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Kavanagh T, Drummond E. Insights from a proteomic atlas of human Alzheimer's disease brain tissue. Neural Regen Res 2025; 20:799-800. [PMID: 38886945 DOI: 10.4103/nrr.nrr-d-24-00215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/02/2024] [Indexed: 06/20/2024] Open
Affiliation(s)
- Tomas Kavanagh
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
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Leitner D, Kavanagh T, Kanshin E, Balcomb K, Pires G, Thierry M, Suazo JI, Schneider J, Ueberheide B, Drummond E, Wisniewski T. Differences in the cerebral amyloid angiopathy proteome in Alzheimer's disease and mild cognitive impairment. Acta Neuropathol 2024; 148:9. [PMID: 39039355 PMCID: PMC11263258 DOI: 10.1007/s00401-024-02767-1] [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: 04/04/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024]
Abstract
Cerebral amyloid angiopathy (CAA) is characterized by amyloid beta (Aβ) deposition in cerebrovasculature. It is prevalent with aging and Alzheimer's disease (AD), associated with intracerebral hemorrhage, and contributes to cognitive deficits. To better understand molecular mechanisms, CAA(+) and CAA(-) vessels were microdissected from paraffin-embedded autopsy temporal cortex of age-matched Control (n = 10), mild cognitive impairment (MCI; n = 4), and sporadic AD (n = 6) cases, followed by label-free quantitative mass spectrometry. 257 proteins were differentially abundant in CAA(+) vessels compared to neighboring CAA(-) vessels in MCI, and 289 in AD (p < 0.05, fold-change > 1.5). 84 proteins changed in the same direction in both groups, and many changed in the same direction among proteins significant in at least one group (p < 0.0001, R2 = 0.62). In CAA(+) vessels, proteins significantly increased in both AD and MCI were particularly associated with collagen-containing extracellular matrix, while proteins associated with ribonucleoprotein complex were significantly decreased in both AD and MCI. In neighboring CAA(-) vessels, 61 proteins were differentially abundant in MCI, and 112 in AD when compared to Control cases. Increased proteins in CAA(-) vessels were associated with extracellular matrix, external encapsulating structure, and collagen-containing extracellular matrix in MCI; collagen trimer in AD. Twenty two proteins were increased in CAA(-) vessels of both AD and MCI. Comparison of the CAA proteome with published amyloid-plaque proteomic datasets identified many proteins similarly enriched in CAA and plaques, as well as a protein subset hypothesized as preferentially enriched in CAA when compared to plaques. SEMA3G emerged as a CAA specific marker, validated immunohistochemically and with correlation to pathology levels (p < 0.0001; R2 = 0.90). Overall, the CAA(-) vessel proteomes indicated changes in vessel integrity in AD and MCI in the absence of Aβ, and the CAA(+) vessel proteome was similar in MCI and AD, which was associated with vascular matrix reorganization, protein translation deficits, and blood brain barrier breakdown.
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Affiliation(s)
- Dominique Leitner
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Tomas Kavanagh
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Evgeny Kanshin
- Proteomics Laboratory, Division of Advanced Research Technologies and Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Kaleah Balcomb
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Geoffrey Pires
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Manon Thierry
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Jianina I Suazo
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Julie Schneider
- Department Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison Street, Suite 1000, Chicago, IL, 60612, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
- Department of Pathology, Rush University Medical Center, Chicago, IL, USA
| | - Beatrix Ueberheide
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies and Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Eleanor Drummond
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia.
| | - Thomas Wisniewski
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, 10016, USA.
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3
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Cartas‐Cejudo P, Cortés A, Lachén‐Montes M, Anaya‐Cubero E, Puerta E, Solas M, Fernández‐Irigoyen J, Santamaría E. Neuropathological stage-dependent proteome mapping of the olfactory tract in Alzheimer's disease: From early olfactory-related omics signatures to computational repurposing of drug candidates. Brain Pathol 2024; 34:e13252. [PMID: 38454090 PMCID: PMC11189775 DOI: 10.1111/bpa.13252] [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: 09/27/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia, characterized by an early olfactory dysfunction, progressive memory loss, and behavioral deterioration. Albeit substantial progress has been made in characterizing AD-associated molecular and cellular events, there is an unmet clinical need for new therapies. In this study, olfactory tract proteotyping performed in controls and AD subjects (n = 17/group) showed a Braak stage-dependent proteostatic impairment accompanied by the progressive modulation of amyloid precursor protein and tau functional interactomes. To implement a computational repurposing of drug candidates with the capacity to reverse early AD-related olfactory omics signatures (OMSs), we generated a consensual OMSs database compiling differential omics datasets obtained by mass-spectrometry or RNA-sequencing derived from initial AD across the olfactory axis. Using the Connectivity Map-based drug repurposing approach, PKC, EGFR, Aurora kinase, Glycogen synthase kinase, and CDK inhibitors were the top pharmacologic classes capable to restore multiple OMSs, whereas compounds with targeted activity to inhibit PI3K, Insulin-like growth factor 1 (IGF-1), microtubules, and Polo-like kinase (PLK) represented a family of drugs with detrimental potential to induce olfactory AD-associated gene expression changes. To validate the potential therapeutic effects of the proposed drugs, in vitro assays were performed. These validation experiments revealed that pretreatment of human neuron-like SH-SY5Y cells with the EGFR inhibitor AG-1478 showed a neuroprotective effect against hydrogen peroxide-induced damage while the pretreatment with the Aurora kinase inhibitor Reversine reduced amyloid-beta (Aβ)-induced neurotoxicity. Taken together, our data pointed out that OMSs may be useful as substrates for drug repurposing to propose novel neuroprotective treatments against AD.
