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Denning AE, Ittyerah R, Levorse LM, Sadeghpour N, Athalye C, Chung E, Ravikumar S, Dong M, Duong MT, Li Y, Ilesanmi A, Sreepada LP, Sabatini P, Lowe M, Bahena A, Zablah J, Spencer BE, Watanabe R, Kim B, Sørensen MH, Khandelwal P, Brown C, Hrybouski S, Xie SX, de Flores R, Robinson JL, Schuck T, Ohm DT, Arezoumandan S, Porta S, Detre JA, Insausti R, Wisse LEM, Das SR, Irwin DJ, Lee EB, Wolk DA, Yushkevich PA. Association of quantitative histopathology measurements with antemortem medial temporal lobe cortical thickness in the Alzheimer's disease continuum. Acta Neuropathol 2024; 148:37. [PMID: 39227502 PMCID: PMC11371872 DOI: 10.1007/s00401-024-02789-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/07/2024] [Accepted: 08/15/2024] [Indexed: 09/05/2024]
Abstract
The medial temporal lobe (MTL) is a hotspot for neuropathology, and measurements of MTL atrophy are often used as a biomarker for cognitive decline associated with neurodegenerative disease. Due to the aggregation of multiple proteinopathies in this region, the specific relationship of MTL atrophy to distinct neuropathologies is not well understood. Here, we develop two quantitative algorithms using deep learning to measure phosphorylated tau (p-tau) and TDP-43 (pTDP-43) pathology, which are both known to accumulate in the MTL and are associated with MTL neurodegeneration. We focus on these pathologies in the context of Alzheimer's disease (AD) and limbic predominant age-related TDP-43 encephalopathy (LATE) and apply our deep learning algorithms to distinct histology sections, on which MTL subregions were digitally annotated. We demonstrate that both quantitative pathology measures show high agreement with expert visual ratings of pathology and discriminate well between pathology stages. In 140 cases with antemortem MR imaging, we compare the association of semi-quantitative and quantitative postmortem measures of these pathologies in the hippocampus with in vivo structural measures of the MTL and its subregions. We find widespread associations of p-tau pathology with MTL subregional structural measures, whereas pTDP-43 pathology had more limited associations with the hippocampus and entorhinal cortex. Quantitative measurements of p-tau pathology resulted in a significantly better model of antemortem structural measures than semi-quantitative ratings and showed strong associations with cortical thickness and volume. By providing a more granular measure of pathology, the quantitative p-tau measures also showed a significant negative association with structure in a severe AD subgroup where semi-quantitative ratings displayed a ceiling effect. Our findings demonstrate the advantages of using quantitative neuropathology to understand the relationship of pathology to structure, particularly for p-tau, and motivate the use of quantitative pathology measurements in future studies.
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Affiliation(s)
- Amanda E Denning
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Ranjit Ittyerah
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Lisa M Levorse
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Chinmayee Athalye
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Eunice Chung
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Sadhana Ravikumar
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Mengjin Dong
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Tran Duong
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Yue Li
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ademola Ilesanmi
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Lasya P Sreepada
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Philip Sabatini
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - MaKayla Lowe
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Alejandra Bahena
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jamila Zablah
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Barbara E Spencer
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryohei Watanabe
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Neurodegenerative Disease Research, Institute On Aging, University of Pennsylvania, Philadelphia, PA, USA
| | - Boram Kim
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Neurodegenerative Disease Research, Institute On Aging, University of Pennsylvania, Philadelphia, PA, USA
| | - Maja Højvang Sørensen
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Neurodegenerative Disease Research, Institute On Aging, University of Pennsylvania, Philadelphia, PA, USA
| | - Pulkit Khandelwal
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher Brown
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Sharon X Xie
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Robin de Flores
- UMR-S U1237, PhIND "Physiopathology and Imaging of Neurological Disorders", Institut Blood and Brain @ Caen-Normandie, INSERM, Caen-Normandie University, GIP Cyceron, Caen, France
| | - John L Robinson
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Neurodegenerative Disease Research, Institute On Aging, University of Pennsylvania, Philadelphia, PA, USA
| | - Theresa Schuck
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Neurodegenerative Disease Research, Institute On Aging, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel T Ohm
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Sanaz Arezoumandan
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Sílvia Porta
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Neurodegenerative Disease Research, Institute On Aging, University of Pennsylvania, Philadelphia, PA, USA
| | - John A Detre
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ricardo Insausti
- Human Neuroanatomy Lab, University of Castilla La Mancha, Albacete, Spain
| | - Laura E M Wisse
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Sandhitsu R Das
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - David J Irwin
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward B Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Neurodegenerative Disease Research, Institute On Aging, University of Pennsylvania, Philadelphia, PA, USA
| | - David A Wolk
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul A Yushkevich
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
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Scalco R, Oliveira LC, Lai Z, Harvey DJ, Abujamil L, DeCarli C, Jin LW, Chuah CN, Dugger BN. Machine learning quantification of Amyloid-β deposits in the temporal lobe of 131 brain bank cases. Acta Neuropathol Commun 2024; 12:134. [PMID: 39154006 PMCID: PMC11330038 DOI: 10.1186/s40478-024-01827-7] [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: 05/20/2024] [Accepted: 06/18/2024] [Indexed: 08/19/2024] Open
Abstract
Accurate and scalable quantification of amyloid-β (Aβ) pathology is crucial for deeper disease phenotyping and furthering research in Alzheimer Disease (AD). This multidisciplinary study addresses the current limitations on neuropathology by leveraging a machine learning (ML) pipeline to perform a granular quantification of Aβ deposits and assess their distribution in the temporal lobe. Utilizing 131 whole-slide-images from consecutive autopsied cases at the University of California Davis Alzheimer Disease Research Center, our objectives were threefold: (1) Validate an automatic workflow for Aβ deposit quantification in white matter (WM) and gray matter (GM); (2) define the distributions of different Aβ deposit types in GM and WM, and (3) investigate correlates of Aβ deposits with dementia status and the presence of mixed pathology. Our methodology highlights the robustness and efficacy of the ML pipeline, demonstrating proficiency akin to experts' evaluations. We provide comprehensive insights into the quantification and distribution of Aβ deposits in the temporal GM and WM revealing a progressive increase in tandem with the severity of established diagnostic criteria (NIA-AA). We also present correlations of Aβ load with clinical diagnosis as well as presence/absence of mixed pathology. This study introduces a reproducible workflow, showcasing the practical use of ML approaches in the field of neuropathology, and use of the output data for correlative analyses. Acknowledging limitations, such as potential biases in the ML model and current ML classifications, we propose avenues for future research to refine and expand the methodology. We hope to contribute to the broader landscape of neuropathology advancements, ML applications, and precision medicine, paving the way for deep phenotyping of AD brain cases and establishing a foundation for further advancements in neuropathological research.
