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Bakoev S, Getmantseva L, Kolosova M, Bakoev F, Kolosov A, Romanets E, Shevtsova V, Romanets T, Kolosov Y, Usatov A. Identifying Significant SNPs of the Total Number of Piglets Born and Their Relationship with Leg Bumps in Pigs. BIOLOGY 2024; 13:1034. [PMID: 39765701 PMCID: PMC11673605 DOI: 10.3390/biology13121034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 11/26/2024] [Accepted: 12/09/2024] [Indexed: 01/11/2025]
Abstract
The aim of this study was to identify genetic variants and pathways associated with the total number of piglets born and to investigate the potential negative consequences of the intensive selection for reproductive traits, particularly the formation of bumps on the legs of pigs. We used genome-wide association analysis and methods for identifying selection signatures. As a result, 47 SNPs were identified, localized in genes that play a significant role during sow pregnancy. These genes are involved in follicle growth and development (SGC), early embryonic development (CCDC3, LRRC8C, LRFN3, TNFRSF19), endometrial receptivity and implantation (NEBL), placentation, and embryonic development (ESRRG, GHRHR, TUSC3, NBAS). Several genes are associated with disorders of the nervous system and brain development (BCL11B, CDNF, ULK4, CC2D2A, KCNK2). Additionally, six SNPs are associated with the formation of bumps on the legs of pigs. These variants include intronic variants in the CCDC3, ULK4, and MINDY4 genes, as well as intergenic variants, regulatory region variants, and variants in the exons of non-coding transcripts. The results suggest important biological pathways and genetic variants associated with sow fertility and highlight the potential negative impacts on the health and physical condition of pigs.
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Affiliation(s)
- Siroj Bakoev
- Biotechnological Faculty, Don State Agrarian University, Persianovsky 346493, Russia; (S.B.); (M.K.); (F.B.); (E.R.); (T.R.); (Y.K.)
| | - Lyubov Getmantseva
- Biotechnological Faculty, Don State Agrarian University, Persianovsky 346493, Russia; (S.B.); (M.K.); (F.B.); (E.R.); (T.R.); (Y.K.)
| | - Maria Kolosova
- Biotechnological Faculty, Don State Agrarian University, Persianovsky 346493, Russia; (S.B.); (M.K.); (F.B.); (E.R.); (T.R.); (Y.K.)
| | - Faridun Bakoev
- Biotechnological Faculty, Don State Agrarian University, Persianovsky 346493, Russia; (S.B.); (M.K.); (F.B.); (E.R.); (T.R.); (Y.K.)
| | - Anatoly Kolosov
- All Russian Research Institute of Animal Breeding, Lesnye Polyany 141212, Russia;
| | - Elena Romanets
- Biotechnological Faculty, Don State Agrarian University, Persianovsky 346493, Russia; (S.B.); (M.K.); (F.B.); (E.R.); (T.R.); (Y.K.)
| | - Varvara Shevtsova
- Southern Scientific Center Russian Academy of Sciences, Rostov-on-Don 344006, Russia;
| | - Timofey Romanets
- Biotechnological Faculty, Don State Agrarian University, Persianovsky 346493, Russia; (S.B.); (M.K.); (F.B.); (E.R.); (T.R.); (Y.K.)
| | - Yury Kolosov
- Biotechnological Faculty, Don State Agrarian University, Persianovsky 346493, Russia; (S.B.); (M.K.); (F.B.); (E.R.); (T.R.); (Y.K.)
| | - Alexander Usatov
- Academy of Biology and Biotechnology Named After D.I. Ivanovsky, Southern Federal University, Rostov-on-Don 344006, Russia;
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Zhang H, Yang M, Zhang J, Li L, Guan T, Liu J, Gong X, Yang F, Shen S, Liu M, Han Y. The putative protein kinase Stk36 is essential for ciliogenesis and CSF flow by associating with Ulk4. FASEB J 2023; 37:e23138. [PMID: 37584603 DOI: 10.1096/fj.202300481r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/28/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
Motile cilia lining on the ependymal cells are crucial for cerebrospinal fluid (CSF) flow and its dysfunction is often associated with hydrocephalus. Unc51-like-kinase 4 (Ulk4) was previously linked to CSF flow and motile ciliogenesis in mice, as the hypomorph mutant of Ulk4 (Ulk4tm1a/tm1a ) developed hydrocephalic phenotype resulted from defective ciliogenesis and disturbed ciliary motility, while the underling mechanism is largely obscure. Here, we report that serine/threonine kinase 36 (STK36), a paralog of ULK4, directly interacts with ULK4 and this was demonstrated by yeast two-hybrid (Y2H) in yeast and coimmunoprecipitation (co-IP) assays in HEK293T cells, respectively. The interaction region was confined to their respective N-terminal kinase domain. The hypomorph mutant of Stk36 (Stk36tmE4-/- ) also developed progressive hydrocephalus postnatally and dysfunctional CSF flow, with multiple defects of motile cilia, including reduced ciliary number, disorganized ciliary orientation, defected axonemal structure and inconsistent base body (BB) orientation. Stk36tmE4-/- also disturbed the expression of Foxj1 transcription factor and a range of other ciliogenesis-related genes. All these morphological changes, motile cilia defects and transcriptional dysregulation in the Stk36tmE4-/- are practically copied from that in Ulk4tm1a/tm1a mice. Taken together, we conclude that both Stk36 and Ulk4 are crucial for CSF flow, they cooperate by direct binding with their kinase domain to regulate the Foxj1 transcription factor pathways for ciliogenesis and cilia function, not limited to CSF flow. The underlying molecular mechanism probably conserved in evolution and could be extended to other metazoans.
