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Patrick R, Naval-Sanchez M, Deshpande N, Huang Y, Zhang J, Chen X, Yang Y, Tiwari K, Esmaeili M, Tran M, Mohamed AR, Wang B, Xia D, Ma J, Bayliss J, Wong K, Hun ML, Sun X, Cao B, Cottle DL, Catterall T, Barzilai-Tutsch H, Troskie RL, Chen Z, Wise AF, Saini S, Soe YM, Kumari S, Sweet MJ, Thomas HE, Smyth IM, Fletcher AL, Knoblich K, Watt MJ, Alhomrani M, Alsanie W, Quinn KM, Merson TD, Chidgey AP, Ricardo SD, Yu D, Jardé T, Cheetham SW, Marcelle C, Nilsson SK, Nguyen Q, White MD, Nefzger CM. The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening. Cell Metab 2024; 36:1858-1881.e23. [PMID: 38959897 DOI: 10.1016/j.cmet.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 03/28/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024]
Abstract
A mechanistic connection between aging and development is largely unexplored. Through profiling age-related chromatin and transcriptional changes across 22 murine cell types, analyzed alongside previous mouse and human organismal maturation datasets, we uncovered a transcription factor binding site (TFBS) signature common to both processes. Early-life candidate cis-regulatory elements (cCREs), progressively losing accessibility during maturation and aging, are enriched for cell-type identity TFBSs. Conversely, cCREs gaining accessibility throughout life have a lower abundance of cell identity TFBSs but elevated activator protein 1 (AP-1) levels. We implicate TF redistribution toward these AP-1 TFBS-rich cCREs, in synergy with mild downregulation of cell identity TFs, as driving early-life cCRE accessibility loss and altering developmental and metabolic gene expression. Such remodeling can be triggered by elevating AP-1 or depleting repressive H3K27me3. We propose that AP-1-linked chromatin opening drives organismal maturation by disrupting cell identity TFBS-rich cCREs, thereby reprogramming transcriptome and cell function, a mechanism hijacked in aging through ongoing chromatin opening.
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Affiliation(s)
- Ralph Patrick
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Marina Naval-Sanchez
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Nikita Deshpande
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Yifei Huang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jingyu Zhang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Xiaoli Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Ying Yang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Kanupriya Tiwari
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Mohammadhossein Esmaeili
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Minh Tran
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Amin R Mohamed
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Binxu Wang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Di Xia
- Genome Innovation Hub, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jun Ma
- Genome Innovation Hub, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jacqueline Bayliss
- Department of Anatomy and Physiology, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kahlia Wong
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Michael L Hun
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Xuan Sun
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Benjamin Cao
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Denny L Cottle
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Tara Catterall
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Hila Barzilai-Tutsch
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Institut NeuroMyoGène, University Claude Bernard Lyon 1, 69008 Lyon, France
| | - Robin-Lee Troskie
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Zhian Chen
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Andrea F Wise
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sheetal Saini
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ye Mon Soe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Snehlata Kumari
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Helen E Thomas
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Ian M Smyth
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Anne L Fletcher
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Konstantin Knoblich
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Matthew J Watt
- Department of Anatomy and Physiology, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Majid Alhomrani
- Department of Clinical Laboratories Sciences, Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia; Research Centre for Health Sciences, Taif University, Taif, Saudi Arabia
| | - Walaa Alsanie
- Department of Clinical Laboratories Sciences, Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia; Research Centre for Health Sciences, Taif University, Taif, Saudi Arabia
| | - Kylie M Quinn
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia
| | - Tobias D Merson
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann P Chidgey
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sharon D Ricardo
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Di Yu
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia; Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Thierry Jardé
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Surgery, Cabrini Monash University, Malvern, VIC 3144, Australia
| | - Seth W Cheetham
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Christophe Marcelle
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Institut NeuroMyoGène, University Claude Bernard Lyon 1, 69008 Lyon, France
| | - Susan K Nilsson
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Melanie D White
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Christian M Nefzger
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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Dang W, Gao D, Lyu G, Irwin DM, Shang S, Chen J, Zhang J, Zhang S, Wang Z. A Nonsynonymous Substitution of Lhx3 Leads to Changes in Body Size in Dogs and Mice. Genes (Basel) 2024; 15:739. [PMID: 38927675 PMCID: PMC11202965 DOI: 10.3390/genes15060739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
Lhx3 is a LIM-homeodomain transcription factor that affects body size in mammals by regulating the secretion of pituitary hormones. Akita, Shiba Inu, and Mame Shiba Inu dogs are Japanese native dog breeds that have different body sizes. To determine whether Lhx3 plays a role in the differing body sizes of these three dog breeds, we sequenced the Lhx3 gene in the three breeds, which led to the identification of an SNP in codon 280 (S280N) associated with body size. The allele frequency at this SNP differed significantly between the large Akita and the two kinds of smaller Shiba dogs. To validate the function of this SNP on body size, we introduced this change into the Lhx3 gene of mice. Homozygous mutant mice (S279N+/+) were found to have significantly increased body lengths and weights compared to heterozygous mutant (S279N+/-) and wild-type (S279N-/-) mice several weeks after weaning. These results demonstrate that a nonsynonymous substitution in Lhx3 plays an important role in regulating body size in mammals.
