1
|
Bao LX, Luo ZM, Zhu XL, Xu YY. Automated identification of protein expression intensity and classification of protein cellular locations in mouse brain regions from immunofluorescence images. Med Biol Eng Comput 2024; 62:1105-1119. [PMID: 38150111 DOI: 10.1007/s11517-023-02985-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: 03/30/2023] [Accepted: 11/28/2023] [Indexed: 12/28/2023]
Abstract
Knowledge of protein expression in mammalian brains at regional and cellular levels can facilitate understanding of protein functions and associated diseases. As the mouse brain is a typical mammalian brain considering cell type and structure, several studies have been conducted to analyze protein expression in mouse brains. However, labeling protein expression using biotechnology is costly and time-consuming. Therefore, automated models that can accurately recognize protein expression are needed. Here, we constructed machine learning models to automatically annotate the protein expression intensity and cellular location in different mouse brain regions from immunofluorescence images. The brain regions and sub-regions were segmented through learning image features using an autoencoder and then performing K-means clustering and registration to align with the anatomical references. The protein expression intensities for those segmented structures were computed on the basis of the statistics of the image pixels, and patch-based weakly supervised methods and multi-instance learning were used to classify the cellular locations. Results demonstrated that the models achieved high accuracy in the expression intensity estimation, and the F1 score of the cellular location prediction was 74.5%. This work established an automated pipeline for analyzing mouse brain images and provided a foundation for further study of protein expression and functions.
Collapse
Affiliation(s)
- Lin-Xia Bao
- School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, China
- Guangdong Provincial Key Laboratory of Medical Imaging Processing, Southern Medical University, Guangzhou, 510515, China
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou, 510623, China
| | - Zhuo-Ming Luo
- School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, China
- Guangdong Provincial Key Laboratory of Medical Imaging Processing, Southern Medical University, Guangzhou, 510515, China
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou, 510623, China
| | - Xi-Liang Zhu
- School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, China
- Guangdong Provincial Key Laboratory of Medical Imaging Processing, Southern Medical University, Guangzhou, 510515, China
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou, 510623, China
| | - Ying-Ying Xu
- School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, China.
- Guangdong Provincial Key Laboratory of Medical Imaging Processing, Southern Medical University, Guangzhou, 510515, China.
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou, 510623, China.
| |
Collapse
|
2
|
Huang Y, Driedonks TAP, Cheng L, Rajapaksha H, Turchinovich A, Routenberg DA, Nagaraj R, Redding-Ochoa J, Arab T, Powell BH, Pletnikova O, Troncoso JC, Zheng L, Hill AF, Mahairaki V, Witwer KW. Relationships of APOE Genotypes With Small RNA and Protein Cargo of Brain Tissue Extracellular Vesicles From Patients With Late-Stage AD. Neurol Genet 2022; 8:e200026. [PMID: 36405397 PMCID: PMC9667865 DOI: 10.1212/nxg.0000000000200026] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/20/2022] [Indexed: 11/24/2022]
Abstract
Background and Objectives Variants of the apolipoprotein E (APOE) gene are the greatest known risk factors for sporadic Alzheimer disease (AD). Three major APOE isoform alleles, ε2, ε3, and ε4, encode and produce proteins that differ by only 1-2 amino acids but have different binding partner interactions. Whereas APOE ε2 is protective against AD relative to ε3, ε4 is associated with an increased risk for AD development. However, the role of APOE in gene regulation in AD pathogenesis has remained largely undetermined. Extracellular vesicles (EVs) are lipid bilayer-delimited particles released by cells to dispose of unwanted materials and mediate intercellular communication, and they are implicated in AD pathophysiology. Brain-derived EVs (bdEVs) could act locally in the tissue and reflect cellular changes. To reveal whether APOE genotype affects EV components in AD brains, bdEVs were separated from patients with AD with different APOE genotypes for parallel small RNA and protein profile. Methods bdEVs from late-stage AD brains (BRAAK stages 5-6) from patients with APOE genotypes ε2/3 (n = 5), ε3/3 (n = 5), ε3/4 (n = 6), and ε4/4 (n = 6) were separated using our published protocol into a 10,000g pelleted extracellular fraction (10K) and a further purified EV fraction. Counting, sizing, and multiomic characterization by small RNA sequencing and proteomic analysis were performed for 10K, EVs, and source tissue. Results Comparing APOE genotypes, no significant differences in bdEV total particle concentration or morphology were observed. Overall small RNA and protein profiles of 10K, EVs, and source tissue also did not differ substantially between different APOE genotypes. However, several differences in individual RNAs (including miRNAs and tRNAs) and proteins in 10K and EVs were observed when comparing the highest and lowest risk groups (ε4/4 and ε2/3). Bioinformatic analysis and previous publications indicate a potential regulatory role of these molecules in AD. Discussion For patients with late-stage AD in this study, only a few moderate differences were observed for small RNA and protein profiles between APOE genotypes. Among these, several newly identified 10K and EV-associated molecules may play roles in AD progression. Possibly, larger genotype-related differences exist and are more apparent in or before earlier disease stages.
Collapse
Affiliation(s)
- Yiyao Huang
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Tom A P Driedonks
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Lesley Cheng
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Harinda Rajapaksha
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Andrey Turchinovich
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - David A Routenberg
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Rajini Nagaraj
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Javier Redding-Ochoa
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Tanina Arab
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Bonita H Powell
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Olga Pletnikova
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Juan C Troncoso
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Lei Zheng
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Andrew F Hill
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Vasiliki Mahairaki
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| |
Collapse
|
3
|
Sandebring-Matton A, Axenhus M, Bogdanovic N, Winblad B, Schedin-Weiss S, Nilsson P, Tjernberg LO. Microdissected Pyramidal Cell Proteomics of Alzheimer Brain Reveals Alterations in Creatine Kinase B-Type, 14-3-3-γ, and Heat Shock Cognate 71. Front Aging Neurosci 2021; 13:735334. [PMID: 34867272 PMCID: PMC8641652 DOI: 10.3389/fnagi.2021.735334] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022] Open
Abstract
Novel insights on proteins involved in Alzheimer’s disease (AD) are needed. Since multiple cell types and matrix components are altered in AD, bulk analysis of brain tissue maybe difficult to interpret. In the current study, we isolated pyramidal cells from the cornu ammonis 1 (CA1) region of the hippocampus from five AD and five neurologically healthy donors using laser capture microdissection (LCM). The samples were analyzed by proteomics using 18O-labeled internal standard and nano-high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) for relative quantification. Fold change between AD and control was calculated for the proteins that were identified in at least two individual proteomes from each group. From the 10 cases analyzed, 62 proteins were identified in at least two AD cases and two control cases. Creatine kinase B-type (CKB), 14-3-3-γ, and heat shock cognate 71 (Hsc71), which have not been extensively studied in the context of the human AD brain previously, were selected for further studies by immunohistochemistry (IHC). In hippocampus, semi-quantitative measures of IHC staining of the three proteins confirmed the findings from our proteomic analysis. Studies of the same proteins in the frontal cortex revealed that the alterations remained for CKB and 14-3-3-γ but not for Hsc71. Protein upregulation in CA1 neurons of final stage AD is either a result of detrimental, pathological effects, or from cell-specific protective response mechanisms in surviving neurons. Based on previous findings from experimental studies, CKB and Hsc71 likely exhibit protective effects, whereas 14-3-3-γ may represent a detrimental pathway. These new players could reflect pathways of importance for the development of new therapeutic strategies.