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Affiliation(s)
- Hongye Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Meimei Yang
- Regenerative Medicine Institute, School of Medicine, University of Galway, Galway, Ireland
| | - Jianhua Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Li Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Tianyuan Guan
- Department of Neurology, Hebei General Hospital, Shijiazhuang, China
| | - Jiaxin Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xuanwei Gong
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Fan Yang
- Department of Neurology, Hebei Children's Hospital, Shijiazhuang, China
| | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, University of Galway, Galway, Ireland
| | - Min Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yongfeng Han
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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Huang L, Tang J, Lin L, Wang R, Chen F, Wei Y, Si Y, Fu W. Association of genetic variants in ULK4 with the age of first onset of type B aortic dissection. Front Genet 2022; 13:956866. [PMID: 36118886 PMCID: PMC9478570 DOI: 10.3389/fgene.2022.956866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/28/2022] [Indexed: 11/30/2022] Open
Abstract
Background: The association between autophagy, structural alterations of the aortic wall, and endothelial dysfunction in humans has yet to be fully elucidated. The family of ULK (UNC51-like) enzymes plays critical roles in autophagy and development. This study aimed to evaluate the association between ULK gene family members and patient age of first type B aortic dissection (TBAD) onset. Methods: The genotype data in a TBAD cohort from China and the related summary-level datasets were analyzed. We applied the sequence kernel association test (SKAT) to test the association between single-nucleotide polymorphisms (SNPs) and age of first onset of TBAD controlling for gender, hypertension, and renal function. Next, we performed a 2-sample Mendelian randomization (MR) to explore the potential causal relationship between ULK4 and early onset of TBAD at the level of gene expression coupled with DNA methylation with genetic variants as instrumental variables. Results: A total of 159 TBAD patients with 1,180,097 SNPs were included. Concerning the association between the ULK gene family and the age of first onset of the TBAD, only ULK4 was found to be significant according to SKAT analysis (q-FDR = 0.0088). From 2-sample MR, the high level of ULK4 gene expression was related to a later age of first onset of TBAD (β = 4.58, p = 0.0214). Conclusion: This is the first study of the ULK gene family in TBAD, regarding the association with the first onset age. We demonstrated that the ULK4 gene is associated with the time of onset of TBAD based on both the SKAT and 2-sample MR analyses.
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Affiliation(s)
- Lihong Huang
- Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Biostatistics, Zhongshan Hospital, Fudan University, Shanghai, China
- Clinical Research Unit, Institute of Clinical Science, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Jiaqi Tang
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lijuan Lin
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ruihan Wang
- Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Feng Chen
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yongyue Wei
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yi Si
- Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Yi Si, ; Weiguo Fu,
| | - Weiguo Fu
- Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Yi Si, ; Weiguo Fu,
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Abstract
Stroke is the second leading cause of death worldwide and a complex, heterogeneous condition. In this review, we provide an overview of the current knowledge on monogenic and multifactorial forms of stroke, highlighting recent insight into the continuum between these. We describe how, in recent years, large-scale genome-wide association studies have enabled major progress in deciphering the genetic basis for stroke and its subtypes, although more research is needed to interpret these findings. We cover the potential of stroke genetics to reveal novel pathophysiological processes underlying stroke, to accelerate the discovery of new therapeutic approaches, and to identify individuals in the population who are at high risk of stroke and could be targeted for tailored preventative interventions.
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Affiliation(s)
- Stéphanie Debette
- Bordeaux Population Health Research Center, Inserm U1219, University of Bordeaux, France (S.D.).,Department of Neurology, Bordeaux University Hospital, Institute for Neurodegenerative Diseases, France (S.D.)
| | - Hugh S Markus
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, United Kingdom (H.S.M.)