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Affiliation(s)
- Wanyi Dang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Dali Gao
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Guangqi Lyu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - David M. Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Songyang Shang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Junnan Chen
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Junpeng Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
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Thaiwong T, Corner S, Forge SL, Kiupel M. Dwarfism in Tibetan Terrier dogs with an LHX3 mutation. J Vet Diagn Invest 2021; 33:740-743. [PMID: 33890524 DOI: 10.1177/10406387211007526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Canine pituitary dwarfism in German Shepherd and related dog breeds has been reported to be associated with a 7-bp deletion mutation in intron 5 of the LHX3 gene. This mutation is transmitted as an autosomal recessive trait that results in dwarf dogs with significantly smaller stature and abnormal haircoat, and potentially early death. Phenotypically, affected adult dogs are proportionally dwarfs. These dwarfs also have a soft, woolly puppy coat that fails to transition into the typical adult hair coat, and marked hair loss occurs in some dogs. We report a similar manifestation of dwarfism in Tibetan Terriers with the same LHX3 mutation. Dwarf Tibetan Terrier puppies were born physically normal but failed to gain weight or to grow at the same rate as their normal littermates. The 7-bp deletion mutation of the LHX3 gene was identified in both alleles of 3 Tibetan Terrier dwarfs from 3 litters, which were biologically related. All parents of these dogs are carriers, confirming transmission of dwarfism in an autosomal recessive manner. Recognition and detection of this mutation will help in guiding future breeding plans to eventually eliminate this trait from Tibetan Terriers.
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Affiliation(s)
| | - Sarah Corner
- Veterinary Diagnostic Laboratory, Lansing, MI, USA
| | - Stacey La Forge
- Tibetan Terrier Health and Welfare Foundation, Sebastian, FL, USA
| | - Matti Kiupel
- Veterinary Diagnostic Laboratory, Lansing, MI, USA.,Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, Lansing, MI, USA
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Jullien N, Romanet P, Philippon M, Quentien MH, Beck-Peccoz P, Bergada I, Odent S, Reynaud R, Barlier A, Saveanu A, Brue T, Castinetti F. Heterozygous LHX3 mutations may lead to a mild phenotype of combined pituitary hormone deficiency. Eur J Hum Genet 2018; 27:216-225. [PMID: 30262920 DOI: 10.1038/s41431-018-0264-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 07/03/2018] [Accepted: 08/09/2018] [Indexed: 12/31/2022] Open
Abstract
LHX3 is an LIM domain transcription factor involved in the early steps of pituitary ontogenesis. We report here functional studies of three allelic variants, including the first heterozygous variant of LHX3 NM_178138.5(LHX3):c.587T>C (p.(Leu196Pro)) that may be responsible for a milder phenotype of hypopituitarism. Our functional studies showed that NM_178138.5(LHX3):c.587T>C (p.(Leu196Pro)) was not able to activate target promoters in vitro, as it did not bind DNA, and likely affected LHX3 function via a mechanism of haplo-insufficiency. Our study demonstrates the possibility that patients with a heterozygous variant of LHX3 may have pituitary deficiencies, with a milder phenotype than patients with homozygous variants. It is thus of vital to propose an optimal follow-up of such patients, who, until now, were considered as not being at risk of presenting pituitary deficiency. The second variant NM_178138.5(LHX3):c.622C>G (p.(Arg208Gly)), present in a homozygous state, displayed decreased transactivating ability without loss of binding capacity in vitro, concordant with in silico analysis; it should thus be considered to affect LHX3 function. In contrast, the NM_178138.5(LHX3):c.929G>C (p.(Arg310Pro)) variant, in a heterozygous state, also predicted as deleterious in silico, proved functionally active in vitro, and should thus still be classified as a variant of unknown significance. Our study emphasizes the need for functional studies due to the limits of software-based predictions of new variants, and the possible association of a pituitary phenotype to heterozygous LHX3 variants.
