Changes in adhesion efficiency and vimentin distribution of fibroblasts from familial Alzheimer's disease patients

Integrated Analysis of Cortex Single-Cell Transcriptome and Serum Proteome Reveals the Novel Biomarkers in Alzheimer's Disease

Blood-based proteomic analysis is a routine practice for detecting the biomarkers of human disease. The results obtained from blood alone cannot fully reflect the alterations of nerve cells, including neurons and glia cells, in Alzheimer's disease (AD) brains. Therefore, the present study aimed to investigate novel potential AD biomarker candidates, through an integrated multi-omics approach in AD. We propose a comprehensive strategy to identify high-confidence candidate biomarkers by integrating multi-omics data from AD, including single-nuclei RNA sequencing (snRNA-seq) datasets of the prefrontal and entorhinal cortices, as wells as serum proteomic datasets. We first quantified a total of 124,658 nuclei, 8 cell types, and 3701 differentially expressed genes (DEGs) from snRNA-seq dataset of 30 human cortices, as well as 1291 differentially expressed proteins (DEPs) from serum proteomic dataset of 11 individuals. Then, ten DEGs/DEPs (NEBL, CHSY3, STMN2, MARCKS, VIM, FGD4, EPB41L2, PLEKHG1, PTPRZ1, and PPP1R14A) were identified by integration analysis of snRNA-seq and proteomics data. Finally, four novel candidate biomarkers (NEBL, EPB41L2, FGD4, and MARCKS) for AD further stood out, according to bioinformatics analysis, and they were verified by enzyme-linked immunosorbent assay (ELISA) verification. These candidate biomarkers are related to the regulation process of the actin cytoskeleton, which is involved in the regulation of synaptic loss in the AD brain tissue. Collectively, this study identified novel cell type-related biomarkers for AD by integrating multi-omics datasets from brains and serum. Our findings provided new targets for the clinical treatment and prognosis of AD.

Single-Cell RNA-Seq Analysis of Cells from Degenerating and Non-Degenerating Intervertebral Discs from the Same Individual Reveals New Biomarkers for Intervertebral Disc Degeneration

In this study, we used single-cell transcriptomic analysis to identify new specific biomarkers for nucleus pulposus (NP) and inner annulus fibrosis (iAF) cells, and to define cell populations within non-degenerating (nD) and degenerating (D) human intervertebral discs (IVD) of the same individual. Cluster analysis based on differential gene expression delineated 14 cell clusters. Gene expression profiles at single-cell resolution revealed the potential functional differences linked to degeneration, and among NP and iAF subpopulations. GO and KEGG analyses discovered molecular functions, biological processes, and transcription factors linked to cell type and degeneration state. We propose two lists of biomarkers, one as specific cell type, including C2orf40, MGP, MSMP, CD44, EIF1, LGALS1, RGCC, EPYC, HILPDA, ACAN, MT1F, CHI3L1, ID1, ID3 and TMED2. The second list proposes predictive IVD degeneration genes, including MT1G, SPP1, HMGA1, FN1, FBXO2, SPARC, VIM, CTGF, MGST1, TAF1D, CAPS, SPTSSB, S100A1, CHI3L2, PLA2G2A, TNRSF11B, FGFBP2, MGP, SLPI, DCN, MT-ND2, MTCYB, ADIRF, FRZB, CLEC3A, UPP1, S100A2, PRG4, COL2A1, SOD2 and MT2A. Protein and mRNA expression of MGST1, vimentin, SOD2 and SYF2 (p29) genes validated our scRNA-seq findings. Our data provide new insights into disc cells phenotypes and biomarkers of IVD degeneration that could improve diagnostic and therapeutic options.

No dopamine cell loss or changes in cytoskeleton function in transgenic mice expressing physiological levels of wild type or G2019S mutant LRRK2 and in human fibroblasts