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Luo S, Zheng N, Lang B. ULK4 in Neurodevelopmental and Neuropsychiatric Disorders. Front Cell Dev Biol 2022; 10:873706. [PMID: 35493088 PMCID: PMC9039724 DOI: 10.3389/fcell.2022.873706] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/29/2022] [Indexed: 11/21/2022] Open
Abstract
The gene Unc51-like kinase 4 (ULK4) belongs to the Unc-51-like serine/threonine kinase family and is assumed to encode a pseudokinase with unclear function. Recently, emerging evidence has suggested that ULK4 may be etiologically involved in a spectrum of neuropsychiatric disorders including schizophrenia, but the underlying mechanism remains unaddressed. Here, we summarize the key findings of the structure and function of the ULK4 protein to provide comprehensive insights to better understand ULK4-related neurodevelopmental and neuropsychiatric disorders and to aid in the development of a ULK4-based therapeutic strategy.
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Affiliation(s)
- Shilin Luo
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Provincial Engineering Research Center of Translational Medicine and Innovative Drug, Changsha, China
| | - Nanxi Zheng
- Department of Psychiatry, National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Nanxi Zheng, ; Bing Lang,
| | - Bing Lang
- Department of Psychiatry, National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Nanxi Zheng, ; Bing Lang,
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Alotaibi RN, Howe BJ, Moreno Uribe LM, Sanchez C, Deleyiannis FW, Padilla C, Poletta FA, Orioli IM, Buxó CJ, Wehby GL, Vieira AR, Murray J, Valencia-Ramírez C, Restrepo Muñeton CP, Long RE, Shaffer JR, Reis SE, Weinberg SM, Neiswanger K, McNeil DW, Marazita ML. Genetic Analyses of Enamel Hypoplasia in Multiethnic Cohorts. Hum Hered 2022; 87:000522642. [PMID: 35172313 PMCID: PMC9378791 DOI: 10.1159/000522642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/09/2022] [Indexed: 11/19/2022] Open
Abstract
Enamel hypoplasia causes reduction in the thickness of affected enamel and is one of the most common dental anomalies. This defect is caused by environmental and/or genetic factors that interfere with tooth formation, emphasizing the importance of investigating enamel hypoplasia on an epidemiological and genetic level. A genome-wide association of enamel hypoplasia was performed in multiple cohorts, overall comprising 7,159 individuals ranging in age from 7-82 years. Mixed-models were used to test for genetic association while simultaneously accounting for relatedness and genetic population structure. Meta-analysis was then performed. More than 5 million single-nucleotide polymorphisms were tested in individual cohorts. Analyses of the individual cohorts and meta-analysis identified association signals close to genome-wide significance (P < 510-8), and many suggestive association signals (510-8 < P < 510-6) near genes with plausible roles in tooth/enamel development. The strongest association signal (P = 1.5710-9) was observed near BMP2K in one of the individual cohorts. Additional suggestive signals were observed near genes with plausible roles in tooth development in the meta-analysis, such as SLC4A4 which can influence enamel hypoplasia. Additional human genetic studies are needed to replicate these results and functional studies in model systems are needed to validate our findings.
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Affiliation(s)
- Rasha N. Alotaibi
- Dental Health Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brian J. Howe
- Department of Family Dentistry, College of Dentistry, University of Iowa, Iowa City, Iowa, USA
| | - Lina M. Moreno Uribe
- The Iowa Institute for Oral Health Research, College of Dentistry, University of Iowa, Iowa City, Iowa, USA
- Department of Orthodontics, School of Dentistry, University of Iowa, Iowa City, Iowa, USA
| | - Carla Sanchez
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Carmencita Padilla
- Department of Pediatrics, College of Medicine, University of the Philippines, Manila, Philippines
| | - Fernando A. Poletta
- ECLAMC/INAGEMP CEMIC, Dirección de Investigación A. Galván, Buenos Aires, Argentina
| | - Ieda M. Orioli
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carmen J. Buxó
- School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - George L. Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, Iowa, USA
| | - Alexandre R. Vieira
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jeffrey Murray
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | | | | | - Ross E. Long
- Lancaster Cleft Palate Clinic, Lancaster, Pennsylvania, USA
| | - John R. Shaffer
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Steven E. Reis
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Seth M. Weinberg
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Katherine Neiswanger
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daniel W. McNeil
- Department of Psychology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, West Virginia, USA
- Department of Dental Practice and Rural Health, School of Dentistry, West Virginia University, Morgantown, West Virginia, USA
| | - Mary L. Marazita
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Luo W, Yang J. Schizophrenia predisposition gene Unc-51-like kinase 4 for the improvement of cerebral ischemia/reperfusion injury. Mol Biol Rep 2022; 49:2933-2943. [PMID: 35083612 DOI: 10.1007/s11033-021-07108-z] [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: 09/08/2021] [Accepted: 12/17/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Cerebral ischemia/reperfusion injury (CIRI) has complex pathogenesis, and inhibiting apoptosis and supporting neural progenitor proliferation are extremely beneficial strategies for treating CIRI. Unc-51-like kinase 4 (ULK4), a susceptibility gene for schizophrenia, promotes neural progenitors proliferation. The phosphatidylinositol 3-kinase (PI3K) pathway plays a critical role in CIRI via inhibition of apoptosis. Therefore, the relationship among ULK4, the PI3K pathway, and apoptosis in the context of CIRI has attracted our great interest. METHODS AND RESULTS Primary cortical neurons were subjected to oxygen-glucose deprivation/reperfusion (OGD/R), and rats were subjected to middle cerebral artery occlusion/reperfusion (MCAO/R). Transfection of the ULK4-overexpression lentivirus was performed alone or in combination with PI3K inhibitor treatment. Here, we revealed that ULK4 was poorly expressed in the cortex in MCAO/R rats and OGD/R-treated primary cortical neurons, ULK4 overexpression inhibited apoptosis, and reduced neurological deficit scores, cerebral infarct volume, and histopathological damage. Moreover, ULK4 overexpression increased PI3K expression and the p-protein kinase B/AKT and p-glycogen synthase kinase 3 beta (GSK3β)/GSK3β ratios, and inhibited apoptosis, while a PI3K inhibitor reversed the effects of ULK4 overexpression on CIRI. CONCLUSIONS ULK4 protects against CIRI, and the underlying mechanism involves PI3K pathway activation which in turn inhibits apoptosis.