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Affiliation(s)
| | - Pauline Romanet
- Aix Marseille Univ, APHM, INSERM, MMG, Hôpital de la Conception, Laboratory of Molecular Biology, Marseille, France
| | - Mélanie Philippon
- Aix Marseille Univ, APHM, INSERM, MMG, Hôpital de la Conception, Department of Endocrinology, Marseille, France
| | | | - Paolo Beck-Peccoz
- Institute of Endocrine Sciences, Ospedale Maggiore IRCCS, University of Milan, Milan, Italy
| | - Ignacio Bergada
- Centro de Investigaciones Endocrinologicas (CEDIE) « Dr. César Bergada » Division de Endocrinologia, Hospital de Ninos Ricardo Guttierrez, Buenos Aires, Argentina
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de référence "Maladies Rares" CLAD-Ouest, université de Rennes 1, CNRS UMR6290, Hôpital SUD, Rennes, France
| | - Rachel Reynaud
- Aix Marseille Univ, APHM, INSERM, MMG, Hôpital la Timone Enfants, Department of Pediatrics, Marseille, France
| | - Anne Barlier
- Aix Marseille Univ, APHM, INSERM, MMG, Hôpital de la Conception, Laboratory of Molecular Biology, Marseille, France
| | - Alexandru Saveanu
- Aix Marseille Univ, INSERM, MMG, UMR1251 Faculté de Médecine, Marseille, France
| | - Thierry Brue
- Aix Marseille Univ, APHM, INSERM, MMG, Hôpital de la Conception, Department of Endocrinology, Marseille, France
| | - Frederic Castinetti
- Aix Marseille Univ, APHM, INSERM, MMG, Hôpital de la Conception, Department of Endocrinology, Marseille, France.
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5
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Löf C, Patyra K, Kero A, Kero J. Genetically modified mouse models to investigate thyroid development, function and growth. Best Pract Res Clin Endocrinol Metab 2018; 32:241-256. [PMID: 29779579 DOI: 10.1016/j.beem.2018.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The thyroid gland produces thyroid hormones (TH), which are essential regulators for growth, development and metabolism. The thyroid is mainly controlled by the thyroid-stimulating hormone (TSH) that binds to its receptor (TSHR) on thyrocytes and mediates its action via different G protein-mediated signaling pathways. TSH primarily activates the Gs-pathway, and at higher concentrations also the Gq/11-pathway, leading to an increase of intracellular cAMP and Ca2+, respectively. To date, the physiological importance of other G protein-mediated signaling pathways in thyrocytes is unclear. Congenital hypothyroidism (CH) is defined as the lack of TH at birth. In familial cases, high-throughput sequencing methods have facilitated the identification of novel mutations. Nevertheless, the precise etiology of CH yet remains unraveled in a proportion of cases. Genetically modified mouse models can reveal new pathophysiological mechanisms of thyroid diseases. Here, we will present an overview of genetic mouse models for thyroid diseases, which have provided crucial insights into thyroid gland development, function, and growth with a special focus on TSHR and microRNA signaling.
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Affiliation(s)
- C Löf
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, Turku Center for Disease Modeling, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - K Patyra
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, Turku Center for Disease Modeling, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - A Kero
- Department of Pediatrics, Turku University Hospital, Kiinamyllynkatu 4-8, 20521, Turku, Finland
| | - J Kero
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, Turku Center for Disease Modeling, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland; Department of Pediatrics, Turku University Hospital, Kiinamyllynkatu 4-8, 20521, Turku, Finland.
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6
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Zhao H, He S, Zhu Y, Cao X, Luo R, Cai Y, Xu H, Sun X. A novel 29 bp insertion/deletion (indel) variant of the <i>LHX3</i> gene and its influence on growth traits in four sheep breeds of various fecundity. Arch Anim Breed 2017. [DOI: 10.5194/aab-60-79-2017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Abstract. Belonging to the same LIM homeobox (LHX) family, LHX3 and LHX4 are key transcription factors in animal growth and reproduction. Insertion/deletion (indel) is a relatively simple and effective DNA marker. Therefore, four sheep breeds of various fecundity were used to explore the novel indel variants within the sheep LHX3 and LHX4 gene, as well as to evaluate their effects on growth traits. Herein, only one novel 29 bp indel (NC_019460.2:g.3107494-3107522delGGCCTGGACTGTGATGGGCACCCTCCGGG) within the sheep LHX3 gene was found, and three genotypes were detected. Interestingly, the increasing trends of II (insertion/insertion) genotype frequency and I allelic frequency were the same as the growth of the fertility character. Genotypic frequency and allelic frequency distributions were significantly different between the high-fecundity breeds (HS, STHS and LFTS) and low-fecundity breed (TS) based on a χ2 test (P < 0.05). Association analyses showed that body length was significantly different in female TS and STHS and that chest width was significantly different for the female TS and male STHS (P < 0.05). These findings suggested that the 29 bp indel could extend the spectrum of genetic variations of the LHX3 gene in sheep and provide a valuable theoretical basis for the marker-assisted selection (MAS) in sheep breeding and genetics.
