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Shahidehpour RK, Nelson PT, Bachstetter AD. A pathologic study of Perivascular pTDP-43 Lin bodies in LATE-NC. Acta Neuropathol Commun 2024; 12:114. [PMID: 38997773 PMCID: PMC11241908 DOI: 10.1186/s40478-024-01826-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND TAR DNA-Binding Protein 43 (TDP-43) pathological inclusions are a distinctive feature in dozens of neurodegenerative pathologies, including limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC). Prior investigations identified vascular-associated TDP-43-positive micro-lesions, known as "Lin bodies," located on or near the brain capillaries of some individuals with LATE-NC. This study aimed to investigate the relationship between the accumulation of Lin bodies and glial cells in LATE-NC and the potential co-localization with ferritin, a protein associated with iron storage. Using multiplexed immunohistochemistry and digital pathology tools, we conducted pathological analyses to investigate the relationship between Lin bodies and glial markers (GFAP for astrocytes, IBA1 for microglia) and ferritin. Analyses were conducted on post-mortem brain tissues collected from individuals with pathologically confirmed Alzheimer's disease neuropathological changes (ADNC) and LATE-NC. RESULTS As shown previously, there was a robust association between Lin bodies and GFAP-positive astrocyte processes. Moreover, we also observed Lin bodies frequently co-localizing with ferritin, suggesting a potential link to compromised vascular integrity. Subsequent analyses demonstrated increased astrocytosis near Lin body-positive vessels compared to those without Lin bodies, particularly in ADNC cases. These results suggest that the accumulation of Lin bodies may elicit an increased glial response, particularly among astrocytes, possibly related to impaired vascular integrity. CONCLUSIONS Lin bodies are associated with a local reactive glial response. The strong association of Lin bodies with ferritin suggests that the loss of vascular integrity may be either a cause or a consequence of the pTDP-43 pathology. The reactive glia surrounding the affected vessels could further compromise vascular function.
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Affiliation(s)
- Ryan K Shahidehpour
- Spinal cord and brain injury research center, Sander-Brown Center on Aging, Department of Neuroscience, University of Kentucky, 741 S. Limestone St, Lexington, KY, 40536, USA
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA
| | - Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, University of Kentucky, Lexington, KY, USA
| | - Adam D Bachstetter
- Spinal cord and brain injury research center, Sander-Brown Center on Aging, Department of Neuroscience, University of Kentucky, 741 S. Limestone St, Lexington, KY, 40536, USA.
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA.
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
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2
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Ewald CY, Pulous FE, Lok SWY, Pun FW, Aliper A, Ren F, Zhavoronkov A. TNIK's emerging role in cancer, metabolism, and age-related diseases. Trends Pharmacol Sci 2024; 45:478-489. [PMID: 38777670 DOI: 10.1016/j.tips.2024.04.010] [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: 03/09/2024] [Revised: 04/12/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024]
Abstract
Traf2- and Nck-interacting kinase (TNIK) has emerged as a key regulator of pathological metabolic signaling in several diseases and is a promising drug target. Originally studied for its role in cell migration and proliferation, TNIK possesses several newly identified functions that drive the pathogenesis of multiple diseases. Specifically, we evaluate TNIK's newfound roles in cancer, metabolic disorders, and neuronal function. We emphasize the implications of TNIK signaling in metabolic signaling and evaluate the translational potential of these discoveries. We also highlight how TNIK's role in many biological processes converges upon several hallmarks of aging. We conclude by discussing the therapeutic landscape of TNIK-targeting drugs and the recent success of clinical trials targeting TNIK.
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Affiliation(s)
- Collin Y Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach CH-8603, Switzerland
| | - Fadi E Pulous
- Insilico Medicine US Inc., 345 Park Avenue South, 2nd Floor Suite 006, New York, NY 10010, USA
| | - Sarah Wing Yan Lok
- Insilico Medicine Hong Kong Ltd., Unit 310, 3/F, Building 8W, Hong Kong Science and Technology Park, Hong Kong, SAR, China
| | - Frank W Pun
- Insilico Medicine Hong Kong Ltd., Unit 310, 3/F, Building 8W, Hong Kong Science and Technology Park, Hong Kong, SAR, China
| | - Alex Aliper
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, Masdar City, Abu Dhabi, UAE
| | - Feng Ren
- Insilico Medicine Shanghai Ltd., Suite 902, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong, Shanghai 201203, China
| | - Alex Zhavoronkov
- Insilico Medicine US Inc., 345 Park Avenue South, 2nd Floor Suite 006, New York, NY 10010, USA; Insilico Medicine Hong Kong Ltd., Unit 310, 3/F, Building 8W, Hong Kong Science and Technology Park, Hong Kong, SAR, China; Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, Masdar City, Abu Dhabi, UAE; Insilico Medicine Shanghai Ltd., Suite 902, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong, Shanghai 201203, China; Buck Institute for Research on Aging, Novato, CA 94945, USA.
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3
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Nelson PT, Fardo DW, Wu X, Aung KZ, Cykowski MD, Katsumata Y. Limbic-predominant age-related TDP-43 encephalopathy (LATE-NC): Co-pathologies and genetic risk factors provide clues about pathogenesis. J Neuropathol Exp Neurol 2024; 83:396-415. [PMID: 38613823 PMCID: PMC11110076 DOI: 10.1093/jnen/nlae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2024] Open
Abstract
Limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC) is detectable at autopsy in more than one-third of people beyond age 85 years and is robustly associated with dementia independent of other pathologies. Although LATE-NC has a large impact on public health, there remain uncertainties about the underlying biologic mechanisms. Here, we review the literature from human studies that may shed light on pathogenetic mechanisms. It is increasingly clear that certain combinations of pathologic changes tend to coexist in aging brains. Although "pure" LATE-NC is not rare, LATE-NC often coexists in the same brains with Alzheimer disease neuropathologic change, brain arteriolosclerosis, hippocampal sclerosis of aging, and/or age-related tau astrogliopathy (ARTAG). The patterns of pathologic comorbidities provide circumstantial evidence of mechanistic interactions ("synergies") between the pathologies, and also suggest common upstream influences. As to primary mediators of vulnerability to neuropathologic changes, genetics may play key roles. Genes associated with LATE-NC include TMEM106B, GRN, APOE, SORL1, ABCC9, and others. Although the anatomic distribution of TDP-43 pathology defines the condition, important cofactors for LATE-NC may include Tau pathology, endolysosomal pathways, and blood-brain barrier dysfunction. A review of the human phenomenology offers insights into disease-driving mechanisms, and may provide clues for diagnostic and therapeutic targets.