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Affiliation(s)
- Wen Luo
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China.,Department of Clinical Pharmacy, The Third Hospital of Mianyang/Sichuan Mental Health Center, Mianyang, 621000, China
| | - Junqing Yang
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China.
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Abstract
Cerebral small vessel disease (cSVD) is a leading cause of ischaemic and haemorrhagic stroke and a major contributor to dementia. Covert cSVD, which is detectable with brain MRI but does not manifest as clinical stroke, is highly prevalent in the general population, particularly with increasing age. Advances in technologies and collaborative work have led to substantial progress in the identification of common genetic variants that are associated with cSVD-related stroke (ischaemic and haemorrhagic) and MRI-defined covert cSVD. In this Review, we provide an overview of collaborative studies - mostly genome-wide association studies (GWAS) - that have identified >50 independent genetic loci associated with the risk of cSVD. We describe how these associations have provided novel insights into the biological mechanisms involved in cSVD, revealed patterns of shared genetic variation across cSVD traits, and shed new light on the continuum between rare, monogenic and common, multifactorial cSVD. We consider how GWAS summary statistics have been leveraged for Mendelian randomization studies to explore causal pathways in cSVD and provide genetic evidence for drug effects, and how the combination of findings from GWAS with gene expression resources and drug target databases has enabled identification of putative causal genes and provided proof-of-concept for drug repositioning potential. We also discuss opportunities for polygenic risk prediction, multi-ancestry approaches and integration with other omics data.
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Abashkin DA, Kurishev AO, Karpov DS, Golimbet VE. Cellular Models in Schizophrenia Research. Int J Mol Sci 2021; 22:ijms22168518. [PMID: 34445221 PMCID: PMC8395162 DOI: 10.3390/ijms22168518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia (SZ) is a prevalent functional psychosis characterized by clinical behavioural symptoms and underlying abnormalities in brain function. Genome-wide association studies (GWAS) of schizophrenia have revealed many loci that do not directly identify processes disturbed in the disease. For this reason, the development of cellular models containing SZ-associated variations has become a focus in the post-GWAS research era. The application of revolutionary clustered regularly interspaced palindromic repeats CRISPR/Cas9 gene-editing tools, along with recently developed technologies for cultivating brain organoids in vitro, have opened new perspectives for the construction of these models. In general, cellular models are intended to unravel particular biological phenomena. They can provide the missing link between schizophrenia-related phenotypic features (such as transcriptional dysregulation, oxidative stress and synaptic dysregulation) and data from pathomorphological, electrophysiological and behavioural studies. The objectives of this review are the systematization and classification of cellular models of schizophrenia, based on their complexity and validity for understanding schizophrenia-related phenotypes.
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Affiliation(s)
- Dmitrii A. Abashkin
- Mental Health Research Center, Clinical Genetics Laboratory, Kashirskoe Sh. 34, 115522 Moscow, Russia; (D.A.A.); (A.O.K.); (D.S.K.)
| | - Artemii O. Kurishev
- Mental Health Research Center, Clinical Genetics Laboratory, Kashirskoe Sh. 34, 115522 Moscow, Russia; (D.A.A.); (A.O.K.); (D.S.K.)
| | - Dmitry S. Karpov
- Mental Health Research Center, Clinical Genetics Laboratory, Kashirskoe Sh. 34, 115522 Moscow, Russia; (D.A.A.); (A.O.K.); (D.S.K.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, 119991 Moscow, Russia
| | - Vera E. Golimbet
- Mental Health Research Center, Clinical Genetics Laboratory, Kashirskoe Sh. 34, 115522 Moscow, Russia; (D.A.A.); (A.O.K.); (D.S.K.)
