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Chen Q, Aguirre L, Liang G, Zhao H, Dong T, Borrego F, de Rojas I, Hu Q, Reyes C, Su LY, Zhang B, Lechleiter JD, Göring HHH, De Jager PL, Kleinman JE, Hyde TM, Li PP, Ruiz A, Weinberger DR, Seshadri S, Ma L. Identification of a specific APOE transcript and functional elements associated with Alzheimer's disease. Mol Neurodegener 2024; 19:63. [PMID: 39210471 PMCID: PMC11361112 DOI: 10.1186/s13024-024-00751-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND The APOE gene is the strongest genetic risk factor for late-onset Alzheimer's Disease (LOAD). However, the gene regulatory mechanisms at this locus remain incompletely characterized. METHODS To identify novel AD-linked functional elements within the APOE locus, we integrated SNP variants with multi-omics data from human postmortem brains including 2,179 RNA-seq samples from 3 brain regions and two ancestries (European and African), 667 DNA methylation samples, and ChIP-seq samples. Additionally, we plotted the expression trajectory of APOE transcripts in human brains during development. RESULTS We identified an AD-linked APOE transcript (jxn1.2.2) particularly observed in the dorsolateral prefrontal cortex (DLPFC). The APOE jxn1.2.2 transcript is associated with brain neuropathological features, cognitive impairment, and the presence of the APOE4 allele in DLPFC. We prioritized two independent functional SNPs (rs157580 and rs439401) significantly associated with jxn1.2.2 transcript abundance and DNA methylation levels. These SNPs are located within active chromatin regions and affect brain-related transcription factor-binding affinities. The two SNPs shared effects on the jxn1.2.2 transcript between European and African ethnic groups. CONCLUSION The novel APOE functional elements provide potential therapeutic targets with mechanistic insight into the disease etiology.
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Affiliation(s)
- Qiang Chen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA
| | - Luis Aguirre
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA
| | - Guoming Liang
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Huanhuan Zhao
- Bioinformatics Program, University of Texas at El Paso, El Paso, TX, USA
| | - Tao Dong
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Felix Borrego
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA
| | - Itziar de Rojas
- Research Center and Memory Clinic, Ace Alzheimer Center Barcelona - Universitat Internacional de Catalunya, Barcelona, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Qichan Hu
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA
| | - Christopher Reyes
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA
| | - Ling-Yan Su
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Bao Zhang
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - James D Lechleiter
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Harald H H Göring
- South Texas Diabetes and Obesity Institute and Division of Human Genetics, University of Texas Rio Grande Valley School of Medicine, San Antonio, TX, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pan P Li
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Agustín Ruiz
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA
- Research Center and Memory Clinic, Ace Alzheimer Center Barcelona - Universitat Internacional de Catalunya, Barcelona, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Departments of Neurology, Neuroscience, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA.
- Department of Neurology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA.
| | - Liang Ma
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA.
- Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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Chen Q, Aguirre L, Zhao H, Borrego F, de Rojas I, Su L, Li PP, Zhang B, Kokovay E, Lechleiter JD, Göring HH, De Jager PL, Kleinman JE, Hyde TM, Ruiz A, Weinberger DR, Seshadri S, Ma L. Identification of a specific APOE transcript and functional elements associated with Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.30.23297431. [PMID: 37961425 PMCID: PMC10635228 DOI: 10.1101/2023.10.30.23297431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
INTRODUCTION The APOE gene is the strongest genetic risk factor for late-onset Alzheimer's Disease (LOAD). However, the gene regulatory mechanisms at this locus have not been fully characterized. METHODS To identify novel AD-linked functional elements within the APOE locus, we integrated SNP variants with RNA-seq, DNA methylation, and ChIP-seq data from human postmortem brains. RESULTS We identified an AD-linked APOE transcript (jxn1.2.2) observed in the dorsolateral prefrontal cortex (DLPFC). The APOE jxn1.2.2 transcript is associated with brain neuropathological features in DLPFC. We prioritized an independent functional SNP, rs157580, significantly associated with jxn1.2.2 transcript abundance and DNA methylation levels. rs157580 is located within active chromatin regions and predicted to affect brain-related transcriptional factors binding affinity. rs157580 shared the effects on the jxn1.2.2 transcript between European and African ethnic groups. DISCUSSION The novel APOE functional elements provide potential therapeutic targets with mechanistic insight into the disease's etiology.