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Affiliation(s)
- Peter T Nelson
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky, USA
- Department of Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
| | - David W Fardo
- Department of Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky, USA
| | - Xian Wu
- Department of Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky, USA
| | - Khine Zin Aung
- Department of Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky, USA
| | - Matthew D Cykowski
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Yuriko Katsumata
- Department of Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky, USA
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4
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Sziraki A, Zhong Y, Neltner AM, Niedowicz D, Rogers CB, Wilcock DM, Nehra G, Neltner JH, Smith RR, Hartz AM, Cao J, Nelson PT. A high-throughput single-cell RNA expression profiling method identifies human pericyte markers. Neuropathol Appl Neurobiol 2023; 49:e12942. [PMID: 37812061 PMCID: PMC10842535 DOI: 10.1111/nan.12942] [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: 04/07/2023] [Revised: 09/19/2023] [Accepted: 10/02/2023] [Indexed: 10/10/2023]
Abstract
AIMS We sought to identify and optimise a universally available histological marker for pericytes in the human brain. Such a marker could be a useful tool for researchers. Further, identifying a gene expressed relatively specifically in human pericytes could provide new insights into the biological functions of this fascinating cell type. METHODS We analysed single-cell RNA expression profiles derived from different human and mouse brain regions using a high-throughput and low-cost single-cell transcriptome sequencing method called EasySci. Through this analysis, we were able to identify specific gene markers for pericytes, some of which had not been previously characterised. We then used commercially (and therefore universally) available antibodies to immunolabel the pericyte-specific gene products in formalin-fixed paraffin-embedded (FFPE) human brains and also performed immunoblots to determine whether appropriately sized proteins were recognised. RESULTS In the EasySci data sets, highly pericyte-enriched expression was notable for SLC6A12 and SLC19A1. Antibodies against these proteins recognised bands of approximately the correct size in immunoblots of human brain extracts. Following optimisation of the immunohistochemical technique, staining for both antibodies was strongly positive in small blood vessels and was far more effective than a PDGFRB antibody at staining pericyte-like cells in FFPE human brain sections. In an exploratory sample of other human organs (kidney, lung, liver, muscle), immunohistochemistry did not show the same pericyte-like pattern of staining. CONCLUSIONS The SLC6A12 antibody was well suited for labelling pericytes in human FFPE brain sections, based on the combined results of single-cell RNA-seq analyses, immunoblots and immunohistochemical studies.
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Affiliation(s)
- Andras Sziraki
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Yu Zhong
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
| | - Allison M. Neltner
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
| | - Dana Niedowicz
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
| | - Colin B. Rogers
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
| | - Donna M. Wilcock
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky, USA
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky, USA
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Geetika Nehra
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Janna H. Neltner
- Department of Pathology and Laboratory Science, University of Kentucky, Lexington, Kentucky, USA
| | - Rebecca R. Smith
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Anika M. Hartz
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Junyue Cao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Peter T. Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
- Department of Pathology and Laboratory Science, University of Kentucky, Lexington, Kentucky, USA
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5
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Gonzalez‐Rodriguez M, Villar‐Conde S, Astillero‐Lopez V, Villanueva‐Anguita P, Ubeda‐Banon I, Flores‐Cuadrado A, Martinez‐Marcos A, Saiz‐Sanchez D. Human amygdala involvement in Alzheimer's disease revealed by stereological and dia-PASEF analysis. Brain Pathol 2023; 33:e13180. [PMID: 37331354 PMCID: PMC10467039 DOI: 10.1111/bpa.13180] [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: 03/07/2023] [Accepted: 06/06/2023] [Indexed: 06/20/2023] Open
Abstract
Alzheimer's disease (AD) is characterized by the accumulation of pathological amyloid-β (Aβ) and Tau proteins. According to the prion-like hypothesis, both proteins can seed and disseminate through brain regions through neural connections and glial cells. The amygdaloid complex (AC) is involved early in the disease, and its widespread connections with other brain regions indicate that it is a hub for propagating pathology. To characterize changes in the AC as well as the involvement of neuronal and glial cells in AD, a combined stereological and proteomic analysis was performed in non-Alzheimer's disease and AD human samples. The synaptic alterations identified by proteomic data analysis could be related to the volume reduction observed in AD by the Cavalieri probe without neuronal loss. The pathological markers appeared in a gradient pattern with the medial region (cortical nucleus, Co) being more affected than lateral regions, suggesting the relevance of connections in the distribution of the pathology among different brain regions. Generalized astrogliosis was observed in every AC nucleus, likely related to deposits of pathological proteins. Astrocytes might mediate phagocytic microglial activation, whereas microglia might play a dual role since protective and toxic phenotypes have been described. These results highlight the potential participation of the amygdala in the disease spreading from/to olfactory areas, the temporal lobe and beyond. Proteomic data are available via ProteomeXchange with identifier PXD038322.
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Affiliation(s)
- Melania Gonzalez‐Rodriguez
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La ManchaCiudad RealSpain
| | - Sandra Villar‐Conde
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La ManchaCiudad RealSpain
| | - Veronica Astillero‐Lopez
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La ManchaCiudad RealSpain
| | - Patricia Villanueva‐Anguita
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La ManchaCiudad RealSpain
| | - Isabel Ubeda‐Banon
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La ManchaCiudad RealSpain
| | - Alicia Flores‐Cuadrado
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La ManchaCiudad RealSpain
| | - Alino Martinez‐Marcos
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La ManchaCiudad RealSpain
| | - Daniel Saiz‐Sanchez
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La ManchaCiudad RealSpain
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6
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Meyers TJ, Yin J, Herrera VA, Pressman AR, Hoffmann TJ, Schaefer C, Avins AL, Choquet H. Transcriptome-wide association study identifies novel candidate susceptibility genes for migraine. HGG ADVANCES 2023; 4:100211. [PMID: 37415806 PMCID: PMC10319829 DOI: 10.1016/j.xhgg.2023.100211] [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: 12/15/2022] [Accepted: 06/05/2023] [Indexed: 07/08/2023] Open
Abstract
Genome-wide association studies (GWASs) have identified more than 130 genetic susceptibility loci for migraine; however, how most of these loci impact migraine development is unknown. To identify novel genes associated with migraine and interpret the transcriptional products of those genes, we conducted a transcriptome-wide association study (TWAS). We performed tissue-specific and multi-tissue TWAS analyses to assess associations between imputed gene expression from 53 tissues and migraine susceptibility using FUSION software. Meta-analyzed GWAS summary statistics from 26,052 migraine cases and 487,214 controls, all of European ancestry and from two cohorts (the Kaiser Permanente GERA and the UK Biobank), were used. We evaluated the associations for genes after conditioning on variant-level effects from GWAS, and we tested for colocalization of GWAS migraine-associated loci and expression quantitative trait loci (eQTLs). Across tissue-specific and multi-tissue analyses, we identified 53 genes for which genetically predicted gene expression was associated with migraine after correcting for multiple testing. Of these 53 genes, 10 (ATF5, CNTNAP1, KTN1-AS1, NEIL1, NEK4, NNT, PNKP, RUFY2, TUBG2, and VAT1) did not overlap known migraine-associated loci identified from GWAS. Tissue-specific analysis identified 45 gene-tissue pairs and cardiovascular tissues represented the highest proportion of the Bonferroni-significant gene-tissue pairs (n = 22 [49%]), followed by brain tissues (n = 6 [13%]), and gastrointestinal tissues (n = 4 [9%]). Colocalization analyses provided evidence of shared genetic variants underlying eQTL and GWAS signals in 18 of the gene-tissue pairs (40%). Our TWAS reports novel genes for migraine and highlights the important contribution of brain, cardiovascular, and gastrointestinal tissues in migraine susceptibility.