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Affiliation(s)
- Rebeca Scalco
- Department of Pathology and Laboratory Medicine, University of California Davis, 4645 2nd Ave. 3400a research building III, Sacramento, CA, 95817, USA
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland
| | - Luca C Oliveira
- Department of Pathology and Laboratory Medicine, University of California Davis, 4645 2nd Ave. 3400a research building III, Sacramento, CA, 95817, USA
- Department of Electrical and Computer Engineering, University of California Davis, Davis, CA, USA
| | - Zhengfeng Lai
- Department of Pathology and Laboratory Medicine, University of California Davis, 4645 2nd Ave. 3400a research building III, Sacramento, CA, 95817, USA
- Department of Electrical and Computer Engineering, University of California Davis, Davis, CA, USA
| | - Danielle J Harvey
- Department of Pathology and Laboratory Medicine, University of California Davis, 4645 2nd Ave. 3400a research building III, Sacramento, CA, 95817, USA
- Department of Public Health Sciences, University of California Davis, School of Medicine, Sacramento, CA, USA
| | - Lana Abujamil
- Department of Pathology and Laboratory Medicine, University of California Davis, 4645 2nd Ave. 3400a research building III, Sacramento, CA, 95817, USA
| | - Charles DeCarli
- Department of Neurology, University of California Davis, School of Medicine, Sacramento, CA, USA
| | - Lee-Way Jin
- Department of Pathology and Laboratory Medicine, University of California Davis, 4645 2nd Ave. 3400a research building III, Sacramento, CA, 95817, USA
| | - Chen-Nee Chuah
- Department of Electrical and Computer Engineering, University of California Davis, Davis, CA, USA
| | - Brittany N Dugger
- Department of Pathology and Laboratory Medicine, University of California Davis, 4645 2nd Ave. 3400a research building III, Sacramento, CA, 95817, USA.
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Koga S, Martin NB, Dickson DW. Evaluating the performance of large language models: ChatGPT and Google Bard in generating differential diagnoses in clinicopathological conferences of neurodegenerative disorders. Brain Pathol 2024; 34:e13207. [PMID: 37553205 PMCID: PMC11006994 DOI: 10.1111/bpa.13207] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/31/2023] [Indexed: 08/10/2023] Open
Abstract
This study explores the utility of the large language models (LLMs), specifically ChatGPT and Google Bard, in predicting neuropathologic diagnoses from clinical summaries. A total of 25 cases of neurodegenerative disorders presented at Mayo Clinic brain bank Clinico-Pathological Conferences were analyzed. The LLMs provided multiple pathologic diagnoses and their rationales, which were compared with the final clinical diagnoses made by physicians. ChatGPT-3.5, ChatGPT-4, and Google Bard correctly made primary diagnoses in 32%, 52%, and 40% of cases, respectively, while correct diagnoses were included in 76%, 84%, and 76% of cases, respectively. These findings highlight the potential of artificial intelligence tools like ChatGPT in neuropathology, suggesting they may facilitate more comprehensive discussions in clinicopathological conferences.
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Affiliation(s)
- Shunsuke Koga
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
- Present address:
Department of Pathology and Laboratory MedicineHospital of the University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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Morderer D, Wren MC, Liu F, Kouri N, Maistrenko A, Khalil B, Pobitzer N, Salemi M, Phinney BS, Dickson DW, Murray ME, Rossoll W. Probe-dependent Proximity Profiling (ProPPr) Uncovers Similarities and Differences in Phospho-Tau-Associated Proteomes Between Tauopathies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.585597. [PMID: 38585836 PMCID: PMC10996607 DOI: 10.1101/2024.03.25.585597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Tauopathies represent a diverse group of neurodegenerative disorders characterized by the abnormal aggregation of the microtubule-associated protein tau. Despite extensive research, the precise mechanisms underlying the complexity of different types of tau pathology remain incompletely understood. Here we describe an approach for proteomic profiling of aggregate-associated proteomes on slides with formalin-fixed, paraffin-embedded (FFPE) tissue that utilizes proximity labelling upon high preservation of aggregate morphology, which permits the profiling of pathological aggregates regardless of their size. To comprehensively investigate the common and unique protein interactors associated with the variety of tau lesions present across different human tauopathies, Alzheimer's disease (AD), corticobasal degeneration (CBD), Pick's disease (PiD), and progressive supranuclear palsy (PSP), were selected to represent the major tauopathy diseases. Implementation of our widely applicable Probe-dependent Proximity Profiling (ProPPr) strategy, using the AT8 antibody, permitted identification and quantification of proteins associated with phospho-tau lesions in well-characterized human post-mortem tissue. The analysis revealed both common and disease-specific proteins associated with phospho-tau aggregates, highlighting potential targets for therapeutic intervention and biomarker development. Candidate validation through high-resolution co-immunofluorescence of distinct aggregates across disease and control cases, confirmed the association of retromer complex protein VPS35 with phospho-tau lesions across the studied tauopathies. Furthermore, we discovered disease-specific associations of proteins including ferritin light chain (FTL) and the neuropeptide precursor VGF within distinct pathological lesions. Notably, examination of FTL-positive microglia in CBD astrocytic plaques indicate a potential role for microglial involvement in the pathogenesis of these tau lesions. Our findings provide valuable insights into the proteomic landscape of tauopathies, shedding light on the molecular mechanisms underlying tau pathology. This first comprehensive characterization of tau-associated proteomes across different tauopathies enhances our understanding of disease heterogeneity and provides a resource for future functional investigation, as well as development of targeted therapies and diagnostic biomarkers.