Collapse
Affiliation(s)
- Anna Sandebring-Matton
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden.,Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden.,Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, United Kingdom
| | - Michael Axenhus
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden.,Theme Inflammation and Aging, Karolinska University Hospital, Huddinge, Sweden
| | - Nenad Bogdanovic
- Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden.,Theme Inflammation and Aging, Karolinska University Hospital, Huddinge, Sweden
| | - Bengt Winblad
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden
| | - Sophia Schedin-Weiss
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden
| | - Per Nilsson
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden
| | - Lars O Tjernberg
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden.,Clinical Chemistry, Karolinska University Hospital, Solna, Sweden
| |
Collapse
|
4
|
Fathi E, Yarbro JM, Homayouni R. NIPSNAP protein family emerges as a sensor of mitochondrial health. Bioessays 2021; 43:e2100014. [PMID: 33852167 PMCID: PMC10577685 DOI: 10.1002/bies.202100014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/11/2022]
Abstract
Since their discovery over two decades ago, the molecular and cellular functions of the NIPSNAP family of proteins (NIPSNAPs) have remained elusive until recently. NIPSNAPs interact with a variety of mitochondrial and cytoplasmic proteins. They have been implicated in multiple cellular processes and associated with different physiologic and pathologic conditions, including pain transmission, Parkinson's disease, and cancer. Recent evidence demonstrated a direct role for NIPSNAP1 and NIPSNAP2 proteins in regulation of mitophagy, a process that is critical for cellular health and maintenance. Importantly, NIPSNAPs contain a 110 amino acid domain that is evolutionary conserved from mammals to bacteria. However, the molecular function of the conserved NIPSNAP domain and its potential role in mitophagy have not been explored. It stands to reason that the highly conserved NIPSNAP domain interacts with a substrate that is ubiquitously present across all species and can perhaps act as a sensor for mitochondrial health.
Collapse
Affiliation(s)
- Esmat Fathi
- Department of Biological Sciences, University of Memphis, Memphis, TN, United States
- Beaumont Research Institute, Beaumont Health, Royal Oak, MI, United States
| | - Jay M. Yarbro
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Ramin Homayouni
- Beaumont Research Institute, Beaumont Health, Royal Oak, MI, United States
- Oakland University William Beaumont School of Medicine, Oakland University, Rochester, MI, United States
| |
Collapse
|
5
|
Stepler KE, Mahoney ER, Kofler J, Hohman TJ, Lopez OL, Robinson RAS. Inclusion of African American/Black adults in a pilot brain proteomics study of Alzheimer's disease. Neurobiol Dis 2020; 146:105129. [PMID: 33049317 PMCID: PMC7990397 DOI: 10.1016/j.nbd.2020.105129] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) disproportionately affects certain racial and ethnic subgroups, such as African American/Black and Hispanic adults. Genetic, comorbid, and socioeconomic risk factors contribute to this disparity; however, the molecular contributions have been largely unexplored. Herein, we conducted a pilot proteomics study of postmortem brains from African American/Black and non-Hispanic White adults neuropathologically diagnosed with AD compared to closely-matched cognitively normal individuals. Examination of hippocampus, inferior parietal lobule, and globus pallidus regions using quantitative proteomics resulted in 568 differentially-expressed proteins in AD. These proteins were consistent with the literature and included glial fibrillary acidic protein, peroxiredoxin-1, and annexin A5. In addition, 351 novel proteins in AD were identified, which could partially be due to cohort diversity. From linear regression analyses, we identified 185 proteins with significant race x diagnosis interactions across various brain regions. These differences generally were reflective of differential expression of proteins in AD that occurred in only a single racial/ethnic group. Overall, this pilot study suggests that disease understanding can be furthered by including diversity in racial/ethnic groups; however, this must be done on a larger scale.
Collapse
Affiliation(s)
- Kaitlyn E Stepler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Emily R Mahoney
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN 37212, United States of America; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America
| | - Julia Kofler
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, United States of America
| | - Timothy J Hohman
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN 37212, United States of America; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America; Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America
| | - Oscar L Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, United States of America; Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, United States of America
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America; Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN 37212, United States of America; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America; Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, United States of America.
| |
Collapse
|
6
|
De Pasquale V, Costanzo M, Siciliano RA, Mazzeo MF, Pistorio V, Bianchi L, Marchese E, Ruoppolo M, Pavone LM, Caterino M. Proteomic Analysis of Mucopolysaccharidosis IIIB Mouse Brain. Biomolecules 2020; 10:biom10030355. [PMID: 32111039 PMCID: PMC7175334 DOI: 10.3390/biom10030355] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 02/17/2020] [Accepted: 02/24/2020] [Indexed: 02/07/2023] Open
Abstract
Mucopolysaccharidosis IIIB (MPS IIIB) is an inherited metabolic disease due to deficiency of α-N-Acetylglucosaminidase (NAGLU) enzyme with subsequent storage of undegraded heparan sulfate (HS). The main clinical manifestations of the disease are profound intellectual disability and neurodegeneration. A label-free quantitative proteomic approach was applied to compare the proteome profile of brains from MPS IIIB and control mice to identify altered neuropathological pathways of MPS IIIB. Proteins were identified through a bottom up analysis and 130 were significantly under-represented and 74 over-represented in MPS IIIB mouse brains compared to wild type (WT). Multiple bioinformatic analyses allowed to identify three major clusters of the differentially abundant proteins: proteins involved in cytoskeletal regulation, synaptic vesicle trafficking, and energy metabolism. The proteome profile of NAGLU-/- mouse brain could pave the way for further studies aimed at identifying novel therapeutic targets for the MPS IIIB. Data are available via ProteomeXchange with the identifier PXD017363.
Collapse
Affiliation(s)
- Valeria De Pasquale
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; (V.D.P.); (M.C.); (V.P.); (M.R.); (M.C.)
| | - Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; (V.D.P.); (M.C.); (V.P.); (M.R.); (M.C.)
- CEINGE-Biotecnologie Avanzate scarl, 80145 Naples, Italy;
| | | | | | - Valeria Pistorio
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; (V.D.P.); (M.C.); (V.P.); (M.R.); (M.C.)
| | - Laura Bianchi
- Laboratory of Functional Proteomics, Department of Life Sciences, University of Siena, 53100 Siena, Italy;
| | - Emanuela Marchese
- CEINGE-Biotecnologie Avanzate scarl, 80145 Naples, Italy;
- Department of Mental Health and Preventive Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy
| | - Margherita Ruoppolo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; (V.D.P.); (M.C.); (V.P.); (M.R.); (M.C.)
