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Paryani F, Kwon JS, Ng CW, Jakubiak K, Madden N, Ofori K, Tang A, Lu H, Xia S, Li J, Mahajan A, Davidson SM, Basile AO, McHugh C, Vonsattel JP, Hickman R, Zody MC, Housman DE, Goldman JE, Yoo AS, Menon V, Al-Dalahmah O. Multi-omic analysis of Huntington's disease reveals a compensatory astrocyte state. Nat Commun 2024; 15:6742. [PMID: 39112488 PMCID: PMC11306246 DOI: 10.1038/s41467-024-50626-0] [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: 09/17/2023] [Accepted: 07/09/2024] [Indexed: 08/10/2024] Open
Abstract
The mechanisms underlying the selective regional vulnerability to neurodegeneration in Huntington's disease (HD) have not been fully defined. To explore the role of astrocytes in this phenomenon, we used single-nucleus and bulk RNAseq, lipidomics, HTT gene CAG repeat-length measurements, and multiplexed immunofluorescence on HD and control post-mortem brains. We identified genes that correlated with CAG repeat length, which were enriched in astrocyte genes, and lipidomic signatures that implicated poly-unsaturated fatty acids in sensitizing neurons to cell death. Because astrocytes play essential roles in lipid metabolism, we explored the heterogeneity of astrocytic states in both protoplasmic and fibrous-like (CD44+) astrocytes. Significantly, one protoplasmic astrocyte state showed high levels of metallothioneins and was correlated with the selective vulnerability of distinct striatal neuronal populations. When modeled in vitro, this state improved the viability of HD-patient-derived spiny projection neurons. Our findings uncover key roles of astrocytic states in protecting against neurodegeneration in HD.
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Affiliation(s)
- Fahad Paryani
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ji-Sun Kwon
- Department of Developmental Biology Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Christopher W Ng
- Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, MA, USA
| | - Kelly Jakubiak
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Nacoya Madden
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Kenneth Ofori
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Alice Tang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Hong Lu
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Shengnan Xia
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Juncheng Li
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aayushi Mahajan
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Shawn M Davidson
- Northwestern Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | | | | | - Jean Paul Vonsattel
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Richard Hickman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - David E Housman
- Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, MA, USA
| | - James E Goldman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, New York, NY, USA
| | - Andrew S Yoo
- Department of Developmental Biology Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Vilas Menon
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, New York, NY, USA.
| | - Osama Al-Dalahmah
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, New York, NY, USA.
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2
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Wang L, Hu Y, Xiao K, Zhang C, Shi Q, Chen L. Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics. Brief Bioinform 2024; 25:bbae257. [PMID: 38819253 PMCID: PMC11141295 DOI: 10.1093/bib/bbae257] [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: 01/16/2024] [Revised: 04/13/2024] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Spatially resolved transcriptomics (SRT) has emerged as a powerful tool for investigating gene expression in spatial contexts, providing insights into the molecular mechanisms underlying organ development and disease pathology. However, the expression sparsity poses a computational challenge to integrate other modalities (e.g. histological images and spatial locations) that are simultaneously captured in SRT datasets for spatial clustering and variation analyses. In this study, to meet such a challenge, we propose multi-modal domain adaption for spatial transcriptomics (stMDA), a novel multi-modal unsupervised domain adaptation method, which integrates gene expression and other modalities to reveal the spatial functional landscape. Specifically, stMDA first learns the modality-specific representations from spatial multi-modal data using multiple neural network architectures and then aligns the spatial distributions across modal representations to integrate these multi-modal representations, thus facilitating the integration of global and spatially local information and improving the consistency of clustering assignments. Our results demonstrate that stMDA outperforms existing methods in identifying spatial domains across diverse platforms and species. Furthermore, stMDA excels in identifying spatially variable genes with high prognostic potential in cancer tissues. In conclusion, stMDA as a new tool of multi-modal data integration provides a powerful and flexible framework for analyzing SRT datasets, thereby advancing our understanding of intricate biological systems.
