cox-regression method. In this analysis, TBX2, TBX3, and ZIC4 were independent predictors of progression. On the basis of methylation status of TBX2 and TBX3, patients were divided into three new molecular grade groups. Survival analysis showed that only 8% of patients in the low molecular grade group progressed within 5 years. This was 29 and 63% for the intermediate- and high-molecular grade groups. In conclusion, this new molecular-grade based on the combination of TBX2 and TBX3 methylation is an excellent marker for predicting progression to muscle-invasive bladder cancer in patients with primary pTaG1/2 bladder cancer.
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28
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Papaioannou VE. The T-box gene family: emerging roles in development, stem cells and cancer. Development 2014; 141:3819-33. [PMID: 25294936 DOI: 10.1242/dev.104471] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The T-box family of transcription factors exhibits widespread involvement throughout development in all metazoans. T-box proteins are characterized by a DNA-binding motif known as the T-domain that binds DNA in a sequence-specific manner. In humans, mutations in many of the genes within the T-box family result in developmental syndromes, and there is increasing evidence to support a role for these factors in certain cancers. In addition, although early studies focused on the role of T-box factors in early embryogenesis, recent studies in mice have uncovered additional roles in unsuspected places, for example in adult stem cell populations. Here, I provide an overview of the key features of T-box transcription factors and highlight their roles and mechanisms of action during various stages of development and in stem/progenitor cell populations.
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Affiliation(s)
- Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
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29
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Jiang H, Li L, Yang H, Bai Y, Jiang H, Li Y. Pax2 may play a role in kidney development by regulating the expression of TBX1. Mol Biol Rep 2014; 41:7491-8. [PMID: 25106525 DOI: 10.1007/s11033-014-3639-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 07/21/2014] [Indexed: 11/24/2022]
Abstract
Renal anomaly is commonly found among patients with loss of TBX1 gene, encoding an important transcriptional factor implicated in numerous developmental processes. Pax2 is a member of the "paired-box" (PAX) family of homeotic genes that orchestrates the patterns of gene expression in specific cells during nephrogenesis. In this study, we hypothesized that Pax2 might activate expression of TBX1, a member of T-box family that closely involving in kidney development. Immunohistochemical and immunofluorescence staining was performed to detect TBX1 expression in E16.5 embryonic rat kidney, while luciferase assay, electrophoretic mobility shift assay (EMSA), and chromatin immunoprecipitation (ChIP) assay were used to confirm the interaction between the Pax2 protein and TBX1 genes. TBX1 was expressed in the cytoplasm of renal tubular epithelial cells in the cortex of E16.5 fetal rat kidney. Inspection of the 5'-flanking sequence of the TBX1 gene identified a putative Pax2 recognition motif (TBX1-577). Luciferase assay and EMSA confirmed this novel promoter region of TBX1 that directly interacted with Pax2, and a site mutation could abolish the transcriptional activation of the TBX1 promoter by Pax2. ChIP assay of the Pax2-TBX1 promoter complex from human kidney epithelial cells further confirmed that endogenous Pax2 interacted with TBX1 promoter region. Thus, Pax2 directly regulates TBX1 expression in vivo. These findings suggest that Pax2 may regulate the TBX1 expression through specific binding to the TBX1 promoter, which may shed light on the potential mechanism of Pax2 and TBX1 in nephrogenesis and renal malformations.
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Affiliation(s)
- Hongkun Jiang
- Department of Pediatrics, First Affiliated Hospital of China Medical University, Shenyang, 110001, China,
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30
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Xu YJ, Chen S, Zhang J, Fang SH, Guo QQ, Wang J, Fu QH, Li F, Xu R, Sun K. Novel TBX1 loss-of-function mutation causes isolated conotruncal heart defects in Chinese patients without 22q11.2 deletion. BMC MEDICAL GENETICS 2014; 15:78. [PMID: 24998776 PMCID: PMC4099205 DOI: 10.1186/1471-2350-15-78] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/24/2014] [Indexed: 12/18/2022]
Abstract
Background TBX1 and CRKL haploinsufficiency is thought to cause the cardiac phenotype of the 22q11.2 deletion syndrome. However, few unequivocal mutations of TBX1 and CRKL have been discovered in isolated conotrucal heart defects (CTDs) patients. The aim of the study was to screen the mutation of TBX1 and CRKL in isolated CTDs Chinese patients without 22q11.2 deletion and identify the pathomechanism of the missense mutations. Methods We enrolled 199 non-22q11.2 deletion patients with CTDs and 139 unrelated healthy controls. Gene sequencing were performed for all of them. The functional data of mutations were obtained by in vitro transfection and luciferase experiments and computer modelling. Results Screening of the TBX1 coding sequence identified a de novo missense mutation (c.385G → A; p.E129K) and a known polymorphism (c.928G → A; p.G310S). In vitro experiments demonstrate that the TBX1E129K variant almost lost transactivation activity. The TBX1G310S variant seems to affect the interaction of TBX1 with other factors. Computer molecular dynamics simulations showed the de novo missense mutation is likely to affect TBX1-DNA interaction. No mutation of CRKL gene was found. Conclusions These observations suggest that the TBX1 loss-of-function mutation may be involved in the pathogenesis of isolated CTDs. This is the first human missense mutation showing that TBX1 is a candidate causing isolated CTDs in Chinese patients without 22q11.2 deletion.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Rang Xu
- Department of Pediatric Cardiology, Xinhua hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, China.