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Fan J, Zhang C, Chen Q, Zhou J, Franc JL, Chen Q, Tong Y. Genomic analyses identify agents regulating somatotroph and lactotroph functions. Funct Integr Genomics 2016; 16:693-704. [PMID: 27709372 DOI: 10.1007/s10142-016-0518-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 08/21/2016] [Accepted: 08/25/2016] [Indexed: 11/25/2022]
Abstract
Isolated hormone deficiency might be caused by loss of a specific type of endocrine cells, and regenerating these missing cells may provide a new option for future treatment. It is known that POU1F1 lineage cells can differentiate into thyrotroph, somatotroph, and lactotroph. However, there is no effective way of controlling pituitary stem/progenitor cells to differentiate into a specific type of endocrine cell. We thereby analyzed multiple genomic publications related to POU1F1 and pituitary development in this study to identify genes and agents regulating POU1F1 lineage cell differentiation. ANOVA analyses were performed to obtain differentially expressed genes. Ingenuity pathway analyses were performed to obtain signaling pathways, interaction networks, and upstream regulators. Venn diagram was used to determine the overlapping information between studies. Summary statistics was performed to rank genes according to their frequency of occurrence in these studies. The results from upstream analyses indicated that 326 agents may regulate pituitary cell differentiation. These agents can be categorized into 12 groups, including hormones and related pathways, PKA-cAMP pathways, p53/DNA damaging/cell cycle pathways, immune/inflammation regulators, growth factor and downstream pathways, retinoic/RAR pathways, ROS pathways, histone modifications, CCAAT/enhancer binding protein family, neuron development/degeneration pathways, calcium related and fat acid, and glucose pathways. Additional experiments demonstrated that H2O2 and catalase differentially regulate growth hormone and prolactin expression in somatolactotroph cells, confirming potential roles of ROS pathway on regulating somatotroph and lactotroph functions.
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Affiliation(s)
- Jun Fan
- Basic Medical College, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medicine, Cedars-Sinai Medical Center, UCLA School of Medicine, Room 3021, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA
| | - Cui Zhang
- Basic Medical College, Xinxiang Medical University, Xinxiang, Henan, 453003, China
| | - Qi Chen
- Department of Medicine, Cedars-Sinai Medical Center, UCLA School of Medicine, Room 3021, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA
| | - Jin Zhou
- Division of Epidemiology and Biostatistics, College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Jean-Louis Franc
- Aix-Marseille Université, CNRS, UMR7286, CRN2M, Faculté de Médecine Nord, Marseille, France
| | - Qing Chen
- School of Pharmaceutical Science, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, China
| | - Yunguang Tong
- Basic Medical College, Xinxiang Medical University, Xinxiang, Henan, 453003, China.
- Department of Medicine, Cedars-Sinai Medical Center, UCLA School of Medicine, Room 3021, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA.
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8
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Cheng JM, Gu JW, Kuang YQ, Ma Y, Xia X, Yang T, Lu M, He WQ, Sun ZY, Zhang YC. Multicenter study on adult growth hormone level in postoperative pituitary tumor patients. Cell Biochem Biophys 2014; 71:1239-42. [PMID: 25403160 DOI: 10.1007/s12013-014-0334-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The objective of this study is to observe the adult growth hormone level in postoperative pituitary tumor patients of multi-centers, and explore the change of hypophyseal hormones in postoperative pituitary tumor patients. Sixty patients with pituitary tumor admitted during March, 2011-March, 2012 were selected. Postoperative hypophyseal hormone deficiency and the change of preoperative, intraoperative, and postoperative growth hormone levels were recorded. Growth hormone hypofunction was the most common hormonal hypofunction, which took up to 85.0 %. Adrenocortical hormone hypofunction was next to it and accounted for 58.33 %. GH + ACTH + TSH + Gn deficiency was the most common in postoperative hormone deficiency, which took up to 40.00 %, and GH + ACTH + TSH + Gn + AVP and GH deficiencies were next to it and accounted for 23.33 and 16.67 %, respectively. The hormone levels in patients after total pituitary tumor resection were significantly lower than those after partial pituitary tumor resection, and the difference was statistically significant; growth hormone and serum prolactin levels after surgery in two groups were decreased, and the difference was statistically significant. The incidence rate of growth hormone deficiency in postoperative pituitary tumor patients is high, which is usually complicated with deficiency of various hypophyseal hormones. In clinical, we should pay attention to the levels of the hypopnyseal hormones, and take timely measures to avoid postoperative complications.