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Affiliation(s)
- Lequn Wang
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, No. 320 Yue Yang Road, Xuhui District, Shanghai 200031, China
- University of Chinese Academy of Sciences, No. 80 Zhongguancun East Road, Haidian District, Beijing 100049, China
| | - Yaofeng Hu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Xiangshan Lane, Hangzhou 310024, China
| | - Kai Xiao
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, No. 320 Yue Yang Road, Xuhui District, Shanghai 200031, China
- University of Chinese Academy of Sciences, No. 80 Zhongguancun East Road, Haidian District, Beijing 100049, China
| | - Chuanchao Zhang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Xiangshan Lane, Hangzhou 310024, China
| | - Qianqian Shi
- Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, No. 320 Yue Yang Road, Xuhui District, Shanghai 200031, China
- University of Chinese Academy of Sciences, No. 80 Zhongguancun East Road, Haidian District, Beijing 100049, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Xiangshan Lane, Hangzhou 310024, China
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3
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González-Arnay E, Pérez-Santos I, Jiménez-Sánchez L, Cid E, Gal B, de la Prida LM, Cavada C. Immunohistochemical field parcellation of the human hippocampus along its antero-posterior axis. Brain Struct Funct 2024; 229:359-385. [PMID: 38180568 PMCID: PMC10917878 DOI: 10.1007/s00429-023-02725-9] [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: 04/15/2023] [Accepted: 10/15/2023] [Indexed: 01/06/2024]
Abstract
The primate hippocampus includes the dentate gyrus, cornu ammonis (CA), and subiculum. CA is subdivided into four fields (CA1-CA3, plus CA3h/hilus of the dentate gyrus) with specific pyramidal cell morphology and connections. Work in non-human mammals has shown that hippocampal connectivity is precisely patterned both in the laminar and longitudinal axes. One of the main handicaps in the study of neuropathological semiology in the human hippocampus is the lack of clear laminar and longitudinal borders. The aim of this study was to explore a histochemical segmentation of the adult human hippocampus, integrating field (medio-lateral), laminar, and anteroposterior longitudinal patterning. We provide criteria for head-body-tail field and subfield parcellation of the human hippocampus based on immunodetection of Rabphilin3a (Rph3a), Purkinje-cell protein 4 (PCP4), Chromogranin A and Regulation of G protein signaling-14 (RGS-14). Notably, Rph3a and PCP4 allow to identify the border between CA3 and CA2, while Chromogranin A and RGS-14 give specific staining of CA2. We also provide novel histological data about the composition of human-specific regions of the anterior and posterior hippocampus. The data are given with stereotaxic coordinates along the longitudinal axis. This study provides novel insights for a detailed region-specific parcellation of the human hippocampus useful for human brain imaging and neuropathology.
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Affiliation(s)
- Emilio González-Arnay
- Department of Anatomy, Histology and Neuroscience, Universidad Autónoma de Madrid, Madrid, Spain
- Department of Basic Medical Science-Division of Human Anatomy, Universidad de La Laguna, Santa Cruz de Tenerife, Canary Islands, Spain
| | - Isabel Pérez-Santos
- Department of Anatomy, Histology and Neuroscience, Universidad Autónoma de Madrid, Madrid, Spain
| | - Lorena Jiménez-Sánchez
- Department of Anatomy, Histology and Neuroscience, Universidad Autónoma de Madrid, Madrid, Spain
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Elena Cid
- Instituto Cajal, CSIC, Madrid, Spain
| | - Beatriz Gal
- Instituto Cajal, CSIC, Madrid, Spain
- Universidad CEU-San Pablo, Madrid, Spain
| | | | - Carmen Cavada
- Department of Anatomy, Histology and Neuroscience, Universidad Autónoma de Madrid, Madrid, Spain.
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4
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Huo Y, Guo Y, Wang J, Xue H, Feng Y, Chen W, Li X. Integrating multi-modal information to detect spatial domains of spatial transcriptomics by graph attention network. J Genet Genomics 2023; 50:720-733. [PMID: 37356752 DOI: 10.1016/j.jgg.2023.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/27/2023]
Abstract
Recent advances in spatially resolved transcriptomic technologies have enabled unprecedented opportunities to elucidate tissue architecture and function in situ. Spatial transcriptomics can provide multimodal and complementary information simultaneously, including gene expression profiles, spatial locations, and histology images. However, most existing methods have limitations in efficiently utilizing spatial information and matched high-resolution histology images. To fully leverage the multi-modal information, we propose a SPAtially embedded Deep Attentional graph Clustering (SpaDAC) method to identify spatial domains while reconstructing denoised gene expression profiles. This method can efficiently learn the low-dimensional embeddings for spatial transcriptomics data by constructing multi-view graph modules to capture both spatial location connectives and morphological connectives. Benchmark results demonstrate that SpaDAC outperforms other algorithms on several recent spatial transcriptomics datasets. SpaDAC is a valuable tool for spatial domain detection, facilitating the comprehension of tissue architecture and cellular microenvironment. The source code of SpaDAC is freely available at Github (https://github.com/huoyuying/SpaDAC.git).
