1
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Suvorov A. Modalities of aging in organisms with different strategies of resource allocation. Ageing Res Rev 2022; 82:101770. [PMID: 36330930 PMCID: PMC10435286 DOI: 10.1016/j.arr.2022.101770] [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: 06/23/2022] [Revised: 08/17/2022] [Accepted: 10/24/2022] [Indexed: 01/31/2023]
Abstract
Although the progress of aging research relies heavily on a theoretical framework, today there is no consensus on many critical questions in aging biology. I hypothesize that a systematic analysis of the intersection of different evolutionary mechanisms of aging with diverse resource allocation strategies in different organisms may reconcile aging hypotheses. The application of disposable soma, mutation accumulation, antagonistic pleiotropy, and life-history theory is considered across organisms with asexual reproduction, organisms with sexual reproduction and indeterminate growth in different conditions of extrinsic mortality, and organisms with determinate growth, with endotherms/homeotherms as a subgroup. This review demonstrates that different aging mechanisms are complementary to each other, and in organisms with different resource allocation strategies they form aging modalities ranging from immortality to suicidal programs. It also revamps the role of growth arrest in aging. Growth arrest evolved in many different groups of organisms as a result of resource reallocation from growth to reproduction (e.g., semelparous animals, holometabolic insects), or from growth to nutrient storage (endotherms/homeotherms). Growth arrest in different animal lineages has similar molecular mechanisms and similar consequences for longevity due to the conflict between growth-promoting and growth-suppressing programs and suppression of regenerative capacity.
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Affiliation(s)
- Alexander Suvorov
- Environmental Health Sciences, University of Massachusetts, Amherst 240B Goessmann, 686 Noth Pleasant Str., Amherst, MA 01003, USA.
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2
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Zhang X, Malik B, Young C, Zhang H, Larkin D, Liao XH, Refetoff S, Liu M, Arvan P. Maintaining the thyroid gland in mutant thyroglobulin-induced hypothyroidism requires thyroid cell proliferation that must continue in adulthood. J Biol Chem 2022; 298:102066. [PMID: 35618019 PMCID: PMC9213252 DOI: 10.1016/j.jbc.2022.102066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/14/2022] Open
Abstract
Congenital hypothyroidism with biallelic thyroglobulin (Tg protein, encoded by the TG gene) mutation is an endoplasmic reticulum (ER) storage disease. Many patients (and animal models) grow an enlarged thyroid (goiter), yet some do not. In adulthood, hypothyroid TGcog/cog mice (bearing a Tg-L2263P mutation) exhibit a large goiter, whereas adult WIC rats bearing the TGrdw/rdw mutation (Tg-G2298R) exhibit a hypoplastic thyroid. Homozygous TG mutation has been linked to thyroid cell death, and cytotoxicity of the Tg-G2298R protein was previously thought to explain the lack of goiter in WIC-TGrdw/rdw rats. However, recent studies revealed that TGcog/cog mice also exhibit widespread ER stress–mediated thyrocyte death, yet under continuous feedback stimulation, thyroid cells proliferate in excess of their demise. Here, to examine the relative proteotoxicity of the Tg-G2298R protein, we have used CRISPR–CRISPR-associated protein 9 technology to generate homozygous TGrdw/rdw knock-in mice in a strain background identical to that of TGcog/cog mice. TGrdw/rdw mice exhibit similar phenotypes of defective Tg protein folding, thyroid histological abnormalities, hypothyroidism, and growth retardation. TGrdw/rdw mice do not show evidence of greater ER stress response or stress-mediated cell death than TGcog/cog mice, and both mouse models exhibit sustained thyrocyte proliferation, with comparable goiter growth. In contrast, in WIC-TGrdw/rdw rats, as a function of aging, the thyrocyte proliferation rate declines precipitously. We conclude that the mutant Tg-G2298R protein is not intrinsically more proteotoxic than Tg-L2263P; rather, aging-dependent difference in maintenance of cell proliferation is the limiting factor, which accounts for the absence of goiter in adult WIC-TGrdw/rdw rats.
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Affiliation(s)
- Xiaohan Zhang
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Bhoomanyu Malik
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Crystal Young
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Hao Zhang
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Dennis Larkin
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Xiao-Hui Liao
- Departments of Medicine, Pediatrics, and Committee on Genetics, The University of Chicago, Chicago Illinois, USA
| | - Samuel Refetoff
- Departments of Medicine, Pediatrics, and Committee on Genetics, The University of Chicago, Chicago Illinois, USA
| | - Ming Liu
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China
| | - Peter Arvan
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical Center, Ann Arbor, Michigan, USA.
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Laouari D, Vergnaud P, Hirose T, Zaidan M, Rabant M, Nguyen C, Burtin M, Legendre C, Codogno P, Friedlander G, Anglicheau D, Terzi F. The sexual dimorphism of kidney growth in mice and humans. Kidney Int 2022; 102:78-95. [PMID: 35337891 DOI: 10.1016/j.kint.2022.02.027] [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: 04/30/2021] [Revised: 02/02/2022] [Accepted: 02/16/2022] [Indexed: 10/18/2022]
Abstract
Kidney mass and function are sexually determined, but the cellular events and the molecular mechanisms involved in this dimorphism are poorly characterized. By combining female and male mice with castration/replacement experiments, we showed that male mice exhibited kidney overgrowth from five weeks of age. This effect was organ specific, since liver and heart weight were comparable between males and females, regardless of age. Consistently, the androgen receptor was found to be expressed in the kidneys of males, but not in the liver. In growing mice, androgens led to kidney overgrowth by first inducing a burst of cell proliferation and then an increase of cell size. Remarkably, androgens were also required to maintain cell size in adults. In fact, orchiectomy resulted in smaller kidneys in a matter of few weeks. These changes paralleled the changes of the expression of ornithine decarboxylase and cyclin D1, two known mediators of kidney growth, whereas, unexpectedly, mTORC1 and Hippo pathways did not seem to be involved. Androgens also enhanced kidney autophagy, very likely by increasing transcription factor EB nuclear translocation. Functionally, the increase of tubular mass resulted in increased sodium/phosphate transport. These findings were relevant to humans. Remarkably, by studying living gender-paired kidney donors-recipients, we showed that tubular cell size increased three months after transplantation in men as compared to women, regardless of the donor gender. Thus, our results identify novel signaling pathways that may be involved in androgen-induced kidney growth and homeostasis, and suggest that androgens determine kidney size after transplantation.
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Affiliation(s)
- Denise Laouari
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades (INEM), Département « Croissance et Signalisation », F-75006 Paris, France
| | - Paul Vergnaud
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades (INEM), Département « Croissance et Signalisation », F-75006 Paris, France; Service de Néphrologie Pédiatrique-Hémodialyse-Transplantation, AP-HP, Hôpital Necker, Paris, France
| | - Takuo Hirose
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades (INEM), Département « Croissance et Signalisation », F-75006 Paris, France
| | - Mohamad Zaidan
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades (INEM), Département « Croissance et Signalisation », F-75006 Paris, France; Service de Néphrologie-Transplantation, AP-HP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Marion Rabant
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades (INEM), Département « Croissance et Signalisation », F-75006 Paris, France; Service d'Anatomo-Pathologie, AP-HP, Hôpital Necker, Paris, France
| | - Clément Nguyen
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades (INEM), Département « Croissance et Signalisation », F-75006 Paris, France
| | - Martine Burtin
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades (INEM), Département « Croissance et Signalisation », F-75006 Paris, France
| | - Christophe Legendre
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades (INEM), Département « Croissance et Signalisation », F-75006 Paris, France; Service de Néphrologie-Transplantation, AP-HP, Hôpital Necker, Paris, France
| | - Patrice Codogno
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades (INEM), Département « Croissance et Signalisation », F-75006 Paris, France
| | - Gerard Friedlander
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades (INEM), Département « Croissance et Signalisation », F-75006 Paris, France
| | - Dany Anglicheau
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades (INEM), Département « Croissance et Signalisation », F-75006 Paris, France; Service de Néphrologie-Transplantation, AP-HP, Hôpital Necker, Paris, France
| | - Fabiola Terzi
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades (INEM), Département « Croissance et Signalisation », F-75006 Paris, France.
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Simó I, Faggiani M, Fernandez DA, Sciara AA, Arranz SE. The cellular basis of compensatory muscle growth in the teleost Odontesthes bonariensis. J Exp Biol 2021; 225:273693. [PMID: 34889453 DOI: 10.1242/jeb.242567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 12/06/2021] [Indexed: 11/20/2022]
Abstract
This study evaluates white muscle growth and in vivo cell proliferation during a fasting and refeeding trial, using pejerrey Odontesthes bonariensis as animal model, in order to better understand the cellular basis governing catch-up growth. Experiments consisted in two groups of fish, a control one continuously fed ad libitum, and a group fasted for 2 weeks and then fed for another 2 weeks. We examined how the formation of new muscle fibers and their increase in size were related to muscle precursor cell (MPC) proliferation under both experimental conditions. During fasting, the number of 5-ethynyl-2'-deoxyuridinepositive (EdU+) cells decreased along with myogenic regulatory factors (MRF) mRNA levels related to myoblast proliferation and differentiation, and the muscle stem cell-markerPax7 mRNA level increased. Analysis of myomere cross-sectional area, distribution of muscle fiber sizes and number of fibers per myomere showed that muscle hypertrophy but not hyperplasia was inhibited during fasting. Both higher igf2 mRNA level and the persistence of cell proliferation could be supporting new myofibre formation. On the other hand, an exacerbated MPC proliferation occurred during catch-up growth, and this increase in cell number could be contributing to the growth of both pre-existing and newly form small fibers. The finding that some MPCs proliferate during fasting and that muscle growth mechanisms, hyperplasia and hypertrophy, are differentially regulated could help to explain why re-fed fish could growth at higher rates, and why they return to the lost growth trajectory.
