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Ray NR, Kunkle BW, Hamilton-Nelson K, Kurup JT, Rajabli F, Qiao M, Vardarajan BN, Cosacak MI, Kizil C, Jean-Francois M, Cuccaro M, Reyes-Dumeyer D, Cantwell L, Kuzma A, Vance JM, Gao S, Hendrie HC, Baiyewu O, Ogunniyi A, Akinyemi RO, Lee WP, Martin ER, Wang LS, Beecham GW, Bush WS, Xu W, Jin F, Wang L, Farrer LA, Haines JL, Byrd GS, Schellenberg GD, Mayeux R, Pericak-Vance MA, Reitz C. Extended genome-wide association study employing the African genome resources panel identifies novel susceptibility loci for Alzheimer's disease in individuals of African ancestry. Alzheimers Dement 2024. [PMID: 38958117 DOI: 10.1002/alz.13880] [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: 09/20/2023] [Revised: 04/03/2024] [Accepted: 04/12/2024] [Indexed: 07/04/2024]
Abstract
INTRODUCTION Despite a two-fold risk, individuals of African ancestry have been underrepresented in Alzheimer's disease (AD) genomics efforts. METHODS Genome-wide association studies (GWAS) of 2,903 AD cases and 6,265 controls of African ancestry. Within-dataset results were meta-analyzed, followed by functional genomics analyses. RESULTS A novel AD-risk locus was identified in MPDZ on chromosome (chr) 9p23 (rs141610415, MAF = 0.002, P = 3.68×10-9). Two additional novel common and nine rare loci were identified with suggestive associations (P < 9×10-7). Comparison of association and linkage disequilibrium (LD) patterns between datasets with higher and lower degrees of African ancestry showed differential association patterns at chr12q23.2 (ASCL1), suggesting that this association is modulated by regional origin of local African ancestry. DISCUSSION These analyses identified novel AD-associated loci in individuals of African ancestry and suggest that degree of African ancestry modulates some associations. Increased sample sets covering as much African genetic diversity as possible will be critical to identify additional loci and deconvolute local genetic ancestry effects. HIGHLIGHTS Genetic ancestry significantly impacts risk of Alzheimer's Disease (AD). Although individuals of African ancestry are twice as likely to develop AD, they are vastly underrepresented in AD genomics studies. The Alzheimer's Disease Genetics Consortium has previously identified 16 common and rare genetic loci associated with AD in African American individuals. The current analyses significantly expand this effort by increasing the sample size and extending ancestral diversity by including populations from continental Africa. Single variant meta-analysis identified a novel genome-wide significant AD-risk locus in individuals of African ancestry at the MPDZ gene, and 11 additional novel loci with suggestive genome-wide significance at P < 9×10-7. Comparison of African American datasets with samples of higher degree of African ancestry demonstrated differing patterns of association and linkage disequilibrium at one of these loci, suggesting that degree and/or geographic origin of African ancestry modulates the effect at this locus. These findings illustrate the importance of increasing number and ancestral diversity of African ancestry samples in AD genomics studies to fully disentangle the genetic architecture underlying AD, and yield more effective ancestry-informed genetic screening tools and therapeutic interventions.
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Affiliation(s)
- Nicholas R Ray
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Brian W Kunkle
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Kara Hamilton-Nelson
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Jiji T Kurup
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Farid Rajabli
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Min Qiao
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Badri N Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | | | - Caghan Kizil
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Melissa Jean-Francois
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Michael Cuccaro
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Laura Cantwell
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Amanda Kuzma
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jeffery M Vance
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Sujuan Gao
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Hugh C Hendrie
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | | | | | - Wan-Ping Lee
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Eden R Martin
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, University of Miami, Miami, Florida, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Gary W Beecham
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - William S Bush
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Biomedical Research, Cleveland, Ohio, USA
- Department of Population and Quantitative Health Sciences and Cleveland Institute for Computational Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Wanying Xu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Biomedical Research, Cleveland, Ohio, USA
| | - Fulai Jin
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Biomedical Research, Cleveland, Ohio, USA
- Department of Population and Quantitative Health Sciences and Cleveland Institute for Computational Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Liyong Wang
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Lindsay A Farrer
- Department of Medicine, Biomedical Genetics Section, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
- Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences and Cleveland Institute for Computational Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Goldie S Byrd
- Maya Angelou Center for Health Equity, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Gerard D Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
- Department of Neurology, Columbia University, New York, New York, USA
- Department of Psychiatry, Columbia University, New York, New York, USA
- Epidemiology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, University of Miami, Miami, Florida, USA
| | - Christiane Reitz
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
- Department of Neurology, Columbia University, New York, New York, USA
- Epidemiology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
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Grunin M, Triffon D, Beykin G, Rahmani E, Schweiger R, Tiosano L, Khateb S, Hagbi-Levi S, Rinsky B, Munitz R, Winkler TW, Heid IM, Halperin E, Carmi S, Chowers I. Genome wide association study and genomic risk prediction of age related macular degeneration in Israel. Sci Rep 2024; 14:13034. [PMID: 38844476 PMCID: PMC11156861 DOI: 10.1038/s41598-024-63065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/24/2024] [Indexed: 06/09/2024] Open
Abstract
The risk of developing age-related macular degeneration (AMD) is influenced by genetic background. In 2016, the International AMD Genomics Consortium (IAMDGC) identified 52 risk variants in 34 loci, and a polygenic risk score (PRS) from these variants was associated with AMD. The Israeli population has a unique genetic composition: Ashkenazi Jewish (AJ), Jewish non-Ashkenazi, and Arab sub-populations. We aimed to perform a genome-wide association study (GWAS) for AMD in Israel, and to evaluate PRSs for AMD. Our discovery set recruited 403 AMD patients and 256 controls at Hadassah Medical Center. We genotyped individuals via custom exome chip. We imputed non-typed variants using cosmopolitan and AJ reference panels. We recruited additional 155 cases and 69 controls for validation. To evaluate predictive power of PRSs for AMD, we used IAMDGC summary-statistics excluding our study and developed PRSs via clumping/thresholding or LDpred2. In our discovery set, 31/34 loci reported by IAMDGC were AMD-associated (P < 0.05). Of those, all effects were directionally consistent with IAMDGC and 11 loci had a P-value under Bonferroni-corrected threshold (0.05/34 = 0.0015). At a 5 × 10-5 threshold, we discovered four suggestive associations in FAM189A1, IGDCC4, C7orf50, and CNTNAP4. Only the FAM189A1 variant was AMD-associated in the replication cohort after Bonferroni-correction. A prediction model including LDpred2-based PRS + covariates had an AUC of 0.82 (95% CI 0.79-0.85) and performed better than covariates-only model (P = 5.1 × 10-9). Therefore, previously reported AMD-associated loci were nominally associated with AMD in Israel. A PRS developed based on a large international study is predictive in Israeli populations.