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Affiliation(s)
- Jing-min Cheng
- Department of Neurosurgery, Chengdu Military General Hospital, 270 Rong Du Road, Chengdu, 610083, Sichuan Province, China
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9
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Malik RE, Rhodes SJ. The role of DNA methylation in regulation of the murine Lhx3 gene. Gene 2013; 534:272-81. [PMID: 24183897 DOI: 10.1016/j.gene.2013.10.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 10/09/2013] [Accepted: 10/23/2013] [Indexed: 12/20/2022]
Abstract
LHX3 is a LIM-homeodomain transcription factor with critical roles in pituitary and nervous system development. Mutations in the LHX3 gene are associated with pediatric diseases featuring severe hormone deficiencies, hearing loss, developmental delay, and other symptoms. The mechanisms that govern LHX3/Lhx3 transcription are poorly understood. In this study, we examined the role of DNA methylation in the expression status of the mouse Lhx3 gene. Pituitary cells that do not normally express Lhx3 (Pit-1/0 cells) were treated with 5-aza-2'-deoxycytidine, a demethylating reagent. This treatment leads to activation of Lhx3 gene expression suggesting that methylation contributes to Lhx3 regulation. Treatment of Pit-1/0 pituitary cells with a combination of a demethylating reagent and a histone deacetylase inhibitor led to rapid activation of Lhx3 expression, suggesting possible crosstalk between DNA methylation and histone modification processes. To assess DNA methylation levels, treated and untreated Pit-1/0 genomic DNAs were subjected to bisulfite conversion and sequencing. Treated Pit-1/0 cells had decreased methylation at specific sites in the Lhx3 locus compared to untreated cells. Chromatin immunoprecipitation assays demonstrated interactions between the MeCp2 methyl binding protein and Lhx3 promoter regions in the Pit-1/0 cell line. Overall, this study demonstrates that DNA methylation patterns of the Lhx3 gene are associated with its expression status.
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Affiliation(s)
- Raleigh E Malik
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Simon J Rhodes
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Biology, Indiana University-Purdue University Indianapolis, IN, USA; Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.
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Hunter CS, Malik RE, Witzmann FA, Rhodes SJ. LHX3 interacts with inhibitor of histone acetyltransferase complex subunits LANP and TAF-1β to modulate pituitary gene regulation. PLoS One 2013; 8:e68898. [PMID: 23861948 PMCID: PMC3701669 DOI: 10.1371/journal.pone.0068898] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/07/2013] [Indexed: 01/19/2023] Open
Abstract
LIM-homeodomain 3 (LHX3) is a transcription factor required for mammalian pituitary gland and nervous system development. Human patients and animal models with LHX3 gene mutations present with severe pediatric syndromes that feature hormone deficiencies and symptoms associated with nervous system dysfunction. The carboxyl terminus of the LHX3 protein is required for pituitary gene regulation, but the mechanism by which this domain operates is unknown. In order to better understand LHX3-dependent pituitary hormone gene transcription, we used biochemical and mass spectrometry approaches to identify and characterize proteins that interact with the LHX3 carboxyl terminus. This approach identified the LANP/pp32 and TAF-1β/SET proteins, which are components of the inhibitor of histone acetyltransferase (INHAT) multi-subunit complex that serves as a multifunctional repressor to inhibit histone acetylation and modulate chromatin structure. The protein domains of LANP and TAF-1β that interact with LHX3 were mapped using biochemical techniques. Chromatin immunoprecipitation experiments demonstrated that LANP and TAF-1β are associated with LHX3 target genes in pituitary cells, and experimental alterations of LANP and TAF-1β levels affected LHX3-mediated pituitary gene regulation. Together, these data suggest that transcriptional regulation of pituitary genes by LHX3 involves regulated interactions with the INHAT complex.
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Affiliation(s)
- Chad S. Hunter
- Department of Biology, Indiana University-Purdue University Indianapolis, Indiana, United States of America
| | - Raleigh E. Malik
- Department of Biochemistry and Molecular Biology, Indiana School of Medicine, Indianapolis, Indiana, United States of America
| | - Frank A. Witzmann
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Simon J. Rhodes
- Department of Biology, Indiana University-Purdue University Indianapolis, Indiana, United States of America
- Department of Biochemistry and Molecular Biology, Indiana School of Medicine, Indianapolis, Indiana, United States of America
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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Prince KL, Colvin SC, Park S, Lai X, Witzmann FA, Rhodes SJ. Developmental analysis and influence of genetic background on the Lhx3 W227ter mouse model of combined pituitary hormone deficiency disease. Endocrinology 2013; 154:738-48. [PMID: 23288907 PMCID: PMC3548188 DOI: 10.1210/en.2012-1790] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Combined pituitary hormone deficiency (CPHD) diseases result in severe outcomes for patients including short stature, developmental delays, and reproductive deficiencies. Little is known about their etiology, especially the developmental profiles and the influences of genetic background on disease progression. Animal models for CPHD provide valuable tools to investigate disease mechanisms and inform diagnostic and treatment protocols. Here we examined hormone production during pituitary development and the influence of genetic background on phenotypic severity in the Lhx3(W227ter/W227ter) mouse model. Lhx3(W227ter/W227ter) embryos have deficiencies of ACTH, α-glycoprotein subunit, GH, PRL, TSHβ, and LHβ during prenatal development. Furthermore, mutant mice have significant reduction in the critical pituitary transcriptional activator-1 (PIT1). Through breeding, the Lhx3(W227ter/W227ter) genotype was placed onto the 129/Sv and C57BL/6 backgrounds. Intriguingly, the genetic background significantly affected viability: whereas Lhx3(W227ter/W227ter) animals were found in the expected frequencies in C57BL/6, homozygous animals were not viable in the 129/Sv genetic environment. The hormone marker and PIT1 reductions observed in Lhx3(W227ter/W227ter) mice on a mixed background were also seen in the separate strains but in some cases were more severe in 129/Sv. To further characterize the molecular changes in diseased mice, we conducted a quantitative proteomic analysis of pituitary proteins. This showed significantly lower levels of PRL, pro-opiomelanocortin (ACTH), and α-glycoprotein subunit proteins in Lhx3(W227ter/W227ter) mice. Together, these data show that hormone deficiency disease is apparent in early prenatal stages in this CPHD model system. Furthermore, as is noted in human disease, genetic background significantly impacts the phenotypic outcome of these monogenic endocrine diseases.