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Affiliation(s)
- Ignacio Simó
- Laboratorio Mixto de Biotecnología Acuática, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Centro Científico, Tecnológico y Educativo Acuario del Río Paraná, Av. Eduardo Carrasco y Cordiviola s/n, Rosario, 2000, Argentina
| | - Mariano Faggiani
- Laboratorio Mixto de Biotecnología Acuática, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Centro Científico, Tecnológico y Educativo Acuario del Río Paraná, Av. Eduardo Carrasco y Cordiviola s/n, Rosario, 2000, Argentina
| | - Daniel A Fernandez
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales (ICPA), Universidad Nacional de Tierra del Fuego (UNTDF), Fuegiabasket 251, V9410BXE Ushuaia, Argentina.,Centro Austral de Investigaciones Científicas (CADIC-CONICET), Bernardo A. Houssay 200, V9410BXE Ushuaia, Argentina
| | - Andrés A Sciara
- Laboratorio Mixto de Biotecnología Acuática, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Centro Científico, Tecnológico y Educativo Acuario del Río Paraná, Av. Eduardo Carrasco y Cordiviola s/n, Rosario, 2000, Argentina
| | - Silvia E Arranz
- Laboratorio Mixto de Biotecnología Acuática, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Centro Científico, Tecnológico y Educativo Acuario del Río Paraná, Av. Eduardo Carrasco y Cordiviola s/n, Rosario, 2000, Argentina
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5
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Rondini EA, Ramseyer VD, Burl RB, Pique-Regi R, Granneman JG. Single cell functional genomics reveals plasticity of subcutaneous white adipose tissue (WAT) during early postnatal development. Mol Metab 2021; 53:101307. [PMID: 34298199 PMCID: PMC8385178 DOI: 10.1016/j.molmet.2021.101307] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE The current study addresses the cellular complexity and plasticity of subcutaneous (inguinal) white adipose tissue (iWAT) in mice during the critical periods of perinatal growth and establishment. METHODS We performed a large-scale single cell transcriptomic (scRNA-seq) and epigenomic (snATAC-seq) characterization of cellular subtypes (adipose stromal cells (ASC) and adipocyte nuclei) during inguinal WAT (subcutaneous; iWAT) development in mice, capturing the early postnatal period (postnatal days (PND) 06 and 18) through adulthood (PND56). RESULTS Perinatal and adult iWAT contain 3 major ASC subtypes that can be independently identified by RNA expression profiles and DNA transposase accessibility. Furthermore, the transcriptomes and enhancer landscapes of both ASC and adipocytes dynamically change during postnatal development. Perinatal ASC (PND06) are highly enriched for several imprinted genes (IGs; e.g., Mest, H19, Igf2) and extracellular matrix proteins whose expression then declines prior to weaning (PND18). By comparison, adult ASC (PND56) are more enriched for transcripts associated with immunoregulation, oxidative stress, and integrin signaling. Two clusters of mature adipocytes, identified through single nuclei RNA sequencing (snRNA-seq), were distinctive for proinflammatory/immune or metabolic gene expression patterns that became more transcriptionally diverse in adult animals. Single nuclei assay for transposase-accessible chromatin (snATAC-seq) revealed that differences in gene expression were associated with developmental changes in chromatin accessibility and predicted transcription factor motifs (e.g., Plagl1, Ar) in both stromal cells and adipocytes. CONCLUSIONS Our data provide new insights into transcriptional and epigenomic signaling networks important during iWAT establishment at a single cell resolution, with important implications for the field of metabolic programming.
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Affiliation(s)
- Elizabeth A Rondini
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Vanesa D Ramseyer
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Rayanne B Burl
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - James G Granneman
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA; Center for Integrative Metabolic and Endocrine Research, Wayne State University, Detroit, MI, USA.
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6
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Chen H, Miao X, Xu J, Pu L, Li L, Han Y, Mao F, Ma Y. Alterations of mRNA and lncRNA profiles associated with the extracellular matrix and spermatogenesis in goats. Anim Biosci 2021; 35:544-555. [PMID: 34530511 PMCID: PMC8902208 DOI: 10.5713/ab.21.0259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/16/2021] [Indexed: 11/27/2022] Open
Abstract
Objective Spermatozoa are produced within the seminiferous tubules after sexual maturity. The expression levels of mRNAs and lncRNAs in testicular tissues are different at each stage of testicular development and are closely related to formation of the extracellular matrix (ECM) and spermatogenesis. Therefore, we set out to study the expression of lncRNAs and mRNAs during the different developmental stages of the goat testis. Methods We constructed 12 RNA libraries using testicular tissues from goats aged 3, 6, and 12 months, and studied the functions of mRNAs and lncRNAs using the gene ontogeny (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases. Relationships between differentially expressed genes (DEGs) were analyzed by lncRNA-mRNA co-expression network and protein-protein interaction network (PPI). Finally, the protein expression levels of matrix metalloproteinase 2 (MMP2), insulin-like growth factor 2 (IGF2), and insulin-like growth factor-binding protein 6 (IGFBP6) were detected by western blotting. Results We found 23, 8, and 135 differentially expressed lncRNAs and 161, 12, and 665 differentially expressed mRNAs that were identified between 3 vs 6, 6 vs 12, and 3 vs 12 months, respectively. GO, KEGG, and PPI analyses showed that the differential genes were mainly related to the ECM. Moreover, MMP2 was a hub gene and co-expressed with the lncRNA TCONS-0002139 and TCONS-00093342. The results of quantitative reverse-transcription polymerase chain reaction verification were consistent with those of RNA-seq sequencing. The expression trends of MMP2, IGF2, and IGFBP6 protein were the same as that of mRNA, which all decreased with age. IGF2 and MMP2 were significantly different in the 3 vs 6-month-old group (p<0.05). Conclusion These results improve our understanding of the molecular mechanisms involved in sexual maturation of the goat testis.
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Affiliation(s)
- Haolin Chen
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730000, China.,Institute of Animal Husbandry and Veterinary, Guizhou Academy of Agricultural Sciences, Guizhou, 550000, China
| | - Xiaomeng Miao
- Institute of Animal Husbandry and Veterinary, Guizhou Academy of Agricultural Sciences, Guizhou, 550000, China
| | - Jinge Xu
- Institute of Animal Husbandry and Veterinary, Guizhou Academy of Agricultural Sciences, Guizhou, 550000, China
| | - Ling Pu
- Institute of Animal Husbandry and Veterinary, Guizhou Academy of Agricultural Sciences, Guizhou, 550000, China
| | - Liang Li
- Institute of Animal Husbandry and Veterinary, Guizhou Academy of Agricultural Sciences, Guizhou, 550000, China
| | - Yong Han
- Institute of Animal Husbandry and Veterinary, Guizhou Academy of Agricultural Sciences, Guizhou, 550000, China
| | - Fengxian Mao
- Guizhou Province Livestock and Poultry Genetic Resources Management Station, Guiyang, Guizhou, 550000, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730000, China
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Changeux JP, Goulas A, Hilgetag CC. A Connectomic Hypothesis for the Hominization of the Brain. Cereb Cortex 2021; 31:2425-2449. [PMID: 33367521 PMCID: PMC8023825 DOI: 10.1093/cercor/bhaa365] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 02/06/2023] Open
Abstract
Cognitive abilities of the human brain, including language, have expanded dramatically in the course of our recent evolution from nonhuman primates, despite only minor apparent changes at the gene level. The hypothesis we propose for this paradox relies upon fundamental features of human brain connectivity, which contribute to a characteristic anatomical, functional, and computational neural phenotype, offering a parsimonious framework for connectomic changes taking place upon the human-specific evolution of the genome. Many human connectomic features might be accounted for by substantially increased brain size within the global neural architecture of the primate brain, resulting in a larger number of neurons and areas and the sparsification, increased modularity, and laminar differentiation of cortical connections. The combination of these features with the developmental expansion of upper cortical layers, prolonged postnatal brain development, and multiplied nongenetic interactions with the physical, social, and cultural environment gives rise to categorically human-specific cognitive abilities including the recursivity of language. Thus, a small set of genetic regulatory events affecting quantitative gene expression may plausibly account for the origins of human brain connectivity and cognition.
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Affiliation(s)
- Jean-Pierre Changeux
- CNRS UMR 3571, Institut Pasteur, 75724 Paris, France
- Communications Cellulaires, Collège de France, 75005 Paris, France
| | - Alexandros Goulas
- Institute of Computational Neuroscience, University Medical Center Eppendorf, Hamburg University, 20246 Hamburg, Germany
| | - Claus C Hilgetag
- Institute of Computational Neuroscience, University Medical Center Eppendorf, Hamburg University, 20246 Hamburg, Germany
- Department of Health Sciences, Boston University, Boston, MA 02115, USA
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Giangreco NP, Elias JE, Tatonetti NP. No population left behind: Improving paediatric drug safety using informatics and systems biology. Br J Clin Pharmacol 2020; 88:1464-1470. [PMID: 33332641 PMCID: PMC8209126 DOI: 10.1111/bcp.14705] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 10/26/2020] [Accepted: 12/05/2020] [Indexed: 12/12/2022] Open
Abstract
Adverse drugs effects (ADEs) in children are common and may result in disability and death. The current paediatric drug safety landscape, including clinical trials, is limited as it rarely includes children and relies on extrapolation from adults. Children are not small adults but go through an evolutionarily conserved and physiologically dynamic process of growth and maturation. Novel quantitative approaches, integrating observations from clinical trials and drug safety databases with dynamic mechanisms, can be used to systematically identify ADEs unique to childhood. In this perspective, we discuss three critical research directions using systems biology methodologies and novel informatics to improve paediatric drug safety, namely child versus adult drug safety profiles, age-dependent drug toxicities and genetic susceptibility of ADEs across childhood. We argue that a data-driven framework that leverages observational data, biomedical knowledge and systems biology modelling will reveal previously unknown mechanisms of pediatric adverse drug events and lead to improved paediatric drug safety.
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Affiliation(s)
- Nicholas P Giangreco
- Department of Biomedical Informatics and Systems Biology, Columbia University, New York, NY, USA
| | - Jonathan E Elias
- Department of Pediatrics, Instructor in Pediatrics, Assistant Medical Director of Information Services, Weill Cornell Medical & NYP Weill Cornell Medical Center, New York, NY, USA
| | - Nicholas P Tatonetti
- Department of Biomedical Informatics and Systems Biology, Columbia University, New York, NY, USA
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McCague EA, Lamichhane R, Holt N, Schrier Vergano SA. Growth charts for individuals with
Coffin‐Siris
syndrome. Am J Med Genet A 2020; 182:2253-2262. [PMID: 32851773 DOI: 10.1002/ajmg.a.61823] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/26/2020] [Accepted: 07/18/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Emily A. McCague
- Master of Public Health Program Eastern Virginia Medical School Norfolk Virginia USA
| | - Rajan Lamichhane
- Department of Clinical Translational Sciences Marshall University Huntington West Virginia USA
| | - Nicole Holt
- Master of Public Health Program Eastern Virginia Medical School Norfolk Virginia USA
| | - Samantha A. Schrier Vergano
- Division of Medical Genetics and Metabolism Children's Hospital of The King's Daughters Norfolk Virginia USA
- Department of Pediatrics Eastern Virginia Medical School Norfolk Virginia USA
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10
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Kumar V, Yang C, Cowley AW. Temporal Expression and Cellular Localization of PAPPA2 in the Developing Kidney of Rat. J Histochem Cytochem 2020; 68:209-222. [PMID: 31989854 DOI: 10.1369/0022155420904478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
PAPPA2 is a metalloproteinase which cleaves insulin-like growth factor binding protein (IGFBP)-3 and IGFBP-5, and its role in pregnancy and postnatal growth is primarily studied. Using exclusion mapping, we reported a subcongenic (26-P) rat where a 0.71-Mbp region containing the pregnancy-associated plasma protein a2 (Pappa2) allele of salt-insensitive Brown Norway (BN) was introgressed into Dahl saltsensitive (SS) genetic background, resulting in the reduction of salt sensitivity. Pappa2 was differentially expressed in the adult kidney of 26-P and SS rats. Here, the expression and cellular localization of Pappa2 in embryonic and postnatal kidneys of 26-P and SS rats were examined. Pappa2 mRNA expression was 5-fold higher in the embryonic kidney (day 20.5) of the 26-P rat compared with the SS rat. Pappa2 mRNA expression progressively increased with the development of kidney, reaching a peak at postnatal day 5 before trending downward in subsequent stages of development in both strains. At all tested time points, Pappa2 remained higher in the 26-P compared with the SS rat kidney. Immunohistochemistry studies localized PAPPA2 in the ureteric bud (UB) and distal part of S-shaped body. PAPPA2 was colocalized with IGFBP-5 in the UB and Na+/K+/2Cl- cotransporter-stained tubules, respectively. Future studies are needed to determine the role of Pappa2 in kidney development and mechanistic pathways involved in this process.