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Affiliation(s)
- Michelle Grunin
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, POB 12271, 9112102, Jerusalem, Israel
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Daria Triffon
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, POB 12271, 9112102, Jerusalem, Israel
| | - Gala Beykin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Elior Rahmani
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Regev Schweiger
- Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
- Department of Genetics, University of Cambridge, CB21TN, Cambridge, UK
| | - Liran Tiosano
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Samer Khateb
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Shira Hagbi-Levi
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Batya Rinsky
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Refael Munitz
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Eran Halperin
- Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
- Department of Anesthesiology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, POB 12271, 9112102, Jerusalem, Israel.
| | - Itay Chowers
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel.
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Ray NR, Kunkle BW, Hamilton-Nelson K, Kurup JT, Rajabli F, Cosacak MI, Kizil C, Jean-Francois M, Cuccaro M, Reyes-Dumeyer D, Cantwell L, Kuzma A, Vance JM, Gao S, Hendrie HC, Baiyewu O, Ogunniyi A, Akinyemi RO, Lee WP, Martin ER, Wang LS, Beecham GW, Bush WS, Farrer LA, Haines JL, Byrd GS, Schellenberg GD, Mayeux R, Pericak-Vance MA, Reitz C. Extended genome-wide association study employing the African Genome Resources Panel identifies novel susceptibility loci for Alzheimer's Disease in individuals of African ancestry. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.29.23294774. [PMID: 37693582 PMCID: PMC10491365 DOI: 10.1101/2023.08.29.23294774] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
INTRODUCTION Despite a two-fold increased risk, individuals of African ancestry have been significantly underrepresented in Alzheimer's Disease (AD) genomics efforts. METHODS GWAS of 2,903 AD cases and 6,265 cognitive controls of African ancestry. Within-dataset results were meta-analyzed, followed by gene-based and pathway analyses, and analysis of RNAseq and whole-genome sequencing data. RESULTS A novel AD risk locus was identified in MPDZ on chromosome 9p23 (rs141610415, MAF=.002, P =3.68×10 -9 ). Two additional novel common and nine novel rare loci approached genome-wide significance at P <9×10 -7 . Comparison of association and LD patterns between datasets with higher and lower degrees of African ancestry showed differential association patterns at chr12q23.2 ( ASCL1 ), suggesting that the association is modulated by regional origin of local African ancestry. DISCUSSION Increased sample sizes and sample sets from Africa covering as much African genetic diversity as possible will be critical to identify additional disease-associated loci and improve deconvolution of local genetic ancestry effects.
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Zhang W, Chen H, Ding L, Huang J, Zhang M, Liu Y, Ma R, Zheng S, Gong J, Piña‐Crespo JC, Zhang Y. Microglial targeted therapy relieves cognitive impairment caused by Cntnap4 deficiency. EXPLORATION (BEIJING, CHINA) 2023; 3:20220160. [PMID: 37933376 PMCID: PMC10624376 DOI: 10.1002/exp.20220160] [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: 11/15/2022] [Accepted: 04/10/2023] [Indexed: 11/08/2023]
Abstract
Contactin-associated protein-like 4 (Cntnap4) is critical for GABAergic transmission in the brain. Impaired Cntnap4 function is implicated in neurological disorders, such as autism; however, the role of Cntnap4 on memory processing is poorly understood. Here, we demonstrate that hippocampal Cntnap4 deficiency in female mice manifests as impaired cognitive function and synaptic plasticity. The underlying mechanisms may involve effects on the pro-inflammatory response resulting in dysfunctional GABAergic transmission and activated tryptophan metabolism. To efficiently and accurately inhibit the pro-inflammatory reaction, we established a biomimetic microglial nanoparticle strategy to deliver FDA-approved PLX3397 (termed MNPs@PLX). We show MNPs@PLX successfully penetrates the blood brain barrier and facilitates microglial-targeted delivery of PLX3397. Furthermore, MNPs@PLX attenuates cognitive decline, dysfunctional synaptic plasticity, and pro-inflammatory response in female heterozygous Cntnap4 knockout mice. Together, our findings show loss of Cntnap4 causes pro-inflammatory cognitive decline that is effectively prevented by supplementation with microglia-specific inhibitors; thus validating the targeting of microglial function as a therapeutic intervention in neurocognitive disorders.