Mutations within the LRRK2 gene have been identified in Parkinson’s disease (PD) patients and have been implicated in the dysfunction of several cellular pathways. Here, we explore how pathogenic mutations and the inhibition of LRRK2 kinase activity affect cytoskeleton dynamics in mouse and human cell systems. We generated and characterized a novel transgenic mouse model expressing physiological levels of human wild type and G2019S-mutant LRRK2. No neuronal loss or neurodegeneration was detected in midbrain dopamine neurons at the age of 12 months. Postnatal hippocampal neurons derived from transgenic mice showed no alterations in the seven parameters examined concerning neurite outgrowth sampled automatically on several hundred neurons using high content imaging. Treatment with the kinase inhibitor LRRK2-IN-1 resulted in no significant changes in the neurite outgrowth. In human fibroblasts we analyzed whether pathogenic LRRK2 mutations change cytoskeleton functions such as cell adhesion. To this end we compared the adhesion characteristics of human skin fibroblasts derived from six PD patients carrying one of three different pathogenic LRRK2 mutations and from four age-matched control individuals. The mutant LRRK2 variants as well as the inhibition of LRRK2 kinase activity did not reveal any significant cell adhesion differences in cultured fibroblasts. In summary, our results in both human and mouse cell systems suggest that neither the expression of wild type or mutant LRRK2, nor the inhibition of LRRK2 kinase activity affect neurite complexity and cellular adhesion.

Significantly reduced expression of the proteoglycan decorin in Alzheimer's disease fibroblasts

Aims-To investigate whether proteoglycan synthesis is altered in skin fibroblasts in patients with Alzheimer's disease compared with normal subjects.Methods-Cell lines obtained from donors with Alzheimer's disease and healthy controls were incubated with radioactive sulphate. The proteoglycans synthesised were determined and analysed by chromatographic, sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and glycosaminoglycans-lyase treatment. The amount of decorin synthesised by each cell line was quantified using western blot analysis. Transcripts for human decorin were determined using northern blot analysis.Results-No significant changes in total sulphate incorporation and glycos-aminoglycan (GAG) composition were detected in the incubation media of these cells. However, chromatographic and SDS-PAGE analysis of the proteoglycans secreted by the cell lines showed that a dermatan sulphate proteoglycan of 150-125 kilodaltons was substantially reduced in Alzheimer's disease fibroblasts. The molecular characteristics of this proteoglycan correspond to decorin. Western blot analysis indicated that decorin was reduced in Alzheimer's disease incubation medium compared with normal medium. Northern blotting indicated that in Alzheimer's disease fibroblasts decorin transcripts were significantly reduced compared with normal fibroblasts. Glypican concentrations, a cell surface heparan sulphate proteoglycan, remained the same.Conclusions-These results strongly suggest that the expression and synthesis of decorin is affected in Alzheimer's disease skin fibroblasts.

Gene expression profiling in cells with enhanced gamma-secretase activity

Background

Processing by γ-secretase of many type-I membrane protein substrates triggers signaling cascades by releasing intracellular domains (ICDs) that, following nuclear translocation, modulate the transcription of different genes regulating a diverse array of cellular and biological processes. Because the list of γ-secretase substrates is growing quickly and this enzyme is a cancer and Alzheimer's disease therapeutic target, the mapping of γ-secretase activity susceptible gene transcription is important for sharpening our view of specific affected genes, molecular functions and biological pathways.

Methodology/Principal Findings

To identify genes and molecular functions transcriptionally affected by γ-secretase activity, the cellular transcriptomes of Chinese hamster ovary (CHO) cells with enhanced and inhibited γ-secretase activity were analyzed and compared by cDNA microarray. The functional clustering by FatiGO of the 1,981 identified genes revealed over- and under-represented groups with multiple activities and functions. Single genes with the most pronounced transcriptional susceptibility to γ-secretase activity were evaluated by real-time PCR. Among the 21 validated genes, the strikingly decreased transcription of PTPRG and AMN1 and increased transcription of UPP1 potentially support data on cell cycle disturbances relevant to cancer, stem cell and neurodegenerative diseases' research. The mapping of interactions of proteins encoded by the validated genes exclusively relied on evidence-based data and revealed broad effects on Wnt pathway members, including WNT3A and DVL3. Intriguingly, the transcription of TERA, a gene of unknown function, is affected by γ-secretase activity and was significantly altered in the analyzed human Alzheimer's disease brain cortices.

Conclusions/Significance

Investigating the effects of γ-secretase activity on gene transcription has revealed several affected clusters of molecular functions and, more specifically, 21 genes that hold significant potential for a better understanding of the biology of γ-secretase and its roles in cancer and Alzheimer's disease pathology.

Ionic and signal transduction alterations in Alzheimer's disease: relevance of studies on peripheral cells

Several lines of evidence indicate that Alzheimer's disease (AD) has systemic expression. Systemic changes are manifested as alterations in a number of molecular and cellular processes. Although, these alterations appear to have little or no consequence in peripheral systems, their parallel expression in the central nervous system (CNS) could account for the principal clinical manifestations of the disease. Recent research seems to indicate that alterations in ion channels, calcium homeostasis, and protein kinase C (PKC) can be linked and thereby constitute a model of pathophysiological relevance. Considering the difficulties of studying dynamic pathophysiological processes in the disease-ridden postmortem AD brain, peripheral tissues such as fibroblasts provide a suitable model to study molecular and cellular aspects of the disease.