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Affiliation(s)
- Kelly L Prince
- Departments of Cellular and Integrative Physiology, Indiana University-Purdue University, Indianapolis, IN 46202, USA
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Sobrier ML, Brachet C, Vié-Luton MP, Perez C, Copin B, Legendre M, Heinrichs C, Amselem S. Symptomatic heterozygotes and prenatal diagnoses in a nonconsanguineous family with syndromic combined pituitary hormone deficiency resulting from two novel LHX3 mutations. J Clin Endocrinol Metab 2012; 97:E503-9. [PMID: 22238406 DOI: 10.1210/jc.2011-2095] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Only 11 mutations have been reported in the transcription factor LHX3, known to be important for the development of the pituitary and motor neurons. All patients were homozygous, with various syndromic forms of combined pituitary hormone deficiency (CPHD), hampering to allocate, in these consanguineous patients, the respective contribution of LHX3 and additional genes to each symptom. OBJECTIVE The aim of the study was to report the family history and the molecular basis of a nonconsanguineous patient with syndromic CPHD. PATIENT The patient, who presented at birth with respiratory distress, had a syndromic CPHD, including severe scoliosis, and normal intelligence. His father and paternal grandmother displayed limited head rotation. RESULTS Two new LHX3 defects were identified. The paternally inherited c.252-3C>G mutation, which disrupts an acceptor splice site, would lead to severely truncated proteins containing a single LIM domain, resembling LIM-only proteins. Coexpression studies revealed the dominant-negative effect of this LIM-only protein over the wild-type LHX3. The maternally inherited p.Cys118Tyr mutation results in partial loss of transcriptional activity and synergy with POU1F1. Given the severity of the patient's phenotype, two prenatal diagnoses were performed: the first led to pregnancy interruption, the second to the birth of a healthy boy. CONCLUSIONS This study of the first nonconsanguineous patient with LHX3 mutations demonstrates the pleiotropic roles of LHX3 during development and its full involvement in the complex disease phenotype. Isolated limitation of head rotation may exist in heterozygous carriers and would result from a dominant-negative effect. These data allowed the first prenatal diagnoses of this severe condition to be performed.
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Affiliation(s)
- Marie-Laure Sobrier
- Institut National de la Santé et de la Recherche Médicale Unité 933, Université Pierre et Marie Curie-Paris 6, Hôpital Armand Trousseau, 26 avenue du Docteur Arnold Netter, 75571 Paris, Cedex 12 France.
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Bechtold-Dalla Pozza S, Hiedl S, Roeb J, Lohse P, Malik RE, Park S, Durán-Prado M, Rhodes SJ. A recessive mutation resulting in a disabling amino acid substitution (T194R) in the LHX3 homeodomain causes combined pituitary hormone deficiency. Horm Res Paediatr 2012; 77:41-51. [PMID: 22286346 PMCID: PMC3355643 DOI: 10.1159/000335929] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 12/06/2011] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND/AIMS Recessive mutations in the LHX3 homeodomain transcription factor gene are associated with developmental disorders affecting the pituitary and nervous system. We describe pediatric patients with combined pituitary hormone deficiency (CPHD) who harbor a novel mutation in LHX3. METHODS Two female siblings from related parents were examined. Both patients had neonatal complications. The index patient had CPHD featuring deficiencies of GH, LH, FSH, PRL, and TSH, with later onset of ACTH deficiency. She also had a hypoplastic anterior pituitary, respiratory distress, hearing impairment, and limited neck rotation. The LHX3 gene was sequenced and the biochemical properties of the predicted altered proteins were characterized. RESULTS A novel homozygous mutation predicted to change amino acid 194 from threonine to arginine (T194R) was detected in both patients. This amino acid is conserved in the DNA-binding homeodomain. Computer modeling predicted that the T194R change would alter the homeodomain structure. The T194R protein did not bind tested LHX3 DNA recognition sites and did not activate the α-glycoprotein and PRL target genes. CONCLUSION The T194R mutation affects a critical residue in the LHX3 protein. This study extends our understanding of the phenotypic features, molecular mechanism, and developmental course associated with mutations in the LHX3 gene.