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Affiliation(s)
- Vikash Kumar
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Chun Yang
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Allen W Cowley
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
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11
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Crespi BJ. Why and How Imprinted Genes Drive Fetal Programming. Front Endocrinol (Lausanne) 2020; 10:940. [PMID: 32117048 PMCID: PMC7025584 DOI: 10.3389/fendo.2019.00940] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/27/2019] [Indexed: 02/06/2023] Open
Abstract
Imprinted genes mediate fetal and childhood growth and development, and early growth patterns drive fetal programming effects. However, predictions and evidence from the kinship theory of imprinting have yet to be directly integrated with data on fetal programming and risks of metabolic disease. I first define paternal-gene and maternal-gene optima with regard to early human growth and development. Next, I review salient evidence with regard to imprinted gene effects on birth weight, body composition, trajectories of feeding and growth, and timing of developmental stages, to evaluate why and how imprinted gene expression influences risks of metabolic disease in later life. I find that metabolic disease risks derive primarily from maternal gene biases that lead to reduced placental efficacy, low birth weight, low relative muscle mass, high relative white fat, increased abdominal adiposity, reduced pancreatic β-cell mass that promotes insulin resistance, reduced appetite and infant sucking efficacy, catch-up fat deposition from family foods after weaning, and early puberty. Paternal gene biases, by contrast, may contribute to metabolic disease via lower rates of brown fat thermiogenesis, and through favoring more rapid postnatal catch-up growth after intrauterine growth restriction from environmental causes. These disease risks can be alleviated through dietary and pharmacological alterations that selectively target imprinted gene expression and relevant metabolic pathways. The kinship theory of imprinting, and mother-offspring conflict more generally, provide a clear predictive framework for guiding future research on fetal programming and metabolic disease.
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Affiliation(s)
- Bernard J. Crespi
- Department of Biological Sciences and Human Evolutionary Studies Program, Simon Fraser University, Burnaby, BC, Canada
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12
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Romanov D, Butenko E, Bakhtadze G, Shkurat T. Genome distance between conserved elements in neighborhoods of growth-regulating genes is correlated with morpho-physiological traits in mammals. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Romanov DE, Butenko EV, Shkurat TP. Genome distance between growth-regulating genes and telomeres is correlated with morpho-physiological traits in mammals. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2018.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Howard BH, Hirai TH, Russanova VR. Epigenome comparisons reveal linkage between gene expression and postnatal remodeling of chromatin domain topology. PLoS One 2018; 13:e0191033. [PMID: 29466355 PMCID: PMC5821309 DOI: 10.1371/journal.pone.0191033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/27/2017] [Indexed: 11/19/2022] Open
Abstract
Substantial evidence has accumulated linking epigenome change to alterations in stem cell function during postnatal development and aging. Yet much remains to be learned about causal relationships, and large gaps remain in our understanding of epigenome-transcriptome interactions. Here we investigate structural features of large histone H3K27me3-enriched regions in human stem cell-like monocytes and their dendritic cell derivatives, where the H3K27me3 modification is considered to demarcate Polycomb (PcG) domains. Both differentiation- and postnatal development-related change are explored, initially by confirming expected reciprocal relationships between transcript abundance and span of PcG domains overlapping transcribed regions. PcG-associated postnatal transcriptome change specific to the stem cell-like monocytes is found to be incompletely explained by conventional measures of PcG region structure. To address this, we introduce algorithms that quantify local nucleosome-scale conservation of PcG-region topology. It is shown that topology-based comparisons can reveal broad statistical linkage between postnatal gene down-regulation and epigenome remodeling; further, such comparisons provide access to a previously unexplored dimension of epigenome architecture.
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Affiliation(s)
- Bruce H. Howard
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Tazuko H. Hirai
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Valya R. Russanova
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
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15
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Abstract
As the popular adage goes, all diseases run into old age and almost all physiological changes are associated with alterations in gene expression, irrespective of whether they are causal or consequential. Therefore, the quest for mechanisms that delay ageing and decrease age-associated diseases has propelled researchers to unravel regulatory factors that lead to changes in chromatin structure and function, which ultimately results in deregulated gene expression. It is therefore essential to bring together literature, which until recently has investigated gene expression and chromatin independently. With advances in biomedical research and the emergence of epigenetic regulators as potential therapeutic targets, enhancing our understanding of mechanisms that 'derail' transcription and identification of causal genes/pathways during ageing will have a significant impact. In this context, this chapter aims to not only summarize the key features of age-associated changes in epigenetics and transcription, but also identifies gaps in the field and proposes aspects that need to be investigated in the future.
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16
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Abstract
Regulation of body growth remains a fascinating and unresolved biological mystery. One key component of body growth is skeletal and longitudinal bone growth. Children grow taller because their bones grew longer, and the predominant driver of longitudinal bone growth is a cartilaginous structure found near the ends of long bone named the growth plate. Numerous recent studies have started to unveil the importance of microRNAs in regulation of growth plate functions, therefore contributing to regulation of linear growth. In addition to longitudinal growth, other organs in our body need to increase in size and cell number as we grow, and the regulation of organ growth involves both systemic factors like hormones; and other intrinsic mechanisms, which we are just beginning to understand. This review aims to summarize some recent important findings on how microRNAs are involved in both of these processes: the regulation of longitudinal bone growth, and the regulation of organs and overall body growth.
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Affiliation(s)
- Julian C Lui
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC Rm 1-3330, 10 Center Drive, MSC-1103, Bethesda, MD, 20892-1103, United States.
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17
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Besson V, Kyryachenko S, Janich P, Benitah SA, Marazzi G, Sassoon D. Expression Analysis of the Stem Cell Marker Pw1/Peg3 Reveals a CD34 Negative Progenitor Population in the Hair Follicle. Stem Cells 2016; 35:1015-1027. [PMID: 27862634 DOI: 10.1002/stem.2540] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 09/10/2016] [Accepted: 10/16/2016] [Indexed: 12/30/2022]
Abstract
Pw1/Peg3 is a parentally imprinted gene expressed in adult stem cells in every tissue thus far examined including the stem cells of the hair follicle. Using a Pw1/Peg3 reporter mouse, we carried out a detailed dissection of the stem cells in the bulge, which is a major stem cell compartment of the hair follicle in mammalian skin. We observed that PW1/Peg3 expression initiates upon placode formation during fetal development, coincident with the establishment of the bulge stem cells. In the adult, we observed that PW1/Peg3 expression is found in both CD34+ and CD34- populations of bulge stem cells. We demonstrate that both populations can give rise to new hair follicles, reconstitute their niche, and self-renew. These results demonstrate that PW1/Peg3 is a reliable marker of the full population of follicle stem cells and reveal a novel CD34- bulge stem-cell population. Stem Cells 2017;35:1015-1027.
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Affiliation(s)
- Vanessa Besson
- Stem Cells and Regenerative Medicine, Institute of Cardiometabolism and Nutrition (ICAN), UMRS 1166 INSERM, University of Pierre and Marie Curie Paris VI, Paris, France
| | - Sergiy Kyryachenko
- Stem Cells and Regenerative Medicine, Institute of Cardiometabolism and Nutrition (ICAN), UMRS 1166 INSERM, University of Pierre and Marie Curie Paris VI, Paris, France
| | - Peggy Janich
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Salvador A Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Giovanna Marazzi
- Stem Cells and Regenerative Medicine, Institute of Cardiometabolism and Nutrition (ICAN), UMRS 1166 INSERM, University of Pierre and Marie Curie Paris VI, Paris, France
| | - David Sassoon
- Stem Cells and Regenerative Medicine, Institute of Cardiometabolism and Nutrition (ICAN), UMRS 1166 INSERM, University of Pierre and Marie Curie Paris VI, Paris, France
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18
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An CI, Ichihashi Y, Peng J, Sinha NR, Hagiwara N. Transcriptome Dynamics and Potential Roles of Sox6 in the Postnatal Heart. PLoS One 2016; 11:e0166574. [PMID: 27832192 PMCID: PMC5104335 DOI: 10.1371/journal.pone.0166574] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 10/31/2016] [Indexed: 01/20/2023] Open
Abstract
The postnatal heart undergoes highly coordinated developmental processes culminating in the complex physiologic properties of the adult heart. The molecular mechanisms of postnatal heart development remain largely unexplored despite their important clinical implications. To gain an integrated view of the dynamic changes in gene expression during postnatal heart development at the organ level, time-series transcriptome analyses of the postnatal hearts of neonatal through adult mice (P1, P7, P14, P30, and P60) were performed using a newly developed bioinformatics pipeline. We identified functional gene clusters by principal component analysis with self-organizing map clustering which revealed organized, discrete gene expression patterns corresponding to biological functions associated with the neonatal, juvenile and adult stages of postnatal heart development. Using weighted gene co-expression network analysis with bootstrap inference for each of these functional gene clusters, highly robust hub genes were identified which likely play key roles in regulating expression of co-expressed, functionally linked genes. Additionally, motivated by the role of the transcription factor Sox6 in the functional maturation of skeletal muscle, the role of Sox6 in the postnatal maturation of cardiac muscle was investigated. Differentially expressed transcriptome analyses between Sox6 knockout (KO) and control hearts uncovered significant upregulation of genes involved in cell proliferation at postnatal day 7 (P7) in the Sox6 KO heart. This result was validated by detecting mitotically active cells in the P7 Sox6 KO heart. The current report provides a framework for the complex molecular processes of postnatal heart development, thus enabling systematic dissection of the developmental regression observed in the stressed and failing adult heart.
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Affiliation(s)
- Chung-Il An
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California Davis, Davis, California, United States of America
- * E-mail: (CA); (YI); (NH)
| | - Yasunori Ichihashi
- Department of Plant Biology, University of California Davis, Davis, California, United States of America
- * E-mail: (CA); (YI); (NH)
| | - Jie Peng
- Department of Statistics, University of California Davis, Davis, California, United States of America
| | - Neelima R. Sinha
- Department of Plant Biology, University of California Davis, Davis, California, United States of America
| | - Nobuko Hagiwara
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California Davis, Davis, California, United States of America
- * E-mail: (CA); (YI); (NH)
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19
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Mlakar V, Huezo-Diaz Curtis P, Satyanarayana Uppugunduri CR, Krajinovic M, Ansari M. Pharmacogenomics in Pediatric Oncology: Review of Gene-Drug Associations for Clinical Use. Int J Mol Sci 2016; 17:ijms17091502. [PMID: 27618021 PMCID: PMC5037779 DOI: 10.3390/ijms17091502] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/02/2016] [Accepted: 08/15/2016] [Indexed: 02/07/2023] Open
Abstract
During the 3rd congress of the European Society of Pharmacogenomics and Personalised Therapy (ESPT) in Budapest in 2015, a preliminary meeting was held aimed at establishing a pediatric individualized treatment in oncology and hematology committees. The main purpose was to facilitate the transfer and harmonization of pharmacogenetic testing from research into clinics, to bring together basic and translational research and to educate health professionals throughout Europe. The objective of this review was to provide the attendees of the meeting as well as the larger scientific community an insight into the compiled evidence regarding current pharmacogenomics knowledge in pediatric oncology. This preliminary evaluation will help steer the committee’s work and should give the reader an idea at which stage researchers and clinicians are, in terms of personalizing medicine for children with cancer. From the evidence presented here, future recommendations to achieve this goal will also be suggested.