Altered adhesion efficiency and fibronectin content in fibroblasts from schizophrenic patients

Cultured fibroblasts from the cutaneous tissue of 16 schizophrenic patients were compared with 16 control cultured fibroblasts from the healthy subjects. The fibroblasts from the schizophrenic patients showed a decreased adhesion efficiency within 30 min after plating compared to that of the control subjects. However, after 90 min, there was no significant difference between the groups, where more than 90% of the cells from both groups had adhesed to the plate. By immunohistochemistry and western blotting using the antibodies against integrin (VLA5), talin, vinculin, fodrin, vimentin, ankyrin, plectin, fibronectin, and focal adhesion kinase (FAK), there was no significant difference in localization and amount between the groups. The amount of fibronectin released into the medium in which the fibroblast had already kept confluency showed no significant difference between the groups. However, the fibronectin content in cell lysate within 48 h after plating was significantly lower in the schizophrenic group.

Decreased adhesiveness and altered cellular distribution of fibronectin in fibroblasts from schizophrenic patients

Relative to those from normal subjects, cultured skin fibroblasts from schizophrenic patients have been found to show abnormal growth characteristics and morphology. This study compared skin fibroblasts from 10 drug-free schizophrenic patients and 10 normal control subjects on cell adhesiveness to the substratum. Relative to fibroblasts from normal controls, those from patients showed significantly decreased cell adhesiveness, with no overlap in distribution between the groups. Since fibronectin, a major cell surface molecule, is known to be involved in the fibroblast adhesion to substratum, its extracellular and intracellular distribution was determined by immunocytochemical analysis. Both extracellular and intracellular levels of fibronectin were significantly lower, and the distribution was altered in fibroblasts from the patients.

Growth properties of familial Alzheimer skin fibroblasts during in vitro aging

Human diploid fibroblasts undergo replicative senescence in vitro, which is strongly correlated with biological aging in vivo. In order to examine whether features compatible with a systemic premature aging are present in familial Alzheimer's disease (FAD) patients, we investigated the growth characteristics of three skin fibroblast lines from FAD patients and from three sex/age-matched controls at different passages until senescence was reached. A kinetic study of the replicative capacity was performed at different culture times by [3H]-thymidine incorporation and crystal violet staining. Data showed no significant difference between the two groups at any studied passage. The life span of the two types of cultures was also comparable. These results suggest that in familial Alzheimer patients there are not systemic signs of accelerated aging.

The puzzle of Alzheimer's disease (AD)

A compromised defensive system of brain cells against aluminium, together with local defects in glucose metabolism, causes AD. Lack of citrate is a driving force and free cis-aconitate or glutamate are potential carriers, which enable the exotoxin to cross lipid membranes. Only a few aluminium ions replace magnesium in key positions. They block the reversibility of phosphorylation reactions, which are important for short term memory: sensitization of the insulin receptor and protein phosphorylations. Due to disturbed phosphorylation of the cytoskeleton, protein synthesis runs out of balance. Efforts to restore the disturbed reactions result in AD specific deposits. Aluminium ions are the common cause for the induction of AD pathogenesis in patients with genetic defects, with mechanical brain lesions or with minor infarcts, as well as with changes in the relation between numbers of neurons and neuron nursing glia cells due to age.

Change in the cytoskeletal system in fibroblasts from patients with familial Alzheimer's disease

1. Fibroblasts were cultured from four patients, two patients from two independent family lines, clinically diagnosed as familial Alzheimer's disease. 2. Adhesion efficiency to the dish was significantly suppressed with fibroblasts from patients with familial Alzheimer's disease compared with the cells from the age-matched control. 3. Cytoskeletal systems were visualized by immunofluorescent staining with antibodies against tubulin, actin, and vimentin, showing unique dearrangement of vimentin fibers in fibroblasts from familial Alzheimer's disease. 4. Regrowth of vimentin fibers after colchicine treatment was slower with fibroblasts from familial Alzheimer's disease than that of the control. 5. Western blotting analysis showed no change in tubulin, actin, and vimentin, but the size of fodrin in familial Alzheimer fibroblasts were different from that of the control cell.