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Affiliation(s)
- Paz Cartas‐Cejudo
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Hospitalario Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Navarra Institute for Health ResearchPamplonaSpain
| | - Adriana Cortés
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Hospitalario Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Navarra Institute for Health ResearchPamplonaSpain
| | - Mercedes Lachén‐Montes
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Hospitalario Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Navarra Institute for Health ResearchPamplonaSpain
| | - Elena Anaya‐Cubero
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Hospitalario Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Navarra Institute for Health ResearchPamplonaSpain
| | - Elena Puerta
- Department of Pharmacology and ToxicologyUniversity of Navarra, IdiSNAPamplonaSpain
| | - Maite Solas
- Department of Pharmacology and ToxicologyUniversity of Navarra, IdiSNAPamplonaSpain
| | - Joaquín Fernández‐Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Hospitalario Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Navarra Institute for Health ResearchPamplonaSpain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Hospitalario Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Navarra Institute for Health ResearchPamplonaSpain
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O'Shea TM, Ao Y, Wang S, Ren Y, Cheng AL, Kawaguchi R, Shi Z, Swarup V, Sofroniew MV. Derivation and transcriptional reprogramming of border-forming wound repair astrocytes after spinal cord injury or stroke in mice. Nat Neurosci 2024:10.1038/s41593-024-01684-6. [PMID: 38907165 DOI: 10.1038/s41593-024-01684-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 05/15/2024] [Indexed: 06/23/2024]
Abstract
Central nervous system (CNS) lesions become surrounded by neuroprotective borders of newly proliferated reactive astrocytes; however, fundamental features of these cells are poorly understood. Here we show that following spinal cord injury or stroke, 90% and 10% of border-forming astrocytes derive, respectively, from proliferating local astrocytes and oligodendrocyte progenitor cells in adult mice of both sexes. Temporal transcriptome analysis, single-nucleus RNA sequencing and immunohistochemistry show that after focal CNS injury, local mature astrocytes dedifferentiate, proliferate and become transcriptionally reprogrammed to permanently altered new states, with persisting downregulation of molecules associated with astrocyte-neuron interactions and upregulation of molecules associated with wound healing, microbial defense and interactions with stromal and immune cells. These wound repair astrocytes share morphologic and transcriptional features with perimeningeal limitans astrocytes and are the predominant source of neuroprotective borders that re-establish CNS integrity around lesions by separating neural parenchyma from stromal and immune cells as occurs throughout the healthy CNS.
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Affiliation(s)
- Timothy M O'Shea
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
| | - Yan Ao
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Shinong Wang
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Yilong Ren
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, PR China
| | - Amy L Cheng
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Riki Kawaguchi
- Departments of Psychiatry and Neurology, University of California Los Angeles, Los Angeles, CA, USA
| | - Zechuan Shi
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, CA, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, CA, USA
| | - Michael V Sofroniew
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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5
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Dubnov S, Bennett ER, Yayon N, Yakov O, Bennett DA, Seshadri S, Mufson E, Tzur Y, Greenberg D, Kuro-O M, Paldor I, Abraham CR, Soreq H. Knockout of the longevity gene Klotho perturbs aging and Alzheimer's disease-linked brain microRNAs and tRNA fragments. Commun Biol 2024; 7:720. [PMID: 38862813 PMCID: PMC11166644 DOI: 10.1038/s42003-024-06407-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: 09/29/2023] [Accepted: 05/31/2024] [Indexed: 06/13/2024] Open
Abstract
Overexpression of the longevity gene Klotho prolongs lifespan, while its knockout shortens lifespan and impairs cognition via perturbation of myelination and synapse formation. However, comprehensive analysis of Klotho knockout effects on mammalian brain transcriptomics is lacking. Here, we report that Klotho knockout alters the levels of aging- and cognition related mRNAs, long non-coding RNAs, microRNAs and tRNA fragments. These include altered neuronal and glial regulators in murine models of aging and Alzheimer's disease and in human Alzheimer's disease post-mortem brains. We further demonstrate interaction of the knockout-elevated tRNA fragments with the spliceosome, possibly affecting RNA processing. Last, we present cell type-specific short RNA-seq datasets from FACS-sorted neurons and microglia of live human brain tissue demonstrating in-depth cell-type association of Klotho knockout-perturbed microRNAs. Together, our findings reveal multiple RNA transcripts in both neurons and glia from murine and human brain that are perturbed in Klotho deficiency and are aging- and neurodegeneration-related.
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Affiliation(s)
- Serafima Dubnov
- The Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Estelle R Bennett
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Nadav Yayon
- The Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Or Yakov
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Sudha Seshadri
- UT Health Medical Arts & Research Center, San Antonio, TX, USA
| | - Elliott Mufson
- Dept. Translational Neuroscience, Barrow Neurological Institute, St. Joseph's Medical Center, Phoenix, AZ, USA
| | - Yonat Tzur
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - David Greenberg
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Makoto Kuro-O
- Division of Anti-aging Medicine, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Iddo Paldor
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
- Dept of Neurosurgery, the Shaare Zedek Medical Center, Jerusalem, Israel
| | - Carmela R Abraham
- Departments of Biochemistry and Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Klogenix LLC., Boston, MA, USA
| | - Hermona Soreq
- The Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.