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Maldonado-Díaz C, Hiya S, Yokoda RT, Farrell K, Marx GA, Kauffman J, Daoud EV, Gonzales MM, Parker AS, Canbeldek L, Kulumani Mahadevan LS, Crary JF, White CL, Walker JM, Richardson TE. Disentangling and quantifying the relative cognitive impact of concurrent mixed neurodegenerative pathologies. Acta Neuropathol 2024; 147:58. [PMID: 38520489 PMCID: PMC10960766 DOI: 10.1007/s00401-024-02716-y] [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: 01/12/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Neurodegenerative pathologies such as Alzheimer disease neuropathologic change (ADNC), Lewy body disease (LBD), limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC), and cerebrovascular disease (CVD) frequently coexist, but little is known about the exact contribution of each pathology to cognitive decline and dementia in subjects with mixed pathologies. We explored the relative cognitive impact of concurrent common and rare neurodegenerative pathologies employing multivariate logistic regression analysis adjusted for age, gender, and level of education. We analyzed a cohort of 6,262 subjects from the National Alzheimer's Coordinating Center database, ranging from 0 to 6 comorbid neuropathologic findings per individual, where 95.7% of individuals had at least 1 neurodegenerative finding at autopsy and 75.5% had at least 2 neurodegenerative findings. We identified which neuropathologic entities correlate most frequently with one another and demonstrated that the total number of pathologies per individual was directly correlated with cognitive performance as assessed by Clinical Dementia Rating (CDR®) and Mini-Mental State Examination (MMSE). We show that ADNC, LBD, LATE-NC, CVD, hippocampal sclerosis, Pick disease, and FTLD-TDP significantly impact overall cognition as independent variables. More specifically, ADNC significantly affected all assessed cognitive domains, LBD affected attention, processing speed, and language, LATE-NC primarily affected tests related to logical memory and language, while CVD and other less common pathologies (including Pick disease, progressive supranuclear palsy, and corticobasal degeneration) had more variable neurocognitive effects. Additionally, ADNC, LBD, and higher numbers of comorbid neuropathologies were associated with the presence of at least one APOE ε4 allele, and ADNC and higher numbers of neuropathologies were inversely correlated with APOE ε2 alleles. Understanding the mechanisms by which individual and concomitant neuropathologies affect cognition and the degree to which each contributes is an imperative step in the development of biomarkers and disease-modifying therapeutics, particularly as these medical interventions become more targeted and personalized.
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Affiliation(s)
- Carolina Maldonado-Díaz
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15.238, 1468 Madison Avenue, New York, NY, 10029, USA
| | - Satomi Hiya
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15.238, 1468 Madison Avenue, New York, NY, 10029, USA
| | - Raquel T Yokoda
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15.238, 1468 Madison Avenue, New York, NY, 10029, USA
| | - Kurt Farrell
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15.238, 1468 Madison Avenue, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Ronal M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gabriel A Marx
- Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Ronal M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Justin Kauffman
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15.238, 1468 Madison Avenue, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Ronal M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Elena V Daoud
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Mitzi M Gonzales
- Department of Neurology, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Neurology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Alicia S Parker
- Department of Neurology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Leyla Canbeldek
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15.238, 1468 Madison Avenue, New York, NY, 10029, USA
| | - Lakshmi Shree Kulumani Mahadevan
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15.238, 1468 Madison Avenue, New York, NY, 10029, USA
| | - John F Crary
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15.238, 1468 Madison Avenue, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Ronal M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Charles L White
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jamie M Walker
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15.238, 1468 Madison Avenue, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Timothy E Richardson
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15.238, 1468 Madison Avenue, New York, NY, 10029, USA.
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Walker JM, Orr ME, Orr TC, Thorn EL, Christie TD, Yokoda RT, Vij M, Ehrenberg AJ, Marx GA, McKenzie AT, Kauffman J, Selmanovic E, Wisniewski T, Drummond E, White CL, Crary JF, Farrell K, Kautz TF, Daoud EV, Richardson TE. Spatial proteomics of hippocampal subfield-specific pathology in Alzheimer's disease and primary age-related tauopathy. Alzheimers Dement 2024; 20:783-797. [PMID: 37777848 PMCID: PMC10916977 DOI: 10.1002/alz.13484] [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: 07/06/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 10/02/2023]
Abstract
INTRODUCTION Alzheimer's disease (AD) and primary age-related tauopathy (PART) both harbor 3R/4R hyperphosphorylated-tau (p-tau)-positive neurofibrillary tangles (NFTs) but differ in the spatial p-tau development in the hippocampus. METHODS Using Nanostring GeoMx Digital Spatial Profiling, we compared protein expression within hippocampal subregions in NFT-bearing and non-NFT-bearing neurons in AD (n = 7) and PART (n = 7) subjects. RESULTS Proteomic measures of synaptic health were inversely correlated with the subregional p-tau burden in AD and PART, and there were numerous differences in proteins involved in proteostasis, amyloid beta (Aβ) processing, inflammation, microglia, oxidative stress, and neuronal/synaptic health between AD and PART and between definite PART and possible PART. DISCUSSION These results suggest subfield-specific proteome differences that may explain some of the differences in Aβ and p-tau distribution and apparent pathogenicity. In addition, hippocampal neurons in possible PART may have more in common with AD than with definite PART, highlighting the importance of Aβ in the pathologic process. HIGHLIGHTS Synaptic health is inversely correlated with local p-tau burden. The proteome of NFT- and non-NFT-bearing neurons is influenced by the presence of Aβ in the hippocampus. Neurons in possible PART cases share more proteomic similarities with neurons in ADNC than they do with neurons in definite PART cases.