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Affiliation(s)
- Vid Mlakar
- Cansearch Research Laboratory, Geneva University Medical School, Avenue de la Roseraie 64, 1205 Geneva, Switzerland.
| | - Patricia Huezo-Diaz Curtis
- Cansearch Research Laboratory, Geneva University Medical School, Avenue de la Roseraie 64, 1205 Geneva, Switzerland.
| | | | - Maja Krajinovic
- Charles-Bruneau Cancer Center, Centre hospitalier universitaire Sainte-Justine, 4515 Rue de Rouen, Montreal, QC H1V 1H1, Canada.
- Department of Pediatrics, University of Montreal, 2900 Boulevard Edouard-Montpetit, Montreal, QC H3T 1J4, Canada.
- Department of Pharmacology, Faculty of Medicine, University of Montreal, 2900 Boulevard Edouard-Montpetit, Montreal, QC H3T 1J4, Canada.
| | - Marc Ansari
- Cansearch Research Laboratory, Geneva University Medical School, Avenue de la Roseraie 64, 1205 Geneva, Switzerland.
- Pediatric Department, Onco-Hematology Unit, Geneva University Hospital, Rue Willy-Donzé 6, 1205 Geneva, Switzerland.
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20
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Beauchemin KJ, Wells JM, Kho AT, Philip VM, Kamir D, Kohane IS, Graber JH, Bult CJ. Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development. PeerJ 2016; 4:e2318. [PMID: 27602285 PMCID: PMC4991849 DOI: 10.7717/peerj.2318] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/12/2016] [Indexed: 12/12/2022] Open
Abstract
To characterize temporal patterns of transcriptional activity during normal lung development, we generated genome wide gene expression data for 26 pre- and post-natal time points in three common inbred strains of laboratory mice (C57BL/6J, A/J, and C3H/HeJ). Using Principal Component Analysis and least squares regression modeling, we identified both strain-independent and strain-dependent patterns of gene expression. The 4,683 genes contributing to the strain-independent expression patterns were used to define a murine Developing Lung Characteristic Subtranscriptome (mDLCS). Regression modeling of the Principal Components supported the four canonical stages of mammalian embryonic lung development (embryonic, pseudoglandular, canalicular, saccular) defined previously by morphology and histology. For postnatal alveolar development, the regression model was consistent with four stages of alveolarization characterized by episodic transcriptional activity of genes related to pulmonary vascularization. Genes expressed in a strain-dependent manner were enriched for annotations related to neurogenesis, extracellular matrix organization, and Wnt signaling. Finally, a comparison of mouse and human transcriptomics from pre-natal stages of lung development revealed conservation of pathways associated with cell cycle, axon guidance, immune function, and metabolism as well as organism-specific expression of genes associated with extracellular matrix organization and protein modification. The mouse lung development transcriptome data generated for this study serves as a unique reference set to identify genes and pathways essential for normal mammalian lung development and for investigations into the developmental origins of respiratory disease and cancer. The gene expression data are available from the Gene Expression Omnibus (GEO) archive (GSE74243). Temporal expression patterns of mouse genes can be investigated using a study specific web resource (http://lungdevelopment.jax.org).
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Affiliation(s)
- Kyle J. Beauchemin
- The Jackson Laboratory, Bar Harbor, ME, United States
- Graduate School of Biomedical Sciences and Engineering, The University of Maine, Orono, ME, United States
| | | | - Alvin T. Kho
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA, United States
| | | | - Daniela Kamir
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Isaac S. Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | | | - Carol J. Bult
- The Jackson Laboratory, Bar Harbor, ME, United States
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21
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Affiliation(s)
| | - Jeffrey Baron
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD.
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22
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Li Y, Xie C, Murphy SK, Skaar D, Nye M, Vidal AC, Cecil KM, Dietrich KN, Puga A, Jirtle RL, Hoyo C. Lead Exposure during Early Human Development and DNA Methylation of Imprinted Gene Regulatory Elements in Adulthood. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:666-73. [PMID: 26115033 PMCID: PMC4858407 DOI: 10.1289/ehp.1408577] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 06/24/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND Lead exposure during early development causes neurodevelopmental disorders by unknown mechanisms. Epidemiologic studies have focused recently on determining associations between lead exposure and global DNA methylation; however, such approaches preclude the identification of loci that may alter human disease risk. OBJECTIVES The objective of this study was to determine whether maternal, postnatal, and early childhood lead exposure can alter the differentially methylated regions (DMRs) that control the monoallelic expression of imprinted genes involved in metabolism, growth, and development. METHODS Questionnaire data and serial blood lead levels were obtained from 105 participants (64 females, 41 males) of the Cincinnati Lead Study from birth to 78 months. When participants were adults, we used Sequenom EpiTYPER assays to test peripheral blood DNA to quantify CpG methylation in peripheral blood leukocytes at DMRs of 22 human imprinted genes. Statistical analyses were conducted using linear regression. RESULTS Mean blood lead concentration from birth to 78 months was associated with a significant decrease in PEG3 DMR methylation (β = -0.0014; 95% CI: -0.0023, -0.0005, p = 0.002), stronger in males (β = -0.0024; 95% CI: -0.0038, -0.0009, p = 0.003) than in females (β = -0.0009; 95% CI: -0.0020, 0.0003, p = 0.1). Elevated mean childhood blood lead concentration was also associated with a significant decrease in IGF2/H19 (β = -0.0013; 95% CI: -0.0023, -0.0003, p = 0.01) DMR methylation, but primarily in females, (β = -0.0017; 95% CI: -0.0029, -0.0006, p = 0.005) rather than in males, (β = -0.0004; 95% CI: -0.0023, 0.0015, p = 0.7). Elevated blood lead concentration during the neonatal period was associated with higher PLAGL1/HYMAI DMR methylation regardless of sex (β = 0.0075; 95% CI: 0.0018, 0.0132, p = 0.01). The magnitude of associations between cumulative lead exposure and CpG methylation remained unaltered from 30 to 78 months. CONCLUSIONS Our findings provide evidence that early childhood lead exposure results in sex-dependent and gene-specific DNA methylation differences in the DMRs of PEG3, IGF2/H19, and PLAGL1/HYMAI in adulthood. CITATION Li Y, Xie C, Murphy SK, Skaar D, Nye M, Vidal AC, Cecil KM, Dietrich KN, Puga A, Jirtle RL, Hoyo C. 2016. Lead exposure during early human development and DNA methylation of imprinted gene regulatory elements in adulthood. Environ Health Perspect 124:666-673; http://dx.doi.org/10.1289/ehp.1408577.
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Affiliation(s)
- Yue Li
- Department of Community and Family Medicine, and
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Changchun Xie
- Division of Epidemiology and Biostatistics, Department of Environmental Health, Center for Clinical and Translational Science and Training, University of Cincinnati (UC), Cincinnati, Ohio, USA
| | - Susan K. Murphy
- Department of Community and Family Medicine, and
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - David Skaar
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University (NCSU), Raleigh, North Carolina, USA
| | - Monica Nye
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Adriana C. Vidal
- Department of Community and Family Medicine, and
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Kim M. Cecil
- Cincinnati Children’s Environmental Health Center, Cincinnati Children’s Hospital Medical Center, UC College of Medicine, Cincinnati, Ohio, USA
- Department of Radiology,
- Department of Pediatrics,
- Department of Environmental Health,
- Center for Environmental Genetics, and
| | - Kim N. Dietrich
- Division of Epidemiology and Biostatistics, UC College of Medicine, Cincinnati, Ohio, USA
| | - Alvaro Puga
- Department of Environmental Health,
- Center for Environmental Genetics, and
| | - Randy L. Jirtle
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University (NCSU), Raleigh, North Carolina, USA
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Sport and Exercise Sciences, Institute of Sport and Physical Activity Research, University of Bedfordshire, Bedford, Bedfordshire, United Kingdom
- Address correspondence to C. Hoyo, Department of Biological Sciences, Center for Human Health and the Environment (CHHE), Program of Epidemiology and Environmental Epigenomics, North Carolina State University (NCSU), Raleigh, NC 27695-7633 USA. Telephone: (919) 515-0540. E-mail: , or R.L. Jirtle, Department of Biological Sciences, CHHE, NCSU, Raleigh, NC 27695-7633 USA. Telephone: (919) 399-3342. E-mail:
| | - Cathrine Hoyo
- Department of Community and Family Medicine, and
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University (NCSU), Raleigh, North Carolina, USA
- Address correspondence to C. Hoyo, Department of Biological Sciences, Center for Human Health and the Environment (CHHE), Program of Epidemiology and Environmental Epigenomics, North Carolina State University (NCSU), Raleigh, NC 27695-7633 USA. Telephone: (919) 515-0540. E-mail: , or R.L. Jirtle, Department of Biological Sciences, CHHE, NCSU, Raleigh, NC 27695-7633 USA. Telephone: (919) 399-3342. E-mail:
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23
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Jee YH, Lebenthal Y, Chaemsaithong P, Yan G, Peran I, Wellstein A, Romero R, Baron J. Midkine and Pleiotrophin Concentrations in Amniotic Fluid in Healthy and Complicated Pregnancies. PLoS One 2016; 11:e0153325. [PMID: 27089523 PMCID: PMC4835047 DOI: 10.1371/journal.pone.0153325] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 03/28/2016] [Indexed: 01/14/2023] Open
Abstract
Background Midkine (MDK) and pleiotrophin (PTN) are heparin-binding growth factors that, in rodents, are highly expressed in early life and decrease to undetectable levels by adulthood. The potential roles of MDK and PTN in human growth and development are not completely elucidated. Method and Findings To delineate the role of MDK and PTN in human development, we developed high sensitivity assays to measure their concentrations in amniotic fluid (AF) at various gestational ages in both healthy and complicated pregnancies. We found that both of these growth factors could be readily measured in AF and that the concentrations were higher than most cytokines previously reported in AF. Conclusion The concentration of MDK but not that of PTN declined with gestational age. Both MDK and PTN concentrations were found to be lower in pregnancies that were complicated by chorioamnionitis at term, raising the possibility that these growth factors might be useful as markers for infection.
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Affiliation(s)
- Youn Hee Jee
- Section on Growth and Development, Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yael Lebenthal
- Section on Growth and Development, Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Piya Chaemsaithong
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Detroit, Michigan, United States of America
| | - Gai Yan
- Department of Oncology, Georgetown University Medical Center and Lombardi Comprehensive Cancer Center, Washington DC, United States of America
| | - Ivana Peran
- Department of Oncology, Georgetown University Medical Center and Lombardi Comprehensive Cancer Center, Washington DC, United States of America
| | - Anton Wellstein
- Department of Oncology, Georgetown University Medical Center and Lombardi Comprehensive Cancer Center, Washington DC, United States of America
| | - Roberto Romero
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Detroit, Michigan, United States of America
| | - Jeffrey Baron
- Section on Growth and Development, Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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24
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Abstract
The regulation of organ size is essential to human health and has fascinated biologists for centuries. Key to the growth process is the ability of most organs to integrate organ-extrinsic cues (eg, nutritional status, inflammatory processes) with organ-intrinsic information (eg, genetic programs, local signals) into a growth response that adapts to changing environmental conditions and ensures that the size of an organ is coordinated with the rest of the body. Paired organs such as the vertebrate limbs and the long bones within them are excellent models for studying this type of regulation because it is possible to manipulate one member of the pair and leave the other as an internal control. During development, growth plates at the end of each long bone produce a transient cartilage model that is progressively replaced by bone. Here, we review how proliferation and differentiation of cells within each growth plate are tightly controlled mainly by growth plate-intrinsic mechanisms that are additionally modulated by extrinsic signals. We also discuss the involvement of several signaling hubs in the integration and modulation of growth-related signals and how they could confer remarkable plasticity to the growth plate. Indeed, long bones have a significant ability for "catch-up growth" to attain normal size after a transient growth delay. We propose that the characterization of catch-up growth, in light of recent advances in physiology and cell biology, will provide long sought clues into the molecular mechanisms that underlie organ growth regulation. Importantly, catch-up growth early in life is commonly associated with metabolic disorders in adulthood, and this association is not completely understood. Further elucidation of the molecules and cellular interactions that influence organ size coordination should allow development of novel therapies for human growth disorders that are noninvasive and have minimal side effects.