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6
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Peng J, Zaman M, Yang S, Huang Y, Yarbro J, Wang Z, Liu D, Soliman H, Hemphill A, Harvey S, Pruett-Miller S, Stewart V, Tanwar A, Kalathur R, Grace C, Turk M, Chittori S, Jiao Y, Wu Z, High A, Wang X, Serrano G, Beach T, Yu G, Yang Y, Chen PC. Midkine Attenuates Aβ Fibril Assembly and AmyloidPlaque Formation. RESEARCH SQUARE 2024:rs.3.rs-4361125. [PMID: 38883748 PMCID: PMC11177971 DOI: 10.21203/rs.3.rs-4361125/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Proteomic profiling of Alzheimer's disease (AD) brains has identified numerous understudied proteins, including midkine (MDK), that are highly upregulated and correlated with Aβ since the early disease stage, but their roles in disease progression are not fully understood. Here we present that MDK attenuates Aβ assembly and influences amyloid formation in the 5xFAD amyloidosis mouse model. MDK protein mitigates fibril formation of both Aβ40 and Aβ42 peptides in Thioflavin T fluorescence assay, circular dichroism, negative stain electron microscopy, and NMR analysis. Knockout of Mdkgene in 5xFAD increases amyloid formation and microglial activation. Further comprehensive mass spectrometry-based profiling of whole proteome and aggregated proteome in these mouse models indicates significant accumulation of Aβ and Aβ-correlated proteins, along with microglial components. Thus, our structural and mouse model studies reveal a protective role of MDK in counteracting amyloid pathology in Alzheimer's disease.
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Affiliation(s)
| | | | - Shu Yang
- St Jude Children's Research Hospital
| | - Ya Huang
- St Jude Children's Research Hospital
| | | | - Zhen Wang
- St Jude Children's Research Hospital
| | | | | | | | | | | | | | | | | | | | | | | | - Yun Jiao
- St Jude Children's Research Hospital
| | | | | | | | | | | | - Gang Yu
- University of Texas Southwestern Medical Center
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Nguyen HD, Kim WK, Huong Vu G. Molecular mechanisms implicated in protein changes in the Alzheimer's disease human hippocampus. Mech Ageing Dev 2024; 219:111930. [PMID: 38554950 DOI: 10.1016/j.mad.2024.111930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/18/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
This study aimed to elucidate the specific biochemical pathways linked to changes in proteins in the Alzheimer's disease (AD) human hippocampus. Our data demonstrate a constant rise in the expression of four proteins (VGF, GFAP, HSPB1, and APP) across all eleven studies. Notably, UBC was the most centrally involved and had increased expression in the hippocampus tissue of individuals with AD. Modified proteins in the hippocampal tissue were found to activate the innate immune system and disrupt communication across chemical synapses. Four hub proteins (CD44, APP, ITGB2, and APOE) are connected to amyloid plaques, whereas two hub proteins (RPL24 and RPS23) are related to neurofibrillary tangles (NFTs). The presence of modified proteins was discovered to trigger the activation of microglia and decrease the functioning of ribosomes and mitochondria in the hippocampus. Three significant microRNAs (hsa-miR-106b-5p, hsa-miR-17-5p, and hsa-miR-16-5p) and transcription factors (MYT1L, PIN1, and CSRNP3) have been discovered to improve our understanding of the alterations in proteins within the hippocampal tissues that lead to the progression of AD. These findings establish a path for possible treatments for AD to employ therapeutic strategies that specifically focus on the proteins or processes linked to the illness.
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Affiliation(s)
- Hai Duc Nguyen
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea; Division of Microbiology, Tulane National Primate Research Center, Tulane University, Louisiana, USA.
| | - Woong-Ki Kim
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Louisiana, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Giang Huong Vu
- Department of Public Health, Hong Bang Health Center, Hai Phong, Vietnam
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Thierry M, Ponce J, Martà-Ariza M, Askenazi M, Faustin A, Leitner D, Pires G, Kanshin E, Drummond E, Ueberheide B, Wisniewski T. The influence of APOE ε4 on the pTau interactome in sporadic Alzheimer's disease. Acta Neuropathol 2024; 147:91. [PMID: 38772917 PMCID: PMC11108952 DOI: 10.1007/s00401-024-02744-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/12/2024] [Accepted: 05/12/2024] [Indexed: 05/23/2024]
Abstract
APOEε4 is the major genetic risk factor for sporadic Alzheimer's disease (AD). Although APOEε4 is known to promote Aβ pathology, recent data also support an effect of APOE polymorphism on phosphorylated Tau (pTau) pathology. To elucidate these potential effects, the pTau interactome was analyzed across APOE genotypes in the frontal cortex of 10 advanced AD cases (n = 5 APOEε3/ε3 and n = 5 APOEε4/ε4), using a combination of anti-pTau pS396/pS404 (PHF1) immunoprecipitation (IP) and mass spectrometry (MS). This proteomic approach was complemented by an analysis of anti-pTau PHF1 and anti-Aβ 4G8 immunohistochemistry, performed in the frontal cortex of 21 advanced AD cases (n = 11 APOEε3/ε3 and n = 10 APOEε4/ε4). Our dataset includes 1130 and 1330 proteins enriched in IPPHF1 samples from APOEε3/ε3 and APOEε4/ε4 groups (fold change ≥ 1.50, IPPHF1 vs IPIgG ctrl). We identified 80 and 68 proteins as probable pTau interactors in APOEε3/ε3 and APOEε4/ε4 groups, respectively (SAINT score ≥ 0.80; false discovery rate (FDR) ≤ 5%). A total of 47/80 proteins were identified as more likely to interact with pTau in APOEε3/ε3 vs APOEε4/ε4 cases. Functional enrichment analyses showed that they were significantly associated with the nucleoplasm compartment and involved in RNA processing. In contrast, 35/68 proteins were identified as more likely to interact with pTau in APOEε4/ε4 vs APOEε3/ε3 cases. They were significantly associated with the synaptic compartment and involved in cellular transport. A characterization of Tau pathology in the frontal cortex showed a higher density of plaque-associated neuritic crowns, made of dystrophic axons and synapses, in APOEε4 carriers. Cerebral amyloid angiopathy was more frequent and severe in APOEε4/ε4 cases. Our study supports an influence of APOE genotype on pTau-subcellular location in AD. These results suggest a facilitation of pTau progression to Aβ-affected brain regions in APOEε4 carriers, paving the way to the identification of new therapeutic targets.
