A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer's disease

BACKGROUND: Alzheimer's disease (AD) is characterized by the intra- and extracellular accumulation of amyloid-β (Aβ) peptides. How Aβ aggregates perturb the proteome in brains of patients and AD transgenic mouse models, remains largely unclear. State-of-the-art mass spectrometry (MS) methods can comprehensively detect proteomic alterations, providing relevant insights unobtainable with transcriptomics investigations. Analyses of the relationship between progressive Aβ aggregation and protein abundance changes in brains of 5xFAD transgenic mice have not been reported previously. METHODS: We quantified progressive Aβ aggregation in hippocampus and cortex of 5xFAD mice and controls with immunohistochemistry and membrane filter assays. Protein changes in different mouse tissues were analyzed by MS-based proteomics using label-free quantification; resulting MS data were processed using an established pipeline. Results were contrasted with existing proteomic data sets from postmortem AD patient brains. Finally, abundance changes in the candidate marker Arl8b were validated in cerebrospinal fluid (CSF) from AD patients and controls using ELISAs. RESULTS: Experiments revealed faster accumulation of Aβ42 peptides in hippocampus than in cortex of 5xFAD mice, with more protein abundance changes in hippocampus, indicating that Aβ42 aggregate deposition is associated with brain region-specific proteome perturbations. Generating time-resolved data sets, we defined Aβ aggregate-correlated and anticorrelated proteome changes, a fraction of which was conserved in postmortem AD patient brain tissue, suggesting that proteome changes in 5xFAD mice mimic disease-relevant changes in human AD. We detected a positive correlation between Aβ42 aggregate deposition in the hippocampus of 5xFAD mice and the abundance of the lysosome-associated small GTPase Arl8b, which accumulated together with axonal lysosomal membranes in close proximity of extracellular Aβ plaques in 5xFAD brains. Abnormal aggregation of Arl8b was observed in human AD brain tissue. Arl8b protein levels were significantly increased in CSF of AD patients. CONCLUSIONS: We report a comprehensive biochemical and proteomic investigation of hippocampal and cortical brain tissue derived from 5xFAD transgenic mice, providing a valuable resource to the neuroscientific community. We identified Arl8b, with significant abundance changes in 5xFAD and AD patient brains. Arl8b might enable the measurement of progressive lysosome accumulation in AD patients and have clinical utility as a candidate biomarker

Hasanoğlan Köy Enstitüsü ve Hasanoğlan Atatürk İlköğretmen Okulu

Ankara : İhsan Doğramacı Bilkent Üniversitesi İktisadi, İdari ve Sosyal Bilimler Fakültesi, Tarih Bölümü, 2015.This work is a student project of the The Department of History, Faculty of Economics, Administrative and Social Sciences, İhsan Doğramacı Bilkent University.by Öztürk, İbrahim Mert

Development of light and pH-dual responsive self-quenching theranostic SPION to make EGFR overexpressing micro tumors glow and destroy

Drug resistant and undetectable tumors easily escape treatment leading metastases and/or recurrence of the lethal disease. Therefore, it is vital to diagnose and destroy micro tumors using simple yet novel approaches. Here, we present fluorescence-based detection and light-based destruction of cancer cells that are known to be resistant to standard therapies. We developed a superparamagnetic iron oxide nanoparticle (SPION)-based theranostic agent that is composed of self-quenching light activated photosensitizer (BPD) and EGFR targeting ligand (Anti-EGFR ScFv or GE11 peptide). Photosensitizer (BPD) was immobilized to PEG-PEI modified SPION with acid-labile linker. Prior to stimulation of the theranostic system by light its accumulation within cancer cells is vital since BPD phototoxicity and fluorescence is activated by lysosomal proteolysis. As BPD is cleaved, the system switches from off to on position which triggers imaging and therapy. Targeting, therapeutic and diagnostic features of the theranostic system were evaluated in high and moderate level EGFR expressing pancreatic cancer cell lines. Our results indicate that the system distinguishes high and moderate EGFR expression levels and yields up to 4.3-fold increase in intracellular fluorescence intensity. Amplification of fluorescence signal was as low as 1.3-fold in the moderate or no EGFR expressing cell lines. Anti-EGFR ScFv targeted SPION caused nearly 2-fold higher cell death via apoptosis in high EGFR expressing Panc-1 cell line. The developed system, possessing advanced targeting, enhanced imaging and effective therapeutic features, is a promising candidate for multi-mode detection and destruction of residual drug-resistant cancer cells

Do histologically aggressive subtypes of papillary thyroid microcarcinoma have worse clinical outcome than non-aggressive rapillary thyroid microcarcinoma subtypes? A multicenter cohort study