- Correspondence:
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Traylor M, Persyn E, Tomppo L, Klasson S, Abedi V, Bakker MK, Torres N, Li L, Bell S, Rutten-Jacobs L, Tozer DJ, Griessenauer CJ, Zhang Y, Pedersen A, Sharma P, Jimenez-Conde J, Rundek T, Grewal RP, Lindgren A, Meschia JF, Salomaa V, Havulinna A, Kourkoulis C, Crawford K, Marini S, Mitchell BD, Kittner SJ, Rosand J, Dichgans M, Jern C, Strbian D, Fernandez-Cadenas I, Zand R, Ruigrok Y, Rost N, Lemmens R, Rothwell PM, Anderson CD, Wardlaw J, Lewis CM, Markus HS. Genetic basis of lacunar stroke: a pooled analysis of individual patient data and genome-wide association studies. Lancet Neurol 2021; 20:351-361. [PMID: 33773637 PMCID: PMC8062914 DOI: 10.1016/s1474-4422(21)00031-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/06/2020] [Accepted: 01/15/2021] [Indexed: 01/07/2023]
Abstract
BACKGROUND The genetic basis of lacunar stroke is poorly understood, with a single locus on 16q24 identified to date. We sought to identify novel associations and provide mechanistic insights into the disease. METHODS We did a pooled analysis of data from newly recruited patients with an MRI-confirmed diagnosis of lacunar stroke and existing genome-wide association studies (GWAS). Patients were recruited from hospitals in the UK as part of the UK DNA Lacunar Stroke studies 1 and 2 and from collaborators within the International Stroke Genetics Consortium. Cases and controls were stratified by ancestry and two meta-analyses were done: a European ancestry analysis, and a transethnic analysis that included all ancestry groups. We also did a multi-trait analysis of GWAS, in a joint analysis with a study of cerebral white matter hyperintensities (an aetiologically related radiological trait), to find additional genetic associations. We did a transcriptome-wide association study (TWAS) to detect genes for which expression is associated with lacunar stroke; identified significantly enriched pathways using multi-marker analysis of genomic annotation; and evaluated cardiovascular risk factors causally associated with the disease using mendelian randomisation. FINDINGS Our meta-analysis comprised studies from Europe, the USA, and Australia, including 7338 cases and 254 798 controls, of which 2987 cases (matched with 29 540 controls) were confirmed using MRI. Five loci (ICA1L-WDR12-CARF-NBEAL1, ULK4, SPI1-SLC39A13-PSMC3-RAPSN, ZCCHC14, ZBTB14-EPB41L3) were found to be associated with lacunar stroke in the European or transethnic meta-analyses. A further seven loci (SLC25A44-PMF1-BGLAP, LOX-ZNF474-LOC100505841, FOXF2-FOXQ1, VTA1-GPR126, SH3PXD2A, HTRA1-ARMS2, COL4A2) were found to be associated in the multi-trait analysis with cerebral white matter hyperintensities (n=42 310). Two of the identified loci contain genes (COL4A2 and HTRA1) that are involved in monogenic lacunar stroke. The TWAS identified associations between the expression of six genes (SCL25A44, ULK4, CARF, FAM117B, ICA1L, NBEAL1) and lacunar stroke. Pathway analyses implicated disruption of the extracellular matrix, phosphatidylinositol 5 phosphate binding, and roundabout binding (false discovery rate <0·05). Mendelian randomisation analyses identified positive associations of elevated blood pressure, history of smoking, and type 2 diabetes with lacunar stroke. INTERPRETATION Lacunar stroke has a substantial heritable component, with 12 loci now identified that could represent future treatment targets. These loci provide insights into lacunar stroke pathogenesis, highlighting disruption of the vascular extracellular matrix (COL4A2, LOX, SH3PXD2A, GPR126, HTRA1), pericyte differentiation (FOXF2, GPR126), TGF-β signalling (HTRA1), and myelination (ULK4, GPR126) in disease risk. FUNDING British Heart Foundation.