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Affiliation(s)
- Travis J. Meyers
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Jie Yin
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Victor A. Herrera
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Alice R. Pressman
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
- Sutter Health, San Francisco, CA 94107, USA
| | - Thomas J. Hoffmann
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Catherine Schaefer
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Andrew L. Avins
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
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7
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Alur V, Raju V, Vastrad B, Vastrad C, Kavatagimath S, Kotturshetti S. Bioinformatics Analysis of Next Generation Sequencing Data Identifies Molecular Biomarkers Associated With Type 2 Diabetes Mellitus. Clin Med Insights Endocrinol Diabetes 2023; 16:11795514231155635. [PMID: 36844983 PMCID: PMC9944228 DOI: 10.1177/11795514231155635] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 01/19/2023] [Indexed: 02/23/2023] Open
Abstract
Background Type 2 diabetes mellitus (T2DM) is the most common metabolic disorder. The aim of the present investigation was to identify gene signature specific to T2DM. Methods The next generation sequencing (NGS) dataset GSE81608 was retrieved from the gene expression omnibus (GEO) database and analyzed to identify the differentially expressed genes (DEGs) between T2DM and normal controls. Then, Gene Ontology (GO) and pathway enrichment analysis, protein-protein interaction (PPI) network, modules, miRNA (micro RNA)-hub gene regulatory network construction and TF (transcription factor)-hub gene regulatory network construction, and topological analysis were performed. Receiver operating characteristic curve (ROC) analysis was also performed to verify the prognostic value of hub genes. Results A total of 927 DEGs (461 were up regulated and 466 down regulated genes) were identified in T2DM. GO and REACTOME results showed that DEGs mainly enriched in protein metabolic process, establishment of localization, metabolism of proteins, and metabolism. The top centrality hub genes APP, MYH9, TCTN2, USP7, SYNPO, GRB2, HSP90AB1, UBC, HSPA5, and SQSTM1 were screened out as the critical genes. ROC analysis provides prognostic value of hub genes. Conclusion The potential crucial genes, especially APP, MYH9, TCTN2, USP7, SYNPO, GRB2, HSP90AB1, UBC, HSPA5, and SQSTM1, might be linked with risk of T2DM. Our study provided novel insights of T2DM into genetics, molecular pathogenesis, and novel therapeutic targets.
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Affiliation(s)
- Varun Alur
- Department of Endocrinology, J.J.M
Medical College, Davanagere, Karnataka, India
| | - Varshita Raju
- Department of Obstetrics and
Gynecology, J.J.M Medical College, Davanagere, Karnataka, India
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry,
K.L.E. College of Pharmacy, Gadag, Karnataka, India
| | | | - Satish Kavatagimath
- Department of Pharmacognosy, K.L.E.
College of Pharmacy, Belagavi, Karnataka, India
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Falker-Gieske C, Paul NF, Spourita M, Gilthorpe JD, Gustmann K, Tetens J. Resistance to chicken amyloid arthropathy is associated with a dysfunctional mutation in serum amyloid A. FASEB J 2023; 37:e22700. [PMID: 36515677 DOI: 10.1096/fj.202200359rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 11/08/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
Abstract
Chicken amyloid arthropathy is a debilitating disease with a major impact on animal welfare. Since the disease is triggered by bacterial infection, preventative treatment also contributes to the widespread overuse of antibiotics. Bacterial infection initiates an acute phase response including increased serum amyloid A (SAA) production by the liver. SAA accumulates at sites of infection and in particular in large joints of affected birds. Interestingly, white egg-laying chickens (WL) are resistant to the disease whilst brown egg-laying chickens (BL) are most affected. Disease susceptibility has an immunological basis but the possible contribution of underlying genetic risk factors is not understood. Using a whole genome sequencing approach, we discovered a novel variant in the SAA gene in WL, which is predicted to result in an arginine to serine substitution at position 90 (SAA.R90S). Surprisingly, when overexpressed in chicken hepatocellular carcinoma cells, SAA.R90S was expressed at a higher rate and secreted to a greater degree than the wild-type SAA protein. Moreover, RNASeq analysis showed that the R90S mutant exerted a differential effect on the expression of core transcription factors linked to cell fate determination and cell differentiation. Comparative analysis of gene expression in murine CD4 T-cells stimulated with IL-6/SAA, suggests that SAA.R90S might block an induced cell fate change toward pro-inflammatory T helper 17 cells, which are required for immunological protection against pathogenic bacteria during an acute phase response. Our results provide first mechanistic insights into the genetic resistance of WL to amyloid arthropathy and could be applied to commercial layer breeding programs to improve animal welfare and reduce the negative effects of the overuse of antibiotics.
