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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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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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Scalco R, Saito N, Beckett L, Nguyen ML, Huie E, Wang HP, Flaherty DA, Honig LS, DeCarli C, Rissman RA, Teich AF, Jin LW, Dugger BN. The neuropathological landscape of Hispanic and non-Hispanic White decedents with Alzheimer disease. Acta Neuropathol Commun 2023; 11:105. [PMID: 37386610 PMCID: PMC10311731 DOI: 10.1186/s40478-023-01574-1] [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: 03/14/2023] [Accepted: 04/30/2023] [Indexed: 07/01/2023] Open
Abstract
Despite the increasing demographic diversity of the United States' aging population, there remain significant gaps in post-mortem research investigating the ethnoracial heterogeneity in the neuropathological landscape of Alzheimer Disease (AD). Most autopsy-based studies have focused on cohorts of non-Hispanic White decedents (NHWD), with few studies including Hispanic decedents (HD). We aimed to characterize the neuropathologic landscape of AD in NHWD (n = 185) and HD (n = 92) evaluated in research programs across three institutions: University of California San Diego, University of California Davis, and Columbia University. Only persons with a neuropathologic diagnosis of intermediate/high AD determined by NIA Reagan and/or NIA-AA criteria were included. A frequency-balanced random sample without replacement was drawn from the NHWD group using a 2:1 age and sex matching scheme with HD. Four brain areas were evaluated: posterior hippocampus, frontal, temporal, and parietal cortices. Sections were stained with antibodies against Aβ (4G8) and phosphorylated tau (AT8). We compared the distribution and semi-quantitative densities for neurofibrillary tangles (NFTs), neuropil threads, core, diffuse, and neuritic plaques. All evaluations were conducted by an expert blinded to demographics and group status. Wilcoxon's two-sample test revealed higher levels of neuritic plaques in the frontal cortex (p = 0.02) and neuropil threads (p = 0.02) in HD, and higher levels of cored plaques in the temporal cortex in NHWD (p = 0.02). Results from ordinal logistic regression controlling for age, sex, and site of origin were similar. In other evaluated brain regions, semi-quantitative scores of plaques, tangles, and threads did not differ statistically between groups. Our results demonstrate HD may be disproportionately burdened by AD-related pathologies in select anatomic regions, particularly tau deposits. Further research is warranted to understand the contributions of demographic, genetic, and environmental factors to heterogeneous pathological presentations.
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Affiliation(s)
- Rebeca Scalco
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Davis, 4645 2Nd Ave, 3400A Research Building III, Sacramento, CA, 95817, USA
| | - Naomi Saito
- Division of Biostatistics, Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - Laurel Beckett
- Division of Biostatistics, Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - My-Le Nguyen
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Davis, 4645 2Nd Ave, 3400A Research Building III, Sacramento, CA, 95817, USA
| | - Emily Huie
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Davis, 4645 2Nd Ave, 3400A Research Building III, Sacramento, CA, 95817, USA
| | - Hsin-Pei Wang
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Davis, 4645 2Nd Ave, 3400A Research Building III, Sacramento, CA, 95817, USA
| | - Delaney A Flaherty
- Taub Institute for Research On Alzheimer's Disease and Aging Brain, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Lawrence S Honig
- Taub Institute for Research On Alzheimer's Disease and Aging Brain, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Charles DeCarli
- Alzheimer's Disease Research Center, Department of Neurology, School of Medicine, University of California Davis, Sacramento, CA, USA
| | - Robert A Rissman
- Department of Neurosciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Andrew F Teich
- Taub Institute for Research On Alzheimer's Disease and Aging Brain, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research On Alzheimer's Disease and Aging Brain, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Lee-Way Jin
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Davis, 4645 2Nd Ave, 3400A Research Building III, Sacramento, CA, 95817, USA
| | - Brittany N Dugger
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Davis, 4645 2Nd Ave, 3400A Research Building III, Sacramento, CA, 95817, USA.