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31
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Interaction between Tbx1 and HoxD10 and connection with TGFβ-BMP signal pathway during kidney development. Gene 2014; 536:197-202. [DOI: 10.1016/j.gene.2012.06.069] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 06/19/2012] [Indexed: 12/22/2022]
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32
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Yao C, Yao GQ, Sun BH, Zhang C, Tommasini SM, Insogna K. The transcription factor T-box 3 regulates colony-stimulating factor 1-dependent Jun dimerization protein 2 expression and plays an important role in osteoclastogenesis. J Biol Chem 2014; 289:6775-6790. [PMID: 24394418 DOI: 10.1074/jbc.m113.499210] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Colony-stimulating factor 1 (CSF1) is known to promote osteoclast progenitor survival, but its roles in osteoclast differentiation and mature osteoclast function are less well understood. In a microarray screen, Jun dimerization protein 2 (JDP2) was identified as significantly induced by CSF1. Recent reports indicate that JDP2 is required for normal osteoclastogenesis and skeletal metabolism. Because there are no reports on the transcriptional regulation of this gene, the DNA sequence from -2612 to +682 bp (relative to the transcription start site) of the JDP2 gene was cloned, and promoter activity was analyzed. The T box-binding element (TBE) between -191 and -141 bp was identified as the cis-element responsible for CSF1-dependent JDP2 expression. Using degenerate PCR, Tbx3 was identified as the major isoform binding the TBE. Overexpression of Tbx3 induced JDP2 promoter activity, whereas suppressing Tbx3 expression substantially attenuated CSF1-induced transcription. Suppressing Tbx3 in osteoclast precursors reduced JDP2 expression and significantly impaired RANKL/CSF1-induced osteoclastogenesis. A MEK1/2-specific inhibitor was found to block CSF1-induced JDP2 expression. Consistent with these data, JDP2(-/-) mice were found to have increased bone mass. In summary, CSF1 up-regulates JDP2 expression by inducing Tbx3 binding to the JDP2 promoter. The downstream signaling cascade from activated c-Fms involves the MEK1/2-ERK1/2 pathway. Tbx3 plays an important role in osteoclastogenesis at least in part by regulating CSF1-dependent expression of JDP2.
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Affiliation(s)
- Chen Yao
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520; Department of Orthopedics, Shanghai No. 6 People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200233, China
| | - Gang-Qing Yao
- Section of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Ben-Hua Sun
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Changqing Zhang
- Department of Orthopedics, Shanghai No. 6 People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200233, China
| | - Steven M Tommasini
- Department of Orthopedics, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Karl Insogna
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520.
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Castillo J, Amaral A, Oliva R. Sperm nuclear proteome and its epigenetic potential. Andrology 2013; 2:326-38. [PMID: 24327354 DOI: 10.1111/j.2047-2927.2013.00170.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 11/08/2013] [Accepted: 11/11/2013] [Indexed: 11/29/2022]
Abstract
The main function of the sperm cell is to transmit the paternal genetic message and epigenetic information to the embryo. Importantly, the majority of the genes in the sperm chromatin are highly condensed by protamines, whereas genes potentially needed in the initial stages of development are associated with histones, representing a form of epigenetic marking. However, so far little attention has been devoted to other sperm chromatin-associated proteins that, in addition to histones and protamines, may also have an epigenetic role. Therefore, with the goal of contributing to cover this subject we have compiled, reviewed and report a list of 581 chromatin or nuclear proteins described in the human sperm cell. Furthermore, we have analysed their Gene Ontology Biological Process enriched terms and have grouped them into different functional categories. Remarkably, we show that 56% of the sperm nuclear proteins have a potential epigenetic activity, being involved in at least one of the following functions: chromosome organization, chromatin organization, protein-DNA complex assembly, DNA packaging, gene expression, transcription, chromatin modification and histone modification. In addition, we have also included and compared the sperm cell proteomes of different model species, demonstrating the existence of common trends in the chromatin composition in the mammalian mature male gamete. Taken together, our analyses suggest that the mammalian sperm cell delivers to the offspring a rich combination of histone variants, transcription factors, chromatin-associated and chromatin-modifying proteins which have the potential to encode and transmit an extremely complex epigenetic information.
