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Severa G, Pennisi A, Barnerias C, Fiorillo C, Scala M, Taglietti V, Cojocaru AI, Jouni D, Tosca L, Tachdjian G, Desguerre I, Authier FJ, Carlier RY, Metay C, Verebi C, Malfatti E. An early onset benign myopathy with glycogen storage caused by a de novo 1.4 Mb-deletion of chromosome 14. Neuromuscul Disord 2023; 33:817-821. [PMID: 37743183 DOI: 10.1016/j.nmd.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/08/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023]
Abstract
Early onset myopathies are a clinically and histologically heterogeneous monogenic diseases linked to approximately 90 genes. Molecular diagnosis is challenging, especially in patients with a mild phenotype. We describe a 26-year-old man with neonatal hypotonia, motor delay and seizures during infancy, and non-progressive, mild muscular weakness in adulthood. Serum Creatine kinase level was normal. Whole-body muscle MRI showed thin muscles, and brain MRI was unremarkable. A deltoid muscle biopsy showed glycogen storage. WGS revealed a de novo 1.4 Mb-deletion of chromosome 14, confirmed by Array-CGH. This microdeletion causes the loss of ten genes including RALGAPA1, encoding for RalA, a regulator of glucose transporter 4 (GLUT4) expression at the membrane of myofibers. GLUT4 was overexpressed in patient's muscle. Here we highlight the importance to search for chromosomal alterations in the diagnostic workup of early onset myopathies.
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Affiliation(s)
- Gianmarco Severa
- Université Paris Est, U955, IMRB, INSERM, APHP, Centre de Référence de Pathologie Neuromusculaire Nord-Est-Ile-de-France, Filnemus, Henri Mondor Hospital, France; Department of Medical, Surgical and Neurological Sciences, Neurology‑Neurophysiology Unit, University of Siena, Policlinico Le Scotte, Viale Bracci 1, 5310 Siena, Italy
| | | | - Christine Barnerias
- Reference Center for Neuromuscular Disorders, Filnemus, EuroNMD, Assistance Publique-Hôpitaux de Paris (APHP) Necker Enfants Malades Hospital, Paris, France
| | - Chiara Fiorillo
- Neurologia Pediatrica e Malattie Muscolari, Istituto G.Gaslini, Genoa, Italy
| | - Marcello Scala
- Neurologia Pediatrica e Malattie Muscolari, Istituto G.Gaslini, Genoa, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università Degli Studi di Genova, Genoa, Italy
| | | | | | - Dima Jouni
- AP-HP. Université Paris Saclay, Hôpital Antoine Béclère, Service d'Histologie, Embryologie et Cytogénétique, 92140 Clamart, France
| | - Lucie Tosca
- AP-HP. Université Paris Saclay, Hôpital Antoine Béclère, Service d'Histologie, Embryologie et Cytogénétique, 92140 Clamart, France
| | - Gérard Tachdjian
- AP-HP. Université Paris Saclay, Hôpital Antoine Béclère, Service d'Histologie, Embryologie et Cytogénétique, 92140 Clamart, France
| | - Isabelle Desguerre
- Reference Center for Neuromuscular Disorders, Filnemus, EuroNMD, Assistance Publique-Hôpitaux de Paris (APHP) Necker Enfants Malades Hospital, Paris, France
| | - François-Jérome Authier
- Université Paris Est, U955, IMRB, INSERM, APHP, Centre de Référence de Pathologie Neuromusculaire Nord-Est-Ile-de-France, Filnemus, Henri Mondor Hospital, France
| | - Robert-Yves Carlier
- AP-HP, GHU Paris Saclay, Hôpital Raymond Poincaré, DMU Smart Imaging, UMR1179 INSERM Garches France
| | - Corinne Metay
- Unité Fonctionnelle de Cardiogénétique et Myogénétique moléculaire et cellulaire. Centre de Génétique Moléculaire et Chromosomique et INSERM UMRS 974, Institut de Myologie. Groupe Hospitalier La Pitié-Salpêtrière-Charles Foix, Paris, INSERM UMRS1166, Sorbonne Université, Paris, France
| | - Camille Verebi
- Service de Médecine Génomique, Maladies de Système et d'Organe - Fédération de Génétique et de Médecine Génomique, DMU BioPhyGen, APHP Centre-Université Paris Cité - Hôpital Cochin, Paris, France
| | - Edoardo Malfatti
- Université Paris Est, U955, IMRB, INSERM, APHP, Centre de Référence de Pathologie Neuromusculaire Nord-Est-Ile-de-France, Filnemus, Henri Mondor Hospital, France.