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Wong DR, Magaki SD, Vinters HV, Yong WH, Monuki ES, Williams CK, Martini AC, DeCarli C, Khacherian C, Graff JP, Dugger BN, Keiser MJ. Learning fast and fine-grained detection of amyloid neuropathologies from coarse-grained expert labels. Commun Biol 2023; 6:668. [PMID: 37355729 PMCID: PMC10290693 DOI: 10.1038/s42003-023-05031-6] [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: 01/25/2023] [Accepted: 06/08/2023] [Indexed: 06/26/2023] Open
Abstract
Precise, scalable, and quantitative evaluation of whole slide images is crucial in neuropathology. We release a deep learning model for rapid object detection and precise information on the identification, locality, and counts of cored plaques and cerebral amyloid angiopathy (CAA). We trained this object detector using a repurposed image-tile dataset without any human-drawn bounding boxes. We evaluated the detector on a new manually-annotated dataset of whole slide images (WSIs) from three institutions, four staining procedures, and four human experts. The detector matched the cohort of neuropathology experts, achieving 0.64 (model) vs. 0.64 (cohort) average precision (AP) for cored plaques and 0.75 vs. 0.51 AP for CAAs at a 0.5 IOU threshold. It provided count and locality predictions that approximately correlated with gold-standard human CERAD-like WSI scoring (p = 0.07 ± 0.10). The openly-available model can quickly score WSIs in minutes without a GPU on a standard workstation.
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Affiliation(s)
- Daniel R Wong
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Shino D Magaki
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Harry V Vinters
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Neurology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - William H Yong
- Department of Pathology & Laboratory Medicine, University of California, Irvine, CA, 92697, USA
| | - Edwin S Monuki
- Department of Pathology & Laboratory Medicine, University of California, Irvine, CA, 92697, USA
| | - Christopher K Williams
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Alessandra C Martini
- Department of Pathology & Laboratory Medicine, University of California, Irvine, CA, 92697, USA
| | - Charles DeCarli
- Department of Neurology, School of Medicine, University of California-Davis, Davis, CA, 95817, USA
| | - Chris Khacherian
- Department of Pathology & Laboratory Medicine, University of California, Irvine, CA, 92697, USA
| | - John P Graff
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Sacramento, CA, 95817, USA
| | - Brittany N Dugger
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Sacramento, CA, 95817, USA.
| | - Michael J Keiser
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, 94158, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, 94158, USA.
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Vizcarra JC, Teich AF, Dugger BN, Gutman DA. Survey of Neuroanatomic Sampling and Staining Procedures in Alzheimer Disease Research Center Brain Banks. FREE NEUROPATHOLOGY 2023; 4:4-6. [PMID: 37347036 PMCID: PMC10280272 DOI: 10.17879/freeneuropathology-2023-4696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/28/2023] [Indexed: 06/23/2023]
Abstract
The collection of post-mortem brain tissue has been a core function of the Alzheimer Disease Research Center's (ADRCs) network located within the United States since its inception. Individual brain banks and centers follow detailed protocols to record, store, and manage complex datasets that include clinical data, demographics, and when post-mortem tissue is available, a detailed neuropathological assessment. Since each institution often has specific research foci, there can be variability in tissue collection and processing workflows. While published guidelines exist for select diseases, such as those put forth by the National Institute on Aging and Alzheimer Association (NIA-AA), it is of importance to denote the current practices across institutions. To this end a survey was developed and sent to United States based brain bank leaders, collecting data on brain region sampling, including anatomic landmarks used, staining (including antibodies used), as well as whole-slide-image scanning hardware. We distributed this survey to 40 brain banks and obtained a response rate of 95% (38 / 40). Most brain banks followed guidelines defined by the NIA-AA, having H&E staining in all recommended regions and targeted region-based amyloid beta, tau, and alpha-synuclein immunohistochemical staining. However, sampling consistency varied related to key anatomic landmarks/locations in select regions, such as the striatum, periventricular white matter, and parietal cortex. This study highlights the diversity and similarities amongst brain banks and discusses considerations when amalgamating data/samples across multiple centers. This survey aids in establishing benchmarks to enhance dialogues on divergent workflows in a feasible way.
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Affiliation(s)
- Juan C. Vizcarra
- Department of Biomedical Engineering, Emory University & Georgia Institute of Technology, Atlanta, USA
| | - Andrew F. Teich
- Department of Pathology and Cell Biology, Department of Neurology, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Brittany N. Dugger
- Department of Pathology and Laboratory Medicine, University of California-Davis, Sacramento, California, USA
| | - David A. Gutman
- Department of Neuropathology, Emory University, Atlanta, Georgia, USA
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