- CEINGE-Biotecnologie Avanzate scarl, 80145 Naples, Italy;
| | - Luigi Michele Pavone
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; (V.D.P.); (M.C.); (V.P.); (M.R.); (M.C.)
- Correspondence: ; Tel.: +39-081-7463043
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; (V.D.P.); (M.C.); (V.P.); (M.R.); (M.C.)
- CEINGE-Biotecnologie Avanzate scarl, 80145 Naples, Italy;
| |
Collapse
|
7
|
Contreras A, Morales L, Del Olmo N, Pérez-García C. Effects of Intermittent versus Chronic-Moderate Ethanol Administration during Adolescence in the Adult Hippocampal Phosphoproteome. Chem Res Toxicol 2020; 33:448-460. [PMID: 31944673 DOI: 10.1021/acs.chemrestox.9b00359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Alcohol consumption during adolescence is known to cause different impairments in the hippocampus that could lead to persistent deficits in adulthood. A common pattern of alcohol use in adolescents consists of excessive and intermittent alcohol consumption over a very short period of time (binge drinking). Protein phosphorylation is a mechanism underlying memory processes and we have previously demonstrated changes in the rat hippocampal phosphoproteome after a single dose of ethanol; however, studies showing the phosphoprotein alterations in the hippocampus after repeated exposition to alcohol are limited. This study focuses on the identification of the phosphoproteins differentially regulated in the adolescent rat hippocampus after repeated ethanol administration by comparing different patterns of alcohol treatments according to dose and frequency of administration ((i) moderate dose-chronic use, (ii) low dose-intermittent use, and (iii) high dose-intermittent use). We have used a proteomic approach, including phosphoprotein enrichment by immobilized metal affinity chromatography, which revealed 21 proteins differentially affected depending on the pattern of alcohol treatment used. Many of these proteins are included in glycolysis and glucagon signaling pathways and are also involved in neurodegeneration, which could reinforce the role of metabolic alterations in the neural damage induced by repeated alcohol exposure during adolescence.
Collapse
Affiliation(s)
- Ana Contreras
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia , Universidad CEU-San Pablo , Madrid 28003 , Spain
| | - Lidia Morales
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia , Universidad CEU-San Pablo , Madrid 28003 , Spain
| | - Nuria Del Olmo
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia , Universidad CEU-San Pablo , Madrid 28003 , Spain
| | - Carmen Pérez-García
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia , Universidad CEU-San Pablo , Madrid 28003 , Spain
| |
Collapse
|
8
|
Abstract
Introduction: Protein thiols are susceptible to oxidation in health and disease. Redox proteomics methods facilitate the identification, quantification, and rationalization of oxidation processes including those involving protein thiols. These residues are crucial to understanding redox homeostasis underpinning normal cell functioning and regulation as well as novel biomarkers of pathology and promising novel drug targets.Areas covered: This article reviews redox proteomic approaches to study of protein thiols in some important human pathologies and assesses the clinical potential of individual Cys residues as novel biomarkers for disease detection and as targets for novel treatments.Expert commentary: Although protein thiols are not as routinely used as redox biomarkers as some other lesions such as carbonylation, there has been growing recent interest in their potential. Driven largely by developments in high-resolution mass spectrometry it is possible now to identify proteins that are redox modified at thiol groups or that interact with regulatory oxidoreductases. Thiols that are specifically susceptible to modification by reactive oxygen species can be routinely identified now and quantitative MS can be used to quantify the proportion of a protein that is redox modified.
Collapse
Affiliation(s)
- David Sheehan
- Department of Chemistry, Khalifa University, Abu Dhabi, United Arab Emirates.,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Brian McDonagh
- Department of Physiology, School of Medicine, National University of Ireland, Galway, Ireland
| |
Collapse
|
9
|
Proteomic signatures of brain regions affected by tau pathology in early and late stages of Alzheimer's disease. Neurobiol Dis 2019; 130:104509. [PMID: 31207390 DOI: 10.1016/j.nbd.2019.104509] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 05/17/2019] [Accepted: 06/13/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common neurodegenerative disorder. Depositions of amyloid β peptide (Aβ) and tau protein are among the major pathological hallmarks of AD. Aβ and tau burden follows predictable spatial patterns during the progression of AD. Nevertheless, it remains obscure why certain brain regions are more vulnerable than others; to investigate this and dysregulated pathways during AD progression, a mass spectrometry-based proteomics study was performed. METHODS In total 103 tissue samples from regions early (entorhinal and parahippocampal cortices - medial temporal lobe (MTL)) and late affected (temporal and frontal cortices - neocortex) by tau pathology were subjected to label-free quantitative proteomics analysis. RESULTS Considering dysregulated proteins during AD progression, the majority (625 out of 737 proteins) was region specific, while some proteins were shared between regions (101 proteins altered in two areas and 11 proteins altered in three areas). Analogously, many dysregulated pathways during disease progression were exclusive to certain regions, but a few pathways altered in two or more areas. Changes in protein expression indicate that synapse loss occurred in all analyzed regions, while translation dysregulation was preponderant in entorhinal, parahippocampal and frontal cortices. Oxidative phosphorylation impairment was prominent in MTL. Differential proteomic analysis of brain areas in health state (controls) showed higher metabolism and increased expression of AD-related proteins in the MTL compared to the neocortex. In addition, several proteins that differentiate brain regions in control tissue were dysregulated in AD. CONCLUSIONS This work provides the comparison of proteomic changes in brain regions affected by tau pathology at different stages of AD. Although we identified commonly regulated proteins and pathways during disease advancement, we found that the dysregulated processes are predominantly region specific. In addition, a distinct proteomic signature was found between MTL and neocortex in healthy subjects that might be related to AD vulnerability. These findings highlight the need for investigating AD's cascade of events throughout the whole brain and studies spanning more brain areas are required to better understand AD etiology and region vulnerability to disease.
Collapse
|
10
|
Drummond E, Goñi F, Liu S, Prelli F, Scholtzova H, Wisniewski T. Potential Novel Approaches to Understand the Pathogenesis and Treat Alzheimer's Disease. J Alzheimers Dis 2019; 64:S299-S312. [PMID: 29562516 DOI: 10.3233/jad-179909] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is growing genetic and proteomic data highlighting the complexity of Alzheimer's disease (AD) pathogenesis. Greater use of unbiased "omics" approaches is being increasingly recognized as essential for the future development of effective AD research, that need to better reflect the multiple distinct pathway abnormalities that can drive AD pathology. The track record of success in AD clinical trials thus far has been very poor. In part, this high failure rate has been related to the premature translation of highly successful results in animal models that mirror only limited aspects of AD pathology to humans. We highlight our recent efforts to increase use of human tissue to gain a better understanding of the AD pathogenesis subtype variety and to develop several distinct therapeutic approaches tailored to address this diversity. These therapeutic approaches include the blocking of the Aβ/apoE interaction, stimulation of innate immunity, and the simultaneous blocking of Aβ/tau oligomer toxicity. We believe that future successful therapeutic approaches will need to be combined to better reflect the complexity of the abnormal pathways triggered in AD pathogenesis.