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Affiliation(s)
| | - Nora-Fabienne Paul
- Department of Animal Sciences, Georg-August-University, Göttingen, Germany
| | - Maria Spourita
- Department of Animal Sciences, Georg-August-University, Göttingen, Germany
| | | | - Karolin Gustmann
- Department of Animal Sciences, Georg-August-University, Göttingen, Germany
| | - Jens Tetens
- Department of Animal Sciences, Georg-August-University, Göttingen, Germany.,Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
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9
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Gal J, Katsumata Y, Zhu H, Srinivasan S, Chen J, Johnson LA, Wang WX, Golden LR, Wilcock DM, Jicha GA, Cykowski MD, Nelson PT. Apolipoprotein E Proteinopathy Is a Major Dementia-Associated Pathologic Biomarker in Individuals with or without the APOE Epsilon 4 Allele. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:564-578. [PMID: 34954207 PMCID: PMC8895423 DOI: 10.1016/j.ajpath.2021.11.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/27/2021] [Accepted: 11/24/2021] [Indexed: 12/14/2022]
Abstract
The amygdala is vulnerable to multiple or "mixed" mis-aggregated proteins associated with neurodegenerative conditions that can manifest clinically with amnestic dementia; the amygdala region is often affected even at earliest disease stages. With the original intent of identifying novel dementia-associated proteins, the detergent-insoluble proteome was characterized from the amygdalae of 40 participants from the University of Kentucky Alzheimer's Disease Center autopsy cohort. These individuals encompassed a spectrum of clinical conditions (cognitively normal to severe amnestic dementia). Polypeptides from the detergent-insoluble fraction were interrogated using liquid chromatography-electrospray ionization-tandem mass spectrometry. As anticipated, portions of peptides previously associated with neurologic diseases were enriched from subjects with dementia. Among all detected peptides, Apolipoprotein E (ApoE) stood out: even more than the expected Tau, APP/Aβ, and α-Synuclein peptides, ApoE peptides were strongly enriched in dementia cases, including from individuals lacking the APOE ε4 genotype. The amount of ApoE protein detected in detergent-insoluble fractions was robustly associated with levels of complement proteins C3 and C4. Immunohistochemical staining of APOE ε3/ε3 subjects' amygdalae confirmed ApoE co-localization with C4 in amyloid plaques. Thus, analyses of human amygdala proteomics indicate that rather than being only an "upstream" genetic risk factor, ApoE is an aberrantly aggregated protein in its own right, and show that the ApoE protein may play active disease-driving mechanistic roles in persons lacking the APOE ε4 allele.
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Affiliation(s)
- Jozsef Gal
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, Kentucky,Department of Neuroscience, University of Kentucky, Lexington, Kentucky
| | - Yuriko Katsumata
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky,Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky,Research & Development, Lexington VA Medical Center, Lexington, Kentucky
| | - Sukanya Srinivasan
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky
| | - Lance Allen Johnson
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky,Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
| | - Wang-Xia Wang
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky,Department of Pathology, University of Kentucky, Lexington, Kentucky
| | | | - Donna M. Wilcock
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky,Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky,Department of Physiology, University of Kentucky, Lexington, Kentucky
| | - Gregory A. Jicha
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky,Department of Neurology, University of Kentucky, Lexington, Kentucky
| | | | - Peter Tobias Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky; Department of Pathology, University of Kentucky, Lexington, Kentucky.
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10
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Srinivasan S, Gal J, Bachstetter A, Nelson PT. Alpha adaptins show isoform-specific association with neurofibrillary tangles in Alzheimer's disease. Neuropathol Appl Neurobiol 2022; 48:e12776. [PMID: 34820873 PMCID: PMC8810620 DOI: 10.1111/nan.12776] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 02/06/2023]
Abstract
AIMS The heterotetrameric assembly protein complex 2 (AP-2) is a central hub for clathrin-dependent endocytosis. The AP-2 α-adaptin subunit has two major isoforms, encoded by two separate genes: AP2A1 and AP2A2. Endocytosis has been implicated in the pathogenesis of neurodegenerative disease, and recent studies linked α-adaptins (gene variants, splicing defects and altered expression) with late-onset Alzheimer's disease (LOAD) risk. Here, we used multiple antibodies to investigate α-adaptin isoforms and their localization in human brains. METHODS The specificities of 10 different α-adaptin antibodies were evaluated using immunoblots after human AP2A1 and AP2A2 plasmid transfection in cultured cells. Additional immunoblot analyses were then performed on protein homogenates from control and LOAD subjects. Formalin-fixed, paraffin-embedded brain sections from control and LOAD subjects were immunohistochemically stained, and immunofluorescence experiments were performed for quantitation of colocalisation with digital image analysis. RESULTS Eight of the 10 evaluated antibodies recognised transfected α-adaptin proteins on immunoblots. The α-adaptin subspecies were relatively uniformly expressed in five different human brain regions. The α-adaptins were present in the detergent-insoluble fraction from cognitively impaired, but less so in control, brains. Immunohistochemical analyses showed colocalisation of AP2A1 with tau pathology in LOAD brains. By contrast, AP2A2 colocalised with microglial cells. CONCLUSIONS These observations provide evidence of isoform-specific changes of α-adaptins in the brains of LOAD subjects. Antibodies that were verified to recognise AP2A1, but not AP2A2, labelled neurofibrillary tangles of LOAD patients. The findings extend our understanding of AP-2 proteins in the human brain in healthy and diseased states.
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Affiliation(s)
- Sukanya Srinivasan
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, 40536
| | - Jozsef Gal
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY, 40536
- Department of Neuroscience, University of Kentucky, Lexington, KY, 40536
| | - Adam Bachstetter
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, 40536
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY, 40536
- Department of Neuroscience, University of Kentucky, Lexington, KY, 40536
| | - Peter T. Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, 40536
- Department of Pathology, University of Kentucky, Lexington, KY, 40536
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11
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Mirabnahrazam G, Ma D, Lee S, Popuri K, Lee H, Cao J, Wang L, Galvin JE, Beg MF. Machine Learning Based Multimodal Neuroimaging Genomics Dementia Score for Predicting Future Conversion to Alzheimer's Disease. J Alzheimers Dis 2022; 87:1345-1365. [PMID: 35466939 PMCID: PMC9195128 DOI: 10.3233/jad-220021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND The increasing availability of databases containing both magnetic resonance imaging (MRI) and genetic data allows researchers to utilize multimodal data to better understand the characteristics of dementia of Alzheimer's type (DAT). OBJECTIVE The goal of this study was to develop and analyze novel biomarkers that can help predict the development and progression of DAT. METHODS We used feature selection and ensemble learning classifier to develop an image/genotype-based DAT score that represents a subject's likelihood of developing DAT in the future. Three feature types were used: MRI only, genetic only, and combined multimodal data. We used a novel data stratification method to better represent different stages of DAT. Using a pre-defined 0.5 threshold on DAT scores, we predicted whether a subject would develop DAT in the future. RESULTS Our results on Alzheimer's Disease Neuroimaging Initiative (ADNI) database showed that dementia scores using genetic data could better predict future DAT progression for currently normal control subjects (Accuracy = 0.857) compared to MRI (Accuracy = 0.143), while MRI can better characterize subjects with stable mild cognitive impairment (Accuracy = 0.614) compared to genetics (Accuracy = 0.356). Combining MRI and genetic data showed improved classification performance in the remaining stratified groups. CONCLUSION MRI and genetic data can contribute to DAT prediction in different ways. MRI data reflects anatomical changes in the brain, while genetic data can detect the risk of DAT progression prior to the symptomatic onset. Combining information from multimodal data appropriately can improve prediction performance.
