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Baer L, Barthelson K, Postlethwait JH, Adelson DL, Pederson SM, Lardelli M. Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis. PLoS Comput Biol 2024; 20:e1011868. [PMID: 38346074 PMCID: PMC10890730 DOI: 10.1371/journal.pcbi.1011868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 02/23/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
In comparisons between mutant and wild-type genotypes, transcriptome analysis can reveal the direct impacts of a mutation, together with the homeostatic responses of the biological system. Recent studies have highlighted that, when the effects of homozygosity for recessive mutations are studied in non-isogenic backgrounds, genes located proximal to the mutation on the same chromosome often appear over-represented among those genes identified as differentially expressed (DE). One hypothesis suggests that DE genes chromosomally linked to a mutation may not reflect functional responses to the mutation but, instead, result from an unequal distribution of expression quantitative trait loci (eQTLs) between sample groups of mutant or wild-type genotypes. This is problematic because eQTL expression differences are difficult to distinguish from genes that are DE due to functional responses to a mutation. Here we show that chromosomally co-located differentially expressed genes (CC-DEGs) are also observed in analyses of dominant mutations in heterozygotes. We define a method and a metric to quantify, in RNA-sequencing data, localised differential allelic representation (DAR) between those sample groups subjected to differential expression analysis. We show how the DAR metric can predict regions prone to eQTL-driven differential expression, and how it can improve functional enrichment analyses through gene exclusion or weighting-based approaches. Advantageously, this improved ability to identify probable eQTLs also reveals examples of CC-DEGs that are likely to be functionally related to a mutant phenotype. This supports a long-standing prediction that selection for advantageous linkage disequilibrium influences chromosome evolution. By comparing the genomes of zebrafish (Danio rerio) and medaka (Oryzias latipes), a teleost with a conserved ancestral karyotype, we find possible examples of chromosomal aggregation of CC-DEGs during evolution of the zebrafish lineage. Our method for DAR analysis requires only RNA-sequencing data, facilitating its application across new and existing datasets.
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Affiliation(s)
- Lachlan Baer
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Karissa Barthelson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - John H. Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - David L. Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Stephen M. Pederson
- Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Michael Lardelli
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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2
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Huang K, Liu X, Zhang Z, Wang T, Xu H, Li Q, Jia Y, Huang L, Kim P, Zhou X. AgeAnnoMO: a knowledgebase of multi-omics annotation for animal aging. Nucleic Acids Res 2024; 52:D822-D834. [PMID: 37850649 PMCID: PMC10767957 DOI: 10.1093/nar/gkad884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/16/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023] Open
Abstract
Aging entails gradual functional decline influenced by interconnected factors. Multiple hallmarks proposed as common and conserved underlying denominators of aging on the molecular, cellular and systemic levels across multiple species. Thus, understanding the function of aging hallmarks and their relationships across species can facilitate the translation of anti-aging drug development from model organisms to humans. Here, we built AgeAnnoMO (https://relab.xidian.edu.cn/AgeAnnoMO/#/), a knowledgebase of multi-omics annotation for animal aging. AgeAnnoMO encompasses an extensive collection of 136 datasets from eight modalities, encompassing 8596 samples from 50 representative species, making it a comprehensive resource for aging and longevity research. AgeAnnoMO characterizes multiple aging regulators across species via multi-omics data, comprehensively annotating aging-related genes, proteins, metabolites, mitochondrial genes, microbiotas and age-specific TCR and BCR sequences tied to aging hallmarks for these species and tissues. AgeAnnoMO not only facilitates a deeper and more generalizable understanding of aging mechanisms, but also provides potential insights of the specificity across tissues and species in aging process, which is important to develop the effective anti-aging interventions for diverse populations. We anticipate that AgeAnnoMO will provide a valuable resource for comprehending and integrating the conserved driving hallmarks in aging biology and identifying the targetable biomarkers for aging research.
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Affiliation(s)
- Kexin Huang
- The Center of Gerontology and Geriatrics and West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Med-X Center for Informatics, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Xi Liu
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Zhaocan Zhang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Tiangang Wang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Haixia Xu
- The Center of Gerontology and Geriatrics and West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Qingxuan Li
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Yuhao Jia
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Liyu Huang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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3
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Lardelli M, Baer L, Hin N, Allen A, Pederson SM, Barthelson K. The Use of Zebrafish in Transcriptome Analysis of the Early Effects of Mutations Causing Early Onset Familial Alzheimer's Disease and Other Inherited Neurodegenerative Conditions. J Alzheimers Dis 2024; 99:S367-S381. [PMID: 37742650 DOI: 10.3233/jad-230522] [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] [Indexed: 09/26/2023]
Abstract
The degree to which non-human animals can be used to model Alzheimer's disease is a contentious issue, particularly as there is still widespread disagreement regarding the pathogenesis of this neurodegenerative dementia. The currently popular transgenic models are based on artificial expression of genes mutated in early onset forms of familial Alzheimer's disease (EOfAD). Uncertainty regarding the veracity of these models led us to focus on heterozygous, single mutations of endogenous genes (knock-in models) as these most closely resemble the genetic state of humans with EOfAD, and so incorporate the fewest assumptions regarding pathological mechanism. We have generated a number of lines of zebrafish bearing EOfAD-like and non-EOfAD-like mutations in genes equivalent to human PSEN1, PSEN2, and SORL1. To analyze the young adult brain transcriptomes of these mutants, we exploited the ability of zebrafish to produce very large families of simultaneous siblings composed of a variety of genotypes and raised in a uniform environment. This "intra-family" analysis strategy greatly reduced genetic and environmental "noise" thereby allowing detection of subtle changes in gene sets after bulk RNA sequencing of entire brains. Changes to oxidative phosphorylation were predicted for all EOfAD-like mutations in the three genes studied. Here we describe some of the analytical lessons learned in our program combining zebrafish genome editing with transcriptomics to understand the molecular pathologies of neurodegenerative disease.