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Rueter J, Rimbach G, Huebbe P. Allelic variation within the major APOE CpG island affects its methylation in the brain of targeted replacement mice expressing human APOE. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194942. [PMID: 37196888 DOI: 10.1016/j.bbagrm.2023.194942] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Affiliation(s)
- Johanna Rueter
- Institute of Human Nutrition and Food Science, University of Kiel, Hermann-Rodewald-Strasse 6, D-24118 Kiel, Germany
| | - Gerald Rimbach
- Institute of Human Nutrition and Food Science, University of Kiel, Hermann-Rodewald-Strasse 6, D-24118 Kiel, Germany.
| | - Patricia Huebbe
- Institute of Human Nutrition and Food Science, University of Kiel, Hermann-Rodewald-Strasse 6, D-24118 Kiel, Germany
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Nikom D, Zheng S. Alternative splicing in neurodegenerative disease and the promise of RNA therapies. Nat Rev Neurosci 2023; 24:457-473. [PMID: 37336982 DOI: 10.1038/s41583-023-00717-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Alternative splicing generates a myriad of RNA products and protein isoforms of different functions from a single gene. Dysregulated alternative splicing has emerged as a new mechanism broadly implicated in the pathogenesis of neurodegenerative diseases such as Alzheimer disease, amyotrophic lateral sclerosis, frontotemporal dementia, Parkinson disease and repeat expansion diseases. Understanding the mechanisms and functional outcomes of abnormal splicing in neurological disorders is vital in developing effective therapies to treat mis-splicing pathology. In this Review, we discuss emerging research and evidence of the roles of alternative splicing defects in major neurodegenerative diseases and summarize the latest advances in RNA-based therapeutic strategies to target these disorders.
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Affiliation(s)
- David Nikom
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA, USA
- Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA, USA
| | - Sika Zheng
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA, USA.
- Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA, USA.
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA, USA.
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Adropin correlates with aging-related neuropathology in humans and improves cognitive function in aging mice. NPJ Aging Mech Dis 2021; 7:23. [PMID: 34462439 PMCID: PMC8405681 DOI: 10.1038/s41514-021-00076-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
The neural functions of adropin, a secreted peptide highly expressed in the brain, have not been investigated. In humans, adropin is highly expressed in astrocytes and peaks during critical postnatal periods of brain development. Gene enrichment analysis of transcripts correlating with adropin expression suggests processes relevant to aging-related neurodegenerative diseases that vary with age and dementia state, possibly indicating survivor bias. In people aged <40 y and 'old-old' (>75 y) diagnosed with dementia, adropin correlates positively with genes involved in mitochondrial processes. In the 'old-old' without dementia adropin expression correlates positively with morphogenesis and synapse function. Potent neurotrophic responses in primary cultured neurons are consistent with adropin supporting the development and function of neural networks. Adropin expression in the 'old-old' also correlates positively with protein markers of tau-related neuropathologies and inflammation, particularly in those without dementia. How variation in brain adropin expression affects neurological aging was investigated using old (18-month) C57BL/6J mice. In mice adropin is expressed in neurons, oligodendrocyte progenitor cells, oligodendrocytes, and microglia and shows correlative relationships with groups of genes involved in neurodegeneration and cellular metabolism. Increasing adropin expression using transgenesis improved spatial learning and memory, novel object recognition, resilience to exposure to new environments, and reduced mRNA markers of inflammation in old mice. Treatment with synthetic adropin peptide also reversed age-related declines in cognitive functions and affected expression of genes involved in morphogenesis and cellular metabolism. Collectively, these results establish a link between adropin expression and neural energy metabolism and indicate a potential therapy against neurological aging.