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Wagner M, Skorobogatko Y, Pode-Shakked B, Powell CM, Alhaddad B, Seibt A, Barel O, Heimer G, Hoffmann C, Demmer LA, Perilla-Young Y, Remke M, Wieczorek D, Navaratnarajah T, Lichtner P, Klee D, Shamseldin HE, Al Mutairi F, Mayatepek E, Strom T, Meitinger T, Alkuraya FS, Anikster Y, Saltiel AR, Distelmaier F. Bi-allelic Variants in RALGAPA1 Cause Profound Neurodevelopmental Disability, Muscular Hypotonia, Infantile Spasms, and Feeding Abnormalities. Am J Hum Genet 2020; 106:246-255. [PMID: 32004447 DOI: 10.1016/j.ajhg.2020.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/06/2020] [Indexed: 12/30/2022] Open
Abstract
Ral (Ras-like) GTPases play an important role in the control of cell migration and have been implicated in Ras-mediated tumorigenicity. Recently, variants in RALA were also described as a cause of intellectual disability and developmental delay, indicating the relevance of this pathway to neuropediatric diseases. Here, we report the identification of bi-allelic variants in RALGAPA1 (encoding Ral GTPase activating protein catalytic alpha subunit 1) in four unrelated individuals with profound neurodevelopmental disability, muscular hypotonia, feeding abnormalities, recurrent fever episodes, and infantile spasms . Dysplasia of corpus callosum with focal thinning of the posterior part and characteristic facial features appeared to be unifying findings. RalGAPA1 was absent in the fibroblasts derived from two affected individuals suggesting a loss-of-function effect of the RALGAPA1 variants. Consequently, RalA activity was increased in these cell lines, which is in keeping with the idea that RalGAPA1 deficiency causes a constitutive activation of RalA. Additionally, levels of RalGAPB, a scaffolding subunit of the RalGAP complex, were dramatically reduced, indicating a dysfunctional RalGAP complex. Moreover, RalGAPA1 deficiency clearly increased cell-surface levels of lipid raft components in detached fibroblasts, which might indicate that anchorage-dependence of cell growth signaling is disturbed. Our findings indicate that the dysregulation of the RalA pathway has an important impact on neuronal function and brain development. In light of the partially overlapping phenotype between RALA- and RALGAPA1-associated diseases, it appears likely that dysregulation of the RalA signaling pathway leads to a distinct group of genetic syndromes that we suggest could be named RALopathies.
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Gladwyn-Ng I, Huang L, Ngo L, Li SS, Qu Z, Vanyai HK, Cullen HD, Davis JM, Heng JIT. Bacurd1/Kctd13 and Bacurd2/Tnfaip1 are interacting partners to Rnd proteins which influence the long-term positioning and dendritic maturation of cerebral cortical neurons. Neural Dev 2016; 11:7. [PMID: 26969432 PMCID: PMC4788816 DOI: 10.1186/s13064-016-0062-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/28/2016] [Indexed: 11/10/2022] Open
Abstract
Background The development of neural circuits within the embryonic cerebral cortex relies on the timely production of neurons, their positioning within the embryonic cerebral cortex as well as their terminal differentiation and dendritic spine connectivity. The RhoA GTPases Rnd2 and Rnd3 are important for neurogenesis and cell migration within the embryonic cortex (Nat Commun 4:1635, 2013), and we recently identified the BTB/POZ domain-containing Adaptor for Cul3-mediated RhoA Degradation family member Bacurd2 (also known as Tnfaip1) as an interacting partner to Rnd2 for the migration of embryonic mouse cortical neurons (Neural Dev 10:9, 2015). Findings We have extended this work and report that Bacurd1/Kctd13 and Bacurd2/Tnfaip1 are interacting partners to Rnd2 and Rnd3 in vitro. Given that these genes are expressed during cortical development, we performed a series of in utero electroporation studies in mice and found that disruptions to Bacurd1/Kctd13 or Bacurd2/Tnfaip1 expression impair the long-term positioning of E14.5-born cortical neurons within the postnatal (P17) mouse cerebral cortex. We also find that forced expression of Bacurd1/Kctd13 and Bacurd2/Tnfaip1 alters the branching and dendritic spine properties of layer II/III projection neurons. Conclusions We identify Bacurd1/Kctd13 and Bacurd2/Tnfaip1 as interacting partners to Rnd proteins which influence the development of cortical neurons. Their neurodevelopmental functions are likely to be relevant to human brain development and disease. Electronic supplementary material The online version of this article (doi:10.1186/s13064-016-0062-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ivan Gladwyn-Ng