Collapse
Affiliation(s)
- Eleanor Drummond
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Fernando Goñi
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Shan Liu
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Frances Prelli
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Henrieta Scholtzova
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| |
Collapse
|
11
|
McLean FH, Campbell FM, Langston RF, Sergi D, Resch C, Grant C, Morris AC, Mayer CD, Williams LM. A high-fat diet induces rapid changes in the mouse hypothalamic proteome. Nutr Metab (Lond) 2019; 16:26. [PMID: 31168311 PMCID: PMC6489262 DOI: 10.1186/s12986-019-0352-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/12/2019] [Indexed: 12/29/2022] Open
Abstract
Background Prolonged over-consumption of a high-fat diet (HFD) commonly leads to obesity and insulin resistance. However, even 3 days of HFD consumption has been linked to inflammation within the key homeostatic brain region, the hypothalamus. Methods Mice were fed either a low-fat diet (LFD) or HFD containing 10% or 60% (Kcal) respectively from fat for 3 days. Mice were weighed, food intake measured and glucose tolerance calculated using intraperitoneal glucose tolerance tests (IPGTT). Proteomic analysis was carried out to determine if hypothalamic proteins were changed by a HFD. The direct effects of dietary fatty acids on mitochondrial morphology and on one of the proteins most changed by a HFD, dihydropyrimidinase-related protein 2 (DRP-2) a microtubule-associated protein which regulates microtubule dynamics, were also tested in mHypoE-N42 (N42) neuronal cells challenged with palmitic acid (PA) and oleic acid (OA). Results Mice on the HFD, as expected, showed increased adiposity and glucose intolerance. Hypothalamic proteomic analysis revealed changes in 104 spots after 3 days on HFD, which, when identified by LC/MS/MS, were found to represent 78 proteins mainly associated with cytoskeleton and synaptic plasticity, stress response, glucose metabolism and mitochondrial function. Over half of the changed proteins have also been reported to be changed in neurodegenerative conditions such as Alzheimer’s disease. Also,in N42 neurons mitochondrial morphology and DRP-2 levels were altered by PA but not by OA. Conclusion These results demonstrate that within 3 days, there is a relatively large effect of HFD on the hypothalamic proteome indicative of cellular stress, altered synaptic plasticity and mitochondrial function, but not inflammation. Changes in N42 cells show an effect of PA but not OA on DRP-2 and on mitochondrial morphology indicating that long-chain saturated fatty acids damage neuronal function. Electronic supplementary material The online version of this article (10.1186/s12986-019-0352-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Fiona H McLean
- 1Rowett Institute, University of Aberdeen Foresterhill Campus, Aberdeen, AB25 2ZD UK.,Division of Neuroscience, University of Dundee, Ninewells Hospital & Medical School, Dundee, DD1 9SY UK
| | - Fiona M Campbell
- 1Rowett Institute, University of Aberdeen Foresterhill Campus, Aberdeen, AB25 2ZD UK
| | - Rosamund F Langston
- Division of Neuroscience, University of Dundee, Ninewells Hospital & Medical School, Dundee, DD1 9SY UK
| | - Domenico Sergi
- 1Rowett Institute, University of Aberdeen Foresterhill Campus, Aberdeen, AB25 2ZD UK.,3Nutrition & Health Substantiation Group, Nutrition and Health Program, Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Adelaide, SA 5000 Australia
| | - Cibell Resch
- 1Rowett Institute, University of Aberdeen Foresterhill Campus, Aberdeen, AB25 2ZD UK
| | - Christine Grant
- 1Rowett Institute, University of Aberdeen Foresterhill Campus, Aberdeen, AB25 2ZD UK
| | - Amanda C Morris
- 1Rowett Institute, University of Aberdeen Foresterhill Campus, Aberdeen, AB25 2ZD UK
| | - Claus D Mayer
- 4Biomathematics and Statistics Scotland, University of Aberdeen, Aberdeen, AB25 2ZD UK
| | - Lynda M Williams
- 1Rowett Institute, University of Aberdeen Foresterhill Campus, Aberdeen, AB25 2ZD UK
| |
Collapse
|
12
|
Stepler KE, Robinson RAS. The Potential of ‘Omics to Link Lipid Metabolism and Genetic and Comorbidity Risk Factors of Alzheimer’s Disease in African Americans. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:1-28. [DOI: 10.1007/978-3-030-05542-4_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
13
|
Mazi AR, Arzuman AS, Gurel B, Sahin B, Tuzuner MB, Ozansoy M, Baykal AT. Neonatal Neurodegeneration in Alzheimer's Disease Transgenic Mouse Model. J Alzheimers Dis Rep 2018; 2:79-91. [PMID: 30480251 PMCID: PMC6159732 DOI: 10.3233/adr-170049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive disorder characterized by a variety of molecular pathologies causing cortical dementia with a prominent memory deficit. Formation of the pathology, which begins decades before the diagnosis of the disease, is highly correlated with the clinical symptoms. Several proteomics studies were performed using animal models to monitor the alterations of the brain tissue proteome at different stages of AD. However, proteome changes in the brain regions of newborn transgenic mouse model have not been investigated yet. To this end, we analyzed protein expression alterations in cortex, hippocampus and cerebellum of transgenic mice carrying five familial AD mutations (5XFAD) at neonatal day-1. Our results indicate a remarkable difference in protein expression profile of newborn 5XFAD brain with region specific variations. Additionally, the proteins, which show similar expression alteration pattern in postmortem human AD brains, were determined. Bioinformatics analysis showed that the molecular alterations were mostly related to the cell morphology, cellular assembly and organization, and neuroinflammation. Moreover, morphological analysis revealed that there is an increase in neurite number of 5XFAD mouse neurons in vitro. We suggest that, molecular alterations in the AD brain exist even at birth, and perhaps the disease is silenced until older ages when the brain becomes vulnerable.
Collapse
Affiliation(s)
- Aise Rumeysa Mazi
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul, Turkey.,Institute of Health Science, Istanbul Medipol University, Istanbul, Turkey.,Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, School of Medicine, Istanbul, Turkey
| | - Aysegul Sumeyye Arzuman
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul, Turkey.,Institute of Health Science, Istanbul Medipol University, Istanbul, Turkey.,Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, School of Medicine, Istanbul, Turkey
| | - Busra Gurel
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul, Turkey.,Institute of Health Science, Istanbul Medipol University, Istanbul, Turkey.,Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, School of Medicine, Istanbul, Turkey
| | - Betul Sahin
- Acibadem Labmed R&D Laboratory, Istanbul, Turkey
| | | | - Mehmet Ozansoy
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul, Turkey.,Department of Physiology, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Acibadem Labmed R&D Laboratory, Istanbul, Turkey.,Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, School of Medicine, Istanbul, Turkey
| |
Collapse
|
14
|
Abstract
Proteomics and lipidomics are powerful tools to the large-scale study of proteins and lipids, respectively. Several methods can be employed with particular benefits and limitations in the study of human brain. This is a review of the rationale use of current techniques with particular attention to limitations and pitfalls inherent to each one of the techniques, and more importantly, to their use in the study of post-mortem brain tissue. These aspects are cardinal to avoid false interpretations, errors and unreal expectancies. Other points are also stressed as exemplified in the analysis of human neurodegenerative diseases which are manifested by disease-, region-, and stage-specific modifications commonly in the context of aging. Information about certain altered protein clusters and proteins oxidatively damaged is summarized for Alzheimer and Parkinson diseases.