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Affiliation(s)
- Michael Lardelli
- Alzheimer's Disease Genetics Laboratory, The University of Adelaide, Adelaide, SA, Australia
| | - Lachlan Baer
- Alzheimer's Disease Genetics Laboratory, The University of Adelaide, Adelaide, SA, Australia
| | - Nhi Hin
- Alkahest Inc., San Carlos, CA, USA
| | - Angel Allen
- Alzheimer's Disease Genetics Laboratory, The University of Adelaide, Adelaide, SA, Australia
| | - Stephen Martin Pederson
- Black Ochre Data Labs, Indigenous Genomics, Telethon Kinds Institute, Adelaide, SA, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Karissa Barthelson
- Alzheimer's Disease Genetics Laboratory, The University of Adelaide, Adelaide, SA, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
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Sande R, Godad A, Doshi G. Zebrafish Experimental Animal Models for AD: A Comprehensive Review. Curr Rev Clin Exp Pharmacol 2024; 19:295-311. [PMID: 38284707 DOI: 10.2174/0127724328279684240104094257] [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: 08/29/2023] [Revised: 11/26/2023] [Accepted: 12/06/2023] [Indexed: 01/30/2024]
Abstract
AD disease (AD) is a multifaceted and intricate neurodegenerative disorder characterized by intracellular neurofibrillary tangle (NFT) formation and the excessive production and deposition of Aβ senile plaques. While transgenic AD models have been found instrumental in unravelling AD pathogenesis, they involve cost and time constraints during the preclinical phase. Zebrafish, owing to their simplicity, well-defined behavioural patterns, and relevance to neurodegenerative research, have emerged as a promising complementary model. Zebrafish possess glutaminergic and cholinergic pathways implicated in learning and memory, actively contributing to our understanding of neural transmission processes. This review sheds light on the molecular mechanisms by which various neurotoxic agents, including okadaic acid (OKA), cigarette smoke extract, metals, and transgenic zebrafish models with genetic similarities to AD patients, induce cognitive impairments and neuronal degeneration in mammalian systems. These insights may facilitate the identification of effective neurotoxic agents for replicating AD pathogenesis in the zebrafish brain. In this comprehensive review, the pivotal role of zebrafish models in advancing our comprehension of AD is emphasized. These models hold immense potential for shaping future research directions and clinical interventions, ultimately contributing to the development of novel AD therapies.
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Affiliation(s)
- Ruksar Sande
- Department of Pharmacology, Toxicology and Therapeutics, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, V L M Road, Vile Parle (w), Mumbai, 400056, India
| | - Angel Godad
- Department of Pharmacology, Toxicology and Therapeutics, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, V L M Road, Vile Parle (w), Mumbai, 400056, India
| | - Gaurav Doshi
- Department of Pharmacology, Toxicology and Therapeutics, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, V L M Road, Vile Parle (w), Mumbai, 400056, India
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Bradford YM, Van Slyke CE, Howe DG, Fashena D, Frazer K, Martin R, Paddock H, Pich C, Ramachandran S, Ruzicka L, Singer A, Taylor R, Tseng WC, Westerfield M. From multiallele fish to nonstandard environments, how ZFIN assigns phenotypes, human disease models, and gene expression annotations to genes. Genetics 2023; 224:iyad032. [PMID: 36864549 PMCID: PMC10158835 DOI: 10.1093/genetics/iyad032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/13/2023] [Indexed: 03/04/2023] Open
Abstract
Danio rerio is a model organism used to investigate vertebrate development. Manipulation of the zebrafish genome and resultant gene products by mutation or targeted knockdown has made the zebrafish a good system for investigating gene function, providing a resource to investigate genetic contributors to phenotype and human disease. Phenotypic outcomes can be the result of gene mutation, targeted knockdown of gene products, manipulation of experimental conditions, or any combination thereof. Zebrafish have been used in various genetic and chemical screens to identify genetic and environmental contributors to phenotype and disease outcomes. The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for genetic, genomic, and phenotypic data that result from research using D. rerio. Here we describe how ZFIN annotates phenotype, expression, and disease model data across various experimental designs, how we computationally determine wild-type gene expression, the phenotypic gene, and how these results allow us to propagate gene expression, phenotype, and disease model data to the correct gene, or gene related entity.
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Affiliation(s)
- Yvonne M Bradford
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Ceri E Van Slyke
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Douglas G Howe
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - David Fashena
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Ken Frazer
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Ryan Martin
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Holly Paddock
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Christian Pich
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | | | - Leyla Ruzicka
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Amy Singer
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Ryan Taylor
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Wei-Chia Tseng
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Monte Westerfield
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
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Liu Y. Zebrafish as a Model Organism for Studying Pathologic Mechanisms of Neurodegenerative Diseases and other Neural Disorders. Cell Mol Neurobiol 2023:10.1007/s10571-023-01340-w. [PMID: 37004595 DOI: 10.1007/s10571-023-01340-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/19/2023] [Indexed: 04/04/2023]
Abstract
Zebrafish are widely considered an excellent vertebrate model for studying the pathogenesis of human diseases because of their transparency of embryonic development, easy breeding, high similarity with human genes, and easy gene manipulation. Previous studies have shown that zebrafish as a model organism provides an ideal operating platform for clarifying the pathological and molecular mechanisms of neurodegenerative diseases and related human diseases. This review mainly summarizes the achievements and prospects of zebrafish used as model organisms in the research of neurodegenerative diseases and other human diseases related to the nervous system in recent years. In the future study of human disease mechanisms, the application of the zebrafish model will continue to provide a valuable operating platform and technical support for investigating and finding better prevention and treatment of these diseases, which has broad application prospects and practical significance. Zebrafish models used in neurodegenerative diseases and other diseases related to the nervous system.