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Vizcarra JC, Pearce TM, Dugger BN, Keiser MJ, Gearing M, Crary JF, Kiely EJ, Morris M, White B, Glass JD, Farrell K, Gutman DA. Toward a generalizable machine learning workflow for neurodegenerative disease staging with focus on neurofibrillary tangles. Acta Neuropathol Commun 2023; 11:202. [PMID: 38110981 PMCID: PMC10726581 DOI: 10.1186/s40478-023-01691-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/19/2023] [Indexed: 12/20/2023] Open
Abstract
Machine learning (ML) has increasingly been used to assist and expand current practices in neuropathology. However, generating large imaging datasets with quality labels is challenging in fields which demand high levels of expertise. Further complicating matters is the often seen disagreement between experts in neuropathology-related tasks, both at the case level and at a more granular level. Neurofibrillary tangles (NFTs) are a hallmark pathological feature of Alzheimer disease, and are associated with disease progression which warrants further investigation and granular quantification at a scale not currently accessible in routine human assessment. In this work, we first provide a baseline of annotator/rater agreement for the tasks of Braak NFT staging between experts and NFT detection using both experts and novices in neuropathology. We use a whole-slide-image (WSI) cohort of neuropathology cases from Emory University Hospital immunohistochemically stained for Tau. We develop a workflow for gathering annotations of the early stage formation of NFTs (Pre-NFTs) and mature intracellular (iNFTs) and show ML models can be trained to learn annotator nuances for the task of NFT detection in WSIs. We utilize a model-assisted-labeling approach and demonstrate ML models can be used to aid in labeling large datasets efficiently. We also show these models can be used to extract case-level features, which predict Braak NFT stages comparable to expert human raters, and do so at scale. This study provides a generalizable workflow for various pathology and related fields, and also provides a technique for accomplishing a high-level neuropathology task with limited human annotations.
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Affiliation(s)
- Juan C Vizcarra
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Dr NW, Atlanta, GA, 30332, USA
| | - Thomas M Pearce
- Department of Pathology, Division of Neuropathology, University of Pittsburgh Medical Center, Room S701 Scaife Hall 3550 Terrace Street, Pittsburgh, PA, 15261, USA
| | - Brittany N Dugger
- Department of Pathology and Laboratory Medicine, University of California-Davis School of Medicine, 3400A Research Building III Sacramento, Davis, CA, 95817, USA
| | - Michael J Keiser
- Department of Pharmaceutical Chemistry, Department of Bioengineering and Therapeutic Sciences, Institute for Neurodegenerative Diseases, Kavli Institute for Fundamental Neuroscience, and Bakar Computational Health Sciences Institute, University of California, 675 Nelson Rising Ln, Box 0518, San Francisco, CA, 94143, USA
| | - Marla Gearing
- Department of Neurology, Emory University School of Medicine, 12 Executive Park Dr NE, Atlanta, GA, 30322, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 1364 Clifton Rd, Atlanta, GA, 30322, USA
| | - John F Crary
- Departments of Pathology, Neuroscience, and Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Neuropathology Brain Bank and Research Core, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, Icahn Building 9th Floor, Room 20A, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Evan J Kiely
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 1364 Clifton Rd, Atlanta, GA, 30322, USA
| | - Meaghan Morris
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21218, USA
| | - Bartholomew White
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02215, USA
| | - Jonathan D Glass
- Department of Neurology, Emory University School of Medicine, 12 Executive Park Dr NE, Atlanta, GA, 30322, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 1364 Clifton Rd, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Whitehead Biomedical Research Building, 615 Michael Street, 5th Floor, Suite 500, Atlanta, GA, 30322, USA
| | - Kurt Farrell
- Departments of Pathology, Neuroscience, and Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Neuropathology Brain Bank and Research Core, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, Icahn Building 9th Floor, L9-02C, 1425 Madison, Avenue, New York, NY, USA
| | - David A Gutman
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 1364 Clifton Rd, Atlanta, GA, 30322, USA.
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8
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Marx GA, Kauffman J, McKenzie AT, Koenigsberg DG, McMillan CT, Morgello S, Karlovich E, Insausti R, Richardson TE, Walker JM, White CL, Babrowicz BM, Shen L, McKee AC, Stein TD, Farrell K, Crary JF. Histopathologic brain age estimation via multiple instance learning. Acta Neuropathol 2023; 146:785-802. [PMID: 37815677 PMCID: PMC10627911 DOI: 10.1007/s00401-023-02636-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/11/2023]
Abstract
Understanding age acceleration, the discordance between biological and chronological age, in the brain can reveal mechanistic insights into normal physiology as well as elucidate pathological determinants of age-related functional decline and identify early disease changes in the context of Alzheimer's and other disorders. Histopathological whole slide images provide a wealth of pathologic data on the cellular level that can be leveraged to build deep learning models to assess age acceleration. Here, we used a collection of digitized human post-mortem hippocampal sections to develop a histological brain age estimation model. Our model predicted brain age within a mean absolute error of 5.45 ± 0.22 years, with attention weights corresponding to neuroanatomical regions vulnerable to age-related changes. We found that histopathologic brain age acceleration had significant associations with clinical and pathologic outcomes that were not found with epigenetic based measures. Our results indicate that histopathologic brain age is a powerful, independent metric for understanding factors that contribute to brain aging.