- EMBL-Australia, The Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC, 3800, Australia.,The Harry Perkins Institute of Medical Research, 6 Verdun St, Crawley, WA, 6009, Australia.,The Centre for Medical Research, The University of Western Australia, Crawley Avenue, Crawley, WA, 6009, Australia
| | - Lieven Huang
- EMBL-Australia, The Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC, 3800, Australia
| | - Linh Ngo
- EMBL-Australia, The Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC, 3800, Australia.,The Harry Perkins Institute of Medical Research, 6 Verdun St, Crawley, WA, 6009, Australia.,The Centre for Medical Research, The University of Western Australia, Crawley Avenue, Crawley, WA, 6009, Australia
| | - Shan Shan Li
- EMBL-Australia, The Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC, 3800, Australia
| | - Zhengdong Qu
- EMBL-Australia, The Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC, 3800, Australia
| | - Hannah Kate Vanyai
- The Harry Perkins Institute of Medical Research, 6 Verdun St, Crawley, WA, 6009, Australia.,The Centre for Medical Research, The University of Western Australia, Crawley Avenue, Crawley, WA, 6009, Australia
| | - Hayley Daniella Cullen
- The Harry Perkins Institute of Medical Research, 6 Verdun St, Crawley, WA, 6009, Australia.,The Centre for Medical Research, The University of Western Australia, Crawley Avenue, Crawley, WA, 6009, Australia
| | - John Michael Davis
- EMBL-Australia, The Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC, 3800, Australia
| | - Julian Ik-Tsen Heng
- EMBL-Australia, The Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC, 3800, Australia. .,The Harry Perkins Institute of Medical Research, 6 Verdun St, Crawley, WA, 6009, Australia. .,The Centre for Medical Research, The University of Western Australia, Crawley Avenue, Crawley, WA, 6009, Australia.
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Gladwyn-Ng IE, Li SS, Qu Z, Davis JM, Ngo L, Haas M, Singer J, Heng JIT. Bacurd2 is a novel interacting partner to Rnd2 which controls radial migration within the developing mammalian cerebral cortex. Neural Dev 2015; 10:9. [PMID: 25888806 PMCID: PMC4433056 DOI: 10.1186/s13064-015-0032-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/23/2015] [Indexed: 12/03/2022] Open
Abstract
Background During fetal brain development in mammals, newborn neurons undergo cell migration to reach their appropriate positions and form functional circuits. We previously reported that the atypical RhoA GTPase Rnd2 promotes the radial migration of mouse cerebral cortical neurons (Nature 455(7209):114–8, 2008; Neuron 69(6):1069–84, 2011), but its downstream signalling pathway is not well understood. Results We have identified BTB-domain containing adaptor for Cul3-mediated RhoA degradation 2 (Bacurd2) as a novel interacting partner to Rnd2, which promotes radial migration within the developing cerebral cortex. We find that Bacurd2 binds Rnd2 at its C-terminus, and this interaction is critical to its cell migration function. We show that forced expression or knockdown of Bacurd2 impairs neuronal migration within the embryonic cortex and alters the morphology of immature neurons. Our in vivo cellular analysis reveals that Bacurd2 influences the multipolar-to-bipolar transition of radially migrating neurons in a cell autonomous fashion. When we addressed the potential signalling relationship between Bacurd2 and Rnd2 using a Bacurd2-Rnd2 chimeric construct, our results suggest that Bacurd2 and Rnd2 could interact to promote radial migration within the embryonic cortex. Conclusions Our studies demonstrate that Bacurd2 is a novel player in neuronal development and influences radial migration within the embryonic cerebral cortex. Electronic supplementary material The online version of this article (doi:10.1186/s13064-015-0032-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ivan Enghian Gladwyn-Ng
- EMBL Australia, The Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, 3800, Australia.
| | - Shan Shan Li
- EMBL Australia, The Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, 3800, Australia.
| | - Zhengdong Qu
- EMBL Australia, The Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, 3800, Australia.