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Affiliation(s)
| | - Da Ma
- School of Engineering, Simon Fraser University, Burnaby, BC, Canada
- School of Medicine, Wake Forest University, Winston-Salem, NC, USA
| | - Sieun Lee
- School of Engineering, Simon Fraser University, Burnaby, BC, Canada
- Mental Health & Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Karteek Popuri
- School of Engineering, Simon Fraser University, Burnaby, BC, Canada
| | - Hyunwoo Lee
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jiguo Cao
- Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, BC, Canada
| | - Lei Wang
- Psychiatry and Behavioral Health, Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - James E Galvin
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mirza Faisal Beg
- School of Engineering, Simon Fraser University, Burnaby, BC, Canada
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12
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Florentinus-Mefailoski A, Bowden P, Scheltens P, Killestein J, Teunissen C, Marshall JG. The plasma peptides of Alzheimer's disease. Clin Proteomics 2021; 18:17. [PMID: 34182925 PMCID: PMC8240224 DOI: 10.1186/s12014-021-09320-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/20/2021] [Indexed: 02/06/2023] Open
Abstract
Background A practical strategy to discover proteins specific to Alzheimer’s dementia (AD) may be to compare the plasma peptides and proteins from patients with dementia to normal controls and patients with neurological conditions like multiple sclerosis or other diseases. The aim was a proof of principle for a method to discover proteins and/or peptides of plasma that show greater observation frequency and/or precursor intensity in AD. The endogenous tryptic peptides of Alzheimer’s were compared to normals, multiple sclerosis, ovarian cancer, breast cancer, female normal, sepsis, ICU Control, heart attack, along with their institution-matched controls, and normal samples collected directly onto ice. Methods Endogenous tryptic peptides were extracted from blinded, individual AD and control EDTA plasma samples in a step gradient of acetonitrile for random and independent sampling by LC–ESI–MS/MS with a set of robust and sensitive linear quadrupole ion traps. The MS/MS spectra were fit to fully tryptic peptides within proteins identified using the X!TANDEM algorithm. Observation frequency of the identified proteins was counted using SEQUEST algorithm. The proteins with apparently increased observation frequency in AD versus AD Control were revealed graphically and subsequently tested by Chi Square analysis. The proteins specific to AD plasma by Chi Square with FDR correction were analyzed by the STRING algorithm. The average protein or peptide log10 precursor intensity was compared across disease and control treatments by ANOVA in the R statistical system. Results Peptides and/or phosphopeptides of common plasma proteins such as complement C2, C7, and C1QBP among others showed increased observation frequency by Chi Square and/or precursor intensity in AD. Cellular gene symbols with large Chi Square values (χ2 ≥ 25, p ≤ 0.001) from tryptic peptides included KIF12, DISC1, OR8B12, ZC3H12A, TNF, TBC1D8B, GALNT3, EME2, CD1B, BAG1, CPSF2, MMP15, DNAJC2, PHACTR4, OR8B3, GCK, EXOSC7, HMGA1 and NT5C3A among others. Similarly, increased frequency of tryptic phosphopeptides were observed from MOK, SMIM19, NXNL1, SLC24A2, Nbla10317, AHRR, C10orf90, MAEA, SRSF8, TBATA, TNIK, UBE2G1, PDE4C, PCGF2, KIR3DP1, TJP2, CPNE8, and NGF amongst others. STRING analysis showed an increase in cytoplasmic proteins and proteins associated with alternate splicing, exocytosis of luminal proteins, and proteins involved in the regulation of the cell cycle, mitochondrial functions or metabolism and apoptosis. Increases in mean precursor intensity of peptides from common plasma proteins such as DISC1, EXOSC5, UBE2G1, SMIM19, NXNL1, PANO, EIF4G1, KIR3DP1, MED25, MGRN1, OR8B3, MGC24039, POLR1A, SYTL4, RNF111, IREB2, ANKMY2, SGKL, SLC25A5, CHMP3 among others were associated with AD. Tryptic peptides from the highly conserved C-terminus of DISC1 within the sequence MPGGGPQGAPAAAGGGGVSHRAGSRDCLPPAACFR and ARQCGLDSR showed a higher frequency and highest intensity in AD compared to all other disease and controls. Conclusion Proteins apparently expressed in the brain that were directly related to Alzheimer’s including Nerve Growth Factor (NFG), Sphingomyelin Phosphodiesterase, Disrupted in Schizophrenia 1 (DISC1), the cell death regulator retinitis pigmentosa (NXNl1) that governs the loss of nerve cells in the retina and the cell death regulator ZC3H12A showed much higher observation frequency in AD plasma vs the matched control. There was a striking agreement between the proteins known to be mutated or dis-regulated in the brains of AD patients with the proteins observed in the plasma of AD patients from endogenous peptides including NBN, BAG1, NOX1, PDCD5, SGK3, UBE2G1, SMPD3 neuronal proteins associated with synapse function such as KSYTL4, VTI1B and brain specific proteins such as TBATA. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-021-09320-2.
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Affiliation(s)
- Angelique Florentinus-Mefailoski
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada
| | - Peter Bowden
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada
| | - Philip Scheltens
- Alzheimer Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Joep Killestein
- MS Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Charlotte Teunissen
- Neurochemistry Lab and Biobank, Dept of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - John G Marshall
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada. .,International Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (Formerly CRP Sante Luxembourg), Strassen, Luxembourg.