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Affiliation(s)
- Gabriel A Marx
- Department of Pathology, Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA
- Department of Artificial Intelligence and Human Health, Nash Family Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA
| | - Justin Kauffman
- Department of Pathology, Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA
- Department of Artificial Intelligence and Human Health, Nash Family Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA
| | - Andrew T McKenzie
- Department of Pathology, Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA
- Department of Artificial Intelligence and Human Health, Nash Family Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel G Koenigsberg
- Department of Pathology, Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA
- Department of Artificial Intelligence and Human Health, Nash Family Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA
| | - Cory T McMillan
- Frontotemporal Degeneration Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan Morgello
- Department of Pathology, Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, New York, NY, USA
| | - Esma Karlovich
- Department of Pathology, Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA
| | - Ricardo Insausti
- Human Neuroanatomy Laboratory, School of Medicine, University of Castilla-La Mancha, Albacete, Spain
| | - Timothy E Richardson
- Department of Pathology, Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA
| | - Jamie M Walker
- Department of Pathology, Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA
| | - Charles L White
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bergan M Babrowicz
- Department of Pathology, Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, New York, NY, USA
| | - Ann C McKee
- Department of Pathology, Alzheimer's Disease and CTE Center, Boston University School of Medicine, Boston, MA, USA
- Department of Veterans Affairs Medical Center, Bedford, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Thor D Stein
- Department of Pathology, Alzheimer's Disease and CTE Center, Boston University School of Medicine, Boston, MA, USA
- Department of Veterans Affairs Medical Center, Bedford, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Kurt Farrell
- Department of Pathology, Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA.
- Department of Artificial Intelligence and Human Health, Nash Family Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA.
| | - John F Crary
- Department of Pathology, Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA.
- Department of Artificial Intelligence and Human Health, Nash Family Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1194, New York, NY, 10029, USA.
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9
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Kapasi A, Poirier J, Hedayat A, Scherlek A, Mondal S, Wu T, Gibbons J, Barnes LL, Bennett DA, Leurgans SE, Schneider JA. High-throughput digital quantification of Alzheimer disease pathology and associated infrastructure in large autopsy studies. J Neuropathol Exp Neurol 2023; 82:976-986. [PMID: 37944065 PMCID: PMC11032710 DOI: 10.1093/jnen/nlad086] [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: 11/12/2023] Open
Abstract
High-throughput digital pathology offers considerable advantages over traditional semiquantitative and manual methods of counting pathology. We used brain tissue from 5 clinical-pathologic cohort studies of aging; the Religious Orders Study, the Rush Memory and Aging Project, the Minority Aging Research Study, the African American Clinical Core, and the Latino Core to (1) develop a workflow management system for digital pathology processes, (2) optimize digital algorithms to quantify Alzheimer disease (AD) pathology, and (3) harmonize data statistically. Data from digital algorithms for the quantification of β-amyloid (Aβ, n = 413) whole slide images and tau-tangles (n = 639) were highly correlated with manual pathology data (r = 0.83 to 0.94). Measures were robust and reproducible across different magnifications and repeated scans. Digital measures for Aβ and tau-tangles across multiple brain regions reproduced established patterns of correlations, even when samples were stratified by clinical diagnosis. Finally, we harmonized newly generated digital measures with historical measures across multiple large autopsy-based studies. We describe a multidisciplinary approach to develop a digital pathology pipeline that reproducibly identifies AD neuropathologies, Aβ load, and tau-tangles. Digital pathology is a powerful tool that can overcome critical challenges associated with traditional microscopy methods.
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Affiliation(s)
- Alifiya Kapasi
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Jennifer Poirier
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Ahmad Hedayat
- Department of Pathology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Ashley Scherlek
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Srabani Mondal
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Tiffany Wu
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - John Gibbons
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Lisa L Barnes
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - David A Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Sue E Leurgans
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Julie A Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
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10
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Morris M, Coste GI, Redding-Ochoa J, Guo H, Graves AR, Troncoso JC, Huganir RL. Hippocampal synaptic alterations associated with tau pathology in primary age-related tauopathy. J Neuropathol Exp Neurol 2023; 82:836-844. [PMID: 37595576 PMCID: PMC10516464 DOI: 10.1093/jnen/nlad064] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023] Open
Abstract
Primary age-related tauopathy (PART) is characterized by aggregation of tau in the mesial temporal lobe in older individuals. High pathologic tau stage (Braak stage) or a high burden of hippocampal tau pathology has been associated with cognitive impairment in PART. However, the potential underlying mechanisms are not well understood. Cognitive impairment in many neurodegenerative diseases correlates with synaptic loss, raising the question of whether synaptic loss also occurs in PART. To address this, we investigated synaptic changes associated with tau Braak stage and high tau pathology burden in PART using synaptophysin and phospho-tau immunofluorescence. We compared 12 cases of definite PART with 6 controls and 6 Alzheimer disease cases. In this study, the hippocampal CA2 region showed loss of synaptophysin puncta and intensity in cases of PART with either a high stage (Braak IV) or a high burden of neuritic tau pathology. There was also loss of synaptophysin intensity in CA3 associated with a high stage or high burden of tau pathology. Loss of synaptophysin was present in Alzheimer disease, but the pattern appeared distinct. These novel findings suggest the presence of synaptic loss associated with either a high hippocampal tau burden or a Braak stage IV in PART.