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Affiliation(s)
- Manon Thierry
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA.
| | - Jackeline Ponce
- Department of Biochemistry and Molecular Pharmacology, Proteomics Laboratory, Grossman School of Medicine, New York University, New York, NY, USA
| | - Mitchell Martà-Ariza
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA
- Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Arline Faustin
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA
| | - Dominique Leitner
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA
- Department of Neurology, Comprehensive Epilepsy Center, Grossman School of Medicine, New York University, New York, NY, USA
| | - Geoffrey Pires
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA
| | - Evgeny Kanshin
- Department of Biochemistry and Molecular Pharmacology, Proteomics Laboratory, Grossman School of Medicine, New York University, New York, NY, USA
| | - Eleanor Drummond
- Brain and Mind Centre, School of Medical Science, University of Sydney, Sydney, Australia
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, Proteomics Laboratory, Grossman School of Medicine, New York University, New York, NY, USA
| | - Thomas Wisniewski
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA.
- Departments of Pathology and Psychiatry, Grossman School of Medicine, New York University, Science Building, Rm 1017, 435 East 30 Street, New York, NY, 10016, USA.
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9
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Yaghoobi A, Malekpour SA. Unraveling the genetic architecture of blood unfolded p-53 among non-demented elderlies: novel candidate genes for early Alzheimer's disease. BMC Genomics 2024; 25:440. [PMID: 38702606 PMCID: PMC11067101 DOI: 10.1186/s12864-024-10363-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a heritable neurodegenerative disease whose long asymptomatic phase makes the early diagnosis of it pivotal. Blood U-p53 has recently emerged as a superior predictive biomarker for AD in the early stages. We hypothesized that genetic variants associated with blood U-p53 could reveal novel loci and pathways involved in the early stages of AD. RESULTS We performed a blood U-p53 Genome-wide association study (GWAS) on 484 healthy and mild cognitively impaired subjects from the ADNI cohort using 612,843 Single nucleotide polymorphisms (SNPs). We performed a pathway analysis and prioritized candidate genes using an AD single-cell gene program. We fine-mapped the intergenic SNPs by leveraging a cell-type-specific enhancer-to-gene linking strategy using a brain single-cell multimodal dataset. We validated the candidate genes in an independent brain single-cell RNA-seq and the ADNI blood transcriptome datasets. The rs279686 between AASS and FEZF1 genes was the most significant SNP (p-value = 4.82 × 10-7). Suggestive pathways were related to the immune and nervous systems. Twenty-three candidate genes were prioritized at 27 suggestive loci. Fine-mapping of 5 intergenic loci yielded nine cell-specific candidate genes. Finally, 15 genes were validated in the independent single-cell RNA-seq dataset, and five were validated in the ADNI blood transcriptome dataset. CONCLUSIONS We underlined the importance of performing a GWAS on an early-stage biomarker of AD and leveraging functional omics datasets for pinpointing causal genes in AD. Our study prioritized nine genes (SORCS1, KIF5C, TMEFF2, TMEM63C, HLA-E, ATAT1, TUBB, ARID1B, and RUNX1) strongly implicated in the early stages of AD.
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Affiliation(s)
- Arash Yaghoobi
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, 19395-5746, Iran
| | - Seyed Amir Malekpour
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, 19395-5746, Iran.
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10
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Seifar F, Fox EJ, Shantaraman A, Liu Y, Dammer EB, Modeste E, Duong DM, Yin L, Trautwig AN, Guo Q, Xu K, Ping L, Reddy JS, Allen M, Quicksall Z, Heath L, Scanlan J, Wang E, Wang M, Linden AV, Poehlman W, Chen X, Baheti S, Ho C, Nguyen T, Yepez G, Mitchell AO, Oatman SR, Wang X, Carrasquillo MM, Runnels A, Beach T, Serrano GE, Dickson DW, Lee EB, Golde TE, Prokop S, Barnes LL, Zhang B, Haroutunian V, Gearing M, Lah JJ, Jager PD, Bennett DA, Greenwood A, Ertekin-Taner N, Levey AI, Wingo A, Wingo T, Seyfried NT. Large-scale Deep Proteomic Analysis in Alzheimer's Disease Brain Regions Across Race and Ethnicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590547. [PMID: 38712030 PMCID: PMC11071432 DOI: 10.1101/2024.04.22.590547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Introduction Alzheimer's disease (AD) is the most prevalent neurodegenerative disease, yet our comprehension predominantly relies on studies within the non-Hispanic White (NHW) population. Here we aimed to provide comprehensive insights into the proteomic landscape of AD across diverse racial and ethnic groups. Methods Dorsolateral prefrontal cortex (DLPFC) and superior temporal gyrus (STG) brain tissues were donated from multiple centers (Mayo Clinic, Emory University, Rush University, Mt. Sinai School of Medicine) and were harmonized through neuropathological evaluation, specifically adhering to the Braak staging and CERAD criteria. Among 1105 DLPFC tissue samples (998 unique individuals), 333 were from African American donors, 223 from Latino Americans, 529 from NHW donors, and the rest were from a mixed or unknown racial background. Among 280 STG tissue samples (244 unique individuals), 86 were African American, 76 Latino American, 116 NHW and the rest were mixed or unknown ethnicity. All tissues were uniformly homogenized and analyzed by tandem mass tag mass spectrometry (TMT-MS). Results As a Quality control (QC) measure, proteins with more than 50% missing values were removed and iterative principal component analysis was conducted to remove outliers within brain regions. After QC, 9,180 and 9,734 proteins remained in the DLPC and STG proteome, respectively, of which approximately 9,000 proteins were shared between regions. Protein levels of microtubule-associated protein tau (MAPT) and amyloid-precursor protein (APP) demonstrated AD-related elevations in DLPFC tissues with a strong association with CERAD and Braak across racial groups. APOE4 protein levels in brain were highly concordant with APOE genotype of the individuals. Discussion This comprehensive region resolved large-scale proteomic dataset provides a resource for the understanding of ethnoracial-specific protein differences in AD brain.
