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Choi H, Kim JA, Cho KO, Kim HJ, Park MH. Case Report: Intellectual disability and borderline intellectual functioning in two sisters with a 12p11.22 loss. Front Genet 2024; 15:1355823. [PMID: 38628577 PMCID: PMC11018894 DOI: 10.3389/fgene.2024.1355823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Multiple genome sequencing studies have identified genetic abnormalities as major causes of severe intellectual disability (ID). However, many children affected by mild ID and borderline intellectual functioning (BIF) lack a genetic diagnosis because known causative ID genetic mutations have not been identified or the role of genetic variants in mild cases is less understood. Genetic variant testing in mild cases is necessary to provide information on prognosis and risk of occurrence. In this study, we report two sibling patients who were 5 years 9 months old and 3 years 3 months old and presented to the hospital due to developmental delay. Clinical assessment and chromosomal microarray analysis were performed. The patients were diagnosed with mild intellectual disability (ID) and borderline intellectual functioning (BIF). Genetic analysis identified a loss of 12p11.22, including the OVCH1-AS1, OVCH1, and TMTC1 genes, which was the only variant that occurred in both sisters. Identical variants were found in their father with probable BIF. Neither patient presented any brain structural abnormalities or dysmorphism, and no exogenous factors or parenting problems were reported. Thus, loss of 12p11.22 may be associated with our patients' cognitive impairment. The OVCH1, OVCH1-AS1 and TMTC1 variants identified in this study are the most likely disease-causing genes in the sisters. Our findings may expand as yet limited knowledge on mild ID and BIF causative variants, which would further support the diagnosis even if the severity is mild.
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Affiliation(s)
- Haemi Choi
- Department of Psychiatry, Eunpyeong St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jeong-A. Kim
- Department of Psychiatry, Eunpyeong St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kyung-Ok Cho
- Department of Pharmacology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, Republic of Korea
- Catholic Neuroscience Institute, The Catholic University of Korea, Seoul, Republic of Korea
- Institute for Aging and Metabolic Diseases, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyun Jung Kim
- Department of Psychiatry, Harvard Medical School, Boston, MA, United States
- Division of Psychotic Disorders, McLean Hospital, Belmont, MA, United States
| | - Min-Hyeon Park
- Department of Psychiatry, Eunpyeong St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, Republic of Korea
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Xia S, Zhao X, Yu H, Li G. Research Note: Identification of breeding-related candidate genes in Tianjin-monkey chickens by transcriptome analysis. Poult Sci 2023; 102:102928. [PMID: 37499610 PMCID: PMC10413196 DOI: 10.1016/j.psj.2023.102928] [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: 05/18/2023] [Revised: 06/20/2023] [Accepted: 07/05/2023] [Indexed: 07/29/2023] Open
Abstract
Tianjin-monkey Chicken is a locally bred dual-purpose naked neck poultry with high tolerance to heat stress and poor reproductive ability. We aim to explore breeding-related genes to promote its growth, reproduction, meat, and egg performances. In this study, purebred, crossbred neck-naked and crossbred neck-feathered Tianjin-monkey Chickens (male = 5 and female = 5 in each group) were sampled for transcriptome analysis. Differential gene expression analysis was performed to identify candidate genes based on mRNA expression profiles. Functional enrichment analyses including GO, KEGG and GSEA analysis were conducted. Forty-five candidate breeding-related genes were identified, which were significantly enriched in 5 KEGG pathways and 37 GO terms. Some of the candidate genes were considered to be valuable in guiding breeding in the future, including SPRY3, CPXM2, FST, HDDC2, TLR1B, CYBB, and EHHADH.
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Affiliation(s)
- Shuli Xia
- Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China; Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin, 300381, China; Tianjin Engineering Research Center of Animal Healthy Farming, Tianjin, 300381, China
| | - Xianghua Zhao
- Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China; Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin, 300381, China; Tianjin Engineering Research Center of Animal Healthy Farming, Tianjin, 300381, China
| | - Haitao Yu
- Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China; Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin, 300381, China; Tianjin Engineering Research Center of Animal Healthy Farming, Tianjin, 300381, China
| | - Guohui Li
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, China.
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Mechanisms of Sperm–Egg Interactions: What Ascidian Fertilization Research Has Taught Us. Cells 2022; 11:cells11132096. [PMID: 35805180 PMCID: PMC9265791 DOI: 10.3390/cells11132096] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 06/18/2022] [Accepted: 06/28/2022] [Indexed: 02/01/2023] Open
Abstract
Fertilization is an essential process in terrestrial organisms for creating a new organism with genetic diversity. Before gamete fusion, several steps are required to achieve successful fertilization. Animal spermatozoa are first activated and attracted to the eggs by egg-derived chemoattractants. During the sperm passage of the egg’s extracellular matrix or upon the sperm binding to the proteinaceous egg coat, the sperm undergoes an acrosome reaction, an exocytosis of acrosome. In hermaphrodites such as ascidians, the self/nonself recognition process occurs when the sperm binds to the egg coat. The activated or acrosome-reacted spermatozoa penetrate through the proteinaceous egg coat. The extracellular ubiquitin–proteasome system, the astacin-like metalloproteases, and the trypsin-like proteases play key roles in this process in ascidians. In the present review, we summarize our current understanding and perspectives on gamete recognition and egg coat lysins in ascidians and consider the general mechanisms of fertilization in animals and plants.