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Jakubauskienė E, Kanopka A. Alternative Splicing and Hypoxia Puzzle in Alzheimer's and Parkinson's Diseases. Genes (Basel) 2021; 12:genes12081272. [PMID: 34440445 PMCID: PMC8394294 DOI: 10.3390/genes12081272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 01/08/2023] Open
Abstract
Alternative pre-mRNA splicing plays a very important role in expanding protein diversity as it generates numerous transcripts from a single protein-coding gene. Therefore, alterations lead this process to neurological human disorders, including Alzheimer’s and Parkinson’s diseases. Moreover, accumulating evidence indicates that the splicing machinery highly contributes to the cells’ ability to adapt to different altered cellular microenvironments, such as hypoxia. Hypoxia is known to have an effect on the expression of proteins involved in a multiple of biological processes, such as erythropoiesis, angiogenesis, and neurogenesis, and is one of the important risk factors in neuropathogenesis. In this review, we discuss the current knowledge of alternatively spliced genes, which, as it is reported, are associated with Alzheimer’s and Parkinson’s diseases. Additionally, we highlight the possible influence of cellular hypoxic microenvironment for the formation of mRNA isoforms contributing to the development of these neurodegenerative diseases.
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Defining early changes in Alzheimer's disease from RNA sequencing of brain regions differentially affected by pathology. Sci Rep 2021; 11:4865. [PMID: 33649380 PMCID: PMC7921390 DOI: 10.1038/s41598-021-83872-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 02/03/2021] [Indexed: 01/01/2023] Open
Abstract
Tau pathology in Alzheimer’s disease (AD) spreads in a predictable pattern that corresponds with disease symptoms and severity. At post-mortem there are cortical regions that range from mildly to severely affected by tau pathology and neuronal loss. A comparison of the molecular signatures of these differentially affected areas within cases and between cases and controls may allow the temporal modelling of disease progression. Here we used RNA sequencing to explore differential gene expression in the mildly affected primary visual cortex and moderately affected precuneus of ten age-, gender- and RNA quality-matched post-mortem brains from AD patients and healthy controls. The two regions in AD cases had similar transcriptomic signatures but there were broader abnormalities in the precuneus consistent with the greater tau load. Both regions were characterised by upregulation of immune-related genes such as those encoding triggering receptor expressed on myeloid cells 2 and membrane spanning 4-domains A6A and milder changes in insulin/IGF1 signalling. The precuneus in AD was also characterised by changes in vesicle secretion and downregulation of the interneuronal subtype marker, somatostatin. The ‘early’ AD transcriptome is characterised by perturbations in synaptic vesicle secretion on a background of neuroimmune dysfunction. In particular, the synaptic deficits that characterise AD may begin with the somatostatin division of inhibitory neurotransmission.
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Li QS, Sun Y, Wang T. Epigenome-wide association study of Alzheimer's disease replicates 22 differentially methylated positions and 30 differentially methylated regions. Clin Epigenetics 2020; 12:149. [PMID: 33069246 PMCID: PMC7568396 DOI: 10.1186/s13148-020-00944-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Growing evidence shows that epigenetic modifications play a role in Alzheimer's disease (AD). We performed an epigenome-wide association study (EWAS) to evaluate the DNA methylation differences using postmortem superior temporal gyrus (STG) and inferior frontal gyrus (IFG) samples. RESULTS Samples from 72 AD patients and 62 age-matched cognitively normal controls were assayed using Illumina© Infinium MethylationEPIC BeadChip. Five and 14 differentially methylated positions (DMPs) associated with pathology (i.e., Braak stage) with p value less than Bonferroni correction threshold of 6.79 × 10-8 in the STG and IFG were identified, respectively. These cytosine-phosphate-guanine (CpG) sites included promoter associated cg26263477 annotated to ABCA7 in the STG (p = 1.21 × 10-11), and cg14058329 annotated to the HOXA5/HOXA3/HOXA-AS3 gene cluster (p = 1.62 × 10-9) and cg09448088 (p = 3.95 × 10-9) annotated to MCF2L in the IFG. These genes were previously reported to harbor DMPs and/or differentially methylated regions (DMRs). Previously reported DMPs annotated to RMGA, GNG7, HOXA3, GPR56, SPG7, PCNT, RP11-961A15.1, MCF2L, RHBDF2, ANK1, PCNT, TPRG1, and RASGEF1C were replicated (p < 0.0001). One hundred twenty-one and 173 DMRs associated with pathology in the STG and IFG, respectively, were additionally identified. Of these, DMRs annotated to 30 unique genes were also identified as significant DMRs in the same brain region in a recent meta-analysis, while additional DMRs annotated to 12 genes were reported as DMRs in a different brain region or in a cross-cortex meta-analysis. The significant DMRs were enriched in promoters, CpG islands, and exons in the genome. Gene set enrichment analysis of DMPs and DMRs showed that gene sets involved in neuroinflammation (e.g., microglia differentiation), neurogenesis, and cognition were enriched (false discovery rate (FDR) < 0.05). CONCLUSIONS Twenty-two DMPs and 30 DMRs associated with pathology were replicated, and novel DMPs and DMRs were discovered.