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Affiliation(s)
- Alberto Roselló-Díez
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065
| | - Alexandra L Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065
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25
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De Leonibus C, Chatelain P, Knight C, Clayton P, Stevens A. Effect of summer daylight exposure and genetic background on growth in growth hormone-deficient children. THE PHARMACOGENOMICS JOURNAL 2015; 16:540-550. [PMID: 26503811 PMCID: PMC5223086 DOI: 10.1038/tpj.2015.67] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 07/06/2015] [Accepted: 07/14/2015] [Indexed: 12/13/2022]
Abstract
The response to growth hormone in humans is dependent on phenotypic, genetic and environmental factors. The present study in children with growth hormone deficiency (GHD) collected worldwide characterised gene–environment interactions on growth response to recombinant human growth hormone (r-hGH). Growth responses in children are linked to latitude, and we found that a correlate of latitude, summer daylight exposure (SDE), was a key environmental factor related to growth response to r-hGH. In turn growth response was determined by an interaction between both SDE and genes known to affect growth response to r-hGH. In addition, analysis of associated networks of gene expression implicated a role for circadian clock pathways and specifically the developmental transcription factor NANOG. This work provides the first observation of gene–environment interactions in children treated with r-hGH.
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Affiliation(s)
- C De Leonibus
- Institute of Human Development, University of Manchester and Royal Manchester Children's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - P Chatelain
- Department Pédiatrie, Hôpital Mère-Enfant-Université Claude Bernard, Lyon, France
| | - C Knight
- University of Manchester, Manchester, UK
| | - P Clayton
- Institute of Human Development, University of Manchester and Royal Manchester Children's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - A Stevens
- Institute of Human Development, University of Manchester and Royal Manchester Children's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
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26
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Abstract
PURPOSE OF REVIEW Recent basic studies have yielded important new insights into the molecular mechanisms that regulate growth locally. Simultaneously, clinical studies have identified new molecular defects that cause growth failure and overgrowth, and genome-wide association studies have elucidated the genetic basis for normal human height variation. RECENT FINDINGS The Hippo pathway has emerged as one of the major mechanisms controlling organ size. In addition, an extensive genetic program has been described that allows rapid body growth in the fetus and infant but then causes growth to slow with age in multiple tissues. In human genome-wide association studies, hundreds of loci associated with adult stature have been identified; many appear to involve genes that function locally in the growth plate. Clinical genetic studies have identified a new genetic abnormality, microduplication of Xq26.3, that is responsible for growth hormone excess, and a gene, DNMT3A, in which mutations cause an overgrowth syndrome through epigenetic mechanisms. SUMMARY These recent advances in our understanding of somatic growth not only provide insight into childhood growth disorders but also have broader medical applications because disruption of these regulatory systems contributes to oncogenesis.
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Affiliation(s)
- Julian C Lui
- Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Presley Garrison
- Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Jeffrey Baron
- Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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Chen X, Yamamoto M, Fujii K, Nagahama Y, Ooshio T, Xin B, Okada Y, Furukawa H, Nishikawa Y. Differential reactivation of fetal/neonatal genes in mouse liver tumors induced in cirrhotic and non-cirrhotic conditions. Cancer Sci 2015; 106:972-81. [PMID: 26011625 PMCID: PMC4556385 DOI: 10.1111/cas.12700] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 05/06/2015] [Accepted: 05/17/2015] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma develops in either chronically injured or seemingly intact livers. To explore the tumorigenic mechanisms underlying these different conditions, we compared the mRNA expression profiles of mouse hepatocellular tumors induced by the repeated injection of CCl4 or a single diethylnitrosamine (DEN) injection using a cDNA microarray. We identified tumor-associated genes that were expressed differentially in the cirrhotic CCl4 model (H19, Igf2, Cbr3, and Krt20) and the non-cirrhotic DEN model (Tff3, Akr1c18, Gpc3, Afp, and Abcd2) as well as genes that were expressed comparably in both models (Ly6d, Slpi, Spink3, Scd2, and Cpe). The levels and patterns of mRNA expression of these genes were validated by quantitative RT-PCR analyses. Most of these genes were highly expressed in mouse livers during the fetal/neonatal periods. We also examined the mRNA expression of these genes in mouse tumors induced by thioacetamide, another cirrhotic inducer, and those that developed spontaneously in non-cirrhotic livers and found that they shared a similar expression profile as that observed in CCl4-induced and DEN-induced tumors, respectively. There was a close relationship between the expression levels of Igf2 and H19 mRNA, which were activated in the cirrhotic models. Our results show that mouse liver tumors reactivate fetal/neonatal genes, some of which are specific to cirrhotic or non-cirrhotic modes of pathogenesis.
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Affiliation(s)
- Xi Chen
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Masahiro Yamamoto
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Kiyonaga Fujii
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Yasuharu Nagahama
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Takako Ooshio
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Bing Xin
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Yoko Okada
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Hiroyuki Furukawa
- Division of Gastroenterological and General Surgery, Department of Surgery, Asahikawa Medical University, Asahikawa, Japan
| | - Yuji Nishikawa
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
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Kamran F, Andrade AC, Nella AA, Clokie SJ, Rezvani G, Nilsson O, Baron J, Lui JC. Evidence That Up-Regulation of MicroRNA-29 Contributes to Postnatal Body Growth Deceleration. Mol Endocrinol 2015; 29:921-32. [PMID: 25866874 DOI: 10.1210/me.2015-1047] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Body growth is rapid in infancy but subsequently slows and eventually ceases due to a progressive decline in cell proliferation that occurs simultaneously in multiple organs. We previously showed that this decline in proliferation is driven in part by postnatal down-regulation of a large set of growth-promoting genes in multiple organs. We hypothesized that this growth-limiting genetic program is orchestrated by microRNAs (miRNAs). Bioinformatic analysis identified target sequences of the miR-29 family of miRNAs to be overrepresented in age-down-regulated genes. Concomitantly, expression microarray analysis in mouse kidney and lung showed that all members of the miR-29 family, miR-29a, -b, and -c, were strongly up-regulated from 1 to 6 weeks of age. Real-time PCR confirmed that miR-29a, -b, and -c were up-regulated with age in liver, kidney, lung, and heart, and their expression levels were higher in hepatocytes isolated from 5-week-old mice than in hepatocytes from embryonic mouse liver at embryonic day 16.5. We next focused on 3 predicted miR-29 target genes (Igf1, Imp1, and Mest), all of which are growth-promoting. A 3'-untranslated region containing the predicted target sequences from each gene was placed individually in a luciferase reporter construct. Transfection of miR-29 mimics suppressed luciferase gene activity for all 3 genes, and this suppression was diminished by mutating the target sequences, suggesting that these genes are indeed regulated by miR-29. Taken together, the findings suggest that up-regulation of miR-29 during juvenile life drives the down-regulation of multiple growth-promoting genes, thus contributing to physiological slowing and eventual cessation of body growth.
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Affiliation(s)
- Fariha Kamran
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Anenisia C Andrade
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Aikaterini A Nella
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Samuel J Clokie
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Geoffrey Rezvani
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Ola Nilsson
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Jeffrey Baron
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Julian C Lui
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
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Stevens A, De Leonibus C, Whatmore A, Hanson D, Murray P, Chatelain P, Westwood M, Clayton P. Pharmacogenomics related to growth disorders. Horm Res Paediatr 2014; 80:477-90. [PMID: 24296333 DOI: 10.1159/000355658] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 09/16/2013] [Indexed: 11/19/2022] Open
Abstract
Growth disorders resulting in short stature are caused by a wide range of underlying pathophysiological processes. To improve height many of these conditions are treated with recombinant human growth hormone (rhGH). However, substantial inter-individual variability in growth response both in the short and long-term is recognised. Over the last decade, disease-specific growth prediction models have been developed that the clinician can use to define a child's potential response to rhGH and to optimise starting and maintenance doses of rhGH. These models, however, are not able to predict all the variations in treatment response. There has, therefore, been recent interest in using genetic information to contribute to the evaluation of responses to rhGH, including high-throughput technologies for assessing DNA markers (genome) and mRNA transcripts (transcriptome) as pharmacogenomic tools. This review will focus on how these pharmacogenomic approaches are being applied to growth disorders.
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Affiliation(s)
- A Stevens
- Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester and Manchester Academic Health Science Centre, Royal Manchester Children's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
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Stevens A, De Leonibus C, Hanson D, Whatmore A, Murray P, Donn R, Meyer S, Chatelain P, Clayton P. Pediatric perspective on pharmacogenomics. Pharmacogenomics 2014; 14:1889-905. [PMID: 24236488 DOI: 10.2217/pgs.13.193] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The advances in high-throughput genomic technologies have improved the understanding of disease pathophysiology and have allowed a better characterization of drug response and toxicity based on individual genetic make up. Pharmacogenomics is being recognized as a valid approach used to identify patients who are more likely to respond to medication, or those in whom there is a high probability of developing severe adverse drug reactions. An increasing number of pharmacogenomic studies are being published, most include only adults. A few studies have shown the impact of pharmacogenomics in pediatrics, highlighting a key difference between children and adults, which is the contribution of developmental changes to therapeutic responses across different age groups. This review focuses on pharmacogenomic research in pediatrics, providing examples from common pediatric conditions and emphasizing their developmental context.
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Affiliation(s)
- Adam Stevens
- Institute of Human Development, Medical & Human Sciences, University of Manchester & Royal Manchester Children's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, 5th Floor Research, Oxford Road, Manchester, M13 9WL, UK
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Delaney A, Padmanabhan V, Rezvani G, Chen W, Forcinito P, Cheung CS, Baron J, Lui JC. Evolutionary conservation and modulation of a juvenile growth-regulating genetic program. J Mol Endocrinol 2014; 52:269-77. [PMID: 24776848 PMCID: PMC4051439 DOI: 10.1530/jme-13-0263] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Body size varies enormously among mammalian species. In small mammals, body growth is typically suppressed rapidly, within weeks, whereas in large mammals, growth is suppressed slowly, over years, allowing for a greater adult size. We recently reported evidence that body growth suppression in rodents is caused in part by a juvenile genetic program that occurs in multiple tissues simultaneously and involves the downregulation of a large set of growth-promoting genes. We hypothesized that this genetic program is conserved in large mammals but that its time course is evolutionarily modulated such that it plays out more slowly, allowing for more prolonged growth. Consistent with this hypothesis, using expression microarray analysis, we identified a set of genes that are downregulated with age in both juvenile sheep kidney and lung. This overlapping gene set was enriched for genes involved in cell proliferation and growth and showed striking similarity to a set of genes downregulated with age in multiple organs of the juvenile mouse and rat, indicating that the multiorgan juvenile genetic program previously described in rodents has been conserved in the 80 million years since sheep and rodents diverged in evolution. Using microarray and real-time PCR, we found that the pace of this program was most rapid in mice, more gradual in rats, and most gradual in sheep. These findings support the hypothesis that a growth-regulating genetic program is conserved among mammalian species but that its pace is modulated to allow more prolonged growth and therefore greater adult body size in larger mammals.