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Affiliation(s)
- Wenlong Zhang
- Department of NeurologyThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Key Laboratory of Neurological Function and HealthSchool of Basic Medical SciencesGuangzhou Medical UniversityGuangzhouChina
- School of Life SciencesWestlake UniversityHangzhouChina
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouChina
| | - Huaqing Chen
- Shenzhen Key Laboratory of Gene and Antibody TherapyCenter for Biotechnology and BiomedicineState Key Laboratory of Chemical OncogenomicsState Key Laboratory of Health Sciences and TechnologyInstitute of Biopharmaceutical and Health EngineeringShenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Liuyan Ding
- Department of NeurologyThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Key Laboratory of Neurological Function and HealthSchool of Basic Medical SciencesGuangzhou Medical UniversityGuangzhouChina
| | - Jie Huang
- Key Laboratory of Neurological Function and HealthSchool of Basic Medical SciencesGuangzhou Medical UniversityGuangzhouChina
| | - Mengran Zhang
- Key Laboratory of Neurological Function and HealthSchool of Basic Medical SciencesGuangzhou Medical UniversityGuangzhouChina
- School of Life SciencesWestlake UniversityHangzhouChina
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouChina
| | - Yan Liu
- School of Traditional Chinese MedicineJinan UniversityGuangzhouChina
| | - Runfang Ma
- Key Laboratory of Neurological Function and HealthSchool of Basic Medical SciencesGuangzhou Medical UniversityGuangzhouChina
- School of Life SciencesWestlake UniversityHangzhouChina
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouChina
| | - Shaohui Zheng
- Key Laboratory of Neurological Function and HealthSchool of Basic Medical SciencesGuangzhou Medical UniversityGuangzhouChina
- School of Life SciencesWestlake UniversityHangzhouChina
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouChina
| | - Junwei Gong
- Key Laboratory of Neurological Function and HealthSchool of Basic Medical SciencesGuangzhou Medical UniversityGuangzhouChina
| | - Juan C. Piña‐Crespo
- Degenerative Diseases ProgramCenter for Genetic Disorders and Aging ResearchSanford Burnham Prebys Medical Discovery InstituteLa JollaCaliforniaUSA
| | - Yunlong Zhang
- Key Laboratory of Neurological Function and HealthSchool of Basic Medical SciencesGuangzhou Medical UniversityGuangzhouChina
- School of Life SciencesWestlake UniversityHangzhouChina
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouChina
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Zhang W, Ding L, Chen H, Zhang M, Ma R, Zheng S, Gong J, Zhang Z, Xu H, Xu P, Zhang Y. Cntnap4 partial deficiency exacerbates α-synuclein pathology through astrocyte-microglia C3-C3aR pathway. Cell Death Dis 2023; 14:285. [PMID: 37087484 PMCID: PMC10122675 DOI: 10.1038/s41419-023-05807-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 04/24/2023]
Abstract
Parkinson's disease (PD) is the most common progressive neurodegenerative movement disorder, which is characterized by dopaminergic (DA) neuron death and the aggregation of neurotoxic α-synuclein. Cntnap4, a risk gene of autism, has been implicated to participate in PD pathogenesis. Here we showed Cntnap4 lacking exacerbates α-synuclein pathology, nigrostriatal DA neuron degeneration and motor impairment, induced by injection of adeno-associated viral vector (AAV)-mediated human α-synuclein overexpression (AAV-hα-Syn). This scenario was further validated in A53T α-synuclein transgenic mice injected with AAV-Cntnap4 shRNA. Mechanistically, α-synuclein derived from damaged DA neuron stimulates astrocytes to release complement C3, activating microglial C3a receptor (C3aR), which in turn triggers microglia to secrete complement C1q and pro-inflammatory cytokines. Thus, the astrocyte-microglia crosstalk further drives DA neuron death and motor dysfunction in PD. Furthermore, we showed that in vivo depletion of microglia and microglial targeted delivery of a novel C3aR antagonist (SB290157) rescue the aggravated α-synuclein pathology resulting from Cntnap4 lacking. Together, our results indicate that Cntnap4 plays a key role in α-synuclein pathogenesis by regulating glial crosstalk and may be a potential target for PD treatment.
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Affiliation(s)
- Wenlong Zhang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Liuyan Ding
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Huaqing Chen
- Shenzhen Key Laboratory of Gene and Antibody Therapy, Center for Biotechnology and Biomedicine, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, 518055, China
| | - Mengran Zhang
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- School of Life Sciences, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, 310024, China
| | - Runfang Ma
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- School of Life Sciences, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, 310024, China
| | - Shaohui Zheng
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- School of Life Sciences, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, 310024, China
| | - Junwei Gong
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Zhiling Zhang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Huaxi Xu
- Institute for Brain Science and Disease, Chongqing Medical University, Chongqing, 400016, China
| | - Pingyi Xu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China.
| | - Yunlong Zhang
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
- School of Life Sciences, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, 310024, China.