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Affiliation(s)
- Yanying Liu
- Department of Basic Medicine, School of Nursing and Health, Qingdao Huanghai University, Qingdao, 266427, China.
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Morello G, La Cognata V, Guarnaccia M, D’Agata V, Cavallaro S. Cracking the Code of Neuronal Cell Fate. Cells 2023; 12:1057. [PMID: 37048129 PMCID: PMC10093029 DOI: 10.3390/cells12071057] [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: 02/15/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Transcriptional regulation is fundamental to most biological processes and reverse-engineering programs can be used to decipher the underlying programs. In this review, we describe how genomics is offering a systems biology-based perspective of the intricate and temporally coordinated transcriptional programs that control neuronal apoptosis and survival. In addition to providing a new standpoint in human pathology focused on the regulatory program, cracking the code of neuronal cell fate may offer innovative therapeutic approaches focused on downstream targets and regulatory networks. Similar to computers, where faults often arise from a software bug, neuronal fate may critically depend on its transcription program. Thus, cracking the code of neuronal life or death may help finding a patch for neurodegeneration and cancer.
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Affiliation(s)
- Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Velia D’Agata
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95124 Catania, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
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Baer L, Barthelson K, Postlethwait J, Adelson D, Pederson S, Lardelli M. Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.02.530865. [PMID: 36945478 PMCID: PMC10028786 DOI: 10.1101/2023.03.02.530865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
In comparisons between mutant and wild-type genotypes, transcriptome analysis can reveal the direct impacts of a mutation, together with the homeostatic responses of the biological system. Recent studies have highlighted that, when homozygous mutations are studied in non-isogenic backgrounds, genes from the same chromosome as a mutation often appear over-represented among differentially expressed (DE) genes. One hypothesis suggests that DE genes chromosomally linked to a mutation may not reflect true biological responses to the mutation but, instead, result from differences in representation of expression quantitative trait loci (eQTLs) between sample groups selected on the basis of mutant or wild-type genotype. This is problematic when inclusion of spurious DE genes in a functional enrichment study results in incorrect inferences of mutation effect. Here we show that chromosomally co-located differentially expressed genes (CC-DEGs) can also be observed in analyses of dominant mutations in heterozygotes. We define a method and a metric to quantify, in RNA-sequencing data, localised differential allelic representation (DAR) between groups of samples subject to differential expression analysis. We show how the DAR metric can predict regions prone to eQTL-driven differential expression, and how it can improve functional enrichment analyses through gene exclusion or weighting of gene-level rankings. Advantageously, this improved ability to identify probable eQTLs also reveals examples of CC-DEGs that are likely to be functionally related to a mutant phenotype. This supports a long-standing prediction that selection for advantageous linkage disequilibrium influences chromosome evolution. By comparing the genomes of zebrafish (Danio rerio) and medaka (Oryzias latipes), a teleost with a conserved ancestral karyotype, we find possible examples of chromosomal aggregation of CC-DEGs during evolution of the zebrafish lineage. The DAR metric provides a solid foundation for addressing the eQTL issue in new and existing datasets because it relies solely on RNA-sequencing data.
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Affiliation(s)
- Lachlan Baer
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Karissa Barthelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | | | - David Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Stephen Pederson
- Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, Australia
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Michael Lardelli
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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Barthelson K, Newman M, Lardelli M. Brain transcriptomes of zebrafish and mouse Alzheimer's disease knock-in models imply early disrupted energy metabolism. Dis Model Mech 2021; 15:273566. [PMID: 34842276 PMCID: PMC8807579 DOI: 10.1242/dmm.049187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 11/17/2021] [Indexed: 11/21/2022] Open
Abstract
Energy production is the most fundamentally important cellular activity supporting all other functions, particularly in highly active organs, such as brains. Here, we summarise transcriptome analyses of young adult (pre-disease) brains from a collection of 11 early-onset familial Alzheimer's disease (EOFAD)-like and non-EOFAD-like mutations in three zebrafish genes. The one cellular activity consistently predicted as affected by only the EOFAD-like mutations is oxidative phosphorylation, which produces most of the energy of the brain. All the mutations were predicted to affect protein synthesis. We extended our analysis to knock-in mouse models of APOE alleles and found the same effect for the late onset Alzheimer's disease risk allele ε4. Our results support a common molecular basis for the initiation of the pathological processes leading to both early and late onset forms of Alzheimer's disease, and illustrate the utility of zebrafish and knock-in single EOFAD mutation models for understanding the causes of this disease. Summary: Young adult zebrafish mutants and a mouse model of a genetic variant promoting early- and late-onset Alzheimer's disease, respectively, share changes in brain gene expression, indicating disturbance of oxidative phosphorylation.