| | - John Michael Davis
- EMBL Australia, The Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, 3800, Australia.
| | - Linh Ngo
- EMBL Australia, The Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, 3800, Australia. .,The Harry Perkins Institute of Medical Research, Perth, Australia.
| | - Matilda Haas
- EMBL Australia, The Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, 3800, Australia.
| | - Jeffrey Singer
- Department of Biology, Portland State University, Portland, Oregon, 96207, USA.
| | - Julian Ik-Tsen Heng
- EMBL Australia, The Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, 3800, Australia. .,The Harry Perkins Institute of Medical Research, Perth, Australia. .,Centre for Medical Research, The University of Western Australia, Perth, Australia. .,Present address: The Harry Perkins Institute of Medical Research, Perth, Australia.
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Parveen N, Masood A, Iftikhar N, Minhas BF, Minhas R, Nawaz U, Abbasi AA. Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers. BMC Genomics 2013; 14:122. [PMID: 23432897 PMCID: PMC3599049 DOI: 10.1186/1471-2164-14-122] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 02/19/2013] [Indexed: 12/03/2022] Open
Abstract
Background Human genome is enriched with thousands of conserved non-coding elements (CNEs). Recently, a medium throughput strategy was employed to analyze the ability of human CNEs to drive tissue specific expression during mouse embryogenesis. These data led to the establishment of publicly available genome wide catalog of functionally defined human enhancers. Scattering of enhancers over larger regions in vertebrate genomes seriously impede attempts to pinpoint their precise target genes. Such associations are prerequisite to explore the significance of this in vivo characterized catalog of human enhancers in development, disease and evolution. Results This study is an attempt to systematically identify the target gene-bodies for functionally defined human CNE-enhancers. For the purpose we adopted the orthology/paralogy mapping approach and compared the CNE induced reporter expression with reported endogenous expression pattern of neighboring genes. This procedure pinpointed specific target gene-bodies for the total of 192 human CNE-enhancers. This enables us to gauge the maximum genomic search space for enhancer hunting: 4 Mb of genomic sequence around the gene of interest (2 Mb on either side). Furthermore, we used human-rodent comparison for a set of 159 orthologous enhancer pairs to infer that the central nervous system (CNS) specific gene expression is closely associated with the cooperative interaction among at least eight distinct transcription factors: SOX5, HFH, SOX17, HNF3β, c-FOS, Tal1beta-E47S, MEF and FREAC. Conclusions In conclusion, the systematic wiring of cis-acting sites and their target gene bodies is an important step to unravel the role of in vivo characterized catalog of human enhancers in development, physiology and medicine.
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Affiliation(s)
- Nazia Parveen
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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Barnett CP, Mencel JJ, Gecz J, Waters W, Kirwin SM, Vinette KMB, Uppill M, Nicholl J. Choreoathetosis, congenital hypothyroidism and neonatal respiratory distress syndrome with intact NKX2-1. Am J Med Genet A 2012; 158A:3168-73. [PMID: 23169673 DOI: 10.1002/ajmg.a.35456] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 04/12/2012] [Indexed: 11/10/2022]
Abstract
Mutations in the NK2 homeobox 1 gene (NKX2-1) cause a rare syndrome known as choreoathetosis, congenital hypothyroidism, and neonatal respiratory distress syndrome (OMIM 610978). Here we present the first reported patient with this condition caused by a 14q13.3 deletion which is adjacent to but does not interrupt NKX2-1, and review the literature on this condition. The infant presented at 23 months with a history of developmental delay, hyperkinesia, recurrent respiratory infections, neonatal respiratory distress, and hypothyroidism. Choreiform movements and delayed motor milestones were first noted at 6-8 months of age. TSH levels had been consistently elevated from 8 months of age. The clinical presentation was suggestive of an NKX2-1 mutation. Sequencing of all exons and splice site junctions of NKX2-1 was performed but was normal. Array CGH was then performed and a 3.29 Mb interstitial deletion at 14q13.1-q13.3 was detected. The distal region of loss of the deletion disrupted the surfactant associated 3 (SFTA3) gene but did disrupt NKX2-1. Findings were confirmed on high resolution SNP array and multiplex semiquanitative PCR. NKX2-1 encodes transcriptional factors involved in the developmental pathways for thyroid, lung, and brain. We hypothesize that the region centromeric to NKX2-1 is important for the normal functioning of this gene and when interrupted produces a phenotype that is typical of the choreoathetosis, congenital hypothyroidism, and neonatal respiratory distress syndrome, as seen in our patient. We conclude that deletions at 14q13.3 adjacent to but not involving NKX2-1 can cause choreoathetosis, congenital hypothyroidism, and neonatal respiratory distress syndrome.