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Affiliation(s)
- Yuying Huo
- School of Software Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Yilang Guo
- School of Software Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Jiakang Wang
- School of Software Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Huijie Xue
- School of Software Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Yujuan Feng
- School of Software Engineering, Beijing University of Technology, Beijing 100124, China
| | | | - Xiangyu Li
- School of Software Engineering, Beijing Jiaotong University, Beijing 100044, China.
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5
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Zhang C, Li X, Huang W, Wang L, Shi Q. Spatially aware self-representation learning for tissue structure characterization and spatial functional genes identification. Brief Bioinform 2023; 24:bbad197. [PMID: 37253698 DOI: 10.1093/bib/bbad197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 06/01/2023] Open
Abstract
Spatially resolved transcriptomics (SRT) enable the comprehensive characterization of transcriptomic profiles in the context of tissue microenvironments. Unveiling spatial transcriptional heterogeneity needs to effectively incorporate spatial information accounting for the substantial spatial correlation of expression measurements. Here, we develop a computational method, SpaSRL (spatially aware self-representation learning), which flexibly enhances and decodes spatial transcriptional signals to simultaneously achieve spatial domain detection and spatial functional genes identification. This novel tunable spatially aware strategy of SpaSRL not only balances spatial and transcriptional coherence for the two tasks, but also can transfer spatial correlation constraint between them based on a unified model. In addition, this joint analysis by SpaSRL deciphers accurate and fine-grained tissue structures and ensures the effective extraction of biologically informative genes underlying spatial architecture. We verified the superiority of SpaSRL on spatial domain detection, spatial functional genes identification and data denoising using multiple SRT datasets obtained by different platforms and tissue sections. Our results illustrate SpaSRL's utility in flexible integration of spatial information and novel discovery of biological insights from spatial transcriptomic datasets.
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Affiliation(s)
- Chuanchao Zhang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Xinxing Li
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wendong Huang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Lequn Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianqian Shi
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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6
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Hu D, Dong X, Wang Q, Liu M, Luo S, Meng Z, Feng Z, Zhou W, Song W. PCP4 Promotes Alzheimer's Disease Pathogenesis by Affecting Amyloid-β Protein Precursor Processing. J Alzheimers Dis 2023:JAD230192. [PMID: 37302034 DOI: 10.3233/jad-230192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
BACKGROUND Down syndrome (DS) is caused by an extra copy of all or part of chromosome 21. The patients with DS develop typical Alzheimer's disease (AD) neuropathology, indicating the role of genes on human chromosome 21 (HSA21) in the pathogenesis of AD. Purkinje cell protein 4 (PCP4), also known as brain-specific protein 19, is a critical gene located on HSA21. However, the role of PCP4 in DS and AD pathogenesis is not clear. OBJECTIVE To explore the role of PCP4 in amyloid-β protein precursor (AβPP) processing in AD. METHODS In this study, we investigated the role of PCP4 in AD progression in vitro and in vivo. In vitro experiments, we overexpressed PCP4 in human Swedish mutant AβPP stable expression or neural cell lines. In vitro experiments, APP23/PS45 double transgenic mice were selected and treated with AAV-PCP4. Multiple topics were detected by western blot, RT-PCR, immunohistochemical and behavioral test. RESULTS We found that PCP4 expression was altered in AD. PCP4 was overexpressed in APP23/PS45 transgenic mice and PCP4 affected the processing of AβPP. The production of amyloid-β protein (Aβ) was also promoted by PCP4. The upregulation of endogenous AβPP expression and the downregulation of ADAM10 were due to the transcriptional regulation of PCP4. In addition, PCP4 increased Aβ deposition and neural plaque formation in the brain, and exuberated learning and memory impairment in transgenic AD model mice. CONCLUSION Our finding reveals that PCP4 contributes to the pathogenesis of AD by affecting AβPP processing and suggests PCP4 as a novel therapeutic target for AD by targeting Aβ pathology.