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Affiliation(s)
- Karissa Barthelson
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Morgan Newman
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Michael Lardelli
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
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Hin N, Newman M, Pederson S, Lardelli M. Iron Responsive Element-Mediated Responses to Iron Dyshomeostasis in Alzheimer's Disease. J Alzheimers Dis 2021; 84:1597-1630. [PMID: 34719489 DOI: 10.3233/jad-210200] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Iron trafficking and accumulation is associated with Alzheimer's disease (AD) pathogenesis. However, the role of iron dyshomeostasis in early disease stages is uncertain. Currently, gene expression changes indicative of iron dyshomeostasis are not well characterized, making it difficult to explore these in existing datasets. OBJECTIVE To identify sets of genes predicted to contain iron responsive elements (IREs) and use these to explore possible iron dyshomeostasis-associated gene expression responses in AD. METHODS Comprehensive sets of genes containing predicted IRE or IRE-like motifs in their 3' or 5' untranslated regions (UTRs) were identified in human, mouse, and zebrafish reference transcriptomes. Further analyses focusing on these genes were applied to a range of cultured cell, human, mouse, and zebrafish gene expression datasets. RESULTS IRE gene sets are sufficiently sensitive to distinguish not only between iron overload and deficiency in cultured cells, but also between AD and other pathological brain conditions. Notably, changes in IRE transcript abundance are among the earliest observable changes in zebrafish familial AD (fAD)-like brains, preceding other AD-typical pathologies such as inflammatory changes. Unexpectedly, while some IREs in the 3' untranslated regions of transcripts show significantly increased stability under iron deficiency in line with current assumptions, many such transcripts instead display decreased stability, indicating that this is not a generalizable paradigm. CONCLUSION Our results reveal IRE gene expression changes as early markers of the pathogenic process in fAD and are consistent with iron dyshomeostasis as an important driver of this disease. Our work demonstrates how differences in the stability of IRE-containing transcripts can be used to explore and compare iron dyshomeostasis-associated gene expression responses across different species, tissues, and conditions.
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Affiliation(s)
- Nhi Hin
- South Australian Genomics Centre, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia.,Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Morgan Newman
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Stephen Pederson
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health & Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Michael Lardelli
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA, Australia
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11
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Barthelson K, Pederson SM, Newman M, Lardelli M. Brain Transcriptome Analysis of a Protein-Truncating Mutation in Sortilin-Related Receptor 1 Associated With Early-Onset Familial Alzheimer's Disease Indicates Early Effects on Mitochondrial and Ribosome Function. J Alzheimers Dis 2021; 79:1105-1119. [PMID: 33386808 DOI: 10.3233/jad-201383] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The early cellular stresses leading to Alzheimer's disease (AD) remain poorly understood because we cannot access living, asymptomatic human AD brains for detailed molecular analyses. Sortilin-related receptor 1 (SORL1) encodes a multi-domain receptor protein genetically associated with both rare, early-onset familial AD (EOfAD) and common, sporadic, late-onset AD (LOAD). SORL1 protein has been shown to act in the trafficking of the amyloid β A4 precursor protein (AβPP) that is proteolysed to form one of the pathological hallmarks of AD, amyloid-β (Aβ) peptide. However, other functions of SORL1 in AD are less well understood. OBJECTIVE To investigate the effects of heterozygosity for an EOfAD-like mutation in SORL1 on the brain transcriptome of young-adult mutation carriers using zebrafish as a model organism. METHODS We performed targeted mutagenesis to generate an EOfAD-like mutation in the zebrafish orthologue of SORL1 and performed RNA-sequencing on mRNA isolated from the young adult brains of siblings in a family of fish either wild type (non-mutant) or heterozygous for the EOfAD-like mutation. RESULTS We identified subtle differences in gene expression indicating changes in mitochondrial and ribosomal function in the mutant fish. These changes appear to be independent of changes in mitochondrial content or the expression of AβPP-related proteins in zebrafish. CONCLUSION These findings provided evidence supporting that EOfAD mutations in SORL1 affect mitochondrial and ribosomal function and provide the basis for future investigation elucidating the nature of these effects.
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Affiliation(s)
- Karissa Barthelson
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Stephen Martin Pederson
- Bioinformatics Hub, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Morgan Newman
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Michael Lardelli
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
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Barthelson K, Dong Y, Newman M, Lardelli M. PRESENILIN 1 Mutations Causing Early-Onset Familial Alzheimer's Disease or Familial Acne Inversa Differ in Their Effects on Genes Facilitating Energy Metabolism and Signal Transduction. J Alzheimers Dis 2021; 82:327-347. [PMID: 34024832 DOI: 10.3233/jad-210128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The most common cause of early-onset familial Alzheimer's disease (EOfAD) is mutations in PRESENILIN 1 (PSEN1) allowing production of mRNAs encoding full-length, but mutant, proteins. In contrast, a single known frameshift mutation in PSEN1 causes familial acne inversa (fAI) without EOfAD. The molecular consequences of heterozygosity for these mutation types, and how they cause completely different diseases, remains largely unexplored. OBJECTIVE To analyze brain transcriptomes of young adult zebrafish to identify similarities and differences in the effects of heterozygosity for psen1 mutations causing EOfAD or fAI. METHODS RNA sequencing was performed on mRNA isolated from the brains of a single family of 6-month-old zebrafish siblings either wild type or possessing a single, heterozygous EOfAD-like or fAI-like mutation in their endogenous psen1 gene. RESULTS Both mutations downregulate genes encoding ribosomal subunits, and upregulate genes involved in inflammation. Genes involved in energy metabolism appeared significantly affected only by the EOfAD-like mutation, while genes involved in Notch, Wnt and neurotrophin signaling pathways appeared significantly affected only by the fAI-like mutation. However, investigation of direct transcriptional targets of Notch signaling revealed possible increases in γ-secretase activity due to heterozygosity for either psen1 mutation. Transcriptional adaptation due to the fAI-like frameshift mutation was evident. CONCLUSION We observed both similar and contrasting effects on brain transcriptomes of the heterozygous EOfAD-like and fAI-like mutations. The contrasting effects may illuminate how these mutation types cause distinct diseases.