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Affiliation(s)
- Christopher P Barnett
- South Australian Clinical Genetics Service, Women's and Children's Hospital/SA Pathology, North Adelaide, South Australia, Australia.
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Shen X, Zeng H, Xie L, He J, Li J, Xie X, Luo C, Xu H, Zhou M, Nie Q, Zhang X. The GTPase activating Rap/RanGAP domain-like 1 gene is associated with chicken reproductive traits. PLoS One 2012; 7:e33851. [PMID: 22496769 PMCID: PMC3322132 DOI: 10.1371/journal.pone.0033851] [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: 05/23/2011] [Accepted: 02/19/2012] [Indexed: 11/28/2022] Open
Abstract
Background Abundant evidence indicates that chicken reproduction is strictly regulated by the hypothalamic-pituitary-gonad (HPG) axis, and the genes included in the HPG axis have been studied extensively. However, the question remains as to whether any other genes outside of the HPG system are involved in regulating chicken reproduction. The present study was aimed to identify, on a genome-wide level, novel genes associated with chicken reproductive traits. Methodology/Principal Finding Suppressive subtractive hybridization (SSH), genome-wide association study (GWAS), and gene-centric GWAS were used to identify novel genes underlying chicken reproduction. Single marker-trait association analysis with a large population and allelic frequency spectrum analysis were used to confirm the effects of candidate genes. Using two full-sib Ningdu Sanhuang (NDH) chickens, GARNL1 was identified as a candidate gene involved in chicken broodiness by SSH analysis. Its expression levels in the hypothalamus and pituitary were significantly higher in brooding chickens than in non-brooding chickens. GWAS analysis with a NDH two tail sample showed that 2802 SNPs were significantly associated with egg number at 300 d of age (EN300). Among the 2802 SNPs, 2 SNPs composed a block overlapping the GARNL1 gene. The gene-centric GWAS analysis with another two tail sample of NDH showed that GARNL1 was strongly associated with EN300 and age at first egg (AFE). Single marker-trait association analysis in 1301 female NDH chickens confirmed that variation in this gene was related to EN300 and AFE. The allelic frequency spectrum of the SNP rs15700989 among 5 different populations supported the above associations. Western blotting, RT-PCR, and qPCR were used to analyze alternative splicing of the GARNL1 gene. RT-PCR detected 5 transcripts and revealed that the transcript, which has a 141 bp insertion, was expressed in a tissue-specific manner. Conclusions/Significance Our findings demonstrate that the GARNL1 gene contributes to chicken reproductive traits.
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Affiliation(s)
- Xu Shen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Hua Zeng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Liang Xie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Institute of Animal Science and Veterinary, Hainan Academy of Agricultural Sciences, Haikou, Hainan, China
| | - Jun He
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Jian Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Xiujuan Xie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Chenglong Luo
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Haiping Xu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Min Zhou
- Biotechnology Institute, Jiang Xi Education College, Nanchang, Jiangxi, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
- * E-mail:
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Bonato V, Baladandayuthapani V, Broom BM, Sulman EP, Aldape KD, Do KA. Bayesian ensemble methods for survival prediction in gene expression data. Bioinformatics 2011; 27:359-67. [PMID: 21148161 PMCID: PMC3031034 DOI: 10.1093/bioinformatics/btq660] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION We propose a Bayesian ensemble method for survival prediction in high-dimensional gene expression data. We specify a fully Bayesian hierarchical approach based on an ensemble 'sum-of-trees' model and illustrate our method using three popular survival models. Our non-parametric method incorporates both additive and interaction effects between genes, which results in high predictive accuracy compared with other methods. In addition, our method provides model-free variable selection of important prognostic markers based on controlling the false discovery rates; thus providing a unified procedure to select relevant genes and predict survivor functions. RESULTS We assess the performance of our method several simulated and real microarray datasets. We show that our method selects genes potentially related to the development of the disease as well as yields predictive performance that is very competitive to many other existing methods. AVAILABILITY http://works.bepress.com/veera/1/.