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13
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Robinson JL, Porta S, Garrett FG, Zhang P, Xie SX, Suh E, Van Deerlin VM, Abner EL, Jicha GA, Barber JM, Lee VMY, Lee EB, Trojanowski JQ, Nelson PT. Limbic-predominant age-related TDP-43 encephalopathy differs from frontotemporal lobar degeneration. Brain 2021; 143:2844-2857. [PMID: 32830216 DOI: 10.1093/brain/awaa219] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/01/2020] [Accepted: 05/21/2020] [Indexed: 12/12/2022] Open
Abstract
TAR-DNA binding protein-43 (TDP-43) proteinopathy is seen in multiple brain diseases. A standardized terminology was recommended recently for common age-related TDP-43 proteinopathy: limbic-predominant, age-related TDP-43 encephalopathy (LATE) and the underlying neuropathological changes, LATE-NC. LATE-NC may be co-morbid with Alzheimer's disease neuropathological changes (ADNC). However, there currently are ill-defined diagnostic classification issues among LATE-NC, ADNC, and frontotemporal lobar degeneration with TDP-43 (FTLD-TDP). A practical challenge is that different autopsy cohorts are composed of disparate groups of research volunteers: hospital- and clinic-based cohorts are enriched for FTLD-TDP cases, whereas community-based cohorts have more LATE-NC cases. Neuropathological methods also differ across laboratories. Here, we combined both cases and neuropathologists' diagnoses from two research centres-University of Pennsylvania and University of Kentucky. The study was designed to compare neuropathological findings between FTLD-TDP and pathologically severe LATE-NC. First, cases were selected from the University of Pennsylvania with pathological diagnoses of either FTLD-TDP (n = 33) or severe LATE-NC (mostly stage 3) with co-morbid ADNC (n = 30). Sections from these University of Pennsylvania cases were cut from amygdala, anterior cingulate, superior/mid-temporal, and middle frontal gyrus. These sections were stained for phospho-TDP-43 immunohistochemically and evaluated independently by two University of Kentucky neuropathologists blinded to case data. A simple set of criteria hypothesized to differentiate FTLD-TDP from LATE-NC was generated based on density of TDP-43 immunoreactive neuronal cytoplasmic inclusions in the neocortical regions. Criteria-based sensitivity and specificity of differentiating severe LATE-NC from FTLD-TDP cases with blind evaluation was ∼90%. Another proposed neuropathological feature related to TDP-43 proteinopathy in aged individuals is 'Alpha' versus 'Beta' in amygdala. Alpha and Beta status was diagnosed by neuropathologists from both universities (n = 5 raters). There was poor inter-rater reliability of Alpha/Beta classification (mean κ = 0.31). We next tested a separate cohort of cases from University of Kentucky with either FTLD-TDP (n = 8) or with relatively 'pure' severe LATE-NC (lacking intermediate or severe ADNC; n = 14). The simple criteria were applied by neuropathologists blinded to the prior diagnoses at University of Pennsylvania. Again, the criteria for differentiating LATE-NC from FTLD-TDP was effective, with sensitivity and specificity ∼90%. If more representative cases from each cohort (including less severe TDP-43 proteinopathy) had been included, the overall accuracy for identifying LATE-NC was estimated at >98% for both cohorts. Also across both cohorts, cases with FTLD-TDP died younger than those with LATE-NC (P < 0.0001). We conclude that in most cases, severe LATE-NC and FTLD-TDP can be differentiated by applying simple neuropathological criteria.
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Affiliation(s)
- John L Robinson
- Alzheimer's Disease Core Center, University of Pennsyvania, Philadelphia, PA, USA.,Center for Neurodegenerative Disease Research, University of Pennsyvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsyvania, Philadelphia, PA, USA
| | - Sílvia Porta
- Alzheimer's Disease Core Center, University of Pennsyvania, Philadelphia, PA, USA.,Center for Neurodegenerative Disease Research, University of Pennsyvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsyvania, Philadelphia, PA, USA
| | - Filip G Garrett
- Department of Pathology, University of Kentucky, Lexington, KY, USA
| | - Panpan Zhang
- Alzheimer's Disease Core Center, University of Pennsyvania, Philadelphia, PA, USA.,Department of Biostatistics, Epidemiology and Informatics, University of Pennsyvania, Philadelphia, PA, USA
| | - Sharon X Xie
- Alzheimer's Disease Core Center, University of Pennsyvania, Philadelphia, PA, USA.,Department of Biostatistics, Epidemiology and Informatics, University of Pennsyvania, Philadelphia, PA, USA
| | - EunRan Suh
- Alzheimer's Disease Core Center, University of Pennsyvania, Philadelphia, PA, USA.,Center for Neurodegenerative Disease Research, University of Pennsyvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsyvania, Philadelphia, PA, USA
| | - Vivianna M Van Deerlin
- Alzheimer's Disease Core Center, University of Pennsyvania, Philadelphia, PA, USA.,Center for Neurodegenerative Disease Research, University of Pennsyvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsyvania, Philadelphia, PA, USA
| | - Erin L Abner
- Department of Epidemiology, University of Kentucky, Lexington, KY, USA.,Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Gregory A Jicha
- Department of Neurology, University of Kentucky, Lexington, KY, USA.,Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Justin M Barber
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Virginia M-Y Lee
- Alzheimer's Disease Core Center, University of Pennsyvania, Philadelphia, PA, USA.,Center for Neurodegenerative Disease Research, University of Pennsyvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsyvania, Philadelphia, PA, USA
| | - Edward B Lee
- Alzheimer's Disease Core Center, University of Pennsyvania, Philadelphia, PA, USA.,Center for Neurodegenerative Disease Research, University of Pennsyvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsyvania, Philadelphia, PA, USA
| | - John Q Trojanowski
- Alzheimer's Disease Core Center, University of Pennsyvania, Philadelphia, PA, USA.,Center for Neurodegenerative Disease Research, University of Pennsyvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsyvania, Philadelphia, PA, USA
| | - Peter T Nelson
- Department of Pathology, University of Kentucky, Lexington, KY, USA.,Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
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14
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Shahidehpour RK, Higdon RE, Crawford NG, Neltner JH, Ighodaro ET, Patel E, Price D, Nelson PT, Bachstetter AD. Dystrophic microglia are associated with neurodegenerative disease and not healthy aging in the human brain. Neurobiol Aging 2021; 99:19-27. [PMID: 33422891 PMCID: PMC8293930 DOI: 10.1016/j.neurobiolaging.2020.12.003] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/31/2020] [Accepted: 12/02/2020] [Indexed: 01/26/2023]
Abstract
Loss of physiological microglial function may increase the propagation of neurodegenerative diseases. Cellular senescence is a hallmark of aging; thus, we hypothesized age could be a cause of dystrophic microglia. Stereological counts were performed for total microglia, 2 microglia morphologies (hypertrophic and dystrophic) across the human lifespan. An age-associated increase in the number of dystrophic microglia was found in the hippocampus and frontal cortex. However, the increase in dystrophic microglia was proportional to the age-related increase in the total number of microglia. Thus, aging alone does not explain the presence of dystrophic microglia. We next tested if dystrophic microglia could be a disease-associated microglia morphology. Compared with controls, the number of dystrophic microglia was greater in cases with either Alzheimer's disease, dementia with Lewy bodies, or limbic-predominant age-related TDP-43 encephalopathy. These results demonstrate that microglia dystrophy, and not hypertrophic microglia, are the disease-associated microglia morphology. Finally, we found strong evidence for iron homeostasis changes in dystrophic microglia, providing a possible molecular mechanism driving the degeneration of microglia in neurodegenerative disease.