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Affiliation(s)
- Qingqin S Li
- Neuroscience, Janssen Research & Development, LLC, 1125 Trenton-Harbourton Road, Titusville, NJ, 08560, USA.
| | - Yu Sun
- Neuroscience, Janssen Research & Development, LLC, 1125 Trenton-Harbourton Road, Titusville, NJ, 08560, USA
- Discovery Science, Janssen Research & Development, LLC, Spring House, PA, USA
| | - Tania Wang
- AccuraScience, LLC, Johnston, IA, USA
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410083, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
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Paasila PJ, Davies DS, Kril JJ, Goldsbury C, Sutherland GT. The relationship between the morphological subtypes of microglia and Alzheimer's disease neuropathology. Brain Pathol 2019; 29:726-740. [PMID: 30803086 DOI: 10.1111/bpa.12717] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/18/2019] [Indexed: 12/13/2022] Open
Abstract
Microglial associations with both the major Alzheimer's disease (AD) pathognomonic entities, β-amyloid-positive plaques and tau-positive neurofibrillary tangles, have been noted in previous investigations of both human tissue and mouse models. However, the precise nature of their role in the pathogenesis of AD is debated; the major working hypothesis is that pro-inflammatory activities of activated microglia contribute to disease progression. In contrast, others have proposed that microglial dystrophy with a loss of physiological and neuroprotective activities promotes neurodegeneration. This immunohistochemical study sought to gain clarity in this area by quantifying the morphological subtypes of microglia in the mildly-affected primary visual cortex (PVC), the moderately affected superior frontal cortex (SFC) and the severely affected inferior temporal cortex (ITC) of 8 AD cases and 15 age and gender-matched, non-demented controls with ranging AD-type pathology. AD cases had increased β-amyloid and tau levels compared to controls in all regions. Neuronal loss was observed in the SFC and ITC, and was associated with atrophy in the latter. A major feature of the ITC in AD was a decrease in ramified (healthy) microglia with image analysis confirming reductions in arborized area and skeletal complexity. Activated microglia were not associated with AD but were increased in non-demented controls with greater AD-type pathology. Microglial clusters were occasionally associated with β-amyloid- and tau-positive plaques but represented less than 2% of the total microglial population. Dystrophic microglia were not associated with AD, but were inversely correlated with brain pH suggesting that agonal events were responsible for this morphological subtype. Overall these novel findings suggest that there is an early microglial reaction to AD-type pathology but a loss of healthy microglia is the prominent feature in severely affected regions of the AD brain.
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Affiliation(s)
- Patrick Jarmo Paasila
- Discipline of Pathology, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | | | - Jillian June Kril
- Discipline of Pathology, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | | | - Greg Trevor Sutherland
- Discipline of Pathology, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
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Youssef P, Chami B, Lim J, Middleton T, Sutherland GT, Witting PK. Evidence supporting oxidative stress in a moderately affected area of the brain in Alzheimer's disease. Sci Rep 2018; 8:11553. [PMID: 30068908 PMCID: PMC6070512 DOI: 10.1038/s41598-018-29770-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/18/2018] [Indexed: 01/15/2023] Open
Abstract
The pathogenesis of Alzheimer's disease (AD) remains to be elucidated. Oxidative damage and excessive beta-amyloid oligomers are components of disease progression but it is unclear how these factors are temporally related. At post mortem, the superior temporal gyrus (STG) of AD cases contains plaques, but displays few tangles and only moderate neuronal loss. The STG at post mortem may represent a brain region that is in the early stages of AD or alternately a region resistant to AD pathogenesis. We evaluated expression profiles and activity of endogenous anti-oxidants, oxidative damage and caspase activity in the STG of apolipoprotein ε4-matched human AD cases and controls. Total superoxide dismutase (SOD) activity was increased, whereas total glutathione peroxidase (GPX), catalase (CAT) and peroxiredoxin (Prx) activities, were decreased in the AD-STG, suggesting that hydrogen peroxide accumulates in this brain region. Transcripts of the transcription factor NFE2L2 and inducible HMOX1, were also increased in the AD-STG, and this corresponded to increased Nuclear factor erythroid 2-related factor (NRF-2) and total heme-oxygenase (HO) activity. The protein oxidation marker 4-hydroxynonenal (4-HNE), remained unchanged in the AD-STG. Similarly, caspase activity was unaltered, suggesting that subtle redox imbalances in early to moderate stages of AD do not impact STG viability.