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Affiliation(s)
| | - Stefan Hiedl
- Pediatric Endocrinology and Diabetology, Ludwig Maximilians University of Munich, Munich, Germany
| | - Julia Roeb
- Pediatric Endocrinology and Diabetology, Ludwig Maximilians University of Munich, Munich, Germany
| | - Peter Lohse
- Clinical Chemistry-Grosshadern, Ludwig Maximilians University of Munich, Munich, Germany
| | - Raleigh E. Malik
- Biochemistry and Molecular Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Ind., USA
| | - Soyoung Park
- Biochemistry and Molecular Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Ind., USA
| | - Mario Durán-Prado
- Medical Sciences, University of Castilla la Mancha, Ciudad Real, Spain
| | - Simon J. Rhodes
- Biochemistry and Molecular Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Ind., USA,Cellular and Integrative Physiology, Indiana University-Purdue University Indianapolis, Indianapolis, Ind., USA,Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Ind., USA,*Simon J. Rhodes, PhD, Cellular and Integrative Physiology, Indiana University School of Medicine, Medical Science Room 362A, 635 N. Barnhill Drive, Indianapolis, IN 46202-5120 (USA), Tel. +1 317 278 1797, E-Mail
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Tsai KL, Noorai RE, Starr-Moss AN, Quignon P, Rinz CJ, Ostrander EA, Steiner JM, Murphy KE, Clark LA. Genome-wide association studies for multiple diseases of the German Shepherd Dog. Mamm Genome 2012; 23:203-11. [PMID: 22105877 PMCID: PMC3509149 DOI: 10.1007/s00335-011-9376-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 10/18/2011] [Indexed: 01/02/2023]
Abstract
The German Shepherd Dog (GSD) is a popular working and companion breed for which over 50 hereditary diseases have been documented. Herein, SNP profiles for 197 GSDs were generated using the Affymetrix v2 canine SNP array for a genome-wide association study to identify loci associated with four diseases: pituitary dwarfism, degenerative myelopathy (DM), congenital megaesophagus (ME), and pancreatic acinar atrophy (PAA). A locus on Chr 9 is strongly associated with pituitary dwarfism and is proximal to a plausible candidate gene, LHX3. Results for DM confirm a major locus encompassing SOD1, in which an associated point mutation was previously identified, but do not suggest modifier loci. Several SNPs on Chr 12 are associated with ME and a 4.7 Mb haplotype block is present in affected dogs. Analysis of additional ME cases for a SNP within the haplotype provides further support for this association. Results for PAA indicate more complex genetic underpinnings. Several regions on multiple chromosomes reach genome-wide significance. However, no major locus is apparent and only two associated haplotype blocks, on Chrs 7 and 12 are observed. These data suggest that PAA may be governed by multiple loci with small effects, or it may be a heterogeneous disorder.
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Affiliation(s)
- Kate L. Tsai
- Department of Genetics and Biochemistry, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Rooksana E. Noorai
- Department of Genetics and Biochemistry, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Alison N. Starr-Moss
- Department of Genetics and Biochemistry, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Pascale Quignon
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. Institut de Génétique et Développement de Rennes, CNRS-UMR6061, Université de Rennes 1, 2 avenue Prof. Léon Bernard, CS34317, Rennes Cedex 35043, France
| | - Caitlin J. Rinz
- Department of Genetics and Biochemistry, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Elaine A. Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jörg M. Steiner
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Keith E. Murphy
- Department of Genetics and Biochemistry, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Leigh Anne Clark
- Department of Genetics and Biochemistry, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
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Mullen RD, Park S, Rhodes SJ. A distal modular enhancer complex acts to control pituitary- and nervous system-specific expression of the LHX3 regulatory gene. Mol Endocrinol 2011; 26:308-19. [PMID: 22194342 DOI: 10.1210/me.2011-1252] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Lin-11, Isl-1, and Mec-3 (LIM)-homeodomain (HD)-class transcription factors are critical for many aspects of mammalian organogenesis. Of these, LHX3 is essential for pituitary gland and nervous system development. Pediatric patients with mutations in coding regions of the LHX3 gene have complex syndromes, including combined pituitary hormone deficiency and nervous system defects resulting in symptoms such as dwarfism, thyroid insufficiency, infertility, and developmental delay. The pathways underlying early pituitary development are poorly understood, and the mechanisms by which the LHX3 gene is regulated in vivo are not known. Using bioinformatic and transgenic mouse approaches, we show that multiple conserved enhancers downstream of the human LHX3 gene direct expression to the developing pituitary and spinal cord in a pattern consistent with endogenous LHX3 expression. Several transferable cis elements can individually guide nervous system expression. However, a single 180-bp minimal enhancer is sufficient to confer specific expression in the developing pituitary. Within this sequence, tandem binding sites recognized by the islet-1 (ISL1) LIM-HD protein are essential for enhancer activity in the pituitary and spine, and a pituitary homeobox 1 (PITX1) bicoid class HD element is required for spatial patterning in the developing pituitary. This study establishes ISL1 as a novel transcriptional regulator of LHX3 and describes a potential mechanism for regulation by PITX1. Moreover, these studies suggest models for analyses of the transcriptional pathways coordinating the expression of other LIM-HD genes and provide tools for the molecular analysis and genetic counseling of pediatric patients with combined pituitary hormone deficiency.