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Zhang W, Huang J, Gao F, You Q, Ding L, Gong J, Zhang M, Ma R, Zheng S, Sun X, Zhang Y. Lactobacillus reuteri normalizes altered fear memory in male Cntnap4 knockout mice. EBioMedicine 2022; 86:104323. [PMID: 36395738 PMCID: PMC9672961 DOI: 10.1016/j.ebiom.2022.104323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a common neurodevelopmental disease, characterized by deficits in social communication, restricted and repetitive behaviours, and impaired fear memory processing. Severe gastrointestinal dysfunction and altered gut microbiome have been reported in ASD patients and animal models. Contactin associated protein-like 4 (CNTNAP4) has been suggested to be a novel risk gene, though its role in ASD remains unelucidated. METHODS Cntnap4-/- mice were generated to explore its role in ASD-related behavioural abnormalities. Electrophysiological recording was employed to examine GABAergic transmission in the basolateral amygdala (BLA) and prefrontal cortex. RNA-sequencing was performed to assess underlying mechanisms. 16S rDNA analysis was performed to explore changes in faecal microbial composition. Male Cntnap4-/- mice were fed with Lactobacillus reuteri (L. reuteri) or faecal microbiota to evaluate the effects of microbiota supplementation on the impaired fear conditioning mediated by Cntnap4 deficiency. FINDINGS Male Cntnap4-/- mice manifested deficiency in social behaviours and tone-cue fear conditioning. Notably, reduced GABAergic transmission and GABA receptor expression were found in the BLA but not the prefrontal cortex. In addition, gut Lactobacillus were less abundant in male Cntnap4-/- mice, and L. reuteri treatment or faecal microbiota transplantation rescued abnormal tone-cued fear memory and improved local GABAergic transmission in the BLA of male Cntnap4-/- mice. INTERPRETATION Cntnap4 shapes GABAergic transmission of amygdala and fear conditioning, and microbial intervention represents a promising therapy in ASD intervention. FUNDING National Natural Science Foundation of China, Science and Technology Planning Project of Guangzhou, Guangzhou Medical University, and China Postdoctoral Science Foundation.
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Affiliation(s)
- Wenlong Zhang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Jie Huang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Feng Gao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Qianglong You
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Liuyan Ding
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Junwei Gong
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Mengran Zhang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Runfang Ma
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Shaohui Zheng
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Xiangdong Sun
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Yunlong Zhang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China.
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Hermanova B, Riedlova P, Dalecka A, Jirik V, Janout V, Sram RJ. Air pollution and molecular changes in age-related diseases. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:772-790. [PMID: 32723182 DOI: 10.1080/09603123.2020.1797643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
Assessment of the impact that air contaminants have on health is difficult as this is a complex mixture of substances that varies depending on the time and place. There are many studies on the association between air pollution and increased morbidity and mortality. Before the effect of polluted air is manifested at the level of the organs, an impact can be observed at the molecular level. These include some new biomarkers, like a shortening of the mean telomere length in DNA, dysregulation of gene expression caused by microRNA levels or a variation in the copy number of mitochondrial DNA. These changes may predispose individuals to premature development of age-related diseases and consequently to shortening of life. The common attribute, shared by changes at the molecular level and the development of diseases, is the presence of oxidative stress.
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Affiliation(s)
- B Hermanova
- Centre for Epidemiological Research, University of Ostrava, Ostrava, Czech Republic
- Department of Epidemiology and Public Health, University of Ostrava, Ostrava, Czech Republic
| | - P Riedlova
- Centre for Epidemiological Research, University of Ostrava, Ostrava, Czech Republic
- Department of Epidemiology and Public Health, University of Ostrava, Ostrava, Czech Republic
| | - A Dalecka
- Centre for Epidemiological Research, University of Ostrava, Ostrava, Czech Republic
- Department of Epidemiology and Public Health, University of Ostrava, Ostrava, Czech Republic
| | - V Jirik
- Centre for Epidemiological Research, University of Ostrava, Ostrava, Czech Republic
- Department of Epidemiology and Public Health, University of Ostrava, Ostrava, Czech Republic
| | - V Janout
- Centre for Epidemiological Research, University of Ostrava, Ostrava, Czech Republic
| | - R J Sram
- Centre for Epidemiological Research, University of Ostrava, Ostrava, Czech Republic
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8
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Zhang W, Zhou M, Lu W, Gong J, Gao F, Li Y, Xu X, Lin Y, Zhang X, Ding L, Zhang Z, Li G, Chen X, Sun X, Zhu X, Xu P, Zhang Y. CNTNAP4 deficiency in dopaminergic neurons initiates parkinsonian phenotypes. Am J Cancer Res 2020; 10:3000-3021. [PMID: 32194851 PMCID: PMC7053186 DOI: 10.7150/thno.40798] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/23/2020] [Indexed: 12/14/2022] Open
Abstract
Rationale: Contactin-associated protein-like 4 (CNTNAP4) belongs to the neurexin superfamily and has critical functions in neurological development and synaptic function. Loss of CNTNAP4 in interneurons has been linked to autism, schizophrenia, and epilepsy. CNTNAP4 is also highly enriched in dopaminergic (DA) neurons in the substantia nigra (SN), however, few studies have investigated the role of CNTNAP4 in DA neurons, and whether CNTNAP4 deficiency in DA neurons contributes to Parkinson's disease (PD) remains unclear. Methods: Effects of CNTNAP4 knockdown or overexpression on the DA MN9D cell line were assessed via Western blotting, immunocytochemistry, and RNA sequencing. An in vivo animal model, including CNTNAP4 knockout mice and stereotaxic injections of adeno-associated viral short-hairpin RNA with the tyrosine-hydroxylase promotor to silence CNTNAP4 in the SN, as well as the resulting physiological/behavioral effects, were evaluated via behavioral tests, Western blotting, immunohistochemistry, and transmission electron microscopy. Enzyme-linked immunosorbent assays (ELISAs) were performed to examine the cerebrospinal fluid (CSF) and plasma CNTNAP4 concentrations in PD patients. Results: We demonstrated that CNTNAP4 knockdown induced mitophagy and increased α-synuclein expression in MN9D cells. CNTNAP4 knockdown in the SN induced PD-like increases in SN-specific α-synuclein expression, DA neuronal degeneration, and motor dysfunction in mice. In addition, CNTNAP4 knockdown in SN-DA neurons increased autophagosomes and reduced synaptic vesicles in the SN. Furthermore, CNTNAP4 knockout mice showed movement deficits, nigral DA degeneration, and increased autophagy, which were consistent with the SN-specific knockdown model. We also found that CSF and plasma CNTNAP4 expression was increased in PD patients; in particular, plasma CNTNAP4 was increased in male PD patients compared with controls or female PD patients. Conclusion: Our findings suggest that CNTNAP4 deficiency may initiate phenotypes relevant to PD, of which we elucidated some of the underlying mechanisms.