Collapse
Affiliation(s)
- Isidro Ferrer
- Pathologic Anatomy Service, Institute of Neuropathology, Bellvitge University Hospital; Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona; and Network Center of Biomedical Research on Neurodegenerative Diseases, Institute Carlos III; Hospitalet de Llobregat, Llobregat, Spain.
| |
Collapse
|
15
|
Gemelli T, de Andrade RB, Rojas DB, Zanatta Â, Schirmbeck GH, Funchal C, Wajner M, Dutra-Filho CS, Wannmacher CMD. Chronic Exposure to β-Alanine Generates Oxidative Stress and Alters Energy Metabolism in Cerebral Cortex and Cerebellum of Wistar Rats. Mol Neurobiol 2017; 55:5101-5110. [DOI: 10.1007/s12035-017-0711-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 08/07/2017] [Indexed: 01/03/2023]
|
16
|
Proteomic differences in amyloid plaques in rapidly progressive and sporadic Alzheimer's disease. Acta Neuropathol 2017; 133:933-954. [PMID: 28258398 DOI: 10.1007/s00401-017-1691-0] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/22/2017] [Accepted: 02/26/2017] [Indexed: 12/16/2022]
Abstract
Rapidly progressive Alzheimer's disease (rpAD) is a particularly aggressive form of Alzheimer's disease, with a median survival time of 7-10 months after diagnosis. Why these patients have such a rapid progression of Alzheimer's disease is currently unknown. To further understand pathological differences between rpAD and typical sporadic Alzheimer's disease (sAD) we used localized proteomics to analyze the protein differences in amyloid plaques in rpAD and sAD. Label-free quantitative LC-MS/MS was performed on amyloid plaques microdissected from rpAD and sAD patients (n = 22 for each patient group) and protein expression differences were quantified. On average, 913 ± 30 (mean ± SEM) proteins were quantified in plaques from each patient and 279 of these proteins were consistently found in plaques from every patient. We found significant differences in protein composition between rpAD and sAD plaques. We found that rpAD plaques contained significantly higher levels of neuronal proteins (p = 0.0017) and significantly lower levels of astrocytic proteins (p = 1.08 × 10-6). Unexpectedly, cumulative protein differences in rpAD plaques did not suggest accelerated typical sAD. Plaques from patients with rpAD were particularly abundant in synaptic proteins, especially those involved in synaptic vesicle release, highlighting the potential importance of synaptic dysfunction in the accelerated development of plaque pathology in rpAD. Combined, our data provide new direct evidence that amyloid plaques do not all have the same protein composition and that the proteomic differences in plaques could provide important insight into the factors that contribute to plaque development. The cumulative protein differences in rpAD plaques suggest rpAD may be a novel subtype of Alzheimer's disease.
Collapse
|
17
|
Do Carmo S, Crynen G, Paradis T, Reed J, Iulita MF, Ducatenzeiler A, Crawford F, Cuello AC. Hippocampal Proteomic Analysis Reveals Distinct Pathway Deregulation Profiles at Early and Late Stages in a Rat Model of Alzheimer's-Like Amyloid Pathology. Mol Neurobiol 2017; 55:3451-3476. [PMID: 28502044 DOI: 10.1007/s12035-017-0580-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/26/2017] [Indexed: 01/01/2023]
Abstract
The cerebral accumulation and cytotoxicity of amyloid beta (Aβ) is central to Alzheimer's pathogenesis. However, little is known about how the amyloid pathology affects the global expression of brain proteins at different disease stages. In order to identify genotype and time-dependent significant changes in protein expression, we employed quantitative proteomics analysis of hippocampal tissue from the McGill-R-Thy1-APP rat model of Alzheimer-like amyloid pathology. McGill transgenic rats were compared to wild-type rats at early and late pathology stages, i.e., when intraneuronal Aβ amyloid burden is conspicuous and when extracellular amyloid plaques are abundant with more pronounced cognitive deficits. After correction for multiple testing, the expression levels of 64 proteins were found to be considerably different in transgenic versus wild-type rats at the pre-plaque stage (3 months), and 86 proteins in the post-plaque group (12 months), with only 9 differentially regulated proteins common to the 2 time-points. This minimal overlap supports the hypothesis that different molecular pathways are affected in the hippocampus at early and late stages of the amyloid pathology throughout its continuum. At early stages, disturbances in pathways related to cellular responses to stress, protein homeostasis, and neuronal structure are predominant, while disturbances in metabolic energy generation dominate at later stages. These results shed new light on the molecular pathways affected by the early accumulation of Aβ and how the evolving amyloid pathology impacts other complex metabolic pathways.
Collapse
Affiliation(s)
- Sonia Do Carmo
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | | | - Tiffany Paradis
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Jon Reed
- Roskamp Institute, Sarasota, FL, USA
| | - M Florencia Iulita
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Adriana Ducatenzeiler
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | | | - A Claudio Cuello
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada. .,Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada. .,Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.
| |
Collapse
|
18
|
Mitochondrial proteins NIP-SNAP-1 and -2 are a target for the immunomodulatory activity of clarithromycin, which involves NF-κB-mediated cytokine production. Biochem Biophys Res Commun 2017; 483:911-916. [DOI: 10.1016/j.bbrc.2016.12.100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 12/15/2016] [Indexed: 11/18/2022]
|
19
|
Yamamoto S, Okamoto T, Ogasawara N, Hashimoto S, Shiraishi T, Sato T, Yamamoto K, Tsutsumi H, Takano K, Himi T, Itoh H, Yokota SI. NIP-SNAP-1 and -2 mitochondrial proteins are maintained by heat shock protein 60. Biochem Biophys Res Commun 2017; 483:917-922. [DOI: 10.1016/j.bbrc.2016.12.133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 12/20/2016] [Indexed: 01/16/2023]
|
20
|
Zelaya MV, Pérez-Valderrama E, de Morentin XM, Tuñon T, Ferrer I, Luquin MR, Fernandez-Irigoyen J, Santamaría E. Olfactory bulb proteome dynamics during the progression of sporadic Alzheimer's disease: identification of common and distinct olfactory targets across Alzheimer-related co-pathologies. Oncotarget 2016; 6:39437-56. [PMID: 26517091 PMCID: PMC4741837 DOI: 10.18632/oncotarget.6254] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/30/2015] [Indexed: 12/30/2022] Open
Abstract
Olfactory dysfunction is present in up to 90% of Alzheimer's disease (AD) patients. Although deposition of hyperphosphorylated tau and β-amyloid substrates are present in olfactory areas, the molecular mechanisms associated with decreased smell function are not completely understood. We have applied mass spectrometry-based quantitative proteomics to probe additional molecular disturbances in postmortem olfactory bulbs (OB) dissected from AD cases respect to neurologically intact controls (n=20, mean age 82.1 years). Relative proteome abundance measurements have revealed protein interaction networks progressively disturbed across AD stages suggesting an early imbalance in splicing factors, subsequent interrupted cycling of neurotransmitters, alteration in toxic and protective mechanisms of β-amyloid, and finally, a mitochondrial dysfunction together with disturbance in neuron-neuron adhesion. We also present novel molecular findings in the OB in an autopsy cohort composed by Lewy body disease (LBD), frontotemporal lobar degeneration (FTLD), mixed dementia, and progressive supranuclear palsy (PSP) cases (n = 41, mean age 79.7 years). Olfactory mediators deregulated during the progression of AD such as Visinin-like protein 1, RUFY3 protein, and Copine 6 were also differentially modulated in the OB in LBD, FTLD, and mixed dementia. Only Dipeptidyl aminopeptidase-like protein 6 showed a specific down-regulation in AD. However, no differences were observed in the olfactory expression of this protein panel in PSP subjects. This study demonstrates an olfactory progressive proteome modulation in AD, unveiling cross-disease similarities and differences especially for specific proteins involved in dendritic and axonic distributions that occur in the OB during the neurodegenerative process.