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Affiliation(s)
- Angela Delaney
- Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institutes of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Vasantha Padmanabhan
- Department of Pediatrics and the Reproductive Sciences Program, The University of Michigan, Ann Arbor, MI
| | - Geoffrey Rezvani
- Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institutes of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Weiping Chen
- Microarray Core Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Patricia Forcinito
- Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institutes of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Crystal S.F. Cheung
- Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institutes of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Jeffrey Baron
- Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institutes of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Julian C.K. Lui
- Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institutes of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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Jones JC, Kroscher KA, Dilger AC. Reductions in expression of growth regulating genes in skeletal muscle with age in wild type and myostatin null mice. BMC PHYSIOLOGY 2014; 14:3. [PMID: 24678801 PMCID: PMC3986603 DOI: 10.1186/1472-6793-14-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 03/25/2014] [Indexed: 12/12/2022]
Abstract
Background Genes that decline in expression with age and are thought to coordinate growth cessation have been identified in various organs, but their expression in skeletal muscle is unknown. Therefore, our objective was to determine expression of these genes (Ezh2, Gpc3, Mdk, Mest, Mycn, Peg3, and Plagl1) in skeletal muscle from birth to maturity. We hypothesized that expression of these genes would decline with age in skeletal muscle but differ between sexes and between wild type and myostatin null mice. Results Female and male wild type and myostatin null mice (C57BL/6J background) were sacrificed by carbon dioxide asphyxiation followed by decapitation at d -7, 0, 21, 42, and 70 days of age. Whole bodies at d -7, all muscles from both hind limbs at d 0, and bicep femoris muscle from d 21, 42 and 70 were collected. Gene expression was determined by quantitative real-time PCR. In general, expression of these growth-regulating genes was reduced at d 21 compared with day 0 and d -7. Expression of Gpc3, Mest, and Peg3 was further reduced at d 42 and 70 compared with d 21, however the expression of Mycn increased from d 21 to d 42 and 70. Myostatin null mice, as expected, were heavier with increased biceps femoris weight at d 70. However, with respect to sex and genotype, there were few differences in expression. Expression of Ezh2 was increased at d 70 and expression of Mdk was increased at d 21 in myostatin null mice compared with wild type, but no other genotype effects were present. Expression of Mdk was increased in females compared to males at d 70, but no other sex effects were present. Conclusions Overall, these data suggest the downregulation of these growth-regulating genes with age might play a role in the coordinated cessation of muscle growth similar to organ growth but likely have a limited role in the differences between sexes or genotypes.
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Affiliation(s)
| | | | - Anna C Dilger
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Stevens A, De Leonibus C, Hanson D, Dowsey AW, Whatmore A, Meyer S, Donn RP, Chatelain P, Banerjee I, Cosgrove KE, Clayton PE, Dunne MJ. Network analysis: a new approach to study endocrine disorders. J Mol Endocrinol 2014; 52:R79-93. [PMID: 24085748 DOI: 10.1530/jme-13-0112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Systems biology is the study of the interactions that occur between the components of individual cells - including genes, proteins, transcription factors, small molecules, and metabolites, and their relationships to complex physiological and pathological processes. The application of systems biology to medicine promises rapid advances in both our understanding of disease and the development of novel treatment options. Network biology has emerged as the primary tool for studying systems biology as it utilises the mathematical analysis of the relationships between connected objects in a biological system and allows the integration of varied 'omic' datasets (including genomics, metabolomics, proteomics, etc.). Analysis of network biology generates interactome models to infer and assess function; to understand mechanisms, and to prioritise candidates for further investigation. This review provides an overview of network methods used to support this research and an insight into current applications of network analysis applied to endocrinology. A wide spectrum of endocrine disorders are included ranging from congenital hyperinsulinism in infancy, through childhood developmental and growth disorders, to the development of metabolic diseases in early and late adulthood, such as obesity and obesity-related pathologies. In addition to providing a deeper understanding of diseases processes, network biology is also central to the development of personalised treatment strategies which will integrate pharmacogenomics with systems biology of the individual.
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Affiliation(s)
- A Stevens
- Faculty of Medical and Human Sciences, Institute of Human Development, University of Manchester, Manchester, UK Manchester Academic Health Science Centre, Royal Manchester Children's Hospital, Central Manchester University Hospitals NHS Foundation Trust, 5th Floor, Oxford Road, Manchester M13 9WL, UK Paediatric and Adolescent Oncology, The University of Manchester, Manchester M13 9WL, UK Stem Cell and Leukaemia Proteomics Laboratory, School of Cancer and Imaging Sciences, The University of Manchester, Manchester M20 4BX, UK Musculoskeletal Research Group, NIHR BRU, University of Manchester, Manchester M13 9PT, UK Department Pediatrie, Hôpital Mère-Enfant, Université Claude Bernard, 69677 Lyon, France Faculty of Life Sciences, University of Manchester, Manchester M13 9NT, UK
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Lui JC, Chen W, Cheung CSF, Baron J. Broad shifts in gene expression during early postnatal life are associated with shifts in histone methylation patterns. PLoS One 2014; 9:e86957. [PMID: 24489814 PMCID: PMC3904965 DOI: 10.1371/journal.pone.0086957] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 12/19/2013] [Indexed: 01/08/2023] Open
Abstract
During early postnatal life, extensive changes in gene expression occur concomitantly in multiple major organs, indicating the existence of a common core developmental genetic program. This program includes hundreds of growth-promoting genes that are downregulated with age in liver, kidney, lung, and heart, and there is evidence that this component of the program drives the widespread decline in cell proliferation that occurs in juvenile life, as organs approach adult sizes. To investigate epigenetic changes that might orchestrate this program, we performed chromatin immunoprecipitation-promoter tiling array to assess temporal changes in histone H3K4 and H3K27 trimethylation (me3) at promoter regions throughout the genome in kidney and lung, comparing 1- to 4-wk-old mice. We found extensive genome-wide shifts in H3K4me3 and H3K27me3 occurring with age in both kidney and lung. The number of genes with concordant changes in the two organs was far greater than expected by chance. Temporal changes in H3K4me3 showed a strong, positive association with changes in gene expression, assessed by microarray, whereas changes in H3K27me3 showed a negative association. Gene ontology analysis indicated that shifts in specific histone methylation marks were associated with specific developmental functions. Of particular interest, genes with decreases in H3K4me3 with age in both organs were strongly implicated in cell cycle and cell proliferation functions. Taken together, the findings suggest that the common core developmental program of gene expression which occurs in multiple organs during juvenile life is associated with a common core developmental program of histone methylation. In particular, declining H3K4me3 is strongly associated with gene downregulation and occurs in the promoter regions of many growth-regulating genes, suggesting that this change in histone methylation may contribute to the component of the genetic program that drives juvenile body growth deceleration.
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Affiliation(s)
- Julian C. Lui
- Section on Growth and Development, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Weiping Chen
- Microarray Core Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Crystal S. F. Cheung
- Section on Growth and Development, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeffrey Baron
- Section on Growth and Development, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
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Fata B, Gottlieb D, Mayer JE, Sacks MS. Estimated in vivo postnatal surface growth patterns of the ovine main pulmonary artery and ascending aorta. J Biomech Eng 2014; 135:71010-12. [PMID: 23757175 DOI: 10.1115/1.4024619] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 05/22/2013] [Indexed: 01/29/2023]
Abstract
Delineating the normal postnatal development of the pulmonary artery (PA) and ascending aorta (AA) can inform our understanding of congenital abnormalities, as well as pulmonary and systolic hypertension. We thus conducted the following study to delineate the PA and AA postnatal growth deformation characteristics in an ovine model. MR images were obtained from endoluminal surfaces of 11 animals whose ages ranged from 1.5 months/15.3 kg mass (very young) to 12 months/56.6 kg mass (adult). A bicubic Hermite finite element surface representation was developed for the each artery from each animal. Under the assumption that the relative locations of surface points were retained during growth, the individual animal surface fits were subsequently used to develop a method to estimate the time-evolving local effective surface growth (relative to the youngest measured animal) in the end-diastolic state. Results indicated that the spatial and temporal surface growth deformation patterns of both arteries, especially in the circumferential direction, were heterogeneous, leading to an increase in taper and increase in cross-sectional ellipticity of the PA. The longitudinal PA growth stretch of a large segment on the posterior wall reached 2.57 ± 0.078 (mean ± SD) at the adult stage. In contrast, the longitudinal growth of the AA was smaller and more uniform (1.80 ± 0.047). Interestingly, a region of the medial wall of both arteries where both arteries are in contact showed smaller circumferential growth stretches-specifically 1.12 ± 0.012 in the PA and 1.43 ± 0.071 in the AA at the adult stage. Overall, our results indicated that contact between the PA and AA resulted in increasing spatial heterogeneity in postnatal growth, with the PA demonstrating the greatest changes. Parametric studies using simplified geometric models of curved arteries during growth suggest that heterogeneous effective surface growth deformations must occur to account for the changes in measured arterial shapes during the postnatal growth period. This result suggests that these first results are a reasonable first-approximation to the actual effective growth patterns. Moreover, this study clearly underscores how functional growth of the PA and AA during postnatal maturation involves complex, local adaptations in tissue formation. Moreover, the present results will help to lay the basis for functional replacement by defining critical geometric metrics.
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Affiliation(s)
- Bahar Fata
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15219, USA
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36
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A genetic program theory of aging using an RNA population model. Ageing Res Rev 2014; 13:46-54. [PMID: 24263168 DOI: 10.1016/j.arr.2013.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 11/08/2013] [Indexed: 12/11/2022]
Abstract
Aging is a common characteristic of multicellular eukaryotes. Copious hypotheses have been proposed to explain the mechanisms of aging, but no single theory is generally acceptable. In this article, we refine the RNA population gene activating model (Lv et al., 2003) based on existing reports as well as on our own latest findings. We propose the RNA population model as a genetic theory of aging. The new model can also be applied to differentiation and tumorigenesis and could explain the biological significance of non-coding DNA, RNA, and repetitive sequence DNA. We provide evidence from the literature as well as from our own findings for the roles of repetitive sequences in gene activation. In addition, we predict several phenomena related to aging and differentiation based on this model.
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Stevens A, Hanson D, Whatmore A, Destenaves B, Chatelain P, Clayton P. Human growth is associated with distinct patterns of gene expression in evolutionarily conserved networks. BMC Genomics 2013; 14:547. [PMID: 23941278 PMCID: PMC3765282 DOI: 10.1186/1471-2164-14-547] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 08/05/2013] [Indexed: 11/25/2022] Open
Abstract
Background A co-ordinated tissue-independent gene expression profile associated with growth is present in rodent models and this is hypothesised to extend to all mammals. Growth in humans has similarities to other mammals but the return to active long bone growth in the pubertal growth spurt is a distinctly human growth event. The aim of this study was to describe gene expression and biological pathways associated with stages of growth in children and to assess tissue-independent expression patterns in relation to human growth. Results We conducted gene expression analysis on a library of datasets from normal children with age annotation, collated from the NCBI Gene Expression Omnibus (GEO) and EBI Arrayexpress databases. A primary data set was generated using cells of lymphoid origin from normal children; the expression of 688 genes (ANOVA false discovery rate modified p-value, q < 0.1) was associated with age, and subsets of these genes formed clusters that correlated with the phases of growth – infancy, childhood, puberty and final height. Network analysis on these clusters identified evolutionarily conserved growth pathways (NOTCH, VEGF, TGFB, WNT and glucocorticoid receptor – Hyper-geometric test, q < 0.05). The greatest degree of network ‘connectivity’ and hence functional significance was present in infancy (Wilcoxon test, p < 0.05), which then decreased through to adulthood. These observations were confirmed in a separate validation data set from lymphoid tissue. Similar biological pathways were observed to be associated with development-related gene expression in other tissues (conjunctival epithelia, temporal lobe brain tissue and bone marrow) suggesting the existence of a tissue-independent genetic program for human growth and maturation. Conclusions Similar evolutionarily conserved pathways have been associated with gene expression and child growth in multiple tissues. These expression profiles associate with the developmental phases of growth including the return to active long bone growth in puberty, a distinctly human event. These observations also have direct medical relevance to pathological changes that induce disease in children. Taking into account development-dependent gene expression profiles for normal children will be key to the appropriate selection of genes and pathways as potential biomarkers of disease or as drug targets.