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9
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The Interaction Between Contactin and Amyloid Precursor Protein and Its Role in Alzheimer’s Disease. Neuroscience 2020; 424:184-202. [DOI: 10.1016/j.neuroscience.2019.10.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 01/06/2023]
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10
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Shangguan Y, Xu X, Ganbat B, Li Y, Wang W, Yang Y, Lu X, Du C, Tian X, Wang X. CNTNAP4 Impacts Epilepsy Through GABAA Receptors Regulation: Evidence From Temporal Lobe Epilepsy Patients and Mouse Models. Cereb Cortex 2019; 28:3491-3504. [PMID: 28968899 DOI: 10.1093/cercor/bhx215] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 12/11/2022] Open
Abstract
Epilepsy is a serious neurological condition characterized by recurrent unprovoked seizures. The exact etiology of epilepsy is not fully understood. Here, we demonstrated that the expression of contactin-associated protein-like 4 (CNTNAP4) was decreased in the temporal neocortex of epileptic patients and in the hippocampus and cortex of epileptic mice. Lentivirus-mediated knock-down of CNTNAP4 in the hippocampus increased mice susceptibility to epilepsy. Conversely, lentivirus-mediated overexpression of CNTNAP4 decreased epileptic behavior in mice. CNTNAP4 affected neuronal excitability and inhibitory synaptic transmission via postsynaptic receptors in Mg2+-free epilepsy cell model. Down-regulation or overexpression of CNTNAP4 in the hippocampus influenced the expression of gamma-aminobutyric acid A receptor β2/3 (GABAARβ2/3) membrane protein, without affecting total GABAARβ2/3 protein concentration in epileptic mice. Protein interactions between CNTNAP4, GABAARβ2/3 and gamma-aminobutyric acid receptor-associated protein (GABARAP) were observed in the hippocampus of epileptic mice. These findings suggest CNTNAP4 may be involved in the occurrence and development of epilepsy through the regulation of GABAAR function, and may be a promising target for the development of epilepsy treatment.
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Affiliation(s)
- Yafei Shangguan
- Department of Neurology, Chongqing Key Laboratory of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Chongqing, China
| | - Xin Xu
- Department of Neurology, Chongqing Key Laboratory of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Chongqing, China
| | - Baigalimaa Ganbat
- Department of Neurology, Chongqing Key Laboratory of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Chongqing, China
| | - Yun Li
- Department of Neurology, Chongqing Key Laboratory of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Chongqing, China
| | - Wei Wang
- Department of Neurology, Chongqing Key Laboratory of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Chongqing, China
| | - Yong Yang
- Department of Neurology, Chongqing Key Laboratory of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Chongqing, China
| | - Xi Lu
- Department of Neurology, Chongqing Key Laboratory of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Chongqing, China
| | - Chao Du
- Department of Neurology, Chongqing Key Laboratory of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Chongqing, China
| | - Xin Tian
- Department of Neurology, Chongqing Key Laboratory of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Chongqing, China
| | - Xuefeng Wang
- Department of Neurology, Chongqing Key Laboratory of Neurology, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Chongqing, China
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11
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Meucci S, Keilholz U, Heim D, Klauschen F, Cacciatore S. Somatic genome alterations in relation to age in lung adenocarcinoma. Int J Cancer 2019; 145:2091-2099. [PMID: 30859574 DOI: 10.1002/ijc.32265] [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: 10/02/2018] [Revised: 02/18/2019] [Accepted: 02/27/2019] [Indexed: 11/11/2022]
Abstract
Lung adenocarcinoma (LUAD) is the most common cause of global cancer-related mortality and the major risk factor is smoking consumption. By analyzing 486 LUAD samples from The Cancer Genome Atlas, we detected a higher mutational burden among younger patients in the global cohort as well as in the TP53-mutated subcohort. The interaction effect of patient age and TP53 mutations significantly affected the mutational rate of younger TP53-mutated patients. Furthermore, we detected a significant enrichment of the smoking-related signature SI4 (SI4) among younger TP53-mutated patients, meanwhile the age-related Signature 1 (SI1) significantly increased in proportion to patient age. Although present and past smoking is reported in the TP53 wild-type patients, we observed a lower average number of somatic mutations, with no correlation with patient age. Overall, TP53 mutations were significantly higher in younger patients and mainly characterized by SI4 and Signature 24 (SI24). Therefore, TP53 seemed to acquire a particular sensitivity to smoking related C>A mutations in younger patients. We hypothesize that TP53 mutations at a younger age might be a crucial factor enhancing the sensitivity to smoking-related mutations leading to a burst of somatic alterations. The mutational profile of cancer cell might reflect the mutational processes operative in aging in a given tissue. Therefore, TP53-mutated and TP53 wild-type patient groups might represent phenotypes which endure aging-related mutational processes with different strength. Our study provides indications of age-dependent differences in mutational backgrounds that might be relevant for cancer prevention and age-adjusted treatment approaches.