Histologically aggressive micropapillary thyroid carcinomas (PTMC) subtypes are thought to be associated with an aggressive clinical course. However, evidence for unfavorable clinical outcomes in patients with aggressive PTMC subtypes is not clear. In this study, we intended to determine the difference in clinical outcomes between patients with aggressive and non-aggressive PTMC subtypes. In this multicenter cohort study, the computer-recorded clinical and histopathological data of patients who underwent thyroid surgery between January 2000 - January 2021 in 9 referral centers and were diagnosed as PTMC were analyzed. A total of 1585 patients [female 1340 (84.5%), male 245 (15.5%), mean age 47.9 +/- 11.63 years), with a mean follow-up time of 66.55 +/- 37.16 months], were included in the study. Ninety-eight cases were diagnosed as aggressive and 1487 as non-aggressive subtypes. Persistent/recurrent disease was observed in 33 (33.7% )and 41 (2.8%) patients with aggressive and non-aggressive subtypes (p 1 cm in size. Therefore, the histopathological subtype of PTMC should be taken into consideration to tailor a personalized management plan

Additional file 2 of A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer’s disease

Additional file 2: Fig. S1. Aβ peptide levels and APP and PSEN1 expression in hippocampus and cortex of 5xFAD mice. Fig. S2. Analysis of Aβ aggregate formation using membrane filter assays and sucrose gradient centrifugations. Fig. S3. Analysis of wild-type expression profiles to assess whether the protein abundance changes detected in 5xFAD brains are more frequent among highly expressed mouse proteins. Fig. S4. Functional analysis of dysregulated proteins defined with a pairwise model in brains of 5xFAD mice. Fig. S5. Enrichment analysis of cell-type-specific marker proteins among dysregulated proteins in brains of 5xFAD mice. Fig. S6. IPA and gene ontology enrichment analysis of differentially expressed proteins defined with the full model in cortical and hippocampal tissues of 5xFAD mice. Fig. S7. Ingenuity pathway analysis of Aβ-correlated and anticorrelated DEPs defined by the pairwise model in brains of 5xFAD mice. Fig. S8. Numbers of pairwise common DEPs in the mouse datasets and datasets from human studies. Fig. S9. Strategy to define mouse protein signatures that are concordantly altered also in AD patient brains. Fig. S10. Investigation of the overlap of DEPs in brains of 5xFAD mice with DEPs in asymptomatic AD brains. Fig. S11. Analysis of the correlation in protein effect sizes between 5xFAD mouse and AD patient brains for proteins present in all studies. Fig. S12. Selection of the neuronal lysosome-associated protein Arl8b by step-by-step data filtering. Fig. S13. Immunofluorescence analysis of 5xFAD brain slices. Fig. S14. Analysis of Arl8b protein aggregates using human brain homogenates derived from AD patients and control individuals

Additional file 1 of A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer’s disease

Additional file 1: Table S1. Commercial antibodies used in this study. Table S2. Characteristics of AD and HD patients and corresponding controls. Table S3. Spearman correlation analysis of Arl8b protein level measurements and AD biomarker levels

Additional file 3 of A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer’s disease

Additional file 3: Supplementary Excel File 1a. DEPs from 5xFAD versus wild-type tissue comparisons in hippocampus and cortex; DEPs were defined using the “pairwise model”; Supplementary Excel File 1b. Summary of the statistical calculations from Supplementary Excel File 1a; Supplementary Excel File 1c. DEPs in both hippocampal and cortical tissues defined through the “full model”; Supplementary Excel File 2. DEPs that correlate or anticorrelate to Aβ aggregate load in both hippocampal and cortical tissues defined through the “pairwise model”; Supplementary Excel File 3. Identified genes differentially down- or upregulatedin cortex or hippocampus of 5xFAD mice; Supplementary Excel File 4. Results of the Ingenuity Pathway Analyses performed in Figures 3g and 4e; Supplementary Excel File 5a. Proteins with significant abundance changes from Johnson et al. 2020; Supplementary Excel File 5b. Proteins with significant abundance changes from Johnson et al. 2022; Supplementary Excel File 5c. Proteins with significant abundance changes from Johnson et al. 2022; Supplementary Excel File 5d. Proteins with significant abundance changes from Drummond et al. 2022; Supplementary Excel File 6. Numbers of common DEPs in mouse and human datasets; Supplementary Excel File 7. DEPs defined using a “pairwise model” and concomitantly altered both in mouse and human brain tissues from J20, J22 and D22. Supplementary Excel File 8a. The step-by-step selection process to identify the potential AD biomarker Arl8b. Supplementary Excel File 8b. The top 25 Aβ-correlated proteins in mouse hippocampal tissues