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Affiliation(s)
| | - Edward J Fox
- Emory University School of Medicine, Atlanta, GA USA
| | | | - Yue Liu
- Emory University School of Medicine, Atlanta, GA USA
| | - Eric B Dammer
- Emory University School of Medicine, Atlanta, GA USA
| | - Erica Modeste
- Emory University School of Medicine, Atlanta, GA USA
| | - Duc M Duong
- Emory University School of Medicine, Atlanta, GA USA
| | - Luming Yin
- Emory University School of Medicine, Atlanta, GA USA
| | | | - Qi Guo
- Emory University School of Medicine, Atlanta, GA USA
| | - Kaiming Xu
- Emory University School of Medicine, Atlanta, GA USA
| | - Lingyan Ping
- Emory University School of Medicine, Atlanta, GA USA
| | - Joseph S Reddy
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL USA
| | - Mariet Allen
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL USA
| | - Zachary Quicksall
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL USA
| | | | | | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | | | | | - Xianfeng Chen
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL USA
| | - Saurabh Baheti
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL USA
| | - Charlotte Ho
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL USA
| | - Thuy Nguyen
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL USA
| | - Geovanna Yepez
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL USA
| | | | | | - Xue Wang
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL USA
| | | | | | - Thomas Beach
- Banner Sun Health Research Institute, Sun City, AR USA
| | | | - Dennis W Dickson
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL USA
| | - Edward B Lee
- Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelpha, PA, USA
| | - Todd E Golde
- Emory University School of Medicine, Atlanta, GA USA
| | | | - Lisa L Barnes
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Varham Haroutunian
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Marla Gearing
- Emory University School of Medicine, Atlanta, GA USA
| | - James J Lah
- Emory University School of Medicine, Atlanta, GA USA
| | | | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL USA
| | | | - Nilüfer Ertekin-Taner
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL USA
- Mayo Clinic Florida, Department of Neurology, Jacksonville, FL USA
| | - Allan I Levey
- Emory University School of Medicine, Atlanta, GA USA
| | - Aliza Wingo
- Emory University School of Medicine, Atlanta, GA USA
| | - Thomas Wingo
- Emory University School of Medicine, Atlanta, GA USA
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11
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Zhang Q, Ma C, Chin LS, Pan S, Li L. Human brain glycoform coregulation network and glycan modification alterations in Alzheimer's disease. SCIENCE ADVANCES 2024; 10:eadk6911. [PMID: 38579000 PMCID: PMC10997212 DOI: 10.1126/sciadv.adk6911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/05/2024] [Indexed: 04/07/2024]
Abstract
Despite the importance of protein glycosylation to brain health, current knowledge of glycosylated proteoforms or glycoforms in human brain and their alterations in Alzheimer's disease (AD) is limited. Here, we report a proteome-wide glycoform profiling study of human AD and control brains using intact glycopeptide-based quantitative glycoproteomics coupled with systems biology. Our study identified more than 10,000 human brain N-glycoforms from nearly 1200 glycoproteins and uncovered disease signatures of altered glycoforms and glycan modifications, including reduced sialylation and N-glycan branching and elongation as well as elevated mannosylation and N-glycan truncation in AD. Network analyses revealed a higher-order organization of brain glycoproteome into networks of coregulated glycoforms and glycans and discovered glycoform and glycan modules associated with AD clinical phenotype, amyloid-β accumulation, and tau pathology. Our findings provide valuable insights into disease pathogenesis and a rich resource of glycoform and glycan changes in AD and pave the way forward for developing glycosylation-based therapies and biomarkers for AD.
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Affiliation(s)
- Qi Zhang
- Department of Pharmacology and Chemical Biology, Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Cheng Ma
- The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lih-Shen Chin
- Department of Pharmacology and Chemical Biology, Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sheng Pan
- The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lian Li
- Department of Pharmacology and Chemical Biology, Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
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12
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Zheng H, Gu C, Yang H. Identification of disease-specific bio-markers through network-based analysis of gene co-expression: A case study on Alzheimer's disease. Heliyon 2024; 10:e27070. [PMID: 38468964 PMCID: PMC10926071 DOI: 10.1016/j.heliyon.2024.e27070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/16/2024] [Accepted: 02/23/2024] [Indexed: 03/13/2024] Open
Abstract
Finding biomarker genes for complex diseases attracts persistent attention due to its application in clinics. In this paper, we propose a network-based method to obtain a set of biomarker genes. The key idea is to construct a gene co-expression network among sensitive genes and cluster the genes into different modules. For each module, we can identify its representative, i.e., the gene with the largest connectivity and the smallest average shortest path length to other genes within the module. We believe these representative genes could serve as a new set of potential biomarkers for diseases. As a typical example, we investigated Alzheimer's disease, obtaining a total of 16 potential representative genes, three of which belong to the non-transcriptome. A total of 11 out of these genes are found in literature from different perspectives and methods. The incipient groups were classified into two different subtypes using machine learning algorithms. We subjected the two subtypes to Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis with healthy groups and moderate groups, respectively. The two sub-type groups were involved in two different biological processes, demonstrating the validity of this approach. This method is disease-specific and independent; hence, it can be extended to classify other kinds of complex diseases.