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Chen Z, Zhang Z, Wang Z, Zhang Z, Wang Q, Pan Y. Heterozygosity and homozygosity regions affect reproductive success and the loss of reproduction: a case study with litter traits in pigs. Comput Struct Biotechnol J 2022; 20:4060-4071. [PMID: 35983229 PMCID: PMC9364102 DOI: 10.1016/j.csbj.2022.07.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/23/2022] Open
Abstract
Runs of heterozygosity (ROHet) and homozygosity (ROH) harbor useful information related to traits of interest. There is a lack of investigating the effect of ROHet and ROH on reproductive success and the loss of reproduction in mammals. Here, we detected and characterized the ROHet and ROH patterns in the genomes of Chinese indigenous pigs (i.e., Jinhua, Chun’an, Longyou Black, and Shengxian Spotted pigs), revealing the similar genetic characteristics of indigenous pigs. Later, we highlighted the underlying litter traits-related ROHet and ROH using association analysis with linear model in these four indigenous pig breeds. To pinpoint the promising candidate genes associated with litter traits, we further in-depth explore the selection patterns of other five pig breeds (i.e., Erhualian, Meishan, Minzhu, Rongchang, and Diqing pigs) with different levels of reproduction performance at the underlying litter traits-related ROHet and ROH using FST and genetic diversity ratio. Then, we identified a set of known and novel candidate genes associated with reproductive performance in pigs. For the novel candidate genes (i.e., CCDC91, SASH1, SAMD5, MACF1, MFSD2A, EPC2, and MBD5), we obtained public available datasets and performed multi-omics analyses integrating transcriptome-wide association studies and comparative single-cell RNA-seq analyses to uncover the roles of them in mammalian reproductive performance. The genes have not been widely reported to be fertility-related genes and can be complementally considered as prior biological information to modify genomic selections models that benefits pig genetic improvement of litter traits. Besides, our findings provide new insights into the function of ROHet and ROH in mammals.
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Hypothalamic and pituitary transcriptome profiling using RNA-sequencing in high-yielding and low-yielding laying hens. Sci Rep 2019; 9:10285. [PMID: 31311989 PMCID: PMC6635495 DOI: 10.1038/s41598-019-46807-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 07/05/2019] [Indexed: 12/21/2022] Open
Abstract
The reproductive physiology and laying performance of laying hens are regulated by the hypothalamus and pituitary. To understand the mechanism of egg laying regulation, we sequenced and analysed the hypothalamus and pituitary expression profiles in high- and low-yielding laying Chinese Dagu Chickens (CDC) using RNA-seq. More than 46 million clean reads and 24,873 tentative genes were obtained using the Gallus gallus genome as a reference. Transcriptome analysis in hypothalamus and pituitary revealed seven and 39 differentially expressed genes (DEGs) between high- and low-yielding CDC hens, respectively. A total of 24 and 22 DEGs were up-regulated and down-regulated, respectively, and 13 novel genes were identified. Functional annotation and pathway enrichment analysis showed that DEGs in the hypothalamus were mainly enriched in glycosaminoglycan biosynthesis. DEGs significantly enriched in the pituitary primarily affected the extracellular matrix, the protein extracellular matrix, and the extracellular space. Pathways involving phenylalanine metabolism, 2-oxocarboxylic acid metabolism, the glycosphingolipid biosynthesis-ganglion series, and local adhesion were significantly enriched in the pituitary. Eight DEGs, PRDX6, TRIB2, OVCH2, CFD, Peptidase M20, SLC7A10, and two other amino acid transporters, are involved in the metabolism and transport of amino acids. To our knowledge, this is the first study comparing the hypothalamus and pituitary transcriptomes of high- and low-yielding laying hens. Our findings suggest that putative differences in gene expression can provide a base for further research in this field. Moreover, we identified increased expression of genes involved in amino acid metabolism, glycosaminoglycan biosynthesis, and oestrogen negative feedback systems in low-yielding laying hens, highlighting their potential as biomarkers of egg production.