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Affiliation(s)
- Dongjie Hu
- Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xiangjun Dong
- Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Qunxian Wang
- Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Mingjing Liu
- Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Shuyue Luo
- Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Zijun Meng
- Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Zijuan Feng
- Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Weihui Zhou
- Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Weihong Song
- Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health and the Affiliated Wenzhou Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Oujiang Laboratory Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang, China
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7
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Martens GA, Geßner C, Osterhof C, Hankeln T, Burmester T. Transcriptomes of Clusterin- and S100B-transfected neuronal cells elucidate protective mechanisms against hypoxia and oxidative stress in the hooded seal (Cystophora cristata) brain. BMC Neurosci 2022; 23:59. [PMID: 36243678 PMCID: PMC9571494 DOI: 10.1186/s12868-022-00744-6] [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: 07/27/2022] [Accepted: 10/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The hooded seal (Cystophora cristata) exhibits impressive diving skills and can tolerate extended durations of asphyxia, hypoxia and oxidative stress, without suffering from irreversible neuronal damage. Thus, when exposed to hypoxia in vitro, neurons of fresh cortical and hippocampal tissue from hooded seals maintained their membrane potential 4-5 times longer than neurons of mice. We aimed to identify the molecular mechanisms underlying the intrinsic neuronal hypoxia tolerance. Previous comparative transcriptomics of the visual cortex have revealed that S100B and clusterin (apolipoprotein J), two stress proteins that are involved in neurological disorders characterized by hypoxic conditions, have a remarkably high expression in hooded seals compared to ferrets. When overexpressed in murine neuronal cells (HN33), S100B and clusterin had neuroprotective effects when cells were exposed to hypoxia. However, their specific roles in hypoxia have remained largely unknown. METHODS In order to shed light on potential molecular pathways or interaction partners, we exposed HN33 cells transfected with either S100B, soluble clusterin (sCLU) or nuclear clusterin (nCLU) to normoxia, hypoxia and oxidative stress for 24 h. We then determined cell viability and compared the transcriptomes of transfected cells to control cells. Potential pathways and upstream regulators were identified via Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA). RESULTS HN33 cells transfected with sCLU and S100B demonstrated improved glycolytic capacity and reduced aerobic respiration at normoxic conditions. Additionally, sCLU appeared to enhance pathways for cellular homeostasis to counteract stress-induced aggregation of proteins. S100B-transfected cells sustained lowered energy-intensive synaptic signaling. In response to hypoxia, hypoxia-inducible factor (HIF) pathways were considerably elevated in nCLU- and sCLU-transfected cells. In a previous study, S100B and sCLU decreased the amount of reactive oxygen species and lipid peroxidation in HN33 cells in response to oxidative stress, but in the present study, these functional effects were not mirrored in gene expression changes. CONCLUSIONS sCLU and S100B overexpression increased neuronal survival by decreasing aerobic metabolism and synaptic signaling in advance to hypoxia and oxidative stress conditions, possibly to reduce energy expenditure and the build-up of deleterious reactive oxygen species (ROS). Thus, a high expression of CLU isoforms and S100B is likely beneficial during hypoxic conditions.
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Affiliation(s)
- Gerrit A Martens
- Institute of Animal Cell and Systems Biology, Biocenter Grindel, University of Hamburg, 20146, Hamburg, Germany.