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Affiliation(s)
- Ryan K Shahidehpour
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, USA; Department of Neuroscience, University of Kentucky, Lexington, KY, USA
| | - Rebecca E Higdon
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, USA; Department of Neuroscience, University of Kentucky, Lexington, KY, USA
| | - Nicole G Crawford
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, USA; Department of Neuroscience, University of Kentucky, Lexington, KY, USA
| | - Janna H Neltner
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA; Department of Pathology and Laboratory Medicine, Division of Neuropathology, University of Kentucky, Lexington, KY, USA
| | - Eseosa T Ighodaro
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA; Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Ela Patel
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Douglas Price
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Peter T Nelson
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA; Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA; Department of Pathology and Laboratory Medicine, Division of Neuropathology, University of Kentucky, Lexington, KY, USA
| | - Adam D Bachstetter
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, USA; Department of Neuroscience, University of Kentucky, Lexington, KY, USA; Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
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15
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Hark TJ, Rao NR, Castillon C, Basta T, Smukowski S, Bao H, Upadhyay A, Bomba-Warczak E, Nomura T, O'Toole ET, Morgan GP, Ali L, Saito T, Guillermier C, Saido TC, Steinhauser ML, Stowell MHB, Chapman ER, Contractor A, Savas JN. Pulse-Chase Proteomics of the App Knockin Mouse Models of Alzheimer's Disease Reveals that Synaptic Dysfunction Originates in Presynaptic Terminals. Cell Syst 2020; 12:141-158.e9. [PMID: 33326751 DOI: 10.1016/j.cels.2020.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/23/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022]
Abstract
Compromised protein homeostasis underlies accumulation of plaques and tangles in Alzheimer's disease (AD). To observe protein turnover at early stages of amyloid beta (Aβ) proteotoxicity, we performed pulse-chase proteomics on mouse brains in three genetic models of AD that knock in alleles of amyloid precursor protein (APP) prior to the accumulation of plaques and during disease progression. At initial stages of Aβ accumulation, the turnover of proteins associated with presynaptic terminals is selectively impaired. Presynaptic proteins with impaired turnover, particularly synaptic vesicle (SV)-associated proteins, have elevated levels, misfold in both a plaque-dependent and -independent manner, and interact with APP and Aβ. Concurrent with elevated levels of SV-associated proteins, we found an enlargement of the SV pool as well as enhancement of presynaptic potentiation. Together, our findings reveal that the presynaptic terminal is particularly vulnerable and represents a critical site for manifestation of initial AD etiology. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Timothy J Hark
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nalini R Rao
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Charlotte Castillon
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Tamara Basta
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Samuel Smukowski
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Huan Bao
- Department of Neuroscience and Howard Hughes Medical Institute, University of Wisconsin, Madison, WI 53706, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Arun Upadhyay
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ewa Bomba-Warczak
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Toshihiro Nomura
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Eileen T O'Toole
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Garry P Morgan
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Laith Ali
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Takashi Saito
- Laboratory of Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan; Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Science, Nagoya, Aichi 467-8601, Japan
| | - Christelle Guillermier
- Center for NanoImaging, Brigham and Women's Hospital and Harvard Medical School, Cambridge, MA 02138, USA
| | - Takaomi C Saido
- Laboratory of Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Matthew L Steinhauser
- Center for NanoImaging, Brigham and Women's Hospital and Harvard Medical School, Cambridge, MA 02138, USA; Department of Medicine, Divisions of Genetics and Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Michael H B Stowell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA; Department of Mechanical Engineering, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Edwin R Chapman
- Department of Neuroscience and Howard Hughes Medical Institute, University of Wisconsin, Madison, WI 53706, USA
| | - Anis Contractor
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Neurobiology, Weinberg College of Arts and Sciences, Northwestern University, Chicago, IL 60611, USA
| | - Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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16
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Kepchia D, Huang L, Dargusch R, Rissman RA, Shokhirev MN, Fischer W, Schubert D. Diverse proteins aggregate in mild cognitive impairment and Alzheimer's disease brain. Alzheimers Res Ther 2020; 12:75. [PMID: 32560738 PMCID: PMC7305608 DOI: 10.1186/s13195-020-00641-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/04/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND All cells accumulate insoluble protein aggregates throughout their lifespan. While many studies have characterized the canonical disease-associated protein aggregates, such as those associated with amyloid plaques, additional, undefined proteins aggregate in the brain and may be directly associated with disease and lifespan. METHODS A proteomics approach was used to identify a large subset of insoluble proteins in the mild cognitively impaired (MCI) and Alzheimer's disease (AD) human brain. Cortical samples from control, MCI, and AD patients were separated into detergent-soluble and detergent-insoluble fractions, and high-resolution LC/MS/MS technology was used to determine which proteins became more insoluble in the disease state. Bioinformatics analyses were used to determine if the alteration of protein aggregation between AD and control patients was associated with any specific biological process. Western blots were used to validate the proteomics data and to assess the levels of secondary protein modifications in MCI and AD. RESULTS There was a stage-dependent increase in detergent-insoluble proteins, with more extreme changes occurring in the AD cohort. Glycolysis was the most significantly overrepresented gene ontology biological process associated with the alteration of protein aggregation between AD and control patients. It was further shown that many low molecular weight proteins that were enriched in the AD brain were also highly aggregated, migrating on SDS-PAGE far above their predicted molecular masses. Glucose-6-phosphate isomerase, ubiquitin carboxyl-terminal hydrolase isoenzyme L1 (UCHL1/PARK5), and the DNA damage repair enzyme KU70 were among the top insoluble proteins identified by proteomics and validated by Western blot to be increased in the insoluble fractions of both MCI and AD brain samples. CONCLUSIONS Diverse proteins became more detergent-insoluble in the brains of both MCI and AD patients compared to age-matched controls, suggesting that multiple proteins aggregate in these diseases, likely posing a direct toxic insult to neurons. Furthermore, detergent-insoluble proteins included those with important biological activities for critical cellular processes such as energetics, proteolysis, and DNA damage repair. Thus, reduced protein solubility likely promotes aggregation and limits functionality, reducing the efficiency of multiple aspects of cell physiology. Pharmaceutical interventions that increase autophagy may provide a useful therapeutic treatment to combat protein aggregation.