Collapse
Affiliation(s)
- María Victoria Zelaya
- Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Fundación Miguel Servet, Proteored-ISCIII, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Estela Pérez-Valderrama
- Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Fundación Miguel Servet, Proteored-ISCIII, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Xabier Martínez de Morentin
- Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Fundación Miguel Servet, Proteored-ISCIII, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Teresa Tuñon
- Pathological Anatomy Department, Navarra Hospital Complex, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Isidro Ferrer
- Institut de Neuropatologia, IDIBELL-Hospital Universitari de Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain.,CIBERNED (Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas), Madrid, Spain
| | - María Rosario Luquin
- Laboratory of Regenerative Therapy, Department of Neurology and Neuroscience Division, Centre for Applied Medical Research (CIMA), University of Navarra, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Joaquín Fernandez-Irigoyen
- Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Fundación Miguel Servet, Proteored-ISCIII, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Enrique Santamaría
- Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Fundación Miguel Servet, Proteored-ISCIII, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| |
Collapse
|
21
|
Funke S, Perumal N, Beck S, Gabel-Scheurich S, Schmelter C, Teister J, Gerbig C, Gramlich OW, Pfeiffer N, Grus FH. Glaucoma related Proteomic Alterations in Human Retina Samples. Sci Rep 2016; 6:29759. [PMID: 27425789 PMCID: PMC4947915 DOI: 10.1038/srep29759] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 06/24/2016] [Indexed: 01/23/2023] Open
Abstract
Glaucoma related proteomic changes have been documented in cell and animal models. However, proteomic studies investigating on human retina samples are still rare. In the present work, retina samples of glaucoma and non-glaucoma control donors have been examined by a state-of-the-art mass spectrometry (MS) workflow to uncover glaucoma related proteomic changes. More than 600 proteins could be identified with high confidence (FDR < 1%) in human retina samples. Distinct proteomic changes have been observed in 10% of proteins encircling mitochondrial and nucleus species. Numerous proteins showed a significant glaucoma related level change (p < 0.05) or distinct tendency of alteration (p < 0.1). Candidates were documented to be involved in cellular development, stress and cell death. Increase of stress related proteins and decrease of new glaucoma related candidates, ADP/ATP translocase 3 (ANT3), PC4 and SRFS1-interacting protein 1 (DFS70) and methyl-CpG-binding protein 2 (MeCp2) could be documented by MS. Moreover, candidates could be validated by Accurate Inclusion Mass Screening (AIMS) and immunostaining and supported for the retinal ganglion cell layer (GCL) by laser capture microdissection (LCM) in porcine and human eye cryosections. The workflow allowed a detailed view into the human retina proteome highlighting new molecular players ANT3, DFS70 and MeCp2 associated to glaucoma.
Collapse
Affiliation(s)
- Sebastian Funke
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Natarajan Perumal
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Sabine Beck
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Silke Gabel-Scheurich
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Carsten Schmelter
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Julia Teister
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Claudia Gerbig
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Oliver W Gramlich
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Johannes Gutenberg University, Mainz, Germany.,Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa, USA
| | - Norbert Pfeiffer
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Franz H Grus
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| |
Collapse
|
22
|
Ianiski FR, Rech VC, Nishihira VSK, Alves CB, Baldissera MD, Wilhelm EA, Luchese C. Amyloid-β peptide absence in short term effects on kinase activity of energy metabolism in mice hippocampus and cerebral cortex. AN ACAD BRAS CIENC 2016; 88:1829-1840. [PMID: 27411072 DOI: 10.1590/0001-3765201620150776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 01/14/2016] [Indexed: 12/20/2022] Open
Abstract
Considering that Alzheimer's disease is a prevalent neurodegenerative disease worldwide, we investigated the activities of three key kinases: creatine kinase, pyruvate kinase and adenylate kinase in the hippocampus and cerebral cortex in Alzheimer's disease model. Male adult Swiss mice received amyloid-β or saline. One day after, mice were treated with blank nanocapsules (17 ml/kg) or meloxicam-loaded nanocapsules (5 mg/kg) or free meloxicam (5 mg/kg). Treatments were performed on alternating days, until the end of the experimental protocol. In the fourteenth day, kinases activities were performed. Amyloid-β did not change the kinases activity in the hippocampus and cerebral cortex of mice. However, free meloxicam decrease the creatine kinase activity in mitochondrial-rich fraction in the group induced by amyloid-β, but for the cytosolic fraction, it has raised in the activity of pyruvate kinase activity in cerebral cortex. Further, meloxicam-loaded nanocapsules administration reduced adenylate kinase activity in the hippocampus of mice injected by amyloid-β. In conclusion we observed absence in short-term effects in kinases activities of energy metabolism in mice hippocampus and cerebral cortex using amyloid-β peptide model. These findings established the foundation to further study the kinases in phosphoryltransfer network changes observed in the brains of patients post-mortem with Alzheimer's disease.