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Affiliation(s)
- Stefano Meucci
- Charité Comprehensive Cancer Center, Charité University Hospital, Charitéplatz 1, 10117, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité University Hospital, Charitéplatz 1, 10117, Berlin, Germany
| | - Daniel Heim
- Institut für Pathologie, Charité University Hospital, Charitéplatz 1, 10117, Berlin, Germany
| | - Frederick Klauschen
- Institut für Pathologie, Charité University Hospital, Charitéplatz 1, 10117, Berlin, Germany
| | - Stefano Cacciatore
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, W120NN, United Kingdom.,Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
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12
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Zhao X, Liu X, Zhang A, Chen H, Huo Q, Li W, Ye R, Chen Z, Liang L, Liu QA, Shen J, Jin X, Li W, Nygaard M, Liu X, Hou Y, Ni T, Bolund L, Gottschalk W, Tao W, Gu J, Tian XL, Yang H, Wang J, Xu X, Lutz MW, Min J, Zeng Y, Nie C. The correlation of copy number variations with longevity in a genome-wide association study of Han Chinese. Aging (Albany NY) 2019; 10:1206-1222. [PMID: 29883365 PMCID: PMC6046244 DOI: 10.18632/aging.101461] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 05/30/2018] [Indexed: 12/13/2022]
Abstract
Copy number variations (CNVs) have been shown to cause numerous diseases, however, their roles in human lifespan remain elusive. In this study, we investigate the association of CNVs with longevity by comparing the Han Chinese genomes of long-lived individuals from 90 to 117 years of age and the middle-aged from 30 to 65. Our data demonstrate that the numbers of CNVs, especially deletions, increase significantly in a direct correlation with longevity. We identify eleven CNVs that strongly associate with longevity; four of them locate in the chromosome bands, 7p11.2, 20q13.33, 19p12 and 8p23.3 and overlap partially with the CNVs identified in long-lived Danish or U.S. populations, while the other seven have not been reported previously. These CNV regions encode nineteen known genes, and some of which have been shown to affect aging-related phenotypes such as the shortening of telomere length (ZNF208), the risk of cancer (FOXA1, LAMA5, ZNF716), and vascular and immune-related diseases (ARHGEF10, TOR2A, SH2D3C). In addition, we found several pathways enriched in long-lived genomes, including FOXA1 and FOXA transcription factor networks involved in regulating aging or age-dependent diseases such as cancer. Thus, our study has identified longevity-associated CNV regions and their affected genes and pathways. Our results suggest that the human genome structures such as CNVs might play an important role in determining a long life in human.
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Affiliation(s)
- Xin Zhao
- BGI Shenzhen, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.,College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Xiaomin Liu
- BGI Shenzhen, Shenzhen 518083, China.,School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | | | - Huashuai Chen
- Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University, Durham NC 27710, USA.,Center for Healthy Aging and Development Studies, Raissun Institute for Advanced Studies, National School of Development, Peking University, Beijing 10080, China.,Business School of Xiangtan University, Xiangtan 411105, China
| | - Qing Huo
- BGI Shenzhen, Shenzhen 518083, China
| | | | - Rui Ye
- BGI Shenzhen, Shenzhen 518083, China
| | | | | | | | - Juan Shen
- BGI Shenzhen, Shenzhen 518083, China
| | - Xin Jin
- BGI Shenzhen, Shenzhen 518083, China
| | - Wenwen Li
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Marianne Nygaard
- The Danish Aging Research Center, Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense C 5000, Denmark
| | - Xiao Liu
- BGI Shenzhen, Shenzhen 518083, China
| | - Yong Hou
- BGI Shenzhen, Shenzhen 518083, China
| | - Ting Ni
- State Key Laboratory of Genetics Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Lars Bolund
- BGI Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - William Gottschalk
- Department of Neurology, Medical Center, Duke University, Durham, NC 27704, USA
| | - Wei Tao
- School of Life Sciences, Peking University, Beijing 100080, China
| | - Jun Gu
- School of Life Sciences, Peking University, Beijing 100080, China
| | - Xiao-Li Tian
- Department of Human Population Genetics, Human Aging Research Institute and School of Life Science Nanchang University, Nanchang 330000, China
| | | | - Jian Wang
- BGI Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI Shenzhen, Shenzhen 518083, China
| | - Michael W Lutz
- Department of Neurology, Medical Center, Duke University, Durham, NC 27704, USA
| | - Junxia Min
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yi Zeng
- Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University, Durham NC 27710, USA.,Center for Healthy Aging and Development Studies, Raissun Institute for Advanced Studies, National School of Development, Peking University, Beijing 10080, China
| | - Chao Nie
- BGI Shenzhen, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
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13
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Mei C, Junjvlieke Z, Raza SHA, Wang H, Cheng G, Zhao C, Zhu W, Zan L. Copy number variation detection in Chinese indigenous cattle by whole genome sequencing. Genomics 2019; 112:831-836. [PMID: 31145994 DOI: 10.1016/j.ygeno.2019.05.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/30/2019] [Accepted: 05/25/2019] [Indexed: 12/15/2022]
Abstract
Copy number variation (CNV) refers to a kind of structural variation, having functional and evolutionary effects on phenotypes. Thus far, further elucidation of the CNVs in different Chinese indigenous cattle breeds by whole genome sequencing have yet not been done. In this study, a comprehensive genomic analysis was performed on 75 cattle individuals including six Chinese indigenous cattle breeds and two non-native specialized beef cattle breeds. Based on the 11,486 CNVRs discovered, population analysis was performed, showed that all the cattle breeds clustered in to three clades, consistent with their lineages Bos taurus, Bos taurus × Bos indicus and Bos indicus. Importantly, a set of CNVRs related genes were found to be associated with the traits of interest, which include meat production or quality (CAST, ACTC1, etc.), adaption (BLA-DQB, EGLN2, etc.) and coat color (KIT, MITF, etc.). These results provide valuable full genome variation resources for Chinese bovine genome research and would be helpful for cattle breeding and selection programs in the future.