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Affiliation(s)
- Vinicius Bonato
- Pfizer Inc., Groton, CT 06340, Department of Biostatistics, Department of Bioinformatics and Computational Biology, Department of Radiation Oncology and Department of Pathology, The University of Texas, M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Veerabhadran Baladandayuthapani
- Pfizer Inc., Groton, CT 06340, Department of Biostatistics, Department of Bioinformatics and Computational Biology, Department of Radiation Oncology and Department of Pathology, The University of Texas, M. D. Anderson Cancer Center, Houston, TX 77030, USA,* To whom correspondence should be addressed
| | - Bradley M. Broom
- Pfizer Inc., Groton, CT 06340, Department of Biostatistics, Department of Bioinformatics and Computational Biology, Department of Radiation Oncology and Department of Pathology, The University of Texas, M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Erik P. Sulman
- Pfizer Inc., Groton, CT 06340, Department of Biostatistics, Department of Bioinformatics and Computational Biology, Department of Radiation Oncology and Department of Pathology, The University of Texas, M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenneth D. Aldape
- Pfizer Inc., Groton, CT 06340, Department of Biostatistics, Department of Bioinformatics and Computational Biology, Department of Radiation Oncology and Department of Pathology, The University of Texas, M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Kim-Anh Do
- Pfizer Inc., Groton, CT 06340, Department of Biostatistics, Department of Bioinformatics and Computational Biology, Department of Radiation Oncology and Department of Pathology, The University of Texas, M. D. Anderson Cancer Center, Houston, TX 77030, USA
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Chen CF, Shiue YL, Yen CJ, Tang PC, Chang HC, Lee YP. Laying traits and underlying transcripts, expressed in the hypothalamus and pituitary gland, that were associated with egg production variability in chickens. Theriogenology 2007; 68:1305-15. [PMID: 17931698 DOI: 10.1016/j.theriogenology.2007.08.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 08/29/2007] [Accepted: 08/11/2007] [Indexed: 10/22/2022]
Abstract
The objective was to characterize the potential laying traits and underlying transcripts expressed in the hypothalamus and pituitary gland that were associated with egg production variability in five genetic stocks of chickens: two commercial lines, Red- (n=12) and Black-feather (n=14) Taiwan country chickens (TCCs); two selected lines of TCCs, B (high body weight/comb size; n=17) and L2 (high-egg production; n=14); and a commercial single comb White Leghorn (WL; n=17). Six laying traits, age at first egg, clutch length, pause length, oviposition lag within clutch, follicle rapid growth period, and rate of yolk accumulation were measured. The significance of differential values among five chicken stocks and correlation coefficients between laying traits and number of eggs to 50 weeks of age or laying rate after first egg, and the expression level of 33 transcripts were determined. Longer clutch length and shorter oviposition lag within clutch contributed to a higher number of eggs to 50 weeks of age or laying rate after first egg in L2 (P<0.05) and WL strains (P<0.05). However, their rate of yolk accumulation (P<0.05) and follicle rapid growth period (P<0.05) were different, indicating the accumulation of different alleles after long-term, independent selection. Across all five strains, numbers of eggs to 50 weeks of age were positive correlated with average clutch length (P<0.05) as well as the rate of yolk accumulation (P<0.05). Expressions of PLAG1, STMN2, PGDS, PARK7, ANP32A, PCDHA@, SCG2, BDH and SAR1A transcripts contributed to number of eggs to 50 weeks of age (P<0.05) or laying rate after first egg (P<0.05). Analysis of correlation coefficients indicated that PLAG1 additionally played roles in decreasing average pause length. Two transcripts, PRL and GARNL1, specifically contributed to number of eggs to 50 weeks of age or laying rate after first egg by reducing oviposition lag within clutch (P<0.05) and/or increasing average clutch length (P<0.05), respectively. Expression level of NCAM1, contributed to laying rate after first egg by association with a shorter oviposition lag within clutch (P<0.05). The current study attributed egg production phenotype in five strains into several laying traits; correlations between these traits and expression levels of underlying transcripts expressed in the hypothalamus and pituitary gland were also established.