Collapse
Affiliation(s)
- Francine R Ianiski
- Programa de Pós-Graduação em Nanociências, Centro de Ciências Tecnológicas, Centro Universitário Franciscano, Rua dos Andradas, 1614, Conjunto I, 97010-032 Santa Maria, RS, Brasil
| | - Virginia C Rech
- Programa de Pós-Graduação em Nanociências, Centro de Ciências Tecnológicas, Centro Universitário Franciscano, Rua dos Andradas, 1614, Conjunto I, 97010-032 Santa Maria, RS, Brasil
| | - Vivian S K Nishihira
- Programa de Pós-Graduação em Nanociências, Centro de Ciências Tecnológicas, Centro Universitário Franciscano, Rua dos Andradas, 1614, Conjunto I, 97010-032 Santa Maria, RS, Brasil
| | - Catiane B Alves
- Programa de Pós-Graduação em Nanociências, Centro de Ciências Tecnológicas, Centro Universitário Franciscano, Rua dos Andradas, 1614, Conjunto I, 97010-032 Santa Maria, RS, Brasil
| | - Matheus D Baldissera
- Departamento de Microbiologia e Parasitologia, Universidade Federal de Santa Maria, Av. Roraima, 1000, Cidade Universitária, Bairro Camobi, 97105-900 Santa Maria, RS, Brasil
| | - Ethel A Wilhelm
- Centro de Ciências Químicas, Farmacêuticas e de Alimentos, Universidade Federal de Pelotas, Campus Universitário, s/n, 96160-000 Capão do Leão, RS, Brasil
| | - Cristiane Luchese
- Centro de Ciências Químicas, Farmacêuticas e de Alimentos, Universidade Federal de Pelotas, Campus Universitário, s/n, 96160-000 Capão do Leão, RS, Brasil
| |
Collapse
|
23
|
Khan AT, Dobson RJB, Sattlecker M, Kiddle SJ. Alzheimer's disease: are blood and brain markers related? A systematic review. Ann Clin Transl Neurol 2016; 3:455-62. [PMID: 27547773 PMCID: PMC4891999 DOI: 10.1002/acn3.313] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/29/2016] [Accepted: 04/07/2016] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVE Peripheral protein biomarkers of Alzheimer's disease (AD) may help identify novel treatment avenues by allowing early diagnosis, recruitment to clinical trials, and treatment initiation. The purpose of this review was to determine which proteins have been found to be differentially expressed in the AD brain and whether these proteins are also found within the blood of AD patients. METHODS A two-stage approach was conducted. The first stage involved conducting a systematic search to identify discovery-based brain proteomic studies of AD. The second stage involved comparing whether proteins found to be differentially expressed in AD brain were also differentially expressed in the blood. RESULTS Across 11 discovery based brain proteomic studies 371 proteins were at different levels in the AD brain. Nine proteins were frequently found, defined as appearing in at least three separate studies. Of these proteins heat-shock cognate 71 kDa, ubiquitin carboxyl-terminal hydrolase isozyme L1, and 2',3'-cyclic nucleotide 3' phosphodiesterase alone were found to share a consistent direction of change, being consistently upregulated in studies they appeared in. Eighteen proteins seen as being differentially expressed within the AD brain were present in blood proteomic studies of AD. Only complement C4a was seen multiple times within both the blood and brain proteomic studies. INTERPRETATION We report a number of proteins appearing in both the blood and brain of AD patients. Of these proteins, C4a may be a good candidate for further follow-up in large-scale replication efforts.
Collapse
Affiliation(s)
- Ali T Khan
- GKT School of Medical Education King's College London London United Kingdom
| | - Richard J B Dobson
- MRC Social, Genetic and Developmental Psychiatry Centre Institute of Psychiatry, Psychology and Neuroscience King's College London London United Kingdom; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia London United Kingdom
| | - Martina Sattlecker
- MRC Social, Genetic and Developmental Psychiatry Centre Institute of Psychiatry, Psychology and Neuroscience King's College London London United Kingdom; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia London United Kingdom
| | - Steven J Kiddle
- MRC Social, Genetic and Developmental Psychiatry Centre Institute of Psychiatry, Psychology and Neuroscience King's College London London United Kingdom; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia London United Kingdom
| |
Collapse
|
24
|
Völgyi K, Háden K, Kis V, Gulyássy P, Badics K, Györffy BA, Simor A, Szabó Z, Janáky T, Drahos L, Dobolyi Á, Penke B, Juhász G, Kékesi KA. Mitochondrial Proteome Changes Correlating with β-Amyloid Accumulation. Mol Neurobiol 2016; 54:2060-2078. [PMID: 26910821 DOI: 10.1007/s12035-015-9682-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 12/23/2015] [Indexed: 01/01/2023]
Abstract
Alzheimer's disease (AD) is a multifactorial disease of wide clinical heterogenity. Overproduction of amyloid precursor protein (APP) and accumulation of β-amyloid (Aβ) and tau proteins are important hallmarks of AD. The identification of early pathomechanisms of AD is critically important for discovery of early diagnosis markers. Decreased brain metabolism is one of the earliest clinical symptoms of AD that indicate mitochondrial dysfunction in the brain. We performed the first comprehensive study integrating synaptic and non-synaptic mitochondrial proteome analysis (two-dimensional differential gel electrophoresis (2D-DIGE) and mass spectrometry) in correlation with Aβ progression in APP/PS1 mice (3, 6, and 9 months of age). We identified changes of 60 mitochondrial proteins that reflect the progressive effect of APP overproduction and Aβ accumulation on mitochondrial processes. Most of the significantly affected proteins play role in the mitochondrial electron transport chain, citric acid cycle, oxidative stress, or apoptosis. Altered expression levels of Htra2 and Ethe1, which showed parallel changes in different age groups, were confirmed also by Western blot. The common regulator bioinformatical analysis suggests the regulatory role of tumor necrosis factor (TNF) in Aβ-mediated mitochondrial protein changes. Our results are in accordance with the previous postmortem human brain proteomic studies in AD in the case of many proteins. Our results could open a new path of research aiming early mitochondrial molecular mechanisms of Aβ accumulation as a prodromal stage of human AD.
Collapse
Affiliation(s)
- Katalin Völgyi
- MTA-ELTE NAP B Laboratory of Molecular and Systems Neurobiology, Hungarian Academy of Sciences and Eötvös Loránd University, Budapest, Hungary.
- Laboratory of Proteomics, Eötvös Loránd University, Budapest, Hungary.