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Affiliation(s)
- J Castillo
- Human Genetics Research Group, IDIBAPS, Faculty of Medicine, University of Barcelona, Barcelona, Spain; Biochemistry and Molecular Genetics Service, Hospital Clinic, Barcelona, Spain
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Davies EG. Immunodeficiency in DiGeorge Syndrome and Options for Treating Cases with Complete Athymia. Front Immunol 2013; 4:322. [PMID: 24198816 PMCID: PMC3814041 DOI: 10.3389/fimmu.2013.00322] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/23/2013] [Indexed: 11/13/2022] Open
Abstract
The commonest association of thymic stromal deficiency resulting in T-cell immunodeficiency is the DiGeorge syndrome (DGS). This results from abnormal development of the third and fourth pharyngeal arches and is most commonly associated with a microdeletion at chromosome 22q11 though other genetic and non-genetic causes have been described. The immunological competence of affected individuals is highly variable, ranging from normal to a severe combined immunodeficiency when there is complete athymia. In the most severe group, correction of the immunodeficiency can be achieved using thymus allografts which can support thymopoiesis even in the absence of donor-recipient matching at the major histocompatibility loci. This review focuses on the causes of DGS, the immunological features of the disorder, and the approaches to correction of the immunodeficiency including the use of thymus transplantation.
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Affiliation(s)
- E Graham Davies
- Centre for Immunodeficiency, Institute of Child Health, University College London and Great Ormond Street Hospital , London , UK
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Thi Thu HN, Haw Tien SF, Loh SL, Bok Yan JS, Korzh V. Tbx2a is required for specification of endodermal pouches during development of the pharyngeal arches. PLoS One 2013; 8:e77171. [PMID: 24130849 PMCID: PMC3795029 DOI: 10.1371/journal.pone.0077171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 09/01/2013] [Indexed: 11/21/2022] Open
Abstract
Tbx2 is a member of the T-box family of transcription factors essential for embryo- and organogenesis. A deficiency in the zebrafish paralogue tbx2a causes abnormalities of the pharyngeal arches in a p53-independent manner. The pharyngeal arches are formed by derivatives of all three embryonic germ layers: endodermal pouches, mesenchymal condensations and neural crest cells. While tbx2a expression is restricted to the endodermal pouches, its function is required for the normal morphogenesis of the entire pharyngeal arches. Given the similar function of Tbx1 in craniofacial development, we explored the possibility of an interaction between Tbx1 and Tbx2a. The use of bimolecular fluorescence complementation revealed the interaction between Tbx2a and Tbx1, thus providing support for the idea that functional interaction between different, co-expressed Tbx proteins could be a common theme across developmental processes in cell lineages and tissues. Together, this work provides mechanistic insight into the role of TBX2 in human disorders affecting the face and neck.
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Affiliation(s)
- Hang Nguyen Thi Thu
- Institute of Molecular and Cell Biology, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Siau Lin Loh
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Jimmy So Bok Yan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Vladimir Korzh
- Institute of Molecular and Cell Biology, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * E-mail:
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Abstract
Developmental transcription factors are key players in animal multicellularity, being members of the T-box family that are among the most important. Until recently, T-box transcription factors were thought to be exclusively present in metazoans. Here, we report the presence of T-box genes in several nonmetazoan lineages, including ichthyosporeans, filastereans, and fungi. Our data confirm that Brachyury is the most ancient member of the T-box family and establish that the T-box family diversified at the onset of Metazoa. Moreover, we demonstrate functional conservation of a homolog of Brachyury of the protist Capsaspora owczarzaki in Xenopus laevis. By comparing the molecular phenotype of C. owczarzaki Brachyury with that of homologs of early branching metazoans, we define a clear difference between unicellular holozoan and metazoan Brachyury homologs, suggesting that the specificity of Brachyury emerged at the origin of Metazoa. Experimental determination of the binding preferences of the C. owczarzaki Brachyury results in a similar motif to that of metazoan Brachyury and other T-box classes. This finding suggests that functional specificity between different T-box classes is likely achieved by interaction with alternative cofactors, as opposed to differences in binding specificity.