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Affiliation(s)
- Meaghan Morris
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Gabrielle I Coste
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Javier Redding-Ochoa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Haidan Guo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Austin R Graves
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Engineering, Baltimore, Maryland, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard L Huganir
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, Maryland, USA
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11
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Stein-O’Brien GL, Palaganas R, Meyer EM, Redding-Ochoa J, Pletnikova O, Guo H, Bell WR, Troncoso JC, Huganir RL, Morris M. Transcriptional Signatures of Hippocampal Tau Pathology in Primary Age-Related Tauopathy and Alzheimer's Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.12.23295440. [PMID: 37745408 PMCID: PMC10516095 DOI: 10.1101/2023.09.12.23295440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Background Tau pathology is common in age-related neurodegenerative diseases. Tau pathology in primary age-related tauopathy (PART) and in Alzheimer's disease (AD) has a similar biochemical structure and anatomic distribution, which is distinct from tau pathology in other diseases. However, the molecular changes associated with intraneuronal tau pathology in PART and AD, and whether these changes are similar in the two diseases, is largely unexplored. Methods Using GeoMx spatial transcriptomics, mRNA was quantified in CA1 pyramidal neurons with tau pathology and adjacent neurons without tau pathology in 6 cases of PART and 6 cases of AD, and compared to 4 control cases without pathology. Transcriptional changes were analyzed for differential gene expression and for coordinated patterns of gene expression associated with both disease state and intraneuronal tau pathology. Results Synaptic gene changes and two novel gene expression signatures associated with intraneuronal tau were identified in PART and AD. Overall, gene expression changes associated with intraneuronal tau pathology were similar in PART and AD. Synaptic gene expression was decreased overall in neurons in AD and PART compared to control cases. However, this decrease was largely driven by neurons lacking tau pathology. Synaptic gene expression was increased in tau-positive neurons compared to tau-negative neurons in disease. Two novel gene expression signatures associated with intraneuronal tau were identified by examining coordinated patterns of gene expression. Genes in the up-regulated expression pattern were enriched in calcium regulation and synaptic function pathways, specifically in synaptic exocytosis. These synaptic gene changes and intraneuronal tau expression signatures were confirmed in a published transcriptional dataset of cortical neurons with tau pathology in AD. Conclusions PART and AD show similar transcriptional changes associated with intraneuronal tau pathology in CA1 pyramidal neurons, raising the possibility of a mechanistic relationship between the tau pathology in the two diseases. Intraneuronal tau pathology was also associated with increased expression of genes associated with synaptic function and calcium regulation compared to tau-negative disease neurons. The findings highlight the power of molecular analysis stratified by pathology in neurodegenerative disease and provide novel insight into common molecular pathways associated with intraneuronal tau in PART and AD.
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Affiliation(s)
- Genevieve L Stein-O’Brien
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Single Cell Training and Analysis Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Baltimore, MD
| | - Ryan Palaganas
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ernest M. Meyer
- UPMC Hillman Cancer Center Cytometry Facility, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Javier Redding-Ochoa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY
| | - Haidan Guo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William R Bell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Richard L Huganir
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Baltimore, MD
| | - Meaghan Morris
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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12
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Murayama MA. The past and present of therapeutic strategy for Alzheimer's diseases: potential for stem cell therapy. Exp Anim 2023; 72:285-293. [PMID: 36878603 PMCID: PMC10435354 DOI: 10.1538/expanim.22-0164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Alzheimer's disease (AD), a progressive neurodegenerative disease characterized by cognitive dysfunction and neuropsychiatric symptoms, is the most prevalent form of dementia among the elderly. Amyloid aggregation, tau hyperphosphorylation, and neural cell loss are the main pathological features. Various hypotheses have been proposed to explain the development of AD. Some therapeutic agents have shown clinical benefits in patients with AD; however, many of these agents have failed. The degree of neural cell loss is associated with the severity of AD. Adult neurogenesis, which governs cognitive and emotional behaviors, occurs in the hippocampus, and some research groups have reported that neural cell transplantation into the hippocampus improves cognitive dysfunction in AD model mice. Based on these clinical findings, stem cell therapy for patients with AD has recently attracted attention. This review provides past and present therapeutic strategies for the management and treatment of AD.
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Affiliation(s)
- Masanori A Murayama
- Department of Animal Models for Human Diseases, Institute of Biomedical Science, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka 573-1010, Japan
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13
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Romero-Fernandez W, Carvajal-Tapia C, Prusky A, Katdare KA, Wang E, Shostak A, Ventura-Antunes L, Harmsen HJ, Lippmann ES, Fuxe K, MacGurn JA, Borroto-Escuela DO, Schrag MS. Detection, visualization and quantification of protein complexes in human Alzheimer's disease brains using proximity ligation assay. Sci Rep 2023; 13:11948. [PMID: 37488165 PMCID: PMC10366145 DOI: 10.1038/s41598-023-38000-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/30/2023] [Indexed: 07/26/2023] Open
Abstract
Examination of healthy and diseased human brain is essential to translational neuroscience. Protein-protein interactions play a pivotal role in physiological and pathological processes, but their detection is difficult, especially in aged and fixed human brain tissue. We used the in-situ proximity ligation assay (PLA) to broaden the range of molecular interactions assessable in-situ in the human neuropathology. We adapted fluorescent in-situ PLA to detect ubiquitin-modified proteins in human brains with Alzheimer's disease (AD), including approaches for the management of autofluorescence and quantification using a high-content image analysis system. We confirmed that phosphorylated microtubule-associated protein tau (Serine202, Threonine205) aggregates were modified by ubiquitin and that phospho-tau-ubiquitin complexes were increased in hippocampal and frontal cortex regions in AD compared to non-AD brains. Overall, we refined PLA for use in human neuropathology, which has revealed a profound change in the distribution of ubiquitin in AD brain and its association with characteristic tau pathologies.