| | - Krisztina Háden
- Laboratory of Proteomics, Eötvös Loránd University, Budapest, Hungary
| | - Viktor Kis
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Péter Gulyássy
- Laboratory of Proteomics, Eötvös Loránd University, Budapest, Hungary
- MTA-TTK NAP B MS Neuroproteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Kata Badics
- Laboratory of Proteomics, Eötvös Loránd University, Budapest, Hungary
| | - Balázs András Györffy
- Laboratory of Proteomics, Eötvös Loránd University, Budapest, Hungary
- MTA-ELTE NAP B Neuroimmunology Research Group, Hungarian Academy of Sciences and Eötvös Loránd University, Budapest, Hungary
| | - Attila Simor
- Laboratory of Proteomics, Eötvös Loránd University, Budapest, Hungary
| | - Zoltán Szabó
- Medical Chemistry Department, University of Szeged, Szeged, Hungary
| | - Tamás Janáky
- Medical Chemistry Department, University of Szeged, Szeged, Hungary
| | - László Drahos
- MTA-TTK NAP B MS Neuroproteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Árpád Dobolyi
- MTA-ELTE NAP B Laboratory of Molecular and Systems Neurobiology, Hungarian Academy of Sciences and Eötvös Loránd University, Budapest, Hungary
| | - Botond Penke
- Medical Chemistry Department, University of Szeged, Szeged, Hungary
| | - Gábor Juhász
- Laboratory of Proteomics, Eötvös Loránd University, Budapest, Hungary
- MTA-TTK NAP B MS Neuroproteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Katalin Adrienna Kékesi
- Laboratory of Proteomics, Eötvös Loránd University, Budapest, Hungary
- Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest, Hungary
| |
Collapse
|
25
|
Adav SS, Gallart-Palau X, Tan KH, Lim SK, Tam JP, Sze SK. Dementia-linked amyloidosis is associated with brain protein deamidation as revealed by proteomic profiling of human brain tissues. Mol Brain 2016; 9:20. [PMID: 26892330 PMCID: PMC4759965 DOI: 10.1186/s13041-016-0200-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/11/2016] [Indexed: 01/25/2023] Open
Abstract
Background Aggregation of malformed proteins is a key feature of many neurodegenerative diseases, but the mechanisms that drive proteinopathy in the brain are poorly understood. We aimed to characterize aggregated proteins in human brain tissues affected by dementia. Results To characterize amyloidal plaque purified from post-mortem brain tissue of dementia patient, we applied ultracentrifugation-electrostatic repulsion hydrophilic interaction chromatography (UC-ERLIC) coupled mass spectrometry-based proteomics technologies. Proteomics profiling of both soluble and aggregated amyloidal plaque demonstrated significant enrichment and deamidation of S100A9, ferritin, hemoglobin subunits, creatine kinase and collagen protein among the aggregated brain proteins. Amyloidal plaques were enriched in the deamidated variant of protein S100A9, and structural analysis indicated that both the low- and high-affinity calcium binding motifs of S100A9 were deamidated exclusively in the aggregated fraction, suggesting altered charge state and function of this protein in brain tissues affected by dementia. The multiple deamidated residues of S100A9 predicts introduction of negative charge that alter Ca++ binding, suggesting increased capacity to form pathological aggregates in the brain. Conclusion UC-coupled proteomics revealed that brain amyloidal plaques are enriched in deamidated proteins, and suggested that altered charge state and calcium-binding capacity of S100A9 may enhance protein aggregation and promote neurodegeneration in the human brain. Electronic supplementary material The online version of this article (doi:10.1186/s13041-016-0200-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sunil S Adav
- School of Biological Sciences, Division of Structural Biology and Biochemistry, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. .,Department of Maternal Fetal Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, 229899, Singapore, Singapore.
| | - Xavier Gallart-Palau
- School of Biological Sciences, Division of Structural Biology and Biochemistry, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Kok Hian Tan
- Department of Maternal Fetal Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, 229899, Singapore, Singapore.
| | - Sai Kiang Lim
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, 138648, Singapore, Singapore.
| | - James P Tam
- School of Biological Sciences, Division of Structural Biology and Biochemistry, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Siu Kwan Sze
- School of Biological Sciences, Division of Structural Biology and Biochemistry, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| |
Collapse
|
26
|
Vicente-Rodríguez M, Herradón G, Ferrer-Alcón M, Uribarri M, Pérez-García C. Chronic Cocaine Use Causes Changes in the Striatal Proteome Depending on the Endogenous Expression of Pleiotrophin. Chem Res Toxicol 2015; 28:1443-54. [DOI: 10.1021/acs.chemrestox.5b00130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marta Vicente-Rodríguez
- Pharmacology Laboratory, Department of
Pharmaceutical and Health Sciences, Facultad de Farmacia, Universidad CEU San Pablo, Madrid, Spain
| | - Gonzalo Herradón
- Pharmacology Laboratory, Department of
Pharmaceutical and Health Sciences, Facultad de Farmacia, Universidad CEU San Pablo, Madrid, Spain
| | | | - María Uribarri
- BRAINco Biopharma, S.L., Bizkaia Technology Park, Vizcaya, Spain
| | - Carmen Pérez-García
- Pharmacology Laboratory, Department of
Pharmaceutical and Health Sciences, Facultad de Farmacia, Universidad CEU San Pablo, Madrid, Spain
| |
Collapse
|
27
|
Beta-amyloid oligomers induce early loss of presynaptic proteins in primary neurons by caspase-dependent and proteasome-dependent mechanisms. Neuroreport 2015; 25:1281-8. [PMID: 25275636 DOI: 10.1097/wnr.0000000000000260] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Beta-amyloid is a major pathogenic molecule for Alzheimer's disease (AD) and can be aggregated into a soluble oligomer, which is a toxic intermediate, before amyloid fibril formation. Beta-amyloid oligomers are associated closely with early synaptic loss in AD. However, it is still unknown which synaptic proteins are involved in the synaptotoxicity, and a direct comparison among the synaptic proteins should also be addressed. Here, we investigated changes in the expression of several presynaptic and postsynaptic proteins in primary neurons after treatment with a low-molecular weight and a high-molecular weight beta-amyloid oligomer. Both oligomers induced early neuronal dysfunction after 4 h and significantly reduced presynaptic protein (synaptophysin, syntaxin, synapsin, and synaptotagmin) expression. However, the expression of postsynaptic proteins (PSD95, NMDAR2A/B, and GluR2/3), except NMDAR1 was not reduced, and some protein expression levels were increased. Glutamate treatment, which is correlated with postsynaptic activation, showed more postsynaptic-specific protein loss compared with beta-amyloid oligomer treatment. Finally, the caspase inhibitor zVAD and the proteasomal inhibitor MG132 attenuated presynaptic protein loss. Thus, our data showed changes in synaptic proteins by beta-amyloid oligomers, which provides an understanding of early synaptotoxicity and suggests new approaches for AD treatment.
Collapse
|
28
|
Brinkmalm A, Portelius E, Öhrfelt A, Brinkmalm G, Andreasson U, Gobom J, Blennow K, Zetterberg H. Explorative and targeted neuroproteomics in Alzheimer's disease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:769-78. [PMID: 25619854 DOI: 10.1016/j.bbapap.2015.01.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/23/2014] [Accepted: 01/16/2015] [Indexed: 01/08/2023]
Abstract
Alzheimer's disease (AD) is a progressive brain amyloidosis that injures brain regions involved in memory consolidation and other higher brain functions. Neuropathologically, the disease is characterized by accumulation of a 42 amino acid peptide called amyloid β (Aβ42) in extracellular senile plaques, intraneuronal inclusions of hyperphosphorylated tau protein in neurofibrillary tangles, and neuronal and axonal degeneration and loss. Biomarker assays capturing these pathologies have been developed for use on cerebrospinal fluid samples but there are additional molecular pathways that most likely contribute to the neurodegeneration and full clinical expression of AD. One way of learning more about AD pathogenesis is to identify novel biomarkers for these pathways and examine them in longitudinal studies of patients in different stages of the disease. Here, we discuss targeted proteomic approaches to study AD and AD-related pathologies in closer detail and explorative approaches to discover novel pathways that may contribute to the disease. This article is part of a Special Issue entitled: Neuroproteomics: Applications in neuroscience and neurology.
Collapse
Affiliation(s)
- Ann Brinkmalm
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden.
| | - Erik Portelius
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Annika Öhrfelt
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Gunnar Brinkmalm
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Ulf Andreasson
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Johan Gobom
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden; UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom.
| |
Collapse
|