| | - Cornelia Geßner
- Institute of Animal Cell and Systems Biology, Biocenter Grindel, University of Hamburg, 20146, Hamburg, Germany
| | - Carina Osterhof
- Institute of Organismic and Molecular Evolution, Molecular Genetics & Genome Analysis, Johannes Gutenberg University Mainz, 55128, Mainz, Germany
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics & Genome Analysis, Johannes Gutenberg University Mainz, 55128, Mainz, Germany
| | - Thorsten Burmester
- Institute of Animal Cell and Systems Biology, Biocenter Grindel, University of Hamburg, 20146, Hamburg, Germany
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8
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Neums L, Koestler DC, Xia Q, Hu J, Patel S, Bell-Glenn S, Pei D, Zhang B, Boyd S, Chalise P, Thompson JA. Assessing equivalent and inverse change in genes between diverse experiments. FRONTIERS IN BIOINFORMATICS 2022; 2:893032. [PMID: 36304274 PMCID: PMC9580844 DOI: 10.3389/fbinf.2022.893032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/22/2022] [Indexed: 05/26/2024] Open
Abstract
Background: It is important to identify when two exposures impact a molecular marker (e.g., a gene's expression) in similar ways, for example, to learn that a new drug has a similar effect to an existing drug. Currently, statistically robust approaches for making comparisons of equivalence of effect sizes obtained from two independently run treatment vs. control comparisons have not been developed. Results: Here, we propose two approaches for evaluating the question of equivalence between effect sizes of two independent studies: a bootstrap test of the Equivalent Change Index (ECI), which we previously developed, and performing Two One-Sided t-Tests (TOST) on the difference in log-fold changes directly. The ECI of a gene is computed by taking the ratio of the effect size estimates obtained from the two different studies, weighted by the maximum of the two p-values and giving it a sign indicating if the effects are in the same or opposite directions, whereas TOST is a test of whether the difference in log-fold changes lies outside a region of equivalence. We used a series of simulation studies to compare the two tests on the basis of sensitivity, specificity, balanced accuracy, and F1-score. We found that TOST is not efficient for identifying equivalently changed gene expression values (F1-score = 0) because it is too conservative, while the ECI bootstrap test shows good performance (F1-score = 0.95). Furthermore, applying the ECI bootstrap test and TOST to publicly available microarray expression data from pancreatic cancer showed that, while TOST was not able to identify any equivalently or inversely changed genes, the ECI bootstrap test identified genes associated with pancreatic cancer. Additionally, when investigating publicly available RNAseq data of smoking vs. vaping, no equivalently changed genes were identified by TOST, but ECI bootstrap test identified genes associated with smoking. Conclusion: A bootstrap test of the ECI is a promising new statistical approach for determining if two diverse studies show similarity in the differential expression of genes and can help to identify genes which are similarly influenced by a specific treatment or exposure. The R package for the ECI bootstrap test is available at https://github.com/Hecate08/ECIbootstrap.
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Affiliation(s)
- Lisa Neums
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Devin C. Koestler
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Qing Xia
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Jinxiang Hu
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Shachi Patel
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Shelby Bell-Glenn
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Dong Pei
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Bo Zhang
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
| | - Samuel Boyd
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Prabhakar Chalise
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Jeffrey A. Thompson
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
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9
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Sanders M, Petrasch-Parwez E, Habbes HW, Düring MV, Förster E. Postnatal Developmental Expression Profile Classifies the Indusium Griseum as a Distinct Subfield of the Hippocampal Formation. Front Cell Dev Biol 2021; 8:615571. [PMID: 33511122 PMCID: PMC7835525 DOI: 10.3389/fcell.2020.615571] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/07/2020] [Indexed: 11/13/2022] Open
Abstract
The indusium griseum (IG) is a cortical structure overlying the corpus callosum along its anterior–posterior extent. It has been classified either as a vestige of the hippocampus or as an extension of the dentate gyrus via the fasciola cinerea, but its attribution to a specific hippocampal subregion is still under debate. To specify the identity of IG neurons more precisely, we investigated the spatiotemporal expression of calbindin, secretagogin, Necab2, PCP4, and Prox1 in the postnatal mouse IG, fasciola cinerea, and hippocampus. We identified the calcium-binding protein Necab2 as a first reliable marker for the IG and fasciola cinerea throughout postnatal development into adulthood. In contrast, calbindin, secretagogin, and PCP4 were expressed each with a different individual time course during maturation, and at no time point, IG or fasciola cinerea principal neurons expressed Prox1, a transcription factor known to define dentate granule cell fate. Concordantly, in a transgenic mouse line expressing enhanced green fluorescent protein (eGFP) in dentate granule cells, neurons of IG and fasciola cinerea were eGFP-negative. Our findings preclude that IG neurons represent dentate granule cells, as earlier hypothesized, and strongly support the view that the IG is an own hippocampal subfield composed of a distinct neuronal population.