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Chen J. Impaired cardiovascular function caused by different stressors elicits a common pathological and transcriptional response in zebrafish embryos. Zebrafish 2013; 10:389-400. [PMID: 23837677 DOI: 10.1089/zeb.2013.0875] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Zebrafish embryos have been widely used to study the genes and processes needed for normal vertebrate heart development. We recently observed that exposure to 2,3,7,8-tetra-chlorodibenzo-p-dioxin (TCDD) or retinoic acid (RA) produces very similar signs of heart failure in developing zebrafish via divergent molecular pathways. The fact that diverse stressors and mutations cause severe pericardial edema and circulatory collapse in developing zebrafish has been largely unexplored. We hypothesized that unrelated chemicals can trigger a common pathological response leading to the same end-stage heart failure. To test this hypothesis, we compared the effects of TCDD, RA, carbaryl, valproic acid, and morpholino oligonucleotide (MO) knockdown of TBX5 on the developing heart in zebrafish embryos. These model stressors have all been previously reported to affect zebrafish heart development, and elicited very similar signs of embryonic heart failure. Microarray analysis showed that one cluster of 92 transcripts affected by these different treatments was significantly downregulated by all treatments. This gene cluster is composed of transcripts required for chromosome assembly, DNA replication, and cell cycle progression. We refer to this cluster as the cell cycle gene cluster (CCGC). Immunohistochemistry revealed that downregulation of the CCGC precedes a halt in cardiomyocyte proliferation in the hearts of zebrafish exposed to any of the treatments. Previous work has shown that the initial response to TCDD is a decrease in cardiac output. Since this precedes the signs of edema, heart failure, and fall in CCGC expression, we postulated that any factor that decreases cardiac output will produce the same syndrome of heart failure responses. To test this, we used MO knockdown of cardiac troponin T2 (TNNT2) to specifically block contractility. The TNNT2-MO produced exactly the same signs of cardiotoxicity as the other treatments, including downregulation of the signature CCGC. Our results indicate that agents altering cardiac output can have amplified consequences during specific periods in development.
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Affiliation(s)
- Jing Chen
- Institute of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China.
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Jang EJ, Park HR, Hong JH, Hwang ES. Lysine 313 of T-box is crucial for modulation of protein stability, DNA binding, and threonine phosphorylation of T-bet. THE JOURNAL OF IMMUNOLOGY 2013; 190:5764-70. [PMID: 23616576 DOI: 10.4049/jimmunol.1203403] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A T-box-containing protein expressed in T cells (T-bet) is a key transcription factor involved in the regulation of Th cell differentiation. Although T-bet-deficient CD4(+) T cells fail to produce IFN-γ and typically differentiate into Th2 cells in vitro, ectopic overexpression of T-bet elevates IFN-γ and suppresses production of IL-2 and Th2 cytokines through different mechanisms. Despite the importance of the T-bet protein level, the regulatory mechanisms that control T-bet protein stability are largely unknown. In this study, we found that T-bet underwent proteasomal degradation via ubiquitination at Lys-313. Despite its robust accumulation following lysine mutation, T-bet(K313R) failed to increase IFN-γ production because of diminished DNA binding activity, as demonstrated in the crystal structure of T-bet-DNA complex. Strikingly, T-bet(K313R) entirely lost the ability to suppress IL-2 production and Th2 cell development; this was due to loss of its interaction with NFAT1. We further identified that the T-bet(K313R) reduced the phosphorylation of T-bet at Thr-302, and that threonine phosphorylation was essential for T-bet interaction with NFAT1 and suppression of NFAT1 activity. Retroviral transduction of T-bet(T302A) into T-bet-deficient cells restored IFN-γ levels compared with those induced by wild-type T-bet, but this mutant failed to inhibit IL-2 and Th2 cytokine production. Collectively, these data show that Lys-313 in the T-box domain is essential for controlling T-bet protein stability via ubiquitin-dependent degradation, T-bet binding to the IFN-γ promoter, and for the interaction with and suppression of NFAT1. Thus, multiple posttranslational modifications of T-bet are involved in fine-tuning cytokine production during Th cell development.