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Affiliation(s)
- Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zainaguli Junjvlieke
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Chuping Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wenjuan Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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14
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Meucci S, Keilholz U, Heim D, Klauschen F, Cacciatore S. Somatic genome alterations in relation to age in lung squamous cell carcinoma. Oncotarget 2018; 9:32161-32172. [PMID: 30181806 PMCID: PMC6114948 DOI: 10.18632/oncotarget.25848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/12/2018] [Indexed: 12/31/2022] Open
Abstract
Lung squamous cell carcinoma (LUSC) is the most common cause of global cancer-related mortality and the major risk factors is smoking consumption. By analyzing ∼500 LUSC samples from The Cancer Genome Atlas, we detected a higher mutational burden as well as a higher level of methylation changes in younger patients. The SNPs mutational profiling showed enrichments of smoking-related signature 4 and defective DNA mismatch repair (MMR)-related signature 6 in younger patients, while the defective DNA MMR signature 26 was enriched among older patients. Furthermore, gene set enrichment analysis was performed in order to explore functional effect of somatic alterations in relation to patient age. Extracellular Matrix-Receptor Interaction, Nucleotide Excision Repair and Axon Guidance seem crucial disrupted pathways in younger patients. We hypothesize that a higher sensitivity to smoking-related damages and the enrichment of defective DNA MMR related mutations may contribute to the higher mutational burden of younger patients. The two distinct age-related defective DNA MMR signatures 6 and 26 might be crucial mutational patterns in LUSC tumorigenesis which may develop distinct phenotypes. Our study provides indications of age-dependent differences in mutational backgrounds (SNPs and CNVs) as well as epigenetic patterns that might be relevant for age adjusted treatment approaches.
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Affiliation(s)
- Stefano Meucci
- Charité Comprehensive Cancer Center, Charité University Hospital, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité University Hospital, Berlin, Germany
| | - Daniel Heim
- Institut für Pathologie, Charité University Hospital, Berlin, Germany
| | | | - Stefano Cacciatore
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, England, UK
- International Centre for Genetic Engineering and Biotechnology, Cancer Genomics Group, Cape Town, South Africa
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15
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Andriani GA, Vijg J, Montagna C. Mechanisms and consequences of aneuploidy and chromosome instability in the aging brain. Mech Ageing Dev 2017; 161:19-36. [PMID: 27013377 PMCID: PMC5490080 DOI: 10.1016/j.mad.2016.03.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/17/2016] [Accepted: 03/19/2016] [Indexed: 01/31/2023]
Abstract
Aneuploidy and polyploidy are a form of Genomic Instability (GIN) known as Chromosomal Instability (CIN) characterized by sporadic abnormalities in chromosome copy numbers. Aneuploidy is commonly linked to pathological states. It is a hallmark of spontaneous abortions and birth defects and it is observed virtually in every human tumor, therefore being generally regarded as detrimental for the development or the maturation of tissues under physiological conditions. Polyploidy however, occurs as part of normal physiological processes during maturation and differentiation of some mammalian cell types. Surprisingly, high levels of aneuploidy are present in the brain, and their frequency increases with age suggesting that the brain is able to maintain its functionality in the presence of high levels of mosaic aneuploidy. Because somatic aneuploidy with age can reach exceptionally high levels, it is likely to have long-term adverse effects in this organ. We describe the mechanisms accountable for an abnormal DNA content with a particular emphasis on the CNS where cell division is limited. Next, we briefly summarize the types of GIN known to date and discuss how they interconnect with CIN. Lastly we highlight how several forms of CIN may contribute to genetic variation, tissue degeneration and disease in the CNS.
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Affiliation(s)
- Grasiella A Andriani
- Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department Ophthalmology and Visual Science, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department of Pathology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA.