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Affiliation(s)
- Marie Sanders
- Department of Neuroanatomy and Molecular Brain Research, Ruhr-University Bochum, Bochum, Germany
| | | | - Hans-Werner Habbes
- Department of Neuroanatomy and Molecular Brain Research, Ruhr-University Bochum, Bochum, Germany
| | - Monika V Düring
- Department of Neuroanatomy and Molecular Brain Research, Ruhr-University Bochum, Bochum, Germany
| | - Eckart Förster
- Department of Neuroanatomy and Molecular Brain Research, Ruhr-University Bochum, Bochum, Germany
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10
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Sanfilippo C, Musumeci G, Kazakova M, Mazzone V, Castrogiovanni P, Imbesi R, Di Rosa M. GNG13 Is a Potential Marker of the State of Health of Alzheimer's Disease Patients' Cerebellum. J Mol Neurosci 2020; 71:1046-1060. [PMID: 33057964 DOI: 10.1007/s12031-020-01726-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022]
Abstract
Brain regions such as the cerebellum (CB) have been neglected for a long time in the study of Alzheimer's disease (AD) pathogenesis. In reference to a new emerging hypothesis according to which there is an altered cerebellar synaptic processing in AD, we verified the possible role played by new biomarkers in the CB of AD patients compared with not-demented healthy control subjects (NDHS). Using a bioinformatics approach, we have collected several microarray datasets and obtained 626 cerebella sample biopsies belonging to subjects who did not die from causes related to neurological diseases and 199 cerebella belonging to AD. The analysis of logical relations between the transcriptome dataset highlighted guanine nucleotide-binding protein (G protein) gamma 13 (GNG13) as a potential new biomarker for Purkinje cells (PCs). We have correlated GNG13 expression levels with already widely existing bibliography of PC marker genes, such as Purkinje cell protein 2 (PCP2), Purkinje cell protein 4 (PCP4), and cerebellin 3 (CBLN3). We showed that expression levels of GNG13 and PCP2, PCP4, and CBLN3 were significantly correlated with each other in NDHS and in AD and significantly reduced in AD patients compared with NDHS subjects. In addition, we highlighted a negative correlation between the expression levels of PC biomarkers and age. From the outcome of our investigation, it is possible to conclude that the identification of GNG13 as a potentially biomarker in PCs represents also a state of health of CB, in association with the expression of PCP2, PCP4, and CBLN3.
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Affiliation(s)
- Cristina Sanfilippo
- IRCCS Centro Neurolesi Bonino Pulejo, Strada Statale 113, C.da Casazza, 98124, Messina, Italy
| | - Giuseppe Musumeci
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy
| | - Maria Kazakova
- Department of Medical Biology, Medical Faculty, Medical University, Plovdiv, Bulgaria
| | - Venera Mazzone
- Department G.F. Ingrassia, Anatomy, School of Medicine, University of Catania, Catania, Italy
| | - Paola Castrogiovanni
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy
| | - Rosa Imbesi
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy
| | - Michelino Di Rosa
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy.
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11
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Cang Z, Nie Q. Inferring spatial and signaling relationships between cells from single cell transcriptomic data. Nat Commun 2020; 11:2084. [PMID: 32350282 PMCID: PMC7190659 DOI: 10.1038/s41467-020-15968-5] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 03/27/2020] [Indexed: 01/20/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) provides details for individual cells; however, crucial spatial information is often lost. We present SpaOTsc, a method relying on structured optimal transport to recover spatial properties of scRNA-seq data by utilizing spatial measurements of a relatively small number of genes. A spatial metric for individual cells in scRNA-seq data is first established based on a map connecting it with the spatial measurements. The cell-cell communications are then obtained by "optimally transporting" signal senders to target signal receivers in space. Using partial information decomposition, we next compute the intercellular gene-gene information flow to estimate the spatial regulations between genes across cells. Four datasets are employed for cross-validation of spatial gene expression prediction and comparison to known cell-cell communications. SpaOTsc has broader applications, both in integrating non-spatial single-cell measurements with spatial data, and directly in spatial single-cell transcriptomics data to reconstruct spatial cellular dynamics in tissues.
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Affiliation(s)
- Zixuan Cang
- Department of Mathematics, University of California, Irvine, Irvine, CA, 92697, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, 92697, USA
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA, 92697, USA.
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA.
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, 92697, USA.