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Affiliation(s)
- Eun Jung Jang
- College of Pharmacy and Global Top 5 Research Program, Ewha Womans University, Seoul 120-750, South Korea
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Choudhry P, Trede NS. DiGeorge syndrome gene tbx1 functions through wnt11r to regulate heart looping and differentiation. PLoS One 2013; 8:e58145. [PMID: 23533583 PMCID: PMC3606275 DOI: 10.1371/journal.pone.0058145] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 01/31/2013] [Indexed: 01/31/2023] Open
Abstract
DiGeorge syndrome (DGS) is the most common microdeletion syndrome, and is characterized by congenital cardiac, craniofacial and immune system abnormalities. The cardiac defects in DGS patients include conotruncal and ventricular septal defects. Although the etiology of DGS is critically regulated by TBX1 gene, the molecular pathways underpinning TBX1's role in heart development are not fully understood. In this study, we characterized heart defects and downstream signaling in the zebrafish tbx1−/− mutant, which has craniofacial and immune defects similar to DGS patients. We show that tbx1−/− mutants have defective heart looping, morphology and function. Defective heart looping is accompanied by failure of cardiomyocytes to differentiate normally and failure to change shape from isotropic to anisotropic morphology in the outer curvatures of the heart. This is the first demonstration of tbx1's role in regulating heart looping, cardiomyocyte shape and differentiation, and may explain how Tbx1 regulates conotruncal development in humans. Next we elucidated tbx1's molecular signaling pathway guided by the cardiac phenotype of tbx1−/− mutants. We show for the first time that wnt11r (wnt11 related), a member of the non-canonical Wnt pathway, and its downstream effector gene alcama (activated leukocyte cell adhesion molecule a) regulate heart looping and differentiation similarly to tbx1. Expression of both wnt11r and alcama are downregulated in tbx1−/− mutants. In addition, both wnt11r−/− mutants and alcama morphants have heart looping and differentiation defects similar to tbx1−/− mutants. Strikingly, heart looping and differentiation in tbx1−/− mutants can be partially rescued by ectopic expression of wnt11r or alcama, supporting a model whereby heart looping and differentiation are regulated by tbx1 in a linear pathway through wnt11r and alcama. This is the first study linking tbx1 and non-canonical Wnt signaling and extends our understanding of DGS and heart development.
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Affiliation(s)
- Priya Choudhry
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail: (PC) (PC); (NT) (NT)
| | - Nikolaus S. Trede
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail: (PC) (PC); (NT) (NT)
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The transcription factors TBX2 and TBX3 interact with human papillomavirus 16 (HPV16) L2 and repress the long control region of HPVs. J Virol 2013; 87:4461-74. [PMID: 23388722 DOI: 10.1128/jvi.01803-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The minor capsid protein L2 of human papillomaviruses (HPVs) has multiple functions during the viral life cycle. Although L2 is required for effective invasion and morphogenesis, only a few cellular interaction partners are known so far. Using yeast two-hybrid screening, we identified the transcription factor TBX2 as a novel interaction partner of HPV type 16 (HPV16) L2. Coimmunoprecipitations and immunofluorescence analyses confirmed the L2-TBX2 interaction and revealed that L2 also interacts with TBX3, another member of the T-box family. Transcription of the early genes during HPV infection is under the control of an upstream enhancer and early promoter region, the long control region (LCR). In promoter-reporter gene assays, we observed that TBX2 and TBX3 repress transcription from the LCR and that this effect is enhanced by L2. Repression of the HPV LCR by TBX2/3 seems to be a conserved mechanism, as it was also observed with the LCRs of different HPV types. Finally, interaction of TBX2 with the LCR was detected by chromatin immunoprecipitation, and we found a strong colocalization of L2 and TBX2 in HPV16-positive cervical intraepithelial neoplasia (CIN) I-II tissue sections. These results suggest that TBX2/3 might play a role in the regulation of HPV gene expression during the viral life cycle.
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Aguirre CE, Murgan S, Carrasco AE, López SL. An intact brachyury function is necessary to prevent spurious axial development in Xenopus laevis. PLoS One 2013; 8:e54777. [PMID: 23359630 PMCID: PMC3554630 DOI: 10.1371/journal.pone.0054777] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 12/17/2012] [Indexed: 11/19/2022] Open
Abstract
We have previously shown that the member of the HES family hairy2 induces the ectopic expression of dorsal markers when it is overexpressed in the ventral side of Xenopus embryos. Intriguingly, hairy2 represses the mesoderm transcription factor brachyury (bra) throughout its domain in the marginal zone. Here we show that in early gastrula, bra and hairy2 are expressed in complementary domains. Overexpression of bra repressed hairy2. Interference of bra function with a dominant-negative construct expanded the hairy2 domain and, like hairy2 overexpression, promoted ectopic expression of dorsal axial markers in the ventral side and induced secondary axes without head and notochord. Hairy2 depletion rescued the ectopic dorsal development induced by interference of bra function. We concluded that an intact bra function is necessary to exclude hairy2 expression from the non-organiser field, to impede the ectopic specification of dorsal axial fates and the appearance of incomplete secondary axes. This evidence supports a previously unrecognised role for bra in maintaining the dorsal fates inhibited in the ventral marginal zone, preventing the appearance of trunk duplications.