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Affiliation(s)
- Priscilla Youssef
- Redox Biology Group, Discipline of Pathology, University of Sydney, Sydney, NSW, 2006, Australia
| | - Belal Chami
- Redox Biology Group, Discipline of Pathology, University of Sydney, Sydney, NSW, 2006, Australia
| | - Julia Lim
- Neuropathology Group, Discipline of Pathology, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Terry Middleton
- Neuropathology Group, Discipline of Pathology, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Greg T Sutherland
- Neuropathology Group, Discipline of Pathology, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Paul K Witting
- Redox Biology Group, Discipline of Pathology, University of Sydney, Sydney, NSW, 2006, Australia.
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12
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Miller JA, Guillozet-Bongaarts A, Gibbons LE, Postupna N, Renz A, Beller AE, Sunkin SM, Ng L, Rose SE, Smith KA, Szafer A, Barber C, Bertagnolli D, Bickley K, Brouner K, Caldejon S, Chapin M, Chua ML, Coleman NM, Cudaback E, Cuhaciyan C, Dalley RA, Dee N, Desta T, Dolbeare TA, Dotson NI, Fisher M, Gaudreault N, Gee G, Gilbert TL, Goldy J, Griffin F, Habel C, Haradon Z, Hejazinia N, Hellstern LL, Horvath S, Howard K, Howard R, Johal J, Jorstad NL, Josephsen SR, Kuan CL, Lai F, Lee E, Lee F, Lemon T, Li X, Marshall DA, Melchor J, Mukherjee S, Nyhus J, Pendergraft J, Potekhina L, Rha EY, Rice S, Rosen D, Sapru A, Schantz A, Shen E, Sherfield E, Shi S, Sodt AJ, Thatra N, Tieu M, Wilson AM, Montine TJ, Larson EB, Bernard A, Crane PK, Ellenbogen RG, Keene CD, Lein E. Neuropathological and transcriptomic characteristics of the aged brain. eLife 2017; 6. [PMID: 29120328 PMCID: PMC5679757 DOI: 10.7554/elife.31126] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/22/2017] [Indexed: 12/11/2022] Open
Abstract
As more people live longer, age-related neurodegenerative diseases are an increasingly important societal health issue. Treatments targeting specific pathologies such as amyloid beta in Alzheimer’s disease (AD) have not led to effective treatments, and there is increasing evidence of a disconnect between traditional pathology and cognitive abilities with advancing age, indicative of individual variation in resilience to pathology. Here, we generated a comprehensive neuropathological, molecular, and transcriptomic characterization of hippocampus and two regions cortex in 107 aged donors (median = 90) from the Adult Changes in Thought (ACT) study as a freely-available resource (http://aging.brain-map.org/). We confirm established associations between AD pathology and dementia, albeit with increased, presumably aging-related variability, and identify sets of co-expressed genes correlated with pathological tau and inflammation markers. Finally, we demonstrate a relationship between dementia and RNA quality, and find common gene signatures, highlighting the importance of properly controlling for RNA quality when studying dementia.