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Affiliation(s)
- Adam Stevens
- Manchester Academic Health Sciences Centre, Faculty of Medical and Human Sciences, Royal Manchester Children's Hospital and the Institute of Human Development, University of Manchester, Manchester, United Kingdom.
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Transcriptional profiling of mRNAs and microRNAs in human bone marrow precursor B cells identifies subset- and age-specific variations. PLoS One 2013; 8:e70721. [PMID: 23936243 PMCID: PMC3728296 DOI: 10.1371/journal.pone.0070721] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 06/20/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Molecular mechanisms explaining age-related changes in the bone marrow with reduced precursor B cell output are poorly understood. METHODS We studied the transcriptome of five precursor B cell subsets in individual bone marrow samples from 4 healthy children and 4 adults employing GeneChip® Human Exon 1.0 ST Arrays (Affymetrix®) and TaqMan® Array MicroRNA Cards (Life Technologies™). RESULTS A total of 1796 mRNAs (11%) were at least once differentially expressed between the various precursor B cell subsets in either age group (FDR 0.1%, p≤1.13×10(-4)) with more marked cell stage specific differences than those related to age. In contrast, microRNA profiles of the various precursor B cell subsets showed less hierarchical clustering as compared to the corresponding mRNA profiles. However, 17 of the 667 microRNA assays (2.5%) were at least once differentially expressed between the subsets (FDR 10%, p≤0.004). From target analysis (Ingenuity® Systems), functional assignment between postulated interacting mRNAs and microRNAs showed especially association to cellular growth, proliferation and cell cycle regulation. One functional network connected up-regulation of the differentiation inhibitor ID2 mRNA to down-regulation of the hematopoiesis- or cell cycle regulating miR-125b-5p, miR-181a-5p, miR-196a-5p, miR-24-3p and miR-320d in adult PreBII large cells. Noteworthy was also the stage-dependent expression of the growth promoting miR-17-92 cluster, showing a partly inverse trend with age, reaching statistical significance at the PreBII small stage (up 3.1-12.9 fold in children, p = 0.0084-0.0270). CONCLUSIONS The global mRNA profile is characteristic for each precursor B cell developmental stage and largely similar in children and adults. The microRNA profile is much cell stage specific and not changing much with age. Importantly, however, specific age-dependent differences involving key networks like differentiation and cellular growth may indicate biological divergence and possibly also altered production potential with age.
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Abstract
In mammals, after a period of growth inhibition, body growth often does not just return to a normal rate but actually exceeds the normal rate, resulting in catch-up growth. Recent evidence suggests that catch-up growth occurs because growth-inhibiting conditions delay progression of the physiological mechanisms that normally cause body growth to slow and cease with age. As a result, following the period of growth inhibition, tissues retain a greater proliferative capacity than normal, and therefore grow more rapidly than normal for age. There is evidence that this mechanism contributes both to catch-up growth in terms of body length, which involves proliferation in the growth plate, and to catch-up growth in terms of organ mass, which involves proliferation in multiple nonskeletal tissues.
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Affiliation(s)
- G P Finkielstain
- Centro de Investigaciones Endocrinológicas (CEDIE-CONICET), División de Endocrinología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
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Khan QES, Sehic A, Skalleberg N, Landin MA, Khuu C, Risnes S, Osmundsen H. Expression of delta-like 1 homologue and insulin-like growth factor 2 through epigenetic regulation of the genes during development of mouse molar. Eur J Oral Sci 2013; 120:292-302. [PMID: 22813219 DOI: 10.1111/j.1600-0722.2012.00976.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Delta-like 1 homolog (Dlk1) and insulin-like growth factor 2 (Igf2) are two of six well-studied mouse imprinted gene clusters that are paternally expressed. Their expression is also linked to their maternally expressed non-coding RNAs, encoded by Gene trap locus 2 (Gtl2) and Imprinted maternally expressed transcript (H19), co-located as imprinted gene clusters. Using deoxyoligonucleotide microarrays and real-time RT-PCR analysis we showed Dlk1 and Gtl2 to exhibit a time-course of expression during tooth development that was similar to that of Igf2 and H19. Western blot analysis of proteins encoded by Dlk1 and Igf2 suggested that the levels of these proteins reflected those of the corresponding mRNAs. Immunohistochemical studies of DLK1 in murine molars detected the protein in both epithelial and mesenchymal regions, in developing cusp mesenchyme, and in newly synthesized enamel and dentin tubules. IGF2 protein was detected primarily at prenatal stages, suggesting that it may be active before birth. Analysis of methylation of cytosine-phosphate-guanine (CpG) islands in both Dlk1 and Igf2 suggested the presence of an increasing fraction of hypermethylated bases with increasing time of development. The increased levels of hypermethylation coincided both with the diminished levels of expression of Dlk1 and Igf2 and with decreased levels of DLK1 and IGF2 proteins in the tooth germ, suggesting that their expression is regulated via methylation of CpG islands present in these genes.
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Lui JC, Nilsson O, Chan Y, Palmer CD, Andrade AC, Hirschhorn JN, Baron J. Synthesizing genome-wide association studies and expression microarray reveals novel genes that act in the human growth plate to modulate height. Hum Mol Genet 2012; 21:5193-201. [PMID: 22914739 DOI: 10.1093/hmg/dds347] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Previous meta-analysis of genome-wide association (GWA) studies has identified 180 loci that influence adult height. However, each GWA locus typically comprises a set of contiguous genes, only one of which presumably modulates height. We reasoned that many of the causative genes within these loci influence height because they are expressed in and function in the growth plate, a cartilaginous structure that causes bone elongation and thus determines stature. Therefore, we used expression microarray studies of mouse and rat growth plate, human disease databases and a mouse knockout phenotype database to identify genes within the GWAS loci that are likely required for normal growth plate function. Each of these approaches identified significantly more genes within the GWA height loci than at random genomic locations (P < 0.0001 each), supporting the validity of the approach. The combined analysis strongly implicates 78 genes in growth plate function, including multiple genes that participate in PTHrP-IHH, BMP and CNP signaling, and many genes that have not previously been implicated in the growth plate. Thus, this analysis reveals a large number of novel genes that regulate human growth plate chondrogenesis and thereby contribute to the normal variations in human adult height. The analytic approach developed for this study may be applied to GWA studies for other common polygenic traits and diseases, thus providing a new general strategy to identify causative genes within GWA loci and to translate genetic associations into mechanistic biological insights.
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Affiliation(s)
- Julian C Lui
- Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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Miranda RC. MicroRNAs and Fetal Brain Development: Implications for Ethanol Teratology during the Second Trimester Period of Neurogenesis. Front Genet 2012; 3:77. [PMID: 22623924 PMCID: PMC3353139 DOI: 10.3389/fgene.2012.00077] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 04/23/2012] [Indexed: 11/29/2022] Open
Abstract
Maternal ethanol consumption during pregnancy can lead to a stereotypic cluster of fetal craniofacial, cardiovascular, skeletal, and neurological deficits that are collectively termed the fetal alcohol spectrum disorder (FASD). Fetal ethanol exposure is a leading non-genetic cause of mental retardation. Mechanisms underlying the etiology of ethanol teratology are varied and complex. This review will focus on the developing brain as an important and vulnerable ethanol target. Near the end of the first trimester, and during the second trimester, fetal neural stem cells (NSCs) produce most of the neurons of the adult brain, and ethanol has been shown to influence NSC renewal and maturation. We will discuss the neural developmental and teratological implications of the biogenesis and function of microRNAs (miRNAs), a class of small non-protein-coding RNAs that control the expression of gene networks by translation repression. A small but growing body of research has identified ethanol-sensitive miRNAs at different stages of NSC and brain maturation. While many miRNAs appear to be vulnerable to ethanol at specific developmental stages, a few, like the miR-9 family, appear to exhibit broad vulnerability to ethanol across multiple stages of NSC differentiation. An assessment of the regulation and function of these miRNAs provides important clues about the mechanisms that underlie fetal vulnerability to alterations in the maternal-fetal environment and yields insights into the genesis of FASD.
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Santana-Farré R, Mirecki-Garrido M, Bocos C, Henríquez-Hernández LA, Kahlon N, Herrera E, Norstedt G, Parini P, Flores-Morales A, Fernández-Pérez L. Influence of neonatal hypothyroidism on hepatic gene expression and lipid metabolism in adulthood. PLoS One 2012; 7:e37386. [PMID: 22666351 PMCID: PMC3354003 DOI: 10.1371/journal.pone.0037386] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 04/19/2012] [Indexed: 11/30/2022] Open
Abstract
Thyroid hormones are required for normal growth and development in mammals. Congenital-neonatal hypothyroidism (CH) has a profound impact on physiology, but its specific influence in liver is less understood. Here, we studied how CH influences the liver gene expression program in adulthood. Pregnant rats were given the antithyroid drug methimazole (MMI) from GD12 until PND30 to induce CH in male offspring. Growth defects due to CH were evident as reductions in body weight and tail length from the second week of life. Once the MMI treatment was discontinued, the feed efficiency increased in CH, and this was accompanied by significant catch-up growth. On PND80, significant reductions in body mass, tail length, and circulating IGF-I levels remained in CH rats. Conversely, the mRNA levels of known GH target genes were significantly upregulated. The serum levels of thyroid hormones, cholesterol, and triglycerides showed no significant differences. In contrast, CH rats showed significant changes in the expression of hepatic genes involved in lipid metabolism, including an increased transcription of PPARα and a reduced expression of genes involved in fatty acid and cholesterol uptake, cellular sterol efflux, triglyceride assembly, bile acid synthesis, and lipogenesis. These changes were associated with a decrease of intrahepatic lipids. Finally, CH rats responded to the onset of hypothyroidism in adulthood with a reduction of serum fatty acids and hepatic cholesteryl esters and to T3 replacement with an enhanced activation of malic enzyme. In summary, we provide in vivo evidence that neonatal hypothyroidism influences the hepatic transcriptional program and tissue sensitivity to hormone treatment in adulthood. This highlights the critical role that a euthyroid state during development plays on normal liver physiology in adulthood.
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Affiliation(s)
- Ruymán Santana-Farré
- Department of Clinical Sciences, Molecular and Translational Endocrinology Group, University of Las Palmas de GC - Cancer Research Institute of The Canary Islands, Las Palmas de Gran Canaria, Spain.
