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Cukier HN, Duarte CL, Laverde-Paz MJ, Simon SA, Van Booven DJ, Miyares AT, Whitehead PL, Hamilton-Nelson KL, Adams LD, Carney RM, Cuccaro ML, Vance JM, Pericak-Vance MA, Griswold AJ, Dykxhoorn DM. An Alzheimer's disease risk variant in TTC3 modifies the actin cytoskeleton organization and the PI3K-Akt signaling pathway in iPSC-derived forebrain neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542316. [PMID: 37292815 PMCID: PMC10246004 DOI: 10.1101/2023.05.25.542316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A missense variant in the tetratricopeptide repeat domain 3 ( TTC3 ) gene (rs377155188, p.S1038C, NM_003316.4:c.3113C>G) was found to segregate with disease in a multigenerational family with late onset Alzheimer's disease. This variant was introduced into induced pluripotent stem cells (iPSCs) derived from a cognitively intact individual using CRISPR genome editing and the resulting isogenic pair of iPSC lines were differentiated into cortical neurons. Transcriptome analysis showed an enrichment for genes involved in axon guidance, regulation of actin cytoskeleton, and GABAergic synapse. Functional analysis showed that the TTC3 p.S1038C iPSC-derived neuronal progenitor cells had altered 3D morphology and increased migration, while the corresponding neurons had longer neurites, increased branch points, and altered expression levels of synaptic proteins. Pharmacological treatment with small molecules that target the actin cytoskeleton could revert many of these cellular phenotypes, suggesting a central role for actin in mediating the cellular phenotypes associated with the TTC3 p.S1038C variant. Highlights The AD risk variant TTC3 p.S1038C reduces the expression levels of TTC3 The variant modifies the expression of AD specific genes BACE1 , INPP5F , and UNC5C Neurons with the variant are enriched for genes in the PI3K-Akt pathwayiPSC-derived neurons with the alteration have increased neurite length and branchingThe variant interferes with actin cytoskeleton and is ameliorated by Cytochalasin D.
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Peeters D, Pico-Knijnenburg I, Wieringa D, Rad M, Cuperus R, Ruige M, Froeling F, Zijp GW, van der Burg M, Driessen GJA. AKT Hyperphosphorylation and T Cell Exhaustion in Down Syndrome. Front Immunol 2022; 13:724436. [PMID: 35222360 PMCID: PMC8866941 DOI: 10.3389/fimmu.2022.724436] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 01/24/2022] [Indexed: 12/22/2022] Open
Abstract
Down syndrome (DS) is associated with increased susceptibility to infections, auto-immunity, immunodeficiency and haematological malignancies. The exact underlying immunological pathophysiology is still unclear. The immunophenotype and clinical characteristics of DS resemble those of Activated PI3K Delta Syndrome (APDS), in which the PI3K/AKT/mTOR pathway is overactivated. We hypothesized that T cell exhaustion and the hyperactivation of the AKT signalling pathway is also present in immune cells of children with DS. In this observational non-interventional cohort study we collected blood samples of children with DS (n=22) and healthy age-matched controls (n=21) for flowcytometric immunophenotyping, phospho-flow AKT analysis and exhaustion analysis of T cells. The median age was 5 years (range 1-12y). Total T and NK cells were similar for both groups, but absolute values and transitional B cells, naive memory B cells and naive CD4+ and CD8+ T cells were lower in DS. pAKT and AKT were increased for CD3+ and CD4+ T cells and CD20+ B cells in children with DS. Total AKT was also increased in CD8+ T cells. Children with DS showed increased expression of inhibitory markers Programmed cell dealth-1 (PD-1), CD244 and CD160 on CD8+ T cells and increased PD-1 and CD244+ expression on CD4+ T cells, suggesting T cell exhaustion. Children with DS show increased pAKT and AKT and increased T cell exhaustion, which might contribute to their increased susceptibility to infections, auto immunity and haematological malignancies.
