Explore the vast range of titles available.

Background Specific microglia responses are thought to contribute to the development and progression of neurodegenerative diseases, including Parkinson’s disease (PD). However, the phenotypic acquisition of microglial cells and their role during the underlying neuroinflammatory processes remain largely elusive. Here, according to the multiple-hit hypothesis, which stipulates that PD etiology is determined by a combination of genetics and various environmental risk factors, we investigate microglial transcriptional programs and morphological adaptations under PARK7 /DJ-1 deficiency, a genetic cause of PD, during lipopolysaccharide (LPS)-induced inflammation. Methods Using a combination of single-cell RNA-sequencing, bulk RNA-sequencing, multicolor flow cytometry and immunofluorescence analyses, we comprehensively compared microglial cell phenotypic characteristics in PARK7 /DJ-1 knock-out (KO) with wildtype littermate mice following 6- or 24-h intraperitoneal injection with LPS. For translational perspectives, we conducted corresponding analyses in human PARK7 /DJ-1 mutant induced pluripotent stem cell (iPSC)-derived microglia and murine bone marrow-derived macrophages (BMDMs). Results By excluding the contribution of other immune brain resident and peripheral cells, we show that microglia acutely isolated from PARK7 /DJ-1 KO mice display a distinct phenotype, specially related to type II interferon and DNA damage response signaling, when compared with wildtype microglia, in response to LPS. We also detected discrete signatures in human PARK7 /DJ-1 mutant iPSC-derived microglia and BMDMs from PARK7 /DJ-1 KO mice. These specific transcriptional signatures were reflected at the morphological level, with microglia in LPS-treated PARK7 /DJ-1 KO mice showing a less amoeboid cell shape compared to wildtype mice, both at 6 and 24 h after acute inflammation, as also observed in BMDMs. Conclusions Taken together, our results show that, under inflammatory conditions, PARK7 /DJ-1 deficiency skews microglia towards a distinct phenotype characterized by downregulation of genes involved in type II interferon signaling and a less prominent amoeboid morphology compared to wildtype microglia. These findings suggest that the underlying oxidative stress associated with the lack of PARK7 /DJ-1 affects microglia neuroinflammatory responses, which may play a causative role in PD onset and progression.

The cellular alterations of the hippocampus lead to memory decline, a shared symptom between Alzheimer’s disease (AD) and dementia with Lewy Bodies (DLB) patients. However, the subregional deterioration pattern of the hippocampus differs between AD and DLB with the CA1 subfield being more severely affected in AD. The activation of microglia, the brain immune cells, could play a role in its selective volume loss. How subregional microglia populations vary within AD or DLB and across these conditions remains poorly understood. Furthermore, how the nature of the hippocampal local pathological imprint is associated with microglia responses needs to be elucidated. To this purpose, we employed an automated pipeline for analysis of 3D confocal microscopy images to assess CA1, CA3 and DG/CA4 subfields microglia responses in post-mortem hippocampal samples from late-onset AD ( n  = 10), DLB ( n  = 8) and age-matched control (CTL) ( n  = 11) individuals. In parallel, we performed volumetric analyses of hyperphosphorylated tau (pTau), amyloid-β (Aβ) and phosphorylated α-synuclein (pSyn) loads. For each of the 32,447 extracted microglia, 16 morphological features were measured to classify them into seven distinct morphological clusters. Our results show similar alterations of microglial morphological features and clusters in AD and DLB, but with more prominent changes in AD. We identified two distinct microglia clusters enriched in disease conditions and particularly increased in CA1 and DG/CA4 of AD and CA3 of DLB. Our study confirms frequent concomitance of pTau, Aβ and pSyn loads across AD and DLB but reveals a specific subregional pattern for each type of pathology, along with a generally increased severity in AD. Furthermore, pTau and pSyn loads were highly correlated across subregions and conditions. We uncovered tight associations between microglial changes and the subfield pathological imprint. Our findings suggest that combinations and severity of subregional pTau, Aβ and pSyn pathologies transform local microglia phenotypic composition in the hippocampus. The high burdens of pTau and pSyn associated with increased microglial alterations could be a factor in CA1 vulnerability in AD.