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Affiliation(s)
- Chih-Feng Chen
- Department of Animal Science, National Chung-Hsing University, 402, Kuo-Kuang Road, Taichung, Taiwan
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Schwarzbraun T, Vincent JB, Schumacher A, Geschwind DH, Oliveira J, Windpassinger C, Ofner L, Ledinegg MK, Kroisel PM, Wagner K, Petek E. Cloning, genomic structure, and expression profiles of TULIP1 (GARNL1), a brain-expressed candidate gene for 14q13-linked neurological phenotypes, and its murine homologue. Genomics 2005; 84:577-86. [PMID: 15498464 DOI: 10.1016/j.ygeno.2004.04.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2004] [Revised: 04/30/2004] [Indexed: 10/26/2022]
Abstract
Previously, we have described the clinical and molecular characterization of a de novo 14q13.1-q21.1 microdeletion, less than 3.5 Mb in size, in a patient with severe microcephaly, psychomotor retardation, and other clinical anomalies. Here we report the characterization of the genomic structure of the human tuberin-like protein gene 1 (TULIP1; approved gene symbol GARNL1), a CpGisland-associated, brain-expressed candidate gene for the neurological findings in our patient, and its murine homologue. The human TULIP1 gene was mapped to chromosome band 14q13.2 by fluorescence in situ hybridization of BAC clone RP11-355C3 (GenBank Accession No. AL160231), containing the 3' region of the gene. TULIP1 spans about 271 kb of human genomic DNA and is divided into 41 exons. An untranscribed, processed pseudogene of TULIP1 was found on human chromosome band 9q31.1. The active locus TULIP1, encoding a predicted protein of 2036 amino acids, is expressed ubiquitously in pre- and postnatal human tissues. The murine homologue Tulip1 spans about 220 kb of mouse genomic DNA and is also divided into 41 exons, encoding a predicted protein of 2035 amino acids. No pseudogene could be found in the available mouse sequence data. Several splicing variants were found. Considering the location, expression profile, and predicted function, TULIP1 is a strong candidate for several neurological features seen in 14q deletion patients. Additionally we searched for mutations in the coding region of TULIP1 in subjects from a family with idiopathic basal ganglia calcification (IBGC; Fahr disease), previously linked to chromosome 14q. We identified two novel SNPs in the intron-exon boundaries; however, they did not segregate only with affected subjects in the predicted model of an autosomal dominant disease such as IBGC.
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Affiliation(s)
- Thomas Schwarzbraun
- Institute of Medical Biology and Human Genetics, Medical University of Graz, Harrachgasse 21/8, A-8010 Graz, Austria
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Gridley S, Lane WS, Garner CW, Lienhard GE. Novel insulin-elicited phosphoproteins in adipocytes. Cell Signal 2005; 17:59-66. [PMID: 15451025 DOI: 10.1016/j.cellsig.2004.05.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2004] [Accepted: 05/24/2004] [Indexed: 10/26/2022]
Abstract
Akt is a key insulin-activated protein kinase. We searched for Akt substrates in 3T3-L1 adipocytes by means of immunoprecipitation with an Akt phosphomotif-specific antibody (PAS antibody). Four insulin-elicited phosphoproteins were isolated and identified by mass spectrometry. The identity of each protein was established by isolating the protein from lysates of untreated and insulin-treated adipocytes with an antibody specific for the protein and showing that the PAS antibody reacted only with the protein in the immunoprecipitate from insulin-treated cells. These proteins have sizes of 47, 75, 105, and 250 kDa on SDS PAGE, and have been designated pp47, 75, 105, and 250. The effect of inhibitors on the phosphorylation of the proteins, the identified sites of phosphorylation, and in vitro phosphorylation by recombinant Akt further indicated that pp47, 105, and 250 are likely to be Akt substrates, whereas pp75 may not be. pp47 and 105 are novel proteins with no known or predicted function. pp75 was previously found as a protein that associated with the colony-stimulating factor receptor, designated as Fms-interacting protein. pp250 is a novel protein with a predicted GTPase activating protein (GAP) domain for Rheb and/or Rap at its carboxy terminus. The subcellular and tissue distributions of the four proteins were determined.