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Affiliation(s)
- Cecilia E. Aguirre
- Laboratorio de Embriología Molecular, Instituto de Biología Celular y Neurociencia ‘‘Prof. E. De Robertis’’ (UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Sabrina Murgan
- Laboratorio de Embriología Molecular, Instituto de Biología Celular y Neurociencia ‘‘Prof. E. De Robertis’’ (UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrés E. Carrasco
- Laboratorio de Embriología Molecular, Instituto de Biología Celular y Neurociencia ‘‘Prof. E. De Robertis’’ (UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Silvia L. López
- Laboratorio de Embriología Molecular, Instituto de Biología Celular y Neurociencia ‘‘Prof. E. De Robertis’’ (UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
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Cochella L, Hobert O. Embryonic priming of a miRNA locus predetermines postmitotic neuronal left/right asymmetry in C. elegans. Cell 2012. [PMID: 23201143 DOI: 10.1016/j.cell.2012.10.049] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The mechanisms by which functional left/right asymmetry arises in morphologically symmetric nervous systems are poorly understood. Here, we provide a mechanistic framework for how functional asymmetry in a postmitotic neuron pair is specified in C. elegans. A key feature of this mechanism is a temporally separated, two-step activation of the lsy-6 miRNA locus. The lsy-6 locus is first "primed" by chromatin decompaction in the precursor for the left neuron, but not the right neuron, several divisions before the neurons are born. lsy-6 expression is then "boosted" to functionally relevant levels several divisions later in the mother of the left neuron, through the activity of a bilaterally expressed transcription factor that can only activate lsy-6 in the primed neuron. This study shows how cells can become committed during early developmental stages to execute a specific fate much later in development and provides a conceptual framework for understanding the generation of neuronal diversity.
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Affiliation(s)
- Luisa Cochella
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA.
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Abstract
The heart as a functional organ first appeared in bilaterians as a single peristaltic pump and evolved through arthropods, fish, amphibians, and finally mammals into a four-chambered engine controlling blood-flow within the body. The acquisition of cardiac complexity in the evolving heart was a product of gene duplication events and the co-option of novel signaling pathways to an ancestral cardiac-specific gene network. T-box factors belong to an evolutionary conserved family of transcriptional regulators with diverse roles in development. Their regulatory functions are integral in the initiation and potentiation of heart development, and mutations in these genes are associated with congenital heart defects. In this review we will discuss the evolutionary conserved cardiac regulatory functions of this family as well as their implication in disease in an aim to facilitate future gene-targeted and regenerative therapeutic remedies.
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Affiliation(s)
- Fadi Hariri
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, C.P. 6128, Succursale, Centre-ville Montréal, Quebec, H3C3J7, Canada
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From murine to human nude/SCID: the thymus, T-cell development and the missing link. Clin Dev Immunol 2012; 2012:467101. [PMID: 22474479 PMCID: PMC3303720 DOI: 10.1155/2012/467101] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 12/09/2011] [Indexed: 11/17/2022]
Abstract
Primary immunodeficiencies (PIDs) are disorders of the immune system, which lead to increased susceptibility to infections. T-cell defects, which may affect T-cell development/function, are approximately 11% of reported PIDs. The pathogenic mechanisms are related to molecular alterations not only of genes selectively expressed in hematopoietic cells but also of the stromal component of the thymus that represents the primary lymphoid organ for T-cell differentiation. With this regard, the prototype of athymic disorders due to abnormal stroma is the Nude/SCID syndrome, first described in mice in 1966. In man, the DiGeorge Syndrome (DGS) has long been considered the human prototype of a severe T-cell differentiation defect. More recently, the human equivalent of the murine Nude/SCID has been described, contributing to unravel important issues of the T-cell ontogeny in humans. Both mice and human diseases are due to alterations of the FOXN1, a developmentally regulated transcription factor selectively expressed in skin and thymic epithelia.