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Affiliation(s)
- Wilber Romero-Fernandez
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA.
| | - Cristian Carvajal-Tapia
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA
| | - Alex Prusky
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA
| | - Ketaki A Katdare
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, 37232, USA
| | - Emmeline Wang
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA
| | - Alena Shostak
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA
| | - Lissa Ventura-Antunes
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA
| | - Hannah J Harmsen
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37240, USA
| | - Ethan S Lippmann
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University, Nashville, TN, 37235, USA
| | - Kjell Fuxe
- Department of Neuroscience, Karolinska Institute, Solna, 17177, Stockholm, Sweden
| | - Jason A MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37240, USA
| | - Dasiel O Borroto-Escuela
- Department of Neuroscience, Karolinska Institute, Solna, 17177, Stockholm, Sweden
- Receptomics and Brain Disorders Lab, Department of Human Physiology, Sport and Exercise, Faculty of Medicine, University of Malaga, Edificio Lopez-Penalver, Jimenez Fraud 10, 29071, Málaga, Spain
| | - Matthew S Schrag
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA.
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, 37232, USA.
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University, Nashville, TN, 37235, USA.
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14
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Walker JM, Goette W, Farrell K, Iida MA, Karlovich E, White CL, Crary JF, Richardson TE. The relationship between hippocampal amyloid beta burden and spatial distribution of neurofibrillary degeneration. Alzheimers Dement 2023; 19:3158-3170. [PMID: 36738450 PMCID: PMC11100308 DOI: 10.1002/alz.12966] [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: 11/17/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Neurofibrillary degeneration in Alzheimer's disease (AD) typically involves the entorhinal cortex and CA1 subregion of the hippocampus early in the disease process, whereas in primary age-related tauopathy (PART), there is an early selective vulnerability of the CA2 subregion. METHODS Image analysis-based quantitative pixel assessments were used to objectively evaluate amyloid beta (Aβ) burden in the medial temporal lobe in relation to the distribution of hyperphosphorylated-tau (p-tau) in 142 cases of PART and AD. RESULTS Entorhinal, CA1, CA3, and CA4 p-tau deposition levels are significantly correlated with Aβ burden, while CA2 p-tau is not. Furthermore, the CA2/CA1 p-tau ratio is inversely correlated with Aβ burden and distribution. In addition, cognitive impairment is correlated with overall p-tau burden. DISCUSSION These data indicate that the presence and extent of medial temporal lobe Aβ may determine the distribution and spread of neurofibrillary degeneration. The resulting p-tau distribution patterns may discriminate between PART and AD. HIGHLIGHTS Subregional hyperphosphorylated-tau (p-tau) distribution is influenced by hippocampal amyloid beta burden. Higher CA2/CA1 p-tau ratio is predictive of primary age-related tauopathy-like neuropathology. Cognitive function is correlated with the overall hippocampal p-tau burden.
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Affiliation(s)
- Jamie M. Walker
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - William Goette
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kurt Farrell
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Megan A. Iida
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Esma Karlovich
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - The PART Working Group
- The PART working group is a multi-institutional collaboration. PART working group investigators are listed in the acknowledgments section
| | - Charles L. White
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - John F. Crary
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Timothy E. Richardson
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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15
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Morris M, Coste GI, Redding-Ochoa J, Guo H, Graves AR, Troncoso JC, Huganir RL. Hippocampal Synaptic Alterations Associated with Tau Pathology in Primary Age-Related Tauopathy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.22.23286323. [PMID: 36865237 PMCID: PMC9980270 DOI: 10.1101/2023.02.22.23286323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Primary Age-Related Tauopathy (PART) is characterized by the aggregation of tau in the mesial temporal lobe in older individuals. High pathologic tau stage (Braak stage) or a high burden of hippocampal tau pathology have been associated with cognitive impairment in PART. However, the underlying mechanisms of cognitive impairment in PART are not well understood. Cognitive impairment in many neurodegenerative diseases correlates with synaptic loss, raising the question of whether synaptic loss occurs in PART. To address this, we investigated synaptic changes associated with tau Braak stage and a high tau pathology burden in PART using synaptophysin and phospho-tau immunofluorescence. We compared twelve cases of definite PART with six young controls and six Alzheimer's disease cases. In this study, we identified loss of synaptophysin puncta and intensity in the CA2 region of the hippocampus in cases of PART with either a high stage (Braak IV) or a high burden of neuritic tau pathology. There was also loss of synaptophysin intensity in CA3 associated with a high stage or high burden of tau pathology. Loss of synaptophysin signal was present in AD, but the pattern was distinct from that seen in PART. These novel findings suggest the presence of synaptic loss in PART associated with either a high hippocampal tau burden or a Braak stage IV. These synaptic changes raise the possibility that synaptic loss in PART could contribute to cognitive impairment, though future studies including cognitive assessments are needed to address this question.