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Affiliation(s)
| | | | - Laura E Gibbons
- Department of Medicine, University of Washington, Seattle, United States
| | - Nadia Postupna
- Department of Pathology, University of Washington, Seattle, United States
| | - Anne Renz
- Kaiser Permanente Washington Health Research Institute, Seattle, United States
| | - Allison E Beller
- Department of Pathology, University of Washington, Seattle, United States
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, United States
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, United States
| | - Shannon E Rose
- Department of Pathology, University of Washington, Seattle, United States
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, United States
| | - Chris Barber
- Allen Institute for Brain Science, Seattle, United States
| | | | | | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, United States
| | | | - Mike Chapin
- Allen Institute for Brain Science, Seattle, United States
| | - Mindy L Chua
- Department of Pathology, University of Washington, Seattle, United States
| | - Natalie M Coleman
- Department of Pathology, University of Washington, Seattle, United States
| | - Eiron Cudaback
- Department of Pathology, University of Washington, Seattle, United States
| | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, United States
| | - Tsega Desta
- Allen Institute for Brain Science, Seattle, United States
| | - Tim A Dolbeare
- Allen Institute for Brain Science, Seattle, United States
| | | | - Michael Fisher
- Allen Institute for Brain Science, Seattle, United States
| | | | - Garrett Gee
- Allen Institute for Brain Science, Seattle, United States
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, United States
| | - Fiona Griffin
- Allen Institute for Brain Science, Seattle, United States
| | - Caroline Habel
- Allen Institute for Brain Science, Seattle, United States
| | - Zeb Haradon
- Allen Institute for Brain Science, Seattle, United States
| | - Nika Hejazinia
- Allen Institute for Brain Science, Seattle, United States
| | - Leanne L Hellstern
- Department of Pathology, University of Washington, Seattle, United States
| | - Steve Horvath
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Kim Howard
- Department of Pathology, University of Washington, Seattle, United States
| | - Robert Howard
- Allen Institute for Brain Science, Seattle, United States
| | - Justin Johal
- Allen Institute for Brain Science, Seattle, United States
| | - Nikolas L Jorstad
- Department of Pathology, University of Washington, Seattle, United States
| | - Samuel R Josephsen
- Department of Pathology, University of Washington, Seattle, United States
| | | | - Florence Lai
- Allen Institute for Brain Science, Seattle, United States
| | - Eric Lee
- Allen Institute for Brain Science, Seattle, United States
| | - Felix Lee
- Allen Institute for Brain Science, Seattle, United States
| | - Tracy Lemon
- Allen Institute for Brain Science, Seattle, United States
| | - Xianwu Li
- Department of Pathology, University of Washington, Seattle, United States
| | - Desiree A Marshall
- Department of Pathology, University of Washington, Seattle, United States
| | - Jose Melchor
- Allen Institute for Brain Science, Seattle, United States
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, United States
| | | | | | - Elizabeth Y Rha
- Department of Pathology, University of Washington, Seattle, United States
| | - Samantha Rice
- Department of Pathology, University of Washington, Seattle, United States
| | - David Rosen
- Allen Institute for Brain Science, Seattle, United States
| | - Abharika Sapru
- Department of Pathology, University of Washington, Seattle, United States
| | - Aimee Schantz
- Department of Pathology, University of Washington, Seattle, United States
| | - Elaine Shen
- Allen Institute for Brain Science, Seattle, United States
| | - Emily Sherfield
- Department of Pathology, University of Washington, Seattle, United States
| | - Shu Shi
- Allen Institute for Brain Science, Seattle, United States
| | - Andy J Sodt
- Allen Institute for Brain Science, Seattle, United States
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, United States
| | - Angela M Wilson
- Department of Pathology, University of Washington, Seattle, United States
| | - Thomas J Montine
- Department of Pathology, University of Washington, Seattle, United States
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, United States
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, United States
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle, United States
| | - Richard G Ellenbogen
- Department of Neurological Surgery, University of Washington, Seattle, United States
| | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, United States
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, United States
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13
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Abstract
Neurodegenerative diseases have a variety of different genes contributing to their underlying pathology. Unfortunately, for many of these diseases it is not clear how changes in gene expression affect pathology. Transcriptome analysis of neurodegenerative diseases using ribonucleic acid sequencing (RNA Seq) and real time quantitative polymerase chain reaction (RT-qPCR) provides for a platform to allow investigators to determine the contribution of various genes to the disease phenotype. In Alzheimer's disease (AD) there are several candidate genes reported that may be associated with the underlying pathology and are, in addition, alternatively spliced. Thus, AD is an ideal disease to examine how alternative splicing may affect pathology. In this context, genes of particular interest to AD pathology include the amyloid precursor protein (APP), TAU, and apolipoprotein E (APOE). Here, we review the evidence of alternative splicing of these genes in normal and AD patients, and recent therapeutic approaches to control splicing.
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Affiliation(s)
- Julia E Love
- Department of Biological Sciences, Science Building, Boise State University, USA
| | - Eric J Hayden
- Department of Biological Sciences, Science Building, Boise State University, USA
| | - Troy T Rohn
- Department of Biological Sciences, Science Building, Boise State University, USA
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