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Affiliation(s)
- Nori Satoh
- Marine Genomics Unit; Okinawa Institute of Science and Technology; Onna Okinawa 904-0495 Japan
| | - Kuni Tagawa
- Marine Biological Laboratory; Graduate School of Science; Hiroshima University; Mukaishima Hiroshima 722-0073 Japan
| | - Hiroki Takahashi
- Division of Developmental Biology; National Institute of Basic Biology; Okagaki Aichi 445-8585 Japan
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Kandimalla R, van Tilborg AAG, Kompier LC, Stumpel DJPM, Stam RW, Bangma CH, Zwarthoff EC. Genome-wide analysis of CpG island methylation in bladder cancer identified TBX2, TBX3, GATA2, and ZIC4 as pTa-specific prognostic markers. Eur Urol 2012; 61:1245-56. [PMID: 22284968 DOI: 10.1016/j.eururo.2012.01.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 01/09/2012] [Indexed: 01/05/2023]
Abstract
BACKGROUND DNA methylation markers could serve as useful biomarkers, both as markers for progression and for urine-based diagnostic assays. OBJECTIVE Identify bladder cancer (BCa)-specific methylated DNA sequences for predicting pTa-specific progression and detecting BCa in voided urine. DESIGN, SETTING, AND PARTICIPANTS Genome-wide methylation analysis was performed on 44 bladder tumours using the Agilent 244K Human CpG Island Microarray (Agilent Technologies, Santa Clara, CA, USA). Validation was done using a custom Illumina 384-plex assay (Illumina, San Diego, CA, USA) in a retrospective group of 77 independent tumours. Markers for progression were identified in pTa (n = 24) tumours and validated retrospectively in an independent series of 41 pTa tumours by the SNaPshot method (Applied Biosystems, Foster City, CA, USA). MEASUREMENTS The percentage of methylation in tumour and urine samples was used to identify markers for detection and related to the end point of progression to muscle-invasive disease with Kaplan-Meier models and multivariate analysis. RESULTS AND LIMITATIONS In the validation set, methylation of the T-box 2 (TBX2), T-box 3 (TBX3), GATA binding protein 2 (GATA2), and Zic family member 4 (ZIC4) genes was associated with progression to muscle-invasive disease in pTa tumours (p = 0.003). Methylation of TBX2 alone showed a sensitivity of 100%, a specificity of 80%, a positive predictive value of 78%, and a negative predictive value of 100%, with an area under the curve of 0.96 (p<0.0001) for predicting progression. Multivariate analysis showed that methylation of TBX3 and GATA2 are independent predictors of progression when compared to clinicopathologic variables (p = 0.04 and p = 0.03, respectively). The predictive accuracy improved by 23% by adding methylation of TBX2, TBX3, and GATA2 to the European Organisation for Research and Treatment of Cancer risk scores. We further identified and validated 110 CpG islands (CGIs) that are differentially methylated between tumour cells and control urine. The limitation of this study is the small number of patients analysed for testing and validating the prognostic markers. CONCLUSIONS We have identified four methylation markers that predict progression in pTa tumours, thereby allowing stratification of patients for personalised follow-up. In addition, we identified CGIs that will enable detection of bladder tumours in voided urine.
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Affiliation(s)
- Raju Kandimalla
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
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Thieme R, Ramin N, Fischer S, Püschel B, Fischer B, Santos AN. Gastrulation in rabbit blastocysts depends on insulin and insulin-like-growth-factor 1. Mol Cell Endocrinol 2012; 348:112-9. [PMID: 21827825 DOI: 10.1016/j.mce.2011.07.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 07/24/2011] [Accepted: 07/24/2011] [Indexed: 11/26/2022]
Abstract
Insulin and insulin-like-growth-factor 1 (IGF1) are components of the uterine secretions. As potent growth factors they influence early embryo development. The underlying molecular mechanisms are largely unknown. Here we report on the effects of insulin and IGF1 on early gastrulation in rabbit blastocysts. We have studied blastocysts grown in vivo in metabolically healthy rabbits, in rabbits with type 1 diabetes and in vitro in the presence or absence of insulin or IGF1. Embryonic disc morphology and expression of Brachyury, Wnt3a and Wnt4 were analysed by qPCR and IHC. Pre-gastrulated blastocysts (stage 0/1) cultured with insulin or IGF1 showed a significantly higher capacity to form the posterior mesoderm and primitive streak (stage 2 and 3) than blastocysts cultured without growth factors. In gastrulating blastocysts the levels of the mesoderm-specific transcription factor Brachyury and the Wnt signalling molecules Wnt3a and Wnt4 showed a stage-specific expression pattern with Brachyury transcripts increasing from stage 0/1 to 3. Wnt4 protein was found spread over the whole embryoblast. Insulin induced Wnt3a, Wnt4 and Brachyury expression in a temporal- and stage-specific pattern. Only blastocysts cultured with insulin reached the Wnt3a, Wnt4 and Brachyury expression levels of stage 2 in vivo blastocysts, indicating that insulin is required for Wnt3a, Wnt4 and Brachyury expression during gastrulation. Insulin-induced Wnt3a and Wnt4 expression preceded Brachyury. Wnt3a-induced expression could be depleted by MEK1 inhibition (PD98059). Involvement of insulin in embryonic Wnt3a expression was further shown in vivo with Wnt3a expression being notably down regulated in stage 2 blastocysts from rabbits with type 1 diabetes. Blastocysts grown in diabetic rabbits are retarded in development, a finding which supports our current results that insulin is highly likely required for early mesoderm formation in rabbit blastocysts by inducing a distinct spatiotemporal expression profile of Wnt3a, Wnt4 and Brachyury.