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Affiliation(s)
- Hexiang Zheng
- Department of Systems Science, Business School, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Changgui Gu
- Department of Systems Science, Business School, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Huijie Yang
- Department of Systems Science, Business School, University of Shanghai for Science and Technology, Shanghai, 200093, China
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13
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Leitner D, Pires G, Kavanagh T, Kanshin E, Askenazi M, Ueberheide B, Devinsky O, Wisniewski T, Drummond E. Similar brain proteomic signatures in Alzheimer's disease and epilepsy. Acta Neuropathol 2024; 147:27. [PMID: 38289539 PMCID: PMC10827928 DOI: 10.1007/s00401-024-02683-4] [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: 10/04/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024]
Abstract
The prevalence of epilepsy is increased among Alzheimer's Disease (AD) patients and cognitive impairment is common among people with epilepsy. Epilepsy and AD are linked but the shared pathophysiological changes remain poorly defined. We aim to identify protein differences associated with epilepsy and AD using published proteomics datasets. We observed a highly significant overlap in protein differences in epilepsy and AD: 89% (689/777) of proteins altered in the hippocampus of epilepsy patients were significantly altered in advanced AD. Of the proteins altered in both epilepsy and AD, 340 were altered in the same direction, while 216 proteins were altered in the opposite direction. Synapse and mitochondrial proteins were markedly decreased in epilepsy and AD, suggesting common disease mechanisms. In contrast, ribosome proteins were increased in epilepsy but decreased in AD. Notably, many of the proteins altered in epilepsy interact with tau or are regulated by tau expression. This suggests that tau likely mediates common protein changes in epilepsy and AD. Immunohistochemistry for Aβ and multiple phosphorylated tau species (pTau396/404, pTau217, pTau231) showed a trend for increased intraneuronal pTau217 and pTau231 but no phosphorylated tau aggregates or amyloid plaques in epilepsy hippocampal sections. Our results provide insights into common mechanisms in epilepsy and AD and highlights the potential role of tau in mediating common pathological protein changes in epilepsy and AD.
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Affiliation(s)
- Dominique Leitner
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, 10016, USA
| | - Geoffrey Pires
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA
| | - Tomas Kavanagh
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Evgeny Kanshin
- Proteomics Laboratory, Division of Advanced Research Technologies and Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, 10016, USA
| | | | - Beatrix Ueberheide
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies and Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, 10016, USA
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, 10016, USA
| | - Thomas Wisniewski
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA.
| | - Eleanor Drummond
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA.
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia.
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14
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Das S. Omics Approaches in Alzheimer's Disease Research. J Alzheimers Dis 2024; 99:S183-S185. [PMID: 38640162 DOI: 10.3233/jad-240272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Affiliation(s)
- Sudeshna Das
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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15
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Levites Y, Dammer EB, Ran Y, Tsering W, Duong D, Abreha M, Gadhavi J, Lolo K, Trejo-Lopez J, Phillips JL, Iturbe A, Erqiuzi A, Moore BD, Ryu D, Natu A, Dillon KD, Torrellas J, Moran C, Ladd TB, Afroz KF, Islam T, Jagirdar J, Funk CC, Robinson M, Borchelt DR, Ertekin-Taner N, Kelly JW, Heppner FL, Johnson EC, McFarland K, Levey AL, Prokop S, Seyfried NT, Golde TE. Aβ Amyloid Scaffolds the Accumulation of Matrisome and Additional Proteins in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.568318. [PMID: 38076912 PMCID: PMC10705437 DOI: 10.1101/2023.11.29.568318] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
We report a highly significant correlation in brain proteome changes between Alzheimers disease (AD) and CRND8 APP695NL/F transgenic mice. However, integrating protein changes observed in the CRND8 mice with co-expression networks derived from human AD, reveals both conserved and divergent module changes. For the most highly conserved module (M42, matrisome) we find many proteins accumulate in plaques, cerebrovascular amyloid (CAA), dystrophic processes, or a combination thereof. Overexpression of two M42 proteins, midkine (Mdk) and pleiotrophin (PTN), in CRND8 mice brains leads to increased accumulation of A β ; in plaques and in CAA; further, recombinant MDK and PTN enhance A β ; aggregation into amyloid. Multiple M42 proteins, annotated as heparan sulfate binding proteins, bind to fibrillar A β 42 and a non-human amyloid fibril in vitro. Supporting this binding data, MDK and PTN co-accumulate with transthyretin (TTR) amyloid in the heart and islet amyloid polypeptide (IAPP) amyloid in the pancreas. Our findings establish several critical insights. Proteomic changes in modules observed in human AD brains define an A β ; amyloid responsome that is well conserved from mouse model to human. Further, distinct amyloid structures may serve as scaffolds, facilitating the co-accumulation of proteins with signaling functions. We hypothesize that this co-accumulation may contribute to downstream pathological sequalae. Overall, this contextualized understanding of proteomic changes and their interplay with amyloid deposition provides valuable insights into the complexity of AD pathogenesis and potential biomarkers and therapeutic targets.