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Affiliation(s)
- Scott Gridley
- Department of Biochemistry, Vail Building, Dartmouth Medical School, Hanover, NH 03755, USA
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Lahiri DK, Ge YW, Maloney B, Wavrant-De Vrièze F, Hardy J. Characterization of two APP gene promoter polymorphisms that appear to influence risk of late-onset Alzheimer's disease. Neurobiol Aging 2004; 26:1329-41. [PMID: 16243604 DOI: 10.1016/j.neurobiolaging.2004.11.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Revised: 11/09/2004] [Accepted: 11/10/2004] [Indexed: 11/19/2022]
Abstract
Alzheimer's disease (AD) is characterized by formation of plaques of amyloid beta peptide (Abeta). Autosomally-inherited or "familial" AD had been demonstrated only in connection with coding sequence mutations. We characterized DNA-protein interaction and expression influence of two polymorphisms that occur in the promoter (C<-->T at -3829 and T<-->C at -1023, +1 transcription start site) of the Abeta precursor protein (APP) gene. We report distinct functional differences in reporter expression and in DNA-protein interaction for variant sequences in both -3829 and -1023 polymorphic regions. The -3829T variant has reduced DNA-protein interaction and reporter expression compared to -3829C, while -1023C has greater DNA-protein interaction and reporter expression than -1023T. Our predictions for likely transcription factors for loss of function (-3829T) are ADR1, MIG1, and PuF, and for gain of function (-1023C) are E12/E47, ITF-2, and RFX2. Characterization of the activity of a regulatory polymorphism of the APP gene points towards understanding mechanisms that likely underlie the majority of AD cases and may contribute to promoter-based drug design.
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Affiliation(s)
- Debomoy K Lahiri
- Department of Psychiatry, Institute of Psychiatric Research, Indiana University School of Medicine, 791 N. Union Drive, Indianapolis, IN 46202, USA.
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Ik Tsen Heng J, Tan SS. The role of class I HLH genes in neural development--have they been overlooked? Bioessays 2003; 25:709-16. [PMID: 12815726 DOI: 10.1002/bies.10299] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Helix-loop-helix (HLH) genes encode for transcription factors affecting a whole variety of developmental programs, including neurogenesis. At least seven functional classes (denoted I to VII) of HLH genes exist, (1) with subclass members exhibiting homo- and heterodimerisation for proper DNA binding and transcriptional regulation of downstream target genes. In the developing nervous system, members of class II, V and VI have been most extensively studied concerning their roles in neural programming. In contrast, the function of class I proteins (such as E12 and E47) is poorly defined and the orthodox view relegates them to general dimerisation duties that are necessary for the activity of the other classes. However, closer scrutiny of the spatiotemporal expression patterns of class I factors, combined with recent biochemical evidence, would suggest that class I proteins possess specific functions during early neural differentiation. This essay supports this possibility, in addition to putting forward the hypothesis that, outside their general dimerisation activity, class I genes have independent roles in regulating neurogenesis.
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Affiliation(s)
- Julian Ik Tsen Heng
- Brain Development Group, The Howard Florey Institute, University of Melbourne, Parkville VIC 3010, Melbourne Australia
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Ciarapica R, Rosati J, Cesareni G, Nasi S. Molecular recognition in helix-loop-helix and helix-loop-helix-leucine zipper domains. Design of repertoires and selection of high affinity ligands for natural proteins. J Biol Chem 2003; 278:12182-90. [PMID: 12514181 DOI: 10.1074/jbc.m211991200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Helix-loop-helix (HLH) and helix-loop-helix-leucine zipper (HLHZip) are dimerization domains that mediate selective pairing among members of a large transcription factor family involved in cell fate determination. To investigate the molecular rules underlying recognition specificity and to isolate molecules interfering with cell proliferation and differentiation control, we assembled two molecular repertoires obtained by directed randomization of the binding surface in these two domains. For this strategy we selected the Heb HLH and Max Zip regions as molecular scaffolds for the randomization process and displayed the two resulting molecular repertoires on lambda phage capsids. By affinity selection, many domains were isolated that bound to the proteins Mad, Rox, MyoD, and Id2 with different levels of affinity. Although several residues along an extended surface within each domain appeared to contribute to dimerization, some key residues critically involved in molecular recognition could be identified. Furthermore, a number of charged residues appeared to act as switch points facilitating partner exchange. By successfully selecting ligands for four of four HLH or HLHZip proteins, we have shown that the repertoires assembled are rather general and possibly contain elements that bind with sufficient affinity to any natural HLH or HLHZip molecule. Thus they represent a valuable source of ligands that could be used as reagents for molecular dissection of functional regulatory pathways.
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Affiliation(s)
- Roberta Ciarapica
- Istituto di Biologia and Patologia Molecolari Consiglio Nazionale delle Ricerche, Università La Sapienza, 00185 Roma, Italy
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