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Álvarez-Campos P, Kenny NJ, Verdes A, Fernández R, Novo M, Giribet G, Riesgo A. Delegating Sex: Differential Gene Expression in Stolonizing Syllids Uncovers the Hormonal Control of Reproduction. Genome Biol Evol 2019; 11:295-318. [PMID: 30535381 PMCID: PMC6350857 DOI: 10.1093/gbe/evy265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2018] [Indexed: 12/31/2022] Open
Abstract
Stolonization in syllid annelids is a unique mode of reproduction among animals. During the breeding season, a structure resembling the adult but containing only gametes, called stolon, is formed generally at the posterior end of the animal. When stolons mature, they detach from the adult and gametes are released into the water column. The process is synchronized within each species, and it has been reported to be under environmental and endogenous control, probably via endocrine regulation. To further understand reproduction in syllids and to elucidate the molecular toolkit underlying stolonization, we generated Illumina RNA-seq data from different tissues of reproductive and nonreproductive individuals of Syllis magdalena and characterized gene expression during the stolonization process. Several genes involved in gametogenesis (ovochymase, vitellogenin, testis-specific serine/threonine-kinase), immune response (complement receptor 2), neuronal development (tyrosine-protein kinase Src42A), cell proliferation (alpha-1D adrenergic receptor), and steroid metabolism (hydroxysteroid dehydrogenase 2) were found differentially expressed in the different tissues and conditions analyzed. In addition, our findings suggest that several neurohormones, such as methyl farnesoate, dopamine, and serotonin, might trigger stolon formation, the correct maturation of gametes and the detachment of stolons when gametogenesis ends. The process seems to be under circadian control, as indicated by the expression patterns of r-opsins. Overall, our results shed light into the genes that orchestrate the onset of gamete formation and improve our understanding of how some hormones, previously reported to be involved in reproduction and metamorphosis processes in other invertebrates, seem to also regulate reproduction via stolonization.
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Affiliation(s)
- Patricia Álvarez-Campos
- Facultad de Ciencias, Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Spain
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
- Department of Biological & Medical Sciences, Oxford Brookes University, Headington Campus, Gipsy Lane, Oxford, United Kingdom
| | - Nathan J Kenny
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
| | - Aida Verdes
- Facultad de Ciencias, Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Spain
- Department of Biology, The Graduate Center, City University of New York
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
| | - Rosa Fernández
- Bioinformatics & Genomics Unit, Center for Genomic Regulation, Barcelona, Spain
| | - Marta Novo
- Facultad de Biología, Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Spain
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Ana Riesgo
- Department of Biology, The Graduate Center, City University of New York
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Bakhtiarizadeh MR, Rahimi M, Mohammadi-Sangcheshmeh A, Shariati J V, Salami SA. PrESOgenesis: A two-layer multi-label predictor for identifying fertility-related proteins using support vector machine and pseudo amino acid composition approach. Sci Rep 2018; 8:9025. [PMID: 29899414 PMCID: PMC5998058 DOI: 10.1038/s41598-018-27338-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/25/2018] [Indexed: 11/08/2022] Open
Abstract
Successful spermatogenesis and oogenesis are the two genetically independent processes preceding embryo development. To date, several fertility-related proteins have been described in mammalian species. Nevertheless, further studies are required to discover more proteins associated with the development of germ cells and embryogenesis in order to shed more light on the processes. This work builds on our previous software (OOgenesis_Pred), mainly focusing on algorithms beyond what was previously done, in particular new fertility-related proteins and their classes (embryogenesis, spermatogenesis and oogenesis) based on the support vector machine according to the concept of Chou's pseudo-amino acid composition features. The results of five-fold cross validation, as well as the independent test demonstrated that this method is capable of predicting the fertility-related proteins and their classes with accuracy of more than 80%. Moreover, by using feature selection methods, important properties of fertility-related proteins were identified that allowed for their accurate classification. Based on the proposed method, a two-layer classifier software, named as "PrESOgenesis" ( https://github.com/mrb20045/PrESOgenesis ) was developed. The tool identified a query sequence (protein or transcript) as fertility or non-fertility-related protein at the first layer and then classified the predicted fertility-related protein into different classes of embryogenesis, spermatogenesis or oogenesis at the second layer.
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Affiliation(s)
| | - Maryam Rahimi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | | | - Vahid Shariati J
- Genome Center, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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Varade J, Wang N, Lim CK, Zhang T, Zhang Y, Liu X, Piehl F, Matell R, Cao H, Xu X, Hammarström L. Novel genetic loci associated HLA-B*08:01 positive myasthenia gravis. J Autoimmun 2018; 88:43-49. [DOI: 10.1016/j.jaut.2017.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/02/2017] [Accepted: 10/05/2017] [Indexed: 01/16/2023]
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OOgenesis_Pred: A sequence-based method for predicting oogenesis proteins by six different modes of Chou's pseudo amino acid composition. J Theor Biol 2017; 414:128-136. [DOI: 10.1016/j.jtbi.2016.11.028] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 11/25/2016] [Accepted: 11/29/2016] [Indexed: 12/22/2022]
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