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Affiliation(s)
- Rachel D Mullen
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5120, USA
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Lai X, Wang L, Tang H, Witzmann FA. A novel alignment method and multiple filters for exclusion of unqualified peptides to enhance label-free quantification using peptide intensity in LC-MS/MS. J Proteome Res 2011; 10:4799-812. [PMID: 21888428 DOI: 10.1021/pr2005633] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Though many software packages have been developed to perform label-free quantification of proteins in complex biological samples using peptide intensities generated by LC-MS/MS, two critical issues are generally ignored in this field: (i) peptides have multiple elution patterns across runs in an experiment, and (ii) many peptides cannot be used for protein quantification. To address these two key issues, we have developed a novel alignment method to enable accurate peptide peak retention time determination and multiple filters to eliminate unqualified peptides for protein quantification. Repeatability and linearity have been tested using six very different samples, i.e., standard peptides, kidney tissue lysates, HT29-MTX cell lysates, depleted human serum, human serum albumin-bound proteins, and standard proteins spiked in kidney tissue lysates. At least 90.8% of the proteins (up to 1,390) had CVs ≤ 30% across 10 technical replicates, and at least 93.6% (up to 2,013) had R(2) ≥ 0.9500 across 7 concentrations. Identical amounts of standard protein spiked in complex biological samples achieved a CV of 8.6% across eight injections of two groups. Further assessment was made by comparing mass spectrometric results to immunodetection, and consistent results were obtained. The new approach has novel and specific features enabling accurate label-free quantification.
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Affiliation(s)
- Xianyin Lai
- Department of Cellular & Integrative Physiology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States.
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Prince KL, Walvoord EC, Rhodes SJ. The role of homeodomain transcription factors in heritable pituitary disease. Nat Rev Endocrinol 2011; 7:727-37. [PMID: 21788968 DOI: 10.1038/nrendo.2011.119] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The anterior pituitary gland secretes hormones that regulate developmental and physiological processes, including growth, the stress response, metabolic status, reproduction and lactation. During embryogenesis, cellular determination and differentiation events establish specialized hormone-secreting cell types within the anterior pituitary gland. These developmental decisions are mediated in part by the actions of a cascade of transcription factors, many of which belong to the homeodomain class of DNA-binding proteins. The discovery of some of these regulatory proteins has facilitated genetic analyses of patients with hormone deficiencies. The findings of these studies reveal that congenital defects-ranging from isolated hormone deficiencies to combined pituitary hormone deficiency syndromes-are sometimes associated with mutations in the genes encoding pituitary-acting developmental transcription factors. The phenotypes of affected individuals and animal models have together provided useful insights into the biology of these transcription factors and have suggested new hypotheses for testing in the basic science laboratory. Here, we summarize the gene regulatory pathways that control anterior pituitary development, with emphasis on the role of the homeodomain transcription factors in normal pituitary organogenesis and heritable pituitary disease.
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Affiliation(s)
- Kelly L Prince
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Medical Science Room 362A, 635 North Barnhill Drive, Indianapolis, IN 46202-5120, USA
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Bower DV, Sato Y, Lansford R. Dynamic lineage analysis of embryonic morphogenesis using transgenic quail and 4D multispectral imaging. Genesis 2011; 49:619-43. [PMID: 21509927 DOI: 10.1002/dvg.20754] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 03/27/2011] [Accepted: 03/28/2011] [Indexed: 12/17/2022]
Abstract
We describe the development of transgenic quail that express various fluorescent proteins in targeted manners and their use as a model system that integrates advanced imaging approaches with conventional and emerging molecular genetics technologies. We also review the progression and complications of past fate mapping techniques that led us to generate transgenic quail, which permit dynamic imaging of amniote embryogenesis with unprecedented subcellular resolution.
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Affiliation(s)
- Danielle V Bower
- Department of Biology and the Biological Imaging Center, California Institute of Technology, Pasadena, California 91125, USA
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