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Affiliation(s)
- Daphne Peeters
- Department of Pediatrics, Juliana Children's Hospital, The Hague, Netherlands
| | - Ingrid Pico-Knijnenburg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Centre, Leiden, Netherlands
| | - Douwe Wieringa
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Centre, Leiden, Netherlands
| | - Mandana Rad
- Department of Pediatric Anaesthesiology, Juliana Children's Hospital/Haga Teaching Hospital, The Hague, Netherlands
| | - Roos Cuperus
- Department of Pediatrics, Juliana Children's Hospital, The Hague, Netherlands
| | - Madelon Ruige
- Department of Pediatrics, Juliana Children's Hospital, The Hague, Netherlands
| | - Frank Froeling
- Department of Pediatric Urology, Juliana Children's Hospital, The Hague, Netherlands
| | - Gerda W Zijp
- Department of Paediatric Surgery, Juliana Children's Hospital, The Hague, Netherlands
| | - Mirjam van der Burg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Centre, Leiden, Netherlands
| | - Gertjan J A Driessen
- Department of Pediatrics, Juliana Children's Hospital, The Hague, Netherlands.,Department of Paediatrics, Maastricht University Medical Centre, Maastricht, Netherlands
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Zhang D, Zhou S, Zhou Z, Jiang X, Chen D, Sun HX, Huang J, Qu S, Yang S, Gu Y, Zhang X, Jin X, Gao Y, Shen Y, Chen F. BDdb: a comprehensive platform for exploration and utilization of birth defect multi-omics data. BMC Med Genomics 2021; 14:260. [PMID: 34736471 PMCID: PMC8570004 DOI: 10.1186/s12920-021-01110-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 10/27/2021] [Indexed: 11/10/2022] Open
Abstract
Background Birth defects pose a major challenge to infant health. Thus far, however, the causes of most birth defects remain cryptic. Over the past few decades, considerable effort has been expended on disclosing the underlying mechanisms related to birth defects, yielding myriad treatises and data. To meet the increasing requirements for data resources, we developed a freely accessible birth defect multi-omics database (BDdb, http://t21omics.cngb.org) consisting of multi-omics data and potential disease biomarkers. Results In total, omics datasets from 136 Gene Expression Omnibus (GEO) Series records, including 5245 samples, as well as 869 biomarkers of 22 birth defects in six different species, were integrated into the BDdb. The database provides a user-friendly interface for searching, browsing, and downloading data of interest. The BDdb also enables users to explore the correlations among different sequencing methods, such as chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq) from different studies, to obtain the information on gene expression patterns from diverse aspects. Conclusion To the best of our knowledge, the BDdb is the first comprehensive database associated with birth defects, which should benefit the diagnosis and prevention of birth defects. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01110-x.
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Affiliation(s)
- Dengwei Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,BGI-Shenzhen, Shenzhen, 518083, People's Republic of China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, People's Republic of China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Si Zhou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Ziheng Zhou
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Xiaosen Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Dongsheng Chen
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Hai-Xi Sun
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, People's Republic of China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.,China National Genebank, BGI-Shenzhen, Shenzhen, 518120, People's Republic of China
| | - Jie Huang
- National Institutes for Food and Drug Control (NIFDC), Beijing, 100050, People's Republic of China
| | - Shoufang Qu
- National Institutes for Food and Drug Control (NIFDC), Beijing, 100050, People's Republic of China
| | - Songchen Yang
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Ying Gu
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, People's Republic of China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Xiuqing Zhang
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China. .,Guangdong Provincial Key Laboratory of Human Disease GenomicsShenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen, 518083, People's Republic of China.
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China. .,Shenzhen Engineering Laboratory for Birth Defects Screening, BGI-Shenzhen, Shenzhen, 518083, People's Republic of China.
| | - Yue Shen
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China. .,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, People's Republic of China. .,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, 518083, People's Republic of China. .,MGI, BGI-Shenzhen, Shenzhen, 518083, People's Republic of China.
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Zhou X, Chen X, Hong T, Zhang M, Cai Y, Cui L. TTC3-Mediated Protein Quality Control, A Potential Mechanism for Cognitive Impairment. Cell Mol Neurobiol 2021; 42:1659-1669. [PMID: 33638766 PMCID: PMC9239942 DOI: 10.1007/s10571-021-01060-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/11/2021] [Indexed: 01/14/2023]
Abstract
The tetrapeptide repeat domain 3 (TTC3) gene falls within Down's syndrome (DS) critical region. Cognitive impairment is a common phenotype of DS and Alzheimer’s disease (AD), and overexpression of TTC3 can accelerate cognitive decline, but the specific mechanism is unknown. The TTC3-mediated protein quality control (PQC) mechanism, similar to the PQC system, is divided into three parts: it acts as a cochaperone to assist proteins in folding correctly; it acts as an E3 ubiquitin ligase (E3s) involved in protein degradation processes through the ubiquitin–proteasome system (UPS); and it may also eventually cause autophagy by affecting mitochondrial function. Thus, this article reviews the research progress on the structure, function, and metabolism of TTC3, including the recent research progress on TTC3 in DS and AD; the role of TTC3 in cognitive impairment through PQC in combination with the abovementioned attributes of TTC3; and the potential targets of TTC3 in the treatment of such diseases.
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Affiliation(s)
- Xu Zhou
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Xiongjin Chen
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Tingting Hong
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Miaoping Zhang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Yujie Cai
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Lili Cui
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China.
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