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Affiliation(s)
- Matthew Traylor
- Clinical Pharmacology and The Barts Heart Centre and NIHR Barts Biomedical Research Centre, Barts Health NHS Trust, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Elodie Persyn
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Liisa Tomppo
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Sofia Klasson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Vida Abedi
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Health System, Danville, PA, USA
| | - Mark K Bakker
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Netherlands
| | - Nuria Torres
- Stroke Pharmacogenomics and Genetics, Sant Pau Institute of Research, Hospital de la Santa Creu I Sant Pau, Barcelona, Spain
| | - Linxin Li
- Centre for the Prevention of Stroke and Dementia, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
| | - Steven Bell
- Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Loes Rutten-Jacobs
- Product Development Personalized Health Care, F Hoffmann-La Roche, Basel, Switzerland
| | - Daniel J Tozer
- Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Christoph J Griessenauer
- Neuroscience Institute, Geisinger Health System, Danville, PA, USA; Institute of Neurointervention, Paracelsus Medical University, Salzburg, Austria
| | - Yanfei Zhang
- Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Annie Pedersen
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Pankaj Sharma
- Institute of Cardiovascular Research, Royal Holloway University of London, London, UK
| | - Jordi Jimenez-Conde
- Neurovascular Research Group, Department of Neurology of Hospital del Mar-IMIM (Institut Hospital del Mar d'Investigacions Mediques), Universitat Autonoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Tatjana Rundek
- Evelyn F McKnight Brain Institute, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Raji P Grewal
- Neuroscience Institute, Saint Francis Medical Center, School of Health and Medical Sciences, Seton Hall University, South Orange, NJ, USA
| | - Arne Lindgren
- Department of Neurology, Skane University Hospital, Lund, Sweden; Department of Clinical Sciences Lund, Neurology, Lund University, Lund, Sweden
| | | | - Veikko Salomaa
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aki Havulinna
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM HiLIFE), Helsinki, Finland
| | - Christina Kourkoulis
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Henry and Allison McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, USA; Program in Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Katherine Crawford
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sandro Marini
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Steven J Kittner
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Jonathan Rosand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Henry and Allison McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Program in Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), LMU Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Christina Jern
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Daniel Strbian
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland; Clinical Neurosciences, University of Helsinki, Helsinki, Finland
| | - Israel Fernandez-Cadenas
- Stroke Pharmacogenomics and Genetics, Sant Pau Institute of Research, Hospital de la Santa Creu I Sant Pau, Barcelona, Spain; Neurovascular Research Laboratory and Neurovascular Unit, Institut de Recerca, Hospital Vall d'Hebron, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Ramin Zand
- Neuroscience Institute, Geisinger Health System, Danville, PA, USA
| | - Ynte Ruigrok
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Netherlands
| | - Natalia Rost
- J Philip Kistler Stroke Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Robin Lemmens
- Experimental Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium; VIB Center for Brain & Disease Research, Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Peter M Rothwell
- Centre for the Prevention of Stroke and Dementia, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
| | - Christopher D Anderson
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Henry and Allison McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Program in Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Joanna Wardlaw
- Centre for Clinical Brain Sciences, UK Dementia Research Institute and Row Fogo Centre for Research into the Ageing Brain, University of Edinburgh, Edinburgh, UK
| | - Cathryn M Lewis
- Department of Medical and Molecular Genetics, King's College London, London, UK; Social, Genetic, and Developmental Psychiatry Centre, King's College London, London, UK
| | - Hugh S Markus
- Clinical Neurosciences, University of Cambridge, Cambridge, UK.
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11
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Xi JJ, Yang GH, Liu YN, Qiu JJ, Gong XL, Yan JB, Zeng F. Genome-wide hypermethylation is closely associated with abnormal expression of genes involved in neural development in induced pluripotent stem cells derived from a Down syndrome mouse model. Cell Biol Int 2021; 45:1383-1392. [PMID: 33527608 DOI: 10.1002/cbin.11560] [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: 01/23/2020] [Revised: 06/05/2020] [Accepted: 06/13/2020] [Indexed: 11/10/2022]
Abstract
Mental retardation is the main clinical manifestation of Down syndrome (DS), and neural abnormalities occur during the early embryonic period and continue throughout life. Tc1, a model mouse for DS, carries the majority part of the human chromosome 21 and has multiple neuropathy phenotypes similar to patients with DS. To explore the mechanism of early neural abnormalities of Tc1 mouse, induced pluripotent stem (iPS) cells from Tc1 mice were obtained, and genome-wide gene expression and methylation analysis were performed for Tc1 and wild-type iPS cells. Our results showed hypermethylation profiles for Tc1 iPS cells, and the abnormal genes were shown to be related to neurodevelopment and distributed on multiple chromosomes. In addition, important genes involved in neurogenesis and neurodevelopment were shown to be downregulated in Tc1 iPS cells. In short, our study indicated that genome-wide hypermethylation leads to the disordered expression of genes associated with neurodevelopment in Tc1 mice during early development. Overall, our work provided a useful reference for the study of the molecular mechanism of nervous system abnormalities in DS.