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16
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Nygaard M, Debrabant B, Tan Q, Deelen J, Andersen‐Ranberg K, Craen AJ, Beekman M, Jeune B, Slagboom PE, Christensen K, Christiansen L. Copy number variation associates with mortality in long-lived individuals: a genome-wide assessment. Aging Cell 2016; 15:49-55. [PMID: 26446717 PMCID: PMC4717275 DOI: 10.1111/acel.12407] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2015] [Indexed: 11/30/2022] Open
Abstract
Copy number variants (CNVs) represent a significant source of genetic variation in the human genome and have been implicated in numerous diseases and complex traits. To date, only a few studies have investigated the role of CNVs in human lifespan. To investigate the impact of CNVs on prospective mortality at the extreme end of life, where the genetic component of lifespan appears most profound, we analyzed genomewide CNV data in 603 Danish nonagenarians and centenarians (mean age 96.9 years, range 90.0–102.5 years). Replication was performed in 500 long‐lived individuals from the Leiden Longevity Study (mean age 93.2 years, range 88.9–103.4 years). First, we assessed the association between the CNV burden of each individual (the number of CNVs, the average CNV length, and the total CNV length) and mortality and found a significant increase in mortality per 10 kb increase in the average CNV length, both for all CNVs (hazard ratio (HR) = 1.024, P = 0.002) and for duplications (HR = 1.011, P = 0.005), as well as per 100 kb increase in the total length of deletions (HR = 1.009, P = 0.0005). Next, we assessed the relation between specific deletions and duplications and mortality. Although no genome–wide significant associations were discovered, we identified six deletions and one duplication that showed consistent association with mortality in both or either of the sexes across both study populations. These results indicate that the genome–wide CNV burden, specifically the average CNV length and the total CNV length, associates with higher mortality in long‐lived individuals.
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Affiliation(s)
- Marianne Nygaard
- The Danish Aging Research Center Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark J.B. Winsloews Vej 9B, 5000, Odense C Denmark
- Department of Clinical Genetics Odense University Hospital Sdr. Boulevard 29, 5000, Odense C Denmark
| | - Birgit Debrabant
- The Danish Aging Research Center Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark J.B. Winsloews Vej 9B, 5000, Odense C Denmark
| | - Qihua Tan
- The Danish Aging Research Center Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark J.B. Winsloews Vej 9B, 5000, Odense C Denmark
- Department of Clinical Genetics Odense University Hospital Sdr. Boulevard 29, 5000, Odense C Denmark
| | - Joris Deelen
- Department of Molecular Epidemiology Leiden University Medical Center P.O. Box 9600, 2300 RC Leiden The Netherlands
| | - Karen Andersen‐Ranberg
- The Danish Aging Research Center Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark J.B. Winsloews Vej 9B, 5000, Odense C Denmark
| | - Anton J.M. Craen
- Department of Gerontology and Geriatrics Leiden University Medical Center P.O. Box 9600, 2300 RC Leiden The Netherlands
| | - Marian Beekman
- Department of Molecular Epidemiology Leiden University Medical Center P.O. Box 9600, 2300 RC Leiden The Netherlands
| | - Bernard Jeune
- The Danish Aging Research Center Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark J.B. Winsloews Vej 9B, 5000, Odense C Denmark
| | - Pieternella E. Slagboom
- Department of Molecular Epidemiology Leiden University Medical Center P.O. Box 9600, 2300 RC Leiden The Netherlands
| | - Kaare Christensen
- The Danish Aging Research Center Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark J.B. Winsloews Vej 9B, 5000, Odense C Denmark
- Department of Clinical Genetics Odense University Hospital Sdr. Boulevard 29, 5000, Odense C Denmark
- Department of Clinical Biochemistry and Pharmacology Odense University Hospital Sdr. Boulevard 29, 5000 Odense C Denmark
| | - Lene Christiansen
- The Danish Aging Research Center Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark J.B. Winsloews Vej 9B, 5000, Odense C Denmark
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17
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Iakoubov L, Mossakowska M, Szwed M, Puzianowska-Kuznicka M. A common copy number variation polymorphism in the CNTNAP2 gene: sexual dimorphism in association with healthy aging and disease. Gerontology 2014; 61:24-31. [PMID: 25139204 DOI: 10.1159/000363320] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 04/30/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND New therapeutic targets are needed to fight aging-related diseases and increase life span. A new female-specific association with diseases and limited survival past 80 years was recently reported for a copy number variation (CNV) in the CNTNAP4 gene from the neurexin superfamily. OBJECTIVE We asked whether there are CNVs that are associated with aging phenotypes within other genes from the neurexin superfamily and whether this association is sex specific. METHODS Select CNV polymorphisms were genotyped with proprietary TaqMan qPCR assays. RESULTS A case/control study, in which a group of 81- to 90-year-old community-dwelling Caucasians with no chronic diseases (case) was compared to a similar control group of 65- to 75-year-olds, revealed a negative association with healthy aging for the ins allele of common esv11910 CNV in the CNTNAP2 gene (n = 388; OR = 0.29, 95% CI: 0.14-0.59, p = 0.0004 for males, and OR = 0.82, 95% CI: 0.42-1.57, p = 0.625 for females). This male-specific association was validated in a study of an independent group of 76- to 80-year-olds. To look for a corresponding positive association of the allele with aging-related diseases, two case subgroups of 81- to 90-year-olds, one composed of individuals with cognitive impairment and the other with various diseases not directly related to the nervous system, such as cardiovascular diseases, etc., were compared to a healthy control subgroup of the same age. A positive male-specific association was found for both cases (OR = 2.75, p = 0.008 for association with cognitive impairment, and OR = 3.18, p = 0.002 for other diseases combined). CONCLUSIONS A new male-specific association with aging is reported for a CNV in the CNTNAP2 gene. The polymorphism might be useful for diagnosing individual genetic predispositions to healthy aging versus aging complicated by chronic diseases.
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