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Affiliation(s)
- Karissa Barthelson
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Yang Dong
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Morgan Newman
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Michael Lardelli
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
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13
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Zhao X, Sun Z, Xu H, Song N, Gao T. Transcriptome and co-expression network analyses reveal the regulatory pathways and key genes associated with temperature adaptability in the yellow drum (Nibea albiflora). J Therm Biol 2021; 100:103071. [PMID: 34503808 DOI: 10.1016/j.jtherbio.2021.103071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/14/2021] [Accepted: 08/03/2021] [Indexed: 12/27/2022]
Abstract
The yellow drum (Nibea albiflora) is an important marine economy fish, that is widely distributed in the coastal waters of the Northwest Pacific. To understand the molecular regulatory mechanism of the yellow drum under temperature stress, transcriptome analysis was performed under five temperature conditions (10 °C, 15 °C, 20 °C, 24 °C, 28 °C) in the present study. Compared with 20 °C, 163, 401, 276, and 372 differentially expressed genes (DEGs) were obtained at 10 °C, 15 °C, 24 °C and 28 °C, respectively. Gene Ontology (GO) analysis indicated that the DEGs were mainly involved in cellular processes, metabolic processes, catalytic activity, membrane and binding. Meanwhile, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the temperature adaptive regulation of the yellow drum was mainly involved in signal transduction, metabolism, genetic information and protein processing. Weighted gene co-expression network analysis (WGCNA) showed that HMGB1, STAT4, Noct, C1q and CRT may be the key hub genes in the response of the yellow drum to temperature stress. In addition, 20 genes that may be associated with temperature stress were identified based on comparative analysis between the KEGG enrichment and the WGCNA results. Ten DEGs were selected for further validation using quantitative real-time PCR (qRT-PCR), and the results were consistent with the RNA-seq data. This study explored the transcriptional patterns of the yellow drum under temperature stress and provided fundamental information on the temperature adaptability of this species.
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Affiliation(s)
- Xiang Zhao
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, 266003, China
| | - Zhicheng Sun
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, 266003, China
| | - Hao Xu
- Qingdao Marine Hazard Mitigation Service, Qingdao, Shandong, 266003, China
| | - Na Song
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, 266003, China.
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, China.
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14
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Huang M, Lou D, Charli A, Kong D, Jin H, Zenitsky G, Anantharam V, Kanthasamy A, Wang Z, Kanthasamy AG. Mitochondrial dysfunction-induced H3K27 hyperacetylation perturbs enhancers in Parkinson's disease. JCI Insight 2021; 6:e138088. [PMID: 34494552 PMCID: PMC8492320 DOI: 10.1172/jci.insight.138088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/28/2021] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial dysfunction is a major pathophysiological contributor to the progression of Parkinson’s disease (PD); however, whether it contributes to epigenetic dysregulation remains unknown. Here, we show that both chemically and genetically driven mitochondrial dysfunctions share a common mechanism of epigenetic dysregulation. Under both scenarios, lysine 27 acetylation of likely variant H3.3 (H3.3K27ac) increased in dopaminergic neuronal models of PD, thereby opening that region to active enhancer activity via H3K27ac. These vulnerable epigenomic loci represent potential transcription factor motifs for PD pathogenesis. We further confirmed that mitochondrial dysfunction induces H3K27ac in ex vivo and in vivo (MitoPark) neurodegenerative models of PD. Notably, the significantly increased H3K27ac in postmortem PD brains highlights the clinical relevance to the human PD population. Our results reveal an exciting mitochondrial dysfunction-metabolism-H3K27ac-transcriptome axis for PD pathogenesis. Collectively, the mechanistic insights link mitochondrial dysfunction to epigenetic dysregulation in dopaminergic degeneration and offer potential new epigenetic intervention strategies for PD.
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Affiliation(s)
- Minhong Huang
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Dan Lou
- Laboratory of Environmental Epigenomes, Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Adhithiya Charli
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Dehui Kong
- Laboratory of Environmental Epigenomes, Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA.,State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei Province, China
| | - Huajun Jin
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Gary Zenitsky
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Vellareddy Anantharam
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Arthi Kanthasamy
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Zhibin Wang
- Laboratory of Environmental Epigenomes, Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA.,State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei Province, China
| | - Anumantha G Kanthasamy
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
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15
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Wang X, Zhang JB, He KJ, Wang F, Liu CF. Advances of Zebrafish in Neurodegenerative Disease: From Models to Drug Discovery. Front Pharmacol 2021; 12:713963. [PMID: 34335276 PMCID: PMC8317260 DOI: 10.3389/fphar.2021.713963] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/30/2021] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative disease (NDD), including Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis, are characterized by the progressive loss of neurons which leads to the decline of motor and/or cognitive function. Currently, the prevalence of NDD is rapidly increasing in the aging population. However, valid drugs or treatment for NDD are still lacking. The clinical heterogeneity and complex pathogenesis of NDD pose a great challenge for the development of disease-modifying therapies. Numerous animal models have been generated to mimic the pathological conditions of these diseases for drug discovery. Among them, zebrafish (Danio rerio) models are progressively emerging and becoming a powerful tool for in vivo study of NDD. Extensive use of zebrafish in pharmacology research or drug screening is due to the high conserved evolution and 87% homology to humans. In this review, we summarize the zebrafish models used in NDD studies, and highlight the recent findings on pharmacological targets for NDD treatment. As high-throughput platforms in zebrafish research have rapidly developed in recent years, we also discuss the application prospects of these new technologies in future NDD research.