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16
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Dey KK, Yarbro JM, Liu D, Han X, Wang Z, Jiao Y, Wu Z, Yang S, Lee D, Dasgupta A, Yuan ZF, Wang X, Zhu L, Peng J. Identifying Sex-Specific Serum Patterns of Alzheimer's Mice through Deep TMT Profiling and a Concentration-Dependent Concatenation Strategy. J Proteome Res 2023; 22:3843-3853. [PMID: 37910662 PMCID: PMC10872962 DOI: 10.1021/acs.jproteome.3c00496] [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: 11/03/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent form of dementia, disproportionately affecting women in disease prevalence and progression. Comprehensive analysis of the serum proteome in a common AD mouse model offers potential in identifying possible AD pathology- and gender-associated biomarkers. Here, we introduce a multiplexed, nondepleted mouse serum proteome profiling via tandem mass-tag (TMTpro) labeling. The labeled sample was separated into 475 fractions using basic reversed-phase liquid chromatography (RPLC), which were categorized into low-, medium-, and high-concentration fractions for concatenation. This concentration-dependent concatenation strategy resulted in 128 fractions for acidic RPLC-tandem mass spectrometry (MS/MS) analysis, collecting ∼5 million MS/MS scans and identifying 3972 unique proteins (3413 genes) that cover a dynamic range spanning at least 6 orders of magnitude. The differential expression analysis between wild type and the commonly used AD model (5xFAD) mice exhibited minimal significant protein alterations. However, we detected 60 statistically significant (FDR < 0.05), sex-specific proteins, including complement components, serpins, carboxylesterases, major urinary proteins, cysteine-rich secretory protein 1, pregnancy-associated murine protein 1, prolactin, amyloid P component, epidermal growth factor receptor, fibrinogen-like protein 1, and hepcidin. The results suggest that our platform possesses the sensitivity and reproducibility required to detect sex-specific differentially expressed proteins in mouse serum samples.
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Affiliation(s)
- Kaushik Kumar Dey
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jay M. Yarbro
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee, TN 38163, USA
| | - Danting Liu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Xian Han
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yun Jiao
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Shu Yang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - DongGeun Lee
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Abhijit Dasgupta
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Zuo-Fei Yuan
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Xusheng Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Liqin Zhu
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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17
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Bano D, Ehninger D, Bagetta G. Decoding metabolic signatures in Alzheimer's disease: a mitochondrial perspective. Cell Death Discov 2023; 9:432. [PMID: 38040687 PMCID: PMC10692234 DOI: 10.1038/s41420-023-01732-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/05/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023] Open
Abstract
Alzheimer's disease (AD) is one of the most prevalent age-related neurodegenerative diseases and accounts for the majority of dementia cases worldwide. Tremendous ongoing efforts of basic and clinical research have expanded our knowledge on AD and its complex multifactorial pathogenesis. For sporadic AD, it is widely assumed that silent and early symptomatic stages initiate decades before the irreversible decline in cognitive abilities that ultimately lead to debilitating conditions. In addition to amyloid plaques and tau-containing neurofibrillary tangles as the most prominent hallmarks of AD lesions within the affected brain areas, we now possess a broader collection of pathological signatures that are associated with AD development and progression. In this regard, there is a substantial body of evidence suggesting that hypometabolism occurs in the brains of individuals at the prodromal stage before dementia is diagnosed, which may reflect an early role of metabolic dysfunction in AD. This perspective surveys the vast literature and critically assesses the current evidence demonstrating a mitochondrial contribution to AD. Additionally, we discuss our interpretations of the reported mitochondrial signatures and consider how altered mitochondrial bioenergetics may be an additional risk factor for AD pathogenesis.
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Affiliation(s)
- Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
| | - Dan Ehninger
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Giacinto Bagetta
- Department of Pharmacy, Health Science and Nutrition, University of Calabria, Rende, CS, Italy
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18
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Zhang Q, Ma C, Chin LS, Pan S, Li L. Human brain glycoform co-regulation network and glycan modification alterations in Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566889. [PMID: 38014218 PMCID: PMC10680592 DOI: 10.1101/2023.11.13.566889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Despite the importance of protein glycosylation to brain health, current knowledge of glycosylated proteoforms or glycoforms in human brain and their alterations in Alzheimer's disease (AD) is limited. Here, we present a new paradigm of proteome-wide glycoform profiling study of human AD and control brains using intact glycopeptide-based quantitative glycoproteomics coupled with systems biology. Our study identified over 10,000 human brain N-glycoforms from nearly 1200 glycoproteins and uncovered disease signatures of altered glycoforms and glycan modifications, including reduced sialylation and N-glycan branching as well as elevated mannosylation and N-glycan truncation in AD. Network analyses revealed a higher-order organization of brain glycoproteome into networks of co-regulated glycoforms and glycans and discovered glycoform and glycan modules associated with AD clinical phenotype, amyloid-β accumulation, and tau pathology. Our findings provide novel insights and a rich resource of glycoform and glycan changes in AD and pave the way forward for developing glycosylation-based therapies and biomarkers for AD.
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19
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Shvetcov A, Thomson S, Spathos J, Cho AN, Wilkins HM, Andrews SJ, Delerue F, Couttas TA, Issar JK, Isik F, Kaur S, Drummond E, Dobson-Stone C, Duffy SL, Rogers NM, Catchpoole D, Gold WA, Swerdlow RH, Brown DA, Finney CA. Blood-Based Transcriptomic Biomarkers Are Predictive of Neurodegeneration Rather Than Alzheimer's Disease. Int J Mol Sci 2023; 24:15011. [PMID: 37834458 PMCID: PMC10573468 DOI: 10.3390/ijms241915011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
Alzheimer's disease (AD) is a growing global health crisis affecting millions and incurring substantial economic costs. However, clinical diagnosis remains challenging, with misdiagnoses and underdiagnoses being prevalent. There is an increased focus on putative, blood-based biomarkers that may be useful for the diagnosis as well as early detection of AD. In the present study, we used an unbiased combination of machine learning and functional network analyses to identify blood gene biomarker candidates in AD. Using supervised machine learning, we also determined whether these candidates were indeed unique to AD or whether they were indicative of other neurodegenerative diseases, such as Parkinson's disease (PD) and amyotrophic lateral sclerosis (ALS). Our analyses showed that genes involved in spliceosome assembly, RNA binding, transcription, protein synthesis, mitoribosomes, and NADH dehydrogenase were the best-performing genes for identifying AD patients relative to cognitively healthy controls. This transcriptomic signature, however, was not unique to AD, and subsequent machine learning showed that this signature could also predict PD and ALS relative to controls without neurodegenerative disease. Combined, our results suggest that mRNA from whole blood can indeed be used to screen for patients with neurodegeneration but may be less effective in diagnosing the specific neurodegenerative disease.