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Affiliation(s)
- René Thieme
- Department of Anatomy and Cell Biology, Martin Luther University Faculty of Medicine, 06108 Halle (Saale), Germany.
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Philipp U, Menzel J, Distl O. A rare form of persistent right aorta arch in linkage disequilibrium with the DiGeorge critical region on CFA26 in German Pinschers. ACTA ACUST UNITED AC 2011; 102 Suppl 1:S68-73. [PMID: 21846749 DOI: 10.1093/jhered/esr053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Persistent right aortic arch (PRAA) is a congenital vascular ring anomaly common in several dog breeds. In German Pinscher, the disorder is characterized by a left retroesophageal subclavian artery in combination with a ligamentum arteriosum originating at the aberrant left subclavian artery (PRAA-SA-LA). In this study, we genotyped 38 microsatellite markers on canine chromosome 26 (CFA26) in German Pinschers and tested them for linkage and association. We found a chromosome-wide significantly linked genomic region on CFA26, which corresponds to the human DiGeorge syndrome critical region (DGCR). Therefore, we analyzed sequences from 13 genes of DGCR and the canine t-box gene TBX1. We identified a total of 26 polymorphisms in German Pinschers. Three of these SNPs located within TBX1 and one in the mitochondrial ribosomal protein L40 gene (MRPL40) were associated with the PRAA-SA-LA phenotype in German Pinscher. Despite linkage and association between PRAA-SA-LA and the canine DGCR, none of these mutations appeared responsible for PRAA-SA-LA. As the orthologue human region on HSA22q11.2 is known for high susceptibility to genomic rearrangements, we suspect that in German Pinschers, chromosomal aberrations might cause PRAA-SA-LA.
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Affiliation(s)
- Ute Philipp
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17p, 30559 Hannover, Germany
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El Omari K, De Mesmaeker J, Karia D, Ginn H, Bhattacharya S, Mancini EJ. Structure of the DNA-bound T-box domain of human TBX1, a transcription factor associated with the DiGeorge syndrome. Proteins 2011; 80:655-60. [PMID: 22095455 DOI: 10.1002/prot.23208] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 09/19/2011] [Accepted: 09/20/2011] [Indexed: 12/20/2022]
Affiliation(s)
- Kamel El Omari
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
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Deepak V, Zhang Z, Meng L, Zeng X, Liu W. Reduced activity and cytoplasmic localization of Runx2 is observed in C3h10t1/2 cells overexpressing Tbx3. Cell Biochem Funct 2011; 29:348-50. [PMID: 21455926 DOI: 10.1002/cbf.1753] [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]
Abstract
Tbox3, a T-box containing transcription factor, has been reported to negatively regulate osteoblastogenesis. Here, we studied the effects mediated by Tbx3 on the master osteogenic transcription factor Runx2 in C3h10t1/2 cells. Dual-luciferase assay results showed that Tbx3 interferes in the Runx2-mediated activation of osteopontin promoter by abrogating Runx2 activity. Immunofluorescence study demonstrated that Runx2 was simultaneously localized in the nucleus and the cytoplasm of Tbx3-overexpressing cells. The results obtained in this study indicate that Tbx3 abrogates Runx2 activity and elevated expression levels of Tbx3 in the cells can result in mislocalization of Runx2.
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Affiliation(s)
- Vishwa Deepak
- Institute of Genetics and Cell Biology, Northeast Normal University, Changchun, China
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