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Conforto TL, Waxman DJ. Sex-specific mouse liver gene expression: genome-wide analysis of developmental changes from pre-pubertal period to young adulthood. Biol Sex Differ 2012; 3:9. [PMID: 22475005 PMCID: PMC3350426 DOI: 10.1186/2042-6410-3-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 04/04/2012] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Early liver development and the transcriptional transitions during hepatogenesis are well characterized. However, gene expression changes during the late postnatal/pre-pubertal to young adulthood period are less well understood, especially with regards to sex-specific gene expression. METHODS Microarray analysis of male and female mouse liver was carried out at 3, 4, and 8 wk of age to elucidate developmental changes in gene expression from the late postnatal/pre-pubertal period to young adulthood. RESULTS A large number of sex-biased and sex-independent genes showed significant changes during this developmental period. Notably, sex-independent genes involved in cell cycle, chromosome condensation, and DNA replication were down regulated from 3 wk to 8 wk, while genes associated with metal ion binding, ion transport and kinase activity were up regulated. A majority of genes showing sex differential expression in adult liver did not display sex differences prior to puberty, at which time extensive changes in sex-specific gene expression were seen, primarily in males. Thus, in male liver, 76% of male-specific genes were up regulated and 47% of female-specific genes were down regulated from 3 to 8 wk of age, whereas in female liver 67% of sex-specific genes showed no significant change in expression. In both sexes, genes up regulated from 3 to 8 wk were significantly enriched (p < E-76) in the set of genes positively regulated by the liver transcription factor HNF4α, as determined in a liver-specific HNF4α knockout mouse model, while genes down regulated during this developmental period showed significant enrichment (p < E-65) for negative regulation by HNF4α. Significant enrichment of the developmentally regulated genes in the set of genes subject to positive and negative regulation by pituitary hormone was also observed. Five sex-specific transcriptional regulators showed sex-specific expression at 4 wk (male-specific Ihh; female-specific Cdx4, Cux2, Tox, and Trim24) and may contribute to the developmental changes that lead to global acquisition of liver sex-specificity by 8 wk of age. CONCLUSIONS Overall, the observed changes in gene expression during postnatal liver development reflect the deceleration of liver growth and the induction of specialized liver functions, with widespread changes in sex-specific gene expression primarily occurring in male liver.
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Affiliation(s)
- Tara L Conforto
- Division of Cell and Molecular Biology, Department of Biology, Boston University, Boston, MA 02215, USA.
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A set of imprinted genes required for normal body growth also promotes growth of rhabdomyosarcoma cells. Pediatr Res 2012; 71:32-8. [PMID: 22289848 PMCID: PMC3420822 DOI: 10.1038/pr.2011.6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
INTRODUCTION In many normal tissues, proliferation rates decline postnatally, causing somatic growth to slow. Previous evidence suggests that this decline is due, in part, to decline in the expression of growth-promoting imprinted genes including Mest, Plagl1, Peg3, Dlk1, and Igf2. Embryonal cancers are composed of cells that maintain embryonic characteristics and proliferate rapidly in childhood. We hypothesized that the abnormal persistent rapid proliferation in embryonal cancers occurs in part because of abnormal persistent high expression of growth-promoting imprinted genes. RESULTS Analysis of microarray data showed elevated expression of MEST, PLAGL1, PEG3, DLK1, and IGF2 in various embryonal cancers, especially rhabdomyosarcoma, as compared to nonembryonal cancers and normal tissues. Similarly, mRNA expression, assessed by real-time PCR, of MEST, PEG3, and IGF2 in rhabdomyosarcoma cell lines was increased as compared to nonembryonal cancer cell lines. Furthermore, siRNA-mediated knockdown of MEST, PLAGL1, PEG3, and IGF2 expression inhibited proliferation in Rh30 rhabdomyosarcoma cells. DISCUSSION These findings suggest that the normal postnatal downregulation of growth-promoting imprinted genes fails to occur in some embryonal cancers, particularly rhabdomyosarcoma, and contributes to the persistent rapid proliferation of rhabdomyosarcoma cells and, more generally, that failure of the mechanisms responsible for normal somatic growth deceleration can promote tumorigenesis.
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Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci. Cell Stem Cell 2011; 9:272-81. [PMID: 21885022 DOI: 10.1016/j.stem.2011.07.007] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 06/07/2011] [Accepted: 07/14/2011] [Indexed: 12/23/2022]
Abstract
BMI1 is required for the self-renewal of stem cells in many tissues including the lung epithelial stem cells, Bronchioalveolar Stem Cells (BASCs). Imprinted genes, which exhibit expression from only the maternally or paternally inherited allele, are known to regulate developmental processes, but what their role is in adult cells remains a fundamental question. Many imprinted genes were derepressed in Bmi1 knockout mice, and knockdown of Cdkn1c (p57) and other imprinted genes partially rescued the self-renewal defect of Bmi1 mutant lung cells. Expression of p57 and other imprinted genes was required for lung cell self-renewal in culture and correlated with repair of lung epithelial cell injury in vivo. Our data suggest that BMI1-dependent regulation of expressed alleles at imprinted loci, distinct from imprinting per se, is required for control of lung stem cells. We anticipate that the regulation and function of imprinted genes is crucial for self-renewal in diverse adult tissue-specific stem cells.
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Berg JS, Lin KK, Sonnet C, Boles NC, Weksberg DC, Nguyen H, Holt LJ, Rickwood D, Daly RJ, Goodell MA. Imprinted genes that regulate early mammalian growth are coexpressed in somatic stem cells. PLoS One 2011; 6:e26410. [PMID: 22039481 PMCID: PMC3198398 DOI: 10.1371/journal.pone.0026410] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 09/26/2011] [Indexed: 01/21/2023] Open
Abstract
Lifelong, many somatic tissues are replenished by specialized adult stem cells. These stem cells are generally rare, infrequently dividing, occupy a unique niche, and can rapidly respond to injury to maintain a steady tissue size. Despite these commonalities, few shared regulatory mechanisms have been identified. Here, we scrutinized data comparing genes expressed in murine long-term hematopoietic stem cells with their differentiated counterparts and observed that a disproportionate number were members of the developmentally-important, monoallelically expressed imprinted genes. Studying a subset, which are members of a purported imprinted gene network (IGN), we found their expression in HSCs rapidly altered upon hematopoietic perturbations. These imprinted genes were also predominantly expressed in stem/progenitor cells of the adult epidermis and skeletal muscle in mice, relative to their differentiated counterparts. The parallel down-regulation of these genes postnatally in response to proliferation and differentiation suggests that the IGN could play a mechanistic role in both cell growth and tissue homeostasis.
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Affiliation(s)
- Jonathan S. Berg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kuanyin K. Lin
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Corinne Sonnet
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nathan C. Boles
- Interdepartmental Program of Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - David C. Weksberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hoang Nguyen
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lowenna J. Holt
- Diabetes and Obesity Research Program, Garvan Institute of Medical Research, Sydney, Australia
| | - Danny Rickwood
- Cancer Research Program, Garvan Institute of Medical Research, Sydney, Australia
| | - Roger J. Daly
- Cancer Research Program, Garvan Institute of Medical Research, Sydney, Australia
| | - Margaret A. Goodell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, United States of America
- Interdepartmental Program of Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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Abstract
Recent studies have begun to provide insight into a long-standing mystery in biology-why body growth in animals is rapid in early life but then progressively slows, thus imposing a limit on adult body size. This growth deceleration in mammals is caused by potent suppression of cell proliferation in multiple tissues and is driven primarily by local, rather than systemic, mechanisms. Recent evidence suggests that this progressive decline in proliferation results from a genetic program that occurs in multiple organs and involves the down-regulation of a large set of growth-promoting genes. This program does not appear to be driven simply by time, but rather depends on growth itself, suggesting that the limit on adult body size is imposed by a negative feedback loop. Different organs appear to use different types of information to precisely target their adult size. For example, skeletal and cardiac muscle growth are negatively regulated by myostatin, the concentration of which depends on muscle mass itself. Liver growth appears to be modulated by bile acid flux, a parameter that reflects organ function. In pancreas, organ size appears to be limited by the initial number of progenitor cells, suggesting a mechanism based on cell-cycle counting. Further elucidation of the fundamental mechanisms suppressing juvenile growth is likely to yield important insights into the pathophysiology of childhood growth disorders and of the unrestrained growth of cancer. In addition, improved understanding of these growth-suppressing mechanisms may someday allow their therapeutic suspension in adult tissues to facilitate tissue regeneration.
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Affiliation(s)
- Julian C Lui
- Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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Crespi B. The evolutionary biology of child health. Proc Biol Sci 2011; 278:1441-9. [PMID: 21288946 PMCID: PMC3081756 DOI: 10.1098/rspb.2010.2627] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 01/10/2011] [Indexed: 01/09/2023] Open
Abstract
I apply evolutionary perspectives and conceptual tools to analyse central issues underlying child health, with emphases on the roles of human-specific adaptations and genomic conflicts in physical growth and development. Evidence from comparative primatology, anthropology, physiology and human disorders indicates that child health risks have evolved in the context of evolutionary changes, along the human lineage, affecting the timing, growth-differentiation phenotypes and adaptive significance of prenatal stages, infancy, childhood, juvenility and adolescence. The most striking evolutionary changes in humans are earlier weaning and prolonged subsequent pre-adult stages, which have structured and potentiated maladaptations related to growth and development. Data from human genetic and epigenetic studies, and mouse models, indicate that growth, development and behaviour during pre-adult stages are mediated to a notable degree by effects from genomic conflicts and imprinted genes. The incidence of cancer, the primary cause of non-infectious childhood mortality, mirrors child growth rates from birth to adolescence, with paediatric cancer development impacted by imprinted genes that control aspects of growth. Understanding the adaptive significance of child growth and development phenotypes, in the context of human-evolutionary changes and genomic conflicts, provides novel insights into the causes of disease in childhood.
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Affiliation(s)
- Bernard Crespi
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, Canada.
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Forcinito P, Andrade AC, Finkielstain GP, Baron J, Nilsson O, Lui JC. Growth-inhibiting conditions slow growth plate senescence. J Endocrinol 2011; 208:59-67. [PMID: 20974641 PMCID: PMC6289067 DOI: 10.1677/joe-10-0302] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The mammalian growth plate undergoes programmed senescence during juvenile life, causing skeletal growth to slow with age. We previously found that hypothyroidism in rats slowed both growth plate chondrocyte proliferation and growth plate senescence, suggesting that senescence is not dependent on age per se but rather on chondrocyte proliferation. However, one alternative explanation is that the observed slowing of growth plate senescence is a specific consequence of hypothyroidism. We reasoned that, if delayed senescence is a general consequence of growth inhibition, rather than a specific result of hypothyroidism, then senescence would also be slowed by other growth-inhibiting conditions. In this study, we therefore used tryptophan deficiency to temporarily inhibit growth in newborn rats for 4 weeks. We then allowed the animals to recover and studied the effects on growth plate senescence. We found that structural, functional, and molecular markers of growth plate senescence were delayed by prior tryptophan deficiency, indicating that the developmental program of senescence had occurred more slowly during the period of growth inhibition. Taken together with previous studies in hypothyroid rats, our findings support the hypothesis that delayed senescence is a general consequence of growth inhibition and hence that growth plate senescence is not simply a function of time per se but rather depends on growth.
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Affiliation(s)
- Patricia Forcinito
- Developmental Endocrinology Branch, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC, Room 1-3330, 10 Center Drive, MSC-1103, Bethesda, Maryland 20892-1103, USA
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