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Affiliation(s)
- Artur Shvetcov
- Department of Psychological Medicine, Sydney Children’s Hospitals Network, Sydney, NSW 2031, Australia
- Discipline of Psychiatry and Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Shannon Thomson
- Neuroinflammation Research Group, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- School of Medical Sciences, Faculty of Medicine Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Jessica Spathos
- Neuroinflammation Research Group, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
| | - Ann-Na Cho
- Dementia Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Heather M. Wilkins
- University of Kansas Alzheimer’s Disease Research Centre, Kansas City, KS 66160, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Centre, Kansas City, KS 66160, USA
- Department of Neurology, University of Kansas Medical Centre, Kansas City, KS 66160, USA
| | - Shea J. Andrews
- Department of Psychiatry & Behavioral Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Fabien Delerue
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Timothy A. Couttas
- Brain and Mind Centre, Translational Research Collective, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Jasmeen Kaur Issar
- Molecular Neurobiology Research Laboratory, Kids Research, Children’s Medical Research Institute, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- Kids Neuroscience Centre, Kids Research, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Finula Isik
- Neuroinflammation Research Group, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- School of Medical Sciences, Faculty of Medicine Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Simranpreet Kaur
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia
- Department of Pediatrics, University of Melbourne, Parkville, VIC 3010, Australia
| | - Eleanor Drummond
- School of Medical Sciences, Faculty of Medicine Health, The University of Sydney, Sydney, NSW 2050, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Carol Dobson-Stone
- School of Medical Sciences, Faculty of Medicine Health, The University of Sydney, Sydney, NSW 2050, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Shantel L. Duffy
- Allied Health, Research and Strategic Partnerships, Nepean Blue Mountains Local Health District, Penrith, NSW 2750, Australia
| | - Natasha M. Rogers
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- Renal and Transplant Medicine Unit, Westmead Hospital, Westmead, NSW 2145, Australia
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Daniel Catchpoole
- The Tumor Bank, Kids Research, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- Children’s Cancer Research Institute, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Wendy A. Gold
- School of Medical Sciences, Faculty of Medicine Health, The University of Sydney, Sydney, NSW 2050, Australia
- Molecular Neurobiology Research Laboratory, Kids Research, Children’s Medical Research Institute, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- Kids Neuroscience Centre, Kids Research, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Russell H. Swerdlow
- University of Kansas Alzheimer’s Disease Research Centre, Kansas City, KS 66160, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Centre, Kansas City, KS 66160, USA
- Department of Neurology, University of Kansas Medical Centre, Kansas City, KS 66160, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Centre, Kansas City, KS 66160, USA
| | - David A. Brown
- Neuroinflammation Research Group, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
- Department of Immunopathology, Institute for Clinical Pathology and Medical Research-New South Wales Health Pathology, Sydney, NSW 2145, Australia
| | - Caitlin A. Finney
- Neuroinflammation Research Group, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- School of Medical Sciences, Faculty of Medicine Health, The University of Sydney, Sydney, NSW 2050, Australia
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20
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Krogsaeter EK, McKetney J, Marquez A, Cakir Z, Stevenson E, Jang GM, Rao A, Zhou A, Huang Y, Krogan NJ, Swaney DL. Lysosomal proteomics reveals mechanisms of neuronal apoE4associated lysosomal dysfunction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560519. [PMID: 37873080 PMCID: PMC10592882 DOI: 10.1101/2023.10.02.560519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
ApoE4 is the primary risk factor for Alzheimer's Disease. While apoE is primarily expressed by astrocytes, AD pathology including endosomal abnormalities and mitochondrial dysfunction first occurs in neurons. Lysosomes are poised at the convergence point between these features. We find that apoE4-expressing cells exhibit lysosomal alkalinization, reduced lysosomal proteolysis, and impaired mitophagy. To identify driving factors for this lysosomal dysfunction, we performed quantitative lysosomal proteome profiling. This revealed that apoE4 expression results in lysosomal depletion of Lgals3bp and accumulation of Tmed5 in both Neuro-2a cells and postmitotic human neurons. Modulating the expression of both proteins affected lysosomal function, with Tmed5 knockdown rescuing lysosomal alkalinization in apoE4 cells, and Lgals3bp knockdown causing lysosomal alkalinization and reduced lysosomal density in apoE3 cells. Taken together, our work reveals that apoE4 exerts gain-of-toxicity by alkalinizing the lysosomal lumen, pinpointing lysosomal Tmed5 accumulation and Lgals3bp depletion as apoE4-associated drivers for this phenotype.
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Affiliation(s)
- Einar K. Krogsaeter
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- These authors contributed equally
| | - Justin McKetney
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- These authors contributed equally
| | - Angelica Marquez
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Zeynep Cakir
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Erica Stevenson
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Gwendolyn M. Jang
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Antara Rao
- Gladstone Institute of Neurological Disease, The J. David Gladstone Institutes, San Francisco, USA
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, USA
| | - Anton Zhou
- Gladstone Institute of Neurological Disease, The J. David Gladstone Institutes, San Francisco, USA
| | - Yadong Huang
- Gladstone Institute of Neurological Disease, The J. David Gladstone Institutes, San Francisco, USA
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, USA
- Neuroscience Graduate Program, University of California, San Francisco, USA
- Gladstone Center for Translational Advancement, Gladstone Institutes, San Francisco, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, USA
- Departments of Neurology and Pathology, University of California, San Francisco, USA
| | - Nevan J. Krogan
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Danielle L. Swaney
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
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