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Affiliation(s)
- Xiaobo Wang
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Jin-Bao Zhang
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Kai-Jie He
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Fen Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Chun-Feng Liu
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China.,Department of Neurology, Suqian First Hospital, Suqian, China
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16
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Barthelson K, Baer L, Dong Y, Hand M, Pujic Z, Newman M, Goodhill GJ, Richards RI, Pederson SM, Lardelli M. Zebrafish Chromosome 14 Gene Differential Expression in the fmr1 h u2787 Model of Fragile X Syndrome. Front Genet 2021; 12:625466. [PMID: 34135935 PMCID: PMC8203322 DOI: 10.3389/fgene.2021.625466] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 04/14/2021] [Indexed: 11/13/2022] Open
Abstract
Zebrafish represent a valuable model for investigating the molecular and cellular basis of Fragile X syndrome (FXS). Reduced expression of the zebrafish FMR1 orthologous gene, fmr1, causes developmental and behavioural phenotypes related to FXS. Zebrafish homozygous for the hu2787 non-sense mutation allele of fmr1 are widely used to model FXS, although FXS-relevant phenotypes seen from morpholino antisense oligonucleotide (morpholino) suppression of fmr1 transcript translation were not observed when hu2787 was first described. The subsequent discovery of transcriptional adaptation (a form of genetic compensation), whereby mutations causing non-sense-mediated decay of transcripts can drive compensatory upregulation of homologous transcripts independent of protein feedback loops, suggested an explanation for the differences reported. We examined the whole-embryo transcriptome effects of homozygosity for fmr1 h u2787 at 2 days post fertilisation. We observed statistically significant changes in expression of a number of gene transcripts, but none from genes showing sequence homology to fmr1. Enrichment testing of differentially expressed genes implied effects on lysosome function and glycosphingolipid biosynthesis. The majority of the differentially expressed genes are located, like fmr1, on Chromosome 14. Quantitative PCR tests did not support that this was artefactual due to changes in relative chromosome abundance. Enrichment testing of the "leading edge" differentially expressed genes from Chromosome 14 revealed that their co-location on this chromosome may be associated with roles in brain development and function. The differential expression of functionally related genes due to mutation of fmr1, and located on the same chromosome as fmr1, is consistent with R.A. Fisher's assertion that the selective advantage of co-segregation of particular combinations of alleles of genes will favour, during evolution, chromosomal rearrangements that place them in linkage disequilibrium on the same chromosome. However, we cannot exclude that the apparent differential expression of genes on Chromosome 14 genes was, (if only in part), caused by differences between the expression of alleles of genes unrelated to the effects of the fmr1 h u2787 mutation and made manifest due to the limited, but non-zero, allelic diversity between the genotypes compared.
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Affiliation(s)
- Karissa Barthelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Lachlan Baer
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Yang Dong
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Melanie Hand
- Bioinformatics Hub, University of Adelaide, Adelaide, SA, Australia
| | - Zac Pujic
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
| | - Morgan Newman
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Geoffrey J. Goodhill
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
- School of Mathematics and Physics, University of Queensland, Brisbane, QLD, Australia
| | - Robert I. Richards
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | | | - Michael Lardelli
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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17
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Zhao X, Yao H, Li X. Unearthing of Key Genes Driving the Pathogenesis of Alzheimer's Disease via Bioinformatics. Front Genet 2021; 12:641100. [PMID: 33936168 PMCID: PMC8085575 DOI: 10.3389/fgene.2021.641100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/15/2021] [Indexed: 01/23/2023] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease with unelucidated molecular pathogenesis. Herein, we aimed to identify potential hub genes governing the pathogenesis of AD. The AD datasets of GSE118553 and GSE131617 were collected from the NCBI GEO database. The weighted gene coexpression network analysis (WGCNA), differential gene expression analysis, and functional enrichment analysis were performed to reveal the hub genes and verify their role in AD. Hub genes were validated by machine learning algorithms. We identified modules and their corresponding hub genes from the temporal cortex (TC), frontal cortex (FC), entorhinal cortex (EC), and cerebellum (CE). We obtained 33, 42, 42, and 41 hub genes in modules associated with AD in TC, FC, EC, and CE tissues, respectively. Significant differences were recorded in the expression levels of hub genes between AD and the control group in the TC and EC tissues (P < 0.05). The differences in the expressions of FCGRT, SLC1A3, PTN, PTPRZ1, and PON2 in the FC and CE tissues among the AD and control groups were significant (P < 0.05). The expression levels of PLXNB1, GRAMD3, and GJA1 were statistically significant between the Braak NFT stages of AD. Overall, our study uncovered genes that may be involved in AD pathogenesis and revealed their potential for the development of AD biomarkers and appropriate AD therapeutics targets.