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Affiliation(s)
- Devin Kepchia
- Cellular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
| | - Ling Huang
- The Razavi Newman Integrative Genomics and Bioinformatics Core, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Richard Dargusch
- Cellular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Robert A Rissman
- Department of Neurosciences and Shiley-Marcos Alzheimer's Disease Research Center Neuropathology Core, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Maxim N Shokhirev
- The Razavi Newman Integrative Genomics and Bioinformatics Core, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Wolfgang Fischer
- Cellular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - David Schubert
- Cellular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
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Yagensky O, Kohansal-Nodehi M, Gunaseelan S, Rabe T, Zafar S, Zerr I, Härtig W, Urlaub H, Chua JJ. Increased expression of heme-binding protein 1 early in Alzheimer's disease is linked to neurotoxicity. eLife 2019; 8:47498. [PMID: 31453805 PMCID: PMC6739868 DOI: 10.7554/elife.47498] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/25/2019] [Indexed: 12/15/2022] Open
Abstract
Alzheimer’s disease is the most prevalent neurodegenerative disorder leading to progressive cognitive decline. Despite decades of research, understanding AD progression at the molecular level, especially at its early stages, remains elusive. Here, we identified several presymptomatic AD markers by investigating brain proteome changes over the course of neurodegeneration in a transgenic mouse model of AD (3×Tg-AD). We show that one of these markers, heme-binding protein 1 (Hebp1), is elevated in the brains of both 3×Tg-AD mice and patients affected by rapidly-progressing forms of AD. Hebp1, predominantly expressed in neurons, interacts with the mitochondrial contact site complex (MICOS) and exhibits a perimitochondrial localization. Strikingly, wildtype, but not Hebp1-deficient, neurons showed elevated cytotoxicity in response to heme-induced apoptosis. Increased survivability in Hebp1-deficient neurons is conferred by blocking the activation of the mitochondrial-associated caspase signaling pathway. Taken together, our data highlight a role of Hebp1 in progressive neuronal loss during AD progression.
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Affiliation(s)
- Oleksandr Yagensky
- Research Group Protein Trafficking in Synaptic Development and Function, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Saravanan Gunaseelan
- Interactomics and Intracellular Trafficking Laboratory, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tamara Rabe
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Saima Zafar
- Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan.,Clinical Dementia Center, Department of Neurology, German Center for Neurodegenerative Diseases, University Medical Center Göttingen, Göttingen, Germany
| | - Inga Zerr
- Clinical Dementia Center, Department of Neurology, German Center for Neurodegenerative Diseases, University Medical Center Göttingen, Göttingen, Germany
| | - Wolfgang Härtig
- Paul Flechsig Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - Henning Urlaub
- Research Group Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - John Je Chua
- Research Group Protein Trafficking in Synaptic Development and Function, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Interactomics and Intracellular Trafficking Laboratory, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,LSI Neurobiology Programme, National University of Singapore, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
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18
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Li Y, Xie L, Huang T, Zhang Y, Zhou J, Qi B, Wang X, Chen Z, Li P. Aging Neurovascular Unit and Potential Role of DNA Damage and Repair in Combating Vascular and Neurodegenerative Disorders. Front Neurosci 2019; 13:778. [PMID: 31440124 PMCID: PMC6694749 DOI: 10.3389/fnins.2019.00778] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 07/11/2019] [Indexed: 02/01/2023] Open
Abstract
Progressive neurological deterioration poses enormous burden on the aging population with ischemic stroke and neurodegenerative disease patients, such as Alzheimers’ disease and Parkinson’s disease. The past two decades have witnessed remarkable advances in the research of neurovascular unit dysfunction, which is emerging as an important pathological feature that underlies these neurological disorders. Dysfunction of the unit allows penetration of blood-derived toxic proteins or leukocytes into the brain and contributes to white matter injury, disturbed neurovascular coupling and neuroinflammation, which all eventually lead to cognitive dysfunction. Recent evidences suggest that aging-related oxidative stress, accumulated DNA damage and impaired DNA repair capacities compromises the genome integrity not only in neurons, but also in other cell types of the neurovascular unit, such as endothelial cells, astrocytes and pericytes. Combating DNA damage or enhancing DNA repair capacities in the neurovascular unit represents a promising therapeutic strategy for vascular and neurodegenerative disorders. In this review, we focus on aging related mechanisms that underlie DNA damage and repair in the neurovascular unit and introduce several novel strategies that target the genome integrity in the neurovascular unit to combat the vascular and neurodegenerative disorders in the aging brain.
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Affiliation(s)
- Yan Li
- Department of Anesthesiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lv Xie
- Department of Anesthesiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tingting Huang
- Department of Anesthesiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yueman Zhang
- Department of Anesthesiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Zhou
- Department of Anesthesiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Qi
- Department of Anesthesiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Wang
- Department of Anesthesiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zengai Chen
- Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Peiying Li
- Department of Anesthesiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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19
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TDP-43 proteinopathy in aging: Associations with risk-associated gene variants and with brain parenchymal thyroid hormone levels. Neurobiol Dis 2019; 125:67-76. [PMID: 30682540 DOI: 10.1016/j.nbd.2019.01.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/13/2019] [Accepted: 01/19/2019] [Indexed: 02/08/2023] Open
Abstract
TDP-43 proteinopathy is very prevalent among the elderly (affecting at least 25% of individuals over 85 years of age) and is associated with substantial cognitive impairment. Risk factors implicated in age-related TDP-43 proteinopathy include commonly inherited gene variants, comorbid Alzheimer's disease pathology, and thyroid hormone dysfunction. To test parameters that are associated with aging-related TDP-43 pathology, we performed exploratory analyses of pathologic, genetic, and biochemical data derived from research volunteers in the University of Kentucky Alzheimer's Disease Center autopsy cohort (n = 136 subjects). Digital pathologic methods were used to discriminate and quantify both neuritic and intracytoplasmic TDP-43 pathology in the hippocampal formation. Overall, 46.4% of the cases were positive for TDP-43 intracellular inclusions, which is consistent with results in other prior community-based cohorts. The pathologies were correlated with hippocampal sclerosis of aging (HS-Aging) linked genotypes. We also assayed brain parenchymal thyroid hormone (triiodothyronine [T3] and thyroxine [T4]) levels. In cases with SLCO1A2/IAPP or ABCC9 risk associated genotypes, the T3/T4 ratio tended to be reduced (p = .051 using 2-tailed statistical test), and in cases with low T3/T4 ratios (bottom quintile), there was a higher likelihood of HS-Aging pathology (p = .025 using 2-tailed statistical test). This is intriguing because the SLCO1A2/IAPP and ABCC9 risk associated genotypes have been associated with altered expression of the astrocytic thyroid hormone receptor (protein product of the nearby gene SLCO1C1). These data indicate that dysregulation of thyroid hormone signaling may play a role in age-related TDP-43 proteinopathy.
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