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Affiliation(s)
- Jiao-Jiao Xi
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Guan-Heng Yang
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Yan-Na Liu
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Jia-Jun Qiu
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiu-Li Gong
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Jing-Bin Yan
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Fanyi Zeng
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China.,Department of Histoembryology, Genetics and Development, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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12
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He Q, Li Z, Yin J, Li Y, Yin Y, Lei X, Zhu W. Prognostic Significance of Autophagy-Relevant Gene Markers in Colorectal Cancer. Front Oncol 2021; 11:566539. [PMID: 33937013 PMCID: PMC8081889 DOI: 10.3389/fonc.2021.566539] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 03/22/2021] [Indexed: 12/22/2022] Open
Abstract
Background Colorectal cancer (CRC) is a common malignant solid tumor with an extremely low survival rate after relapse. Previous investigations have shown that autophagy possesses a crucial function in tumors. However, there is no consensus on the value of autophagy-associated genes in predicting the prognosis of CRC patients. This work screens autophagy-related markers and signaling pathways that may participate in the development of CRC, and establishes a prognostic model of CRC based on autophagy-associated genes. Methods Gene transcripts from the TCGA database and autophagy-associated gene data from the GeneCards database were used to obtain expression levels of autophagy-associated genes, followed by Wilcox tests to screen for autophagy-related differentially expressed genes. Then, 11 key autophagy-associated genes were identified through univariate and multivariate Cox proportional hazard regression analysis and used to establish prognostic models. Additionally, immunohistochemical and CRC cell line data were used to evaluate the results of our three autophagy-associated genes EPHB2, NOL3, and SNAI1 in TCGA. Based on the multivariate Cox analysis, risk scores were calculated and used to classify samples into high-risk and low-risk groups. Kaplan-Meier survival analysis, risk profiling, and independent prognosis analysis were carried out. Receiver operating characteristic analysis was performed to estimate the specificity and sensitivity of the prognostic model. Finally, GSEA, GO, and KEGG analysis were performed to identify the relevant signaling pathways. Results A total of 301 autophagy-related genes were differentially expressed in CRC. The areas under the 1-year, 3-year, and 5-year receiver operating characteristic curves of the autophagy-based prognostic model for CRC were 0.764, 0.751, and 0.729, respectively. GSEA analysis of the model showed significant enrichment in several tumor-relevant pathways and cellular protective biological processes. The expression of EPHB2, IL-13, MAP2, RPN2, and TRAF5 was correlated with microsatellite instability (MSI), while the expression of IL-13, RPN2, and TRAF5 was related to tumor mutation burden (TMB). GO analysis showed that the 11 target autophagy genes were chiefly enriched in mRNA processing, RNA splicing, and regulation of the mRNA metabolic process. KEGG analysis showed enrichment mainly in spliceosomes. We constructed a prognostic risk assessment model based on 11 autophagy-related genes in CRC. Conclusion A prognostic risk assessment model based on 11 autophagy-associated genes was constructed in CRC. The new model suggests directions and ideas for evaluating prognosis and provides guidance to choose better treatment strategies for CRC.
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Affiliation(s)
- Qinglian He
- Department of Pathology, Guangdong Medical University, Dongguan, China
| | - Ziqi Li
- Department of Pathology, Guangdong Medical University, Dongguan, China
| | - Jinbao Yin
- Department of Pathology, Guangdong Medical University, Dongguan, China
| | - Yuling Li
- Department of Pathology, Dongguan People's Hospital, Southern Medical University, Dongguan, China
| | - Yuting Yin
- Department of Pathology, Guangdong Medical University, Dongguan, China
| | - Xue Lei
- Department of Pathology, Guangdong Medical University, Dongguan, China
| | - Wei Zhu
- Department of Pathology, Guangdong Medical University, Dongguan, China
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13
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Reyer H, Oster M, Wittenburg D, Murani E, Ponsuksili S, Wimmers K. Genetic Contribution to Variation in Blood Calcium, Phosphorus, and Alkaline Phosphatase Activity in Pigs. Front Genet 2019; 10:590. [PMID: 31316547 PMCID: PMC6610066 DOI: 10.3389/fgene.2019.00590] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 06/04/2019] [Indexed: 12/18/2022] Open
Abstract
Blood values of calcium (Ca), inorganic phosphorus (IP), and alkaline phosphatase activity (ALP) are valuable indicators for mineral status and bone mineralization. The mineral homeostasis is maintained by absorption, retention, and excretion processes employing a number of known and unknown sensing and regulating factors with implications on immunity. Due to the high inter-individual variation of Ca and P levels in the blood of pigs and to clarify molecular contributions to this variation, the genetics of hematological traits related to the Ca and P balance were investigated in a German Landrace population, integrating both single-locus and multi-locus genome-wide association study (GWAS) approaches. Genomic heritability estimates suggest a moderate genetic contribution to the variation of hematological Ca (N = 456), IP (N = 1049), ALP (N = 439), and the Ca/P ratio (N = 455), with values ranging from 0.27 to 0.54. The genome-wide analysis of markers adds a number of genomic regions to the list of quantitative trait loci, some of which overlap with previous results. Despite the gaps in knowledge of genes involved in Ca and P metabolism, genes like THBS2, SHH, PTPRT, PTGS1, and FRAS1 with reported connections to bone metabolism were derived from the significantly associated genomic regions. Additionally, genomic regions included TRAFD1 and genes coding for phosphate transporters (SLC17A1-SLC17A4), which are linked to Ca and P homeostasis. The study calls for improved functional annotation of the proposed candidate genes to derive features involved in maintaining Ca and P balance. This gene information can be exploited to diagnose and predict characteristics of micronutrient utilization, bone development, and a well-functioning musculoskeletal system in pig husbandry and breeding.