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Affiliation(s)
- Xingxing Zhao
- Department of Neurology, Bethune Hospital Affiliated to Shanxi Medical University, Taiyuan, China.,Department of Cardiology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Hongmei Yao
- Department of Cardiology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Xinyi Li
- Department of Neurology, Bethune Hospital Affiliated to Shanxi Medical University, Taiyuan, China
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18
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Stein D, Mizrahi A, Golova A, Saretzky A, Venzor AG, Slobodnik Z, Kaluski S, Einav M, Khrameeva E, Toiber D. Aging and pathological aging signatures of the brain: through the focusing lens of SIRT6. Aging (Albany NY) 2021; 13:6420-6441. [PMID: 33690173 PMCID: PMC7993737 DOI: 10.18632/aging.202755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/21/2021] [Indexed: 02/06/2023]
Abstract
Brain-specific SIRT6-KO mice present increased DNA damage, learning impairments, and neurodegenerative phenotypes, placing SIRT6 as a key protein in preventing neurodegeneration. In the aging brain, SIRT6 levels/activity decline, which is accentuated in Alzheimer's patients. To understand SIRT6 roles in transcript pattern changes, we analyzed transcriptomes of young WT, old WT and young SIRT6-KO mice brains, and found changes in gene expression related to healthy and pathological aging. In addition, we traced these differences in human and mouse samples of Alzheimer's and Parkinson's diseases, healthy aging and calorie restriction (CR). Our results define four gene expression categories that change with age in a pathological or non-pathological manner, which are either reversed or not by CR. We found that each of these gene expression categories is associated with specific transcription factors, thus serving as potential candidates for their category-specific regulation. One of these candidates is YY1, which we found to act together with SIRT6 regulating specific processes. We thus argue that SIRT6 has a pivotal role in preventing age-related transcriptional changes in brains. Therefore, reduced SIRT6 activity may drive pathological age-related gene expression signatures in the brain.
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Affiliation(s)
- Daniel Stein
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Amir Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Anastasia Golova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Adam Saretzky
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Alfredo Garcia Venzor
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Zeev Slobodnik
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Shai Kaluski
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Monica Einav
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Ekaterina Khrameeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Debra Toiber
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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19
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Barthelson K, Newman M, Nowell CJ, Lardelli M. No observed effect on brain vasculature of Alzheimer's disease-related mutations in the zebrafish presenilin 1 gene. Mol Brain 2021; 14:22. [PMID: 33494778 PMCID: PMC7831246 DOI: 10.1186/s13041-021-00734-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/13/2021] [Indexed: 11/10/2022] Open
Abstract
Previously, we found that brains of adult zebrafish heterozygous for Alzheimer's disease-related mutations in their presenilin 1 gene (psen1, orthologous to human PSEN1) show greater basal expression levels of hypoxia responsive genes relative to their wild type siblings under normoxia, suggesting hypoxic stress. In this study, we investigated whether this might be due to changes in brain vasculature. We generated and compared 3D reconstructions of GFP-labelled blood vessels of the zebrafish forebrain from heterozygous psen1 mutant zebrafish and their wild type siblings. We observed no statistically significant differences in vessel density, surface area, overall mean diameter, overall straightness, or total vessel length normalised to the volume of the telencephalon. Our findings do not support that changes in vascular morphology are responsible for the increased basal expression of hypoxia responsive genes in psen1 heterozygous mutant brains.
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Affiliation(s)
- Karissa Barthelson
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia.
| | - Morgan Newman
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
| | - Cameron J Nowell
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3058, Australia
| | - Michael Lardelli
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
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20
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Newman M, Nik HM, Sutherland GT, Hin N, Kim WS, Halliday GM, Jayadev S, Smith C, Laird AS, Lucas CW, Kittipassorn T, Peet DJ, Lardelli M. Accelerated loss of hypoxia response in zebrafish with familial Alzheimer's disease-like mutation of presenilin 1. Hum Mol Genet 2020; 29:2379-2394. [PMID: 32588886 PMCID: PMC8604272 DOI: 10.1093/hmg/ddaa119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/27/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
Ageing is the major risk factor for Alzheimer's disease (AD), a condition involving brain hypoxia. The majority of early-onset familial AD (EOfAD) cases involve dominant mutations in the gene PSEN1. PSEN1 null mutations do not cause EOfAD. We exploited putative hypomorphic and EOfAD-like mutations in the zebrafish psen1 gene to explore the effects of age and genotype on brain responses to acute hypoxia. Both mutations accelerate age-dependent changes in hypoxia-sensitive gene expression supporting that ageing is necessary, but insufficient, for AD occurrence. Curiously, the responses to acute hypoxia become inverted in extremely aged fish. This is associated with an apparent inability to upregulate glycolysis. Wild-type PSEN1 allele expression is reduced in post-mortem brains of human EOfAD mutation carriers (and extremely aged fish), possibly contributing to EOfAD pathogenesis. We also observed that age-dependent loss of HIF1 stabilization under hypoxia is a phenomenon conserved across vertebrate classes.