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12
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Ratié L, Desmaris E, García-Moreno F, Hoerder-Suabedissen A, Kelman A, Theil T, Bellefroid EJ, Molnár Z. Loss of Dmrt5 Affects the Formation of the Subplate and Early Corticogenesis. Cereb Cortex 2019; 30:3296-3312. [PMID: 31845734 PMCID: PMC7197206 DOI: 10.1093/cercor/bhz310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Dmrt5 (Dmrta2) and Dmrt3 are key regulators of cortical patterning and progenitor proliferation and differentiation. In this study, we show an altered apical to intermediate progenitor transition, with a delay in SP neurogenesis and premature birth of Ctip2+ cortical neurons in Dmrt5−/− mice. In addition to the cortical progenitors, DMRT5 protein appears present in postmitotic subplate (SP) and marginal zone neurons together with some migrating cortical neurons. We observed the altered split of preplate and the reduced SP and disturbed radial migration of cortical neurons into cortical plate in Dmrt5−/− brains and demonstrated an increase in the proportion of multipolar cells in primary neuronal cultures from Dmrt5−/− embryonic brains. Dmrt5 affects cortical development with specific time sensitivity that we described in two conditional mice with slightly different deletion time. We only observed a transient SP phenotype at E15.5, but not by E18.5 after early (Dmrt5lox/lox;Emx1Cre), but not late (Dmrt5lox/lox;NestinCre) deletion of Dmrt5. SP was less disturbed in Dmrt5lox/lox;Emx1Cre and Dmrt3−/− brains than in Dmrt5−/− and affects dorsomedial cortex more than lateral and caudal cortex. Our study demonstrates a novel function of Dmrt5 in the regulation of early SP formation and radial cortical neuron migration. Summary Statement Our study demonstrates a novel function of Dmrt5 in regulating marginal zone and subplate formation and migration of cortical neurons to cortical plate.
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Affiliation(s)
- Leslie Ratié
- ULB Neuroscience Institute, Université Libre de Bruxelles, B-6041 Gosselies, Belgium.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Elodie Desmaris
- ULB Neuroscience Institute, Université Libre de Bruxelles, B-6041 Gosselies, Belgium
| | - Fernando García-Moreno
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK.,Achucarro Basque Center for Neuroscience, Parque Científico UPV/EHU Edif. Sede, E-48940 Leioa, Spain.,IKERBASQUE Foundation, 48013 Bilbao, Spain
| | | | - Alexandra Kelman
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Thomas Theil
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Eric J Bellefroid
- ULB Neuroscience Institute, Université Libre de Bruxelles, B-6041 Gosselies, Belgium
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
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13
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Yu YE, Xing Z, Do C, Pao A, Lee EJ, Krinsky-McHale S, Silverman W, Schupf N, Tycko B. Genetic and epigenetic pathways in Down syndrome: Insights to the brain and immune system from humans and mouse models. PROGRESS IN BRAIN RESEARCH 2019; 251:1-28. [PMID: 32057305 PMCID: PMC7286740 DOI: 10.1016/bs.pbr.2019.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The presence of an extra copy of human chromosome 21 (Hsa21) leads to a constellation of phenotypic manifestations in Down syndrome (DS), including prominent effects on the brain and immune system. Intensive efforts to unravel the molecular mechanisms underlying these phenotypes may help developing effective therapies, both in DS and in the general population. Here we review recent progress in genetic and epigenetic analysis of trisomy 21 (Ts21). New mouse models of DS based on syntenic conservation of segments of the mouse and human chromosomes are starting to clarify the contributions of chromosomal subregions and orthologous genes to specific phenotypes in DS. The expression of genes on Hsa21 is regulated by epigenetic mechanisms, and with recent findings of highly recurrent gene-specific changes in DNA methylation patterns in brain and immune system cells with Ts21, the epigenomics of DS has become an active research area. Here we highlight the value of combining human studies with mouse models for defining DS critical genes and understanding the trans-acting effects of a simple chromosomal aneuploidy on genome-wide epigenetic patterning. These genetic and epigenetic studies are starting to uncover fundamental biological mechanisms, leading to insights that may soon become therapeutically relevant.
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Affiliation(s)
- Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States; Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY, United States.
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Catherine Do
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States
| | - Annie Pao
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Eun Joon Lee
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States
| | - Sharon Krinsky-McHale
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, United States
| | - Wayne Silverman
- Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Pediatrics, University of California at Irvine, Irvine, CA, United States
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, United States
| | - Benjamin Tycko
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States.