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Affiliation(s)
- Henry Reyer
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Michael Oster
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Dörte Wittenburg
- Biomathematics and Bioinformatics Unit, Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Eduard Murani
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Functional Genome Analysis Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Klaus Wimmers
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.,Department of Animal Breeding and Genetics, Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
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14
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Tassano E, Uccella S, Giacomini T, Striano P, Severino M, Porta S, Gimelli G, Ronchetto P. Intragenic Microdeletion of ULK4 and Partial Microduplication of BRWD3 in Siblings with Neuropsychiatric Features and Obesity. Cytogenet Genome Res 2018; 156:14-21. [PMID: 30086552 DOI: 10.1159/000491871] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2018] [Indexed: 12/13/2022] Open
Abstract
ULK4 and BRWD3 deletions have been identified in patients with developmental/language delay and intellectual disability. Both genes play pivotal roles in brain development. In particular, ULK4 encodes serine/threonine kinases that are critical for the development and function of the nervous system, while BRWD3 plays a crucial role in ubiquitination, as part of the ubiquitin/proteasome system. We report on 2 brothers, aged 7.6 and 20 years, presenting with cognitive impairment, epilepsy, autistic features, hearing loss, and obesity. Array-CGH analysis demonstrated 2 rare CNVs in both siblings: a paternally inherited microdeletion of ∼145 kb at 3p22.1, disrupting the ULK4 gene, and a maternally inherited microduplication of ∼117 kb at Xq21.1 including only the BRWD3 gene. As already described for other recurrent syndromes with variable phenotype, these findings are challenging in genetic counseling because of an evident variable penetrance. We discuss the possible correlations between the clinical phenotype of our patients and the function of the genes involved in these microrearrangements.
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15
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Liu M, Fitzgibbon M, Wang Y, Reilly J, Qian X, O'Brien T, Clapcote S, Shen S, Roche M. Ulk4 regulates GABAergic signaling and anxiety-related behavior. Transl Psychiatry 2018; 8:43. [PMID: 29391390 PMCID: PMC5804027 DOI: 10.1038/s41398-017-0091-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/09/2017] [Accepted: 11/30/2017] [Indexed: 01/15/2023] Open
Abstract
Excitation/inhibition imbalance has been proposed as a fundamental mechanism in the pathogenesis of neuropsychiatric and neurodevelopmental disorders, in which copy number variations of the Unc-51 like kinase 4 (ULK4) gene encoding a putative Serine/Threonine kinase have been reported in approximately 1/1000 of patients suffering pleiotropic clinical conditions of schizophrenia, depression, autistic spectrum disorder (ASD), developmental delay, language delay, intellectual disability, or behavioral disorder. The current study characterized behavior of heterozygous Ulk4 +/tm1a mice, demonstrating that Ulk4 +/tm1a mice displayed no schizophrenia-like behavior in acoustic startle reactivity and prepulse inhibition tests or depressive-like behavior in the Porsolt swim or tail suspension tests. However, Ulk4 +/tm1a mice exhibited an anxiety-like behavioral phenotype in several tests. Previously identified hypo-anxious (Atp1a2, Ptn, and Mdk) and hyper-anxious (Gria1, Syngap1, and Npy2r) genes were found to be dysregulated accordingly in Ulk4 mutants. Ulk4 was found to be expressed in GABAergic neurons and the Gad67+ interneurons were significantly reduced in the hippocampus and basolateral amygdala of Ulk4 +/tm1a mice. Transcriptome analyses revealed a marked reduction of GABAergic neuronal subtypes, including Pvalb, Sst, Cck, Npy, and Nos3, as well as significant upregulation of GABA receptors, including Gabra1, Gabra3, Gabra4, Gabra5, and Gabrb3. This is the first evidence that Ulk4 plays a major role in regulating GABAergic signaling and anxiety-like behavior, which may have implications for the development of novel anxiolytic treatments.
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Affiliation(s)
- Min Liu
- Regenerative Medicine Institute, School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - Marie Fitzgibbon
- Physiology, School of Medicine, Galway Neuroscience Centre and Centre for Pain Research, National University of Ireland Galway, Galway, Ireland
| | - Yanqin Wang
- Regenerative Medicine Institute, School of Medicine, National University of Ireland Galway, Galway, Ireland
- Department of Physiology, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Jamie Reilly
- Regenerative Medicine Institute, School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - Xiaohong Qian
- National Center for Protein Sciences, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing Institute of Radiation Medicine, Beijing, China
| | - Timothy O'Brien
- Regenerative Medicine Institute, School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - Steve Clapcote
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, National University of Ireland Galway, Galway, Ireland.
| | - Michelle Roche
- Physiology, School of Medicine, Galway Neuroscience Centre and Centre for Pain Research, National University of Ireland Galway, Galway, Ireland.
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