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Affiliation(s)
- Morgan Newman
- School of Biological Sciences, University of
Adelaide, Adelaide, South Australia 5005, Australia
| | - Hani Moussavi Nik
- School of Biological Sciences, University of
Adelaide, Adelaide, South Australia 5005, Australia
| | - Greg T Sutherland
- Discipline of Pathology, School of Medical Sciences and Charles
Perkins Centre, Faculty of Medicine and Health, The University of
Sydney, Camperdown, New South Wales 2006, Australia
| | - Nhi Hin
- School of Biological Sciences, University of
Adelaide, Adelaide, South Australia 5005, Australia
- Bioinformatics Hub, University of
Adelaide, Adelaide, South Australia, Australia
| | - Woojin S Kim
- Brain and Mind Centre, Central Clinical School, Faculty of
Medicine and Health, The University of Sydney, Camperdown, New
South Wales 2052, Australia
- School of Medical Sciences, University of New South
Wales and Neuroscience Research Australia, Randwick, New South Wales,
Australia
| | - Glenda M Halliday
- Brain and Mind Centre, Central Clinical School, Faculty of
Medicine and Health, The University of Sydney, Camperdown, New
South Wales 2052, Australia
- School of Medical Sciences, University of New South
Wales and Neuroscience Research Australia, Randwick, New South Wales,
Australia
| | - Suman Jayadev
- Department of Neurology, University of
Washington, Seattle, Washington 98195, USA
| | - Carole Smith
- Department of Neurology, University of
Washington, Seattle, Washington 98195, USA
| | - Angela S Laird
- Centre for MND Research, Department of Biomedical Sciences,
Faculty of Medicine and Health Sciences, Macquarie University,
New South Wales 2109, Australia
| | - Caitlin W Lucas
- Centre for MND Research, Department of Biomedical Sciences,
Faculty of Medicine and Health Sciences, Macquarie University,
New South Wales 2109, Australia
| | - Thaksaon Kittipassorn
- School of Biological Sciences, University of
Adelaide, Adelaide, South Australia 5005, Australia
- Department of Physiology, Faculty of Medicine Siriraj Hospital,
Mahidol University, Bangkok 10700, Thailand
| | - Dan J Peet
- School of Biological Sciences, University of
Adelaide, Adelaide, South Australia 5005, Australia
| | - Michael Lardelli
- School of Biological Sciences, University of
Adelaide, Adelaide, South Australia 5005, Australia
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21
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Pereira PDC, Henrique EP, Porfírio DM, Crispim CCDS, Campos MTB, de Oliveira RM, Silva IMS, Guerreiro LCF, da Silva TWP, da Silva ADJF, Rosa JBDS, de Azevedo DLF, Lima CGC, Castro de Abreu C, Filho CS, Diniz DLWP, Magalhães NGDM, Guerreiro-Diniz C, Diniz CWP, Diniz DG. Environmental Enrichment Improved Learning and Memory, Increased Telencephalic Cell Proliferation, and Induced Differential Gene Expression in Colossoma macropomum. Front Pharmacol 2020; 11:840. [PMID: 32595498 PMCID: PMC7303308 DOI: 10.3389/fphar.2020.00840] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 05/21/2020] [Indexed: 01/06/2023] Open
Abstract
Fish use spatial cognition based on allocentric cues to navigate, but little is known about how environmental enrichment (EE) affects learning and memory in correlation with hematological changes or gene expression in the fish brain. Here we investigated these questions in Colossoma macropomum (Teleostei). Fish were housed for 192 days in either EE or in an impoverished environment (IE) aquarium. EE contained toys, natural plants, and a 12-h/day water stream for voluntary exercise, whereas IE had no toys, plants, or water stream. A third plus maze aquarium was used for spatial and object recognition tests. Compared with IE, the EE fish showed greater learning rates, body length, and body weight. After behavioral tests, whole brain tissue was taken, stored in RNA-later, and then homogenized for DNA sequencing after conversion of isolated RNA. To compare read mapping and gene expression profiles across libraries for neurotranscriptome differential expression, we mapped back RNA-seq reads to the C. macropomum de novo assembled transcriptome. The results showed significant differential behavior, cell counts and gene expression in EE and IE individuals. As compared with IE, we found a greater number of cells in the telencephalon of individuals maintained in EE but no significant difference in the tectum opticum, suggesting differential plasticity in these areas. A total of 107,669 transcripts were found that ultimately yielded 64 differentially expressed transcripts between IE and EE brains. Another group of adult fish growing in aquaculture conditions were either subjected to exercise using running water flow or maintained sedentary. Flow cytometry analysis of peripheral blood showed a significantly higher density of lymphocytes, and platelets but no significant differences in erythrocytes and granulocytes. Thus, under the influence of contrasting environments, our findings showed differential changes at the behavioral, cellular, and molecular levels. We propose that the differential expression of selected transcripts, number of telencephalic cell counts, learning and memory performance, and selective hematological cell changes may be part of Teleostei adaptive physiological responses triggered by EE visuospatial and somatomotor stimulation. Our findings suggest abundant differential gene expression changes depending on environment and provide a basis for exploring gene regulation mechanisms under EE in C. macropomum.
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Affiliation(s)
- Patrick Douglas Corrêa Pereira
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança, Brazil
| | - Ediely Pereira Henrique
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança, Brazil
| | - Danillo Monteiro Porfírio
- Laboratório de Investigação em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | | | - Maitê Thaís Barros Campos
- Laboratório de Investigação em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | - Renata Melo de Oliveira
- Laboratório de Investigação em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | - Isabella Mesquita Sfair Silva
- Laboratório de Investigação em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | - Luma Cristina Ferreira Guerreiro
- Laboratório de Investigação em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | - Tiago Werley Pires da Silva
- Laboratório de Investigação em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | | | - João Batista da Silva Rosa
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança, Brazil
| | | | - Cecília Gabriella Coutinho Lima
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança, Brazil
| | - Cintya Castro de Abreu
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança, Brazil
| | - Carlos Santos Filho
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança, Brazil
| | | | - Nara Gyzely de Morais Magalhães
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança, Brazil
| | - Cristovam Guerreiro-Diniz
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança, Brazil
| | - Cristovam Wanderley Picanço Diniz
- Laboratório de Investigação em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | - Daniel Guerreiro Diniz
- Laboratório de Investigação em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
- Laboratório de Microscopia Eletrônica, Instituto Evandro Chagas, Belém, Brazil
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