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14
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Tulke S, Haas CA, Häussler U. Expression of brain‐derived neurotrophic factor and structural plasticity in the dentate gyrus and
CA
2 region correlate with epileptiform activity. Epilepsia 2019; 60:1234-1247. [DOI: 10.1111/epi.15540] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 04/17/2019] [Accepted: 04/22/2019] [Indexed: 01/29/2023]
Affiliation(s)
- Susanne Tulke
- Experimental Epilepsy Research Department of Neurosurgery Medical Center - University of Freiburg Faculty of Medicine University of Freiburg Freiburg im Breisgau Germany
- Faculty of Biology University of Freiburg Freiburg im Breisgau Germany
| | - Carola A. Haas
- Experimental Epilepsy Research Department of Neurosurgery Medical Center - University of Freiburg Faculty of Medicine University of Freiburg Freiburg im Breisgau Germany
- BrainLinks‐BrainTools Cluster of Excellence University of Freiburg Freiburg im Breisgau Germany
| | - Ute Häussler
- Experimental Epilepsy Research Department of Neurosurgery Medical Center - University of Freiburg Faculty of Medicine University of Freiburg Freiburg im Breisgau Germany
- BrainLinks‐BrainTools Cluster of Excellence University of Freiburg Freiburg im Breisgau Germany
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15
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BDNF effects on dendritic spine morphology and hippocampal function. Cell Tissue Res 2018; 373:729-741. [DOI: 10.1007/s00441-017-2782-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/22/2017] [Indexed: 12/22/2022]
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16
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Recabarren-Leiva D, Alarcón M. New insights into the gene expression associated to amyotrophic lateral sclerosis. Life Sci 2018; 193:110-123. [DOI: 10.1016/j.lfs.2017.12.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/01/2017] [Accepted: 12/10/2017] [Indexed: 12/11/2022]
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17
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Jiang X, Liu C, Yu T, Zhang L, Meng K, Xing Z, Belichenko PV, Kleschevnikov AM, Pao A, Peresie J, Wie S, Mobley WC, Yu YE. Genetic dissection of the Down syndrome critical region. Hum Mol Genet 2015; 24:6540-51. [PMID: 26374847 DOI: 10.1093/hmg/ddv364] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/02/2015] [Indexed: 01/11/2023] Open
Abstract
Down syndrome (DS), caused by trisomy 21, is the most common chromosomal disorder associated with developmental cognitive deficits. Despite intensive efforts, the genetic mechanisms underlying developmental cognitive deficits remain poorly understood, and no treatment has been proven effective. The previous mouse-based experiments suggest that the so-called Down syndrome critical region of human chromosome 21 is an important region for this phenotype, which is demarcated by Setd4/Cbr1 and Fam3b/Mx2. We first confirmed the importance of the Cbr1-Fam3b region using compound mutant mice, which carry a duplication spanning the entire human chromosome 21 orthologous region on mouse chromosome 16 [Dp(16)1Yey] and Ms1Rhr. By dividing the Setd4-Mx2 region into complementary Setd4-Kcnj6 and Kcnj15-Mx2 intervals, we started an unbiased dissection through generating and analyzing Dp(16)1Yey/Df(16Setd4-Kcnj6)Yey and Dp(16)1Yey/Df(16Kcnj15-Mx2)Yey mice. Surprisingly, the Dp(16)1Yey-associated cognitive phenotypes were not rescued by either deletion in the compound mutants, suggesting the possible presence of at least one causative gene in each of the two regions. The partial rescue by a Dyrk1a mutation in a compound mutant carrying Dp(16)1Yey and the Dyrk1a mutation confirmed the causative role of Dyrk1a, whereas the absence of a similar rescue by Df(16Dyrk1a-Kcnj6)Yey in Dp(16)1Yey/Df(16Dyrk1a-Kcnj6)Yey mice demonstrated the importance of Kcnj6. Our results revealed the high levels of complexities of gene actions and interactions associated with the Setd4/Cbr1-Fam3b/Mx2 region as well as their relationship with developmental cognitive deficits in DS.
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Affiliation(s)
- Xiaoling Jiang
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Chunhong Liu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Tao Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA, Department of Medical Genetics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Li Zhang
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA, Department of Physiology and Pathophysiology, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Kai Meng
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA, Department of Physiology and Pathophysiology, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Pavel V Belichenko
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA and
| | - Alexander M Kleschevnikov
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA and
| | - Annie Pao
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Jennifer Peresie
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Sarah Wie
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - William C Mobley
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA and
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA, Genetics, Genomics and Bioinformatics Program, Department of Cellular and Molecular Biology, Roswell Park Division of Graduate School,State University of New York at Buffalo, Buffalo, NY 14263, USA
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