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Affiliation(s)
- Meaghan Morris
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Gabrielle I Coste
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Javier Redding-Ochoa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Haidan Guo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Austin R Graves
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
- Kavli Neuroscience Discovery Institute, Baltimore, MD
- Department of Biomedical Engineering, Johns Hopkins University School of Engineering, Baltimore, MD
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Richard L Huganir
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
- Kavli Neuroscience Discovery Institute, Baltimore, MD
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Calderón-Garcidueñas L, Hernández-Luna J, Aiello-Mora M, Brito-Aguilar R, Evelson PA, Villarreal-Ríos R, Torres-Jardón R, Ayala A, Mukherjee PS. APOE Peripheral and Brain Impact: APOE4 Carriers Accelerate Their Alzheimer Continuum and Have a High Risk of Suicide in PM 2.5 Polluted Cities. Biomolecules 2023; 13:927. [PMID: 37371506 DOI: 10.3390/biom13060927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
This Review emphasizes the impact of APOE4-the most significant genetic risk factor for Alzheimer's disease (AD)-on peripheral and neural effects starting in childhood. We discuss major mechanistic players associated with the APOE alleles' effects in humans to understand their impact from conception through all life stages and the importance of detrimental, synergistic environmental exposures. APOE4 influences AD pathogenesis, and exposure to fine particulate matter (PM2.5), manufactured nanoparticles (NPs), and ultrafine particles (UFPs) associated with combustion and friction processes appear to be major contributors to cerebrovascular dysfunction, neuroinflammation, and oxidative stress. In the context of outdoor and indoor PM pollution burden-as well as Fe, Ti, and Al alloys; Hg, Cu, Ca, Sn, and Si UFPs/NPs-in placenta and fetal brain tissues, urban APOE3 and APOE4 carriers are developing AD biological disease hallmarks (hyperphosphorylated-tau (P-tau) and amyloid beta 42 plaques (Aβ42)). Strikingly, for Metropolitan Mexico City (MMC) young residents ≤ 40 y, APOE4 carriers have 4.92 times higher suicide odds and 23.6 times higher odds of reaching Braak NFT V stage versus APOE4 non-carriers. The National Institute on Aging and Alzheimer's Association (NIA-AA) framework could serve to test the hypothesis that UFPs and NPs are key players for oxidative stress, neuroinflammation, protein aggregation and misfolding, faulty complex protein quality control, and early damage to cell membranes and organelles of neural and vascular cells. Noninvasive biomarkers indicative of the P-tau and Aβ42 abnormal protein deposits are needed across the disease continuum starting in childhood. Among the 21.8 million MMC residents, we have potentially 4 million APOE4 carriers at accelerated AD progression. These APOE4 individuals are prime candidates for early neuroprotective interventional trials. APOE4 is key in the development of AD evolving from childhood in highly polluted urban centers dominated by anthropogenic and industrial sources of pollution. APOE4 subjects are at higher early risk of AD development, and neuroprotection ought to be implemented. Effective reductions of PM2.5, UFP, and NP emissions from all sources are urgently needed. Alzheimer's Disease prevention ought to be at the core of the public health response and physicians-scientist minority research be supported.
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Affiliation(s)
- Lilian Calderón-Garcidueñas
- College of Health, The University of Montana, Missoula, MT 59812, USA
- Universidad del Valle de México, Mexico City 14370, Mexico
| | | | - Mario Aiello-Mora
- Otorrinolaryngology Department, Instituto Nacional de Cardiología, Mexico City 14080, Mexico
| | | | - Pablo A Evelson
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires C1113 AAD, Argentina
| | | | - Ricardo Torres-Jardón
- Instituto de Ciencias de la Atmósfera y Cambio Climático, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Alberto Ayala
- Sacramento Metropolitan Air Quality Management District, Sacramento, CA 95814, USA
- West Virginia University, Morgantown, WV 26506, USA
| | - Partha S Mukherjee
- Interdisciplinary Statistical Research Unit, Indian Statistical Institute, Kolkata 700108, India
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Romero-Fernandez W, Carvajal-Tapia C, Prusky A, Katdare K, Wang E, Shostak A, Ventura-Antunes L, Harmsen H, Lippmann E, Borroto-Escuela D, MacGurn J, Fuxe K, Schrag M. Detection, Visualization and Quantification of Protein Complexes in Human Alzheimer's Disease Brains using Proximity Ligation Assay. RESEARCH SQUARE 2023:rs.3.rs-2570335. [PMID: 36824944 PMCID: PMC9949263 DOI: 10.21203/rs.3.rs-2570335/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Examination of healthy and diseased human brain is essential to translational neuroscience. Protein-protein interactions play a pivotal role in physiological and pathological processes, but their detection is difficult, especially in aged and fixed human brain tissue. We used the proximity ligation assay (PLA) to broaden the range of molecular interactions assessable in-situ in human neuropathology. We adapted fluorescent in-situ PLA to detect ubiquitin-modified proteins in human brains with Alzheimer's disease (AD), including approaches for the management of autofluorescence and quantification using a high-content image analysis system. We confirmed that hyperphosphorylated microtubule-associated protein tau (Serine202, Threonine205) aggregates were modified by ubiquitin and that phospho-tau-ubiquitin complexes were increased in hippocampal and frontal cortex regions in AD compared to non-AD brains. Overall, we refined PLA for use in human neuropathology, which has revealed a profound change in the distribution of ubiquitin in AD brain and its association with characteristic tau pathologies.
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Novel Strategy for Alzheimer’s Disease Treatment through Oral Vaccine Therapy with Amyloid Beta. Biologics 2023. [DOI: 10.3390/biologics3010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Alzheimer’s disease (AD) is a neuropathology characterized by progressive cognitive impairment and dementia. The disease is attributed to senile plaques, which are aggregates of amyloid beta (Aβ) outside nerve cells; neurofibrillary tangles, which are filamentous accumulations of phosphorylated tau in nerve cells; and loss of neurons in the brain tissue. Immunization of an AD mouse model with Aβ-eliminated pre-existing senile plaque amyloids and prevented new accumulation. Furthermore, its effect showed that cognitive function can be improved by passive immunity without side effects, such as lymphocyte infiltration in AD model mice treated with vaccine therapy, indicating the possibility of vaccine therapy for AD. Further, considering the possibility of side effects due to direct administration of Aβ, the practical use of the safe oral vaccine, which expressed Aβ in plants, is expected. Indeed, administration of this oral vaccine to Alzheimer’s model mice reduced Aβ accumulation in the brain. Moreover, almost no expression of inflammatory IgG was observed. Therefore, vaccination prior to Aβ accumulation or at an early stage of accumulation may prevent Aβ from causing AD.
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