Confocal fluorescent microscopy is a major tool to investigate the molecular orchestration of biomedical samples. The quality of the image acquisition depends critically on the tissue quality and thickness, the type, and concentration of antibodies used, as well as on microscope parameters. Due to these factors, intra-sample and inter-sample variability inevitably arises. Segmentation and quantification of targeted proteins can thus become a challenging process. Image processing techniques need therefore to address the acquisitions variability to minimize the risk of biases originating from changes in signal intensity, background noise, and parameterization. Here, we introduce PaFSe, a parameter-free segmentation algorithm for 3D fluorescent images. The algorithm is based on our established PRAQA approach, which evaluates the dispersion of several pixel intensity neighborhoods allowing for a statistical assessment whether individual subfields of an image can be considered as positive signal or background. PaFSe extends PRAQA by a fully automatic estimate for the segmentation parameters, and thereby provides a completely parameter-free and robust segmentation algorithm. By comparing PaFSe with Ilastik on synthetic examples, we show that our method achieves similar performances as a supervised approach in low-to-moderate noise environments without the need of tedious training. Furthermore, we validate the efficiency of PaFSe by segmenting and quantifying the abundance of hyperphosphorylated Tau protein in post-mortem human brain samples from Alzheimer’s disease patients and age-matched controls, where we obtain quantification values highly correlated with manual neuropathological segmentation. PaFSe is a parameter-free, fast, and adaptive approach for robust segmentation and quantification of protein abundance from complex 3D fluorescent images and is freely available at https://doi.org/10.17881/j20h-pa27 .

The cellular alterations of the hippocampus lead to memory decline, a shared symptom between Alzheimer's disease (AD) and dementia with Lewy Bodies (DLB) patients. However, the subregional deterioration pattern of the hippocampus differs between AD and DLB with the CA1 subfield being more severely affected in AD. The activation of microglia, the brain immune cells, could play a role in its selective volume loss. How subregional microglia populations vary within AD or DLB and across these conditions remains poorly understood. Furthermore, how the nature of the hippocampal local pathological imprint is associated with microglia responses needs to be elucidated. To this purpose, we employed an automated pipeline for analysis of 3D confocal microscopy images to assess CA1, CA3 and DG/CA4 subfields microglia responses in post-mortem hippocampal samples from late-onset AD (n = 10), DLB (n = 8) and age-matched control (CTL) (n = 11) individuals. In parallel, we performed volumetric analyses of hyperphosphorylated tau (pTau), amyloid-[beta] (A[beta]) and phosphorylated [alpha]-synuclein (pSyn) loads. For each of the 32,447 extracted microglia, 16 morphological features were measured to classify them into seven distinct morphological clusters. Our results show similar alterations of microglial morphological features and clusters in AD and DLB, but with more prominent changes in AD. We identified two distinct microglia clusters enriched in disease conditions and particularly increased in CA1 and DG/CA4 of AD and CA3 of DLB. Our study confirms frequent concomitance of pTau, A[beta] and pSyn loads across AD and DLB but reveals a specific subregional pattern for each type of pathology, along with a generally increased severity in AD. Furthermore, pTau and pSyn loads were highly correlated across subregions and conditions. We uncovered tight associations between microglial changes and the subfield pathological imprint. Our findings suggest that combinations and severity of subregional pTau, A[beta] and pSyn pathologies transform local microglia phenotypic composition in the hippocampus. The high burdens of pTau and pSyn associated with increased microglial alterations could be a factor in CA1 vulnerability in AD. Keywords: Alzheimer's disease, Dementia with Lewy Bodies, Hippocampus, Microglia, Amyloid-[beta], Hyperphosphorylated tau, Phosphorylated [alpha]-synuclein

Parkinson’s disease (PD) is a severe and complex multifactorial neurodegenerative disease with still elusive pathophysiology preventing the development of curative treatments. Molecular deep phenotyping by longitudinal multi-omics is a promising approach to identify mechanisms of PD aetiology and its progression. However, the heterogeneous data require new analysis frameworks to understand disease progression across biological entities and processes. Here, we present MONFIT, a holistic analysis pipeline that integrates and mines time-series single-cell RNA-sequencing data with bulk proteomics and metabolomics data by non-negative matrix tri-factorization, enabling prior knowledge incorporation from molecular networks. First, MONIFT integrates time-point-specific data and then holistically mines the integrated data across time points. By applying MONFIT to longitudinal multi-omics data of differentiation of PD and control patient-derived induced pluripotent stem cells into dopaminergic neurons, we identify novel PD-associated genes, emphasize molecular pathways that play important roles in PD pathology, and suggest new intervention opportunities using drug-repurposing. MONFIT is fully adaptable to other multi-omics data sets.

Hippocampal alteration is at the centre of memory decline in the most common age-related neurodegenerative diseases: Alzheimer's disease (AD) and Dementia with Lewy Bodies (DLB). However, the subregional deterioration of the hippocampus differs between both diseases with more severe atrophy in the CA1 subfield of the AD patients. How AD and DLB-typical pathologies compose the various local microenvironment of the hippocampus across AD and DLB needs to be further explored to understand this process. Additionally, microglia responses could further impact the atrophy rate. Some studies suggest that microglia react differently according to the underlying neurodegenerative disorder. How microglia are transformed across hippocampal subfields in AD and DLB, and how their changes are associated with disease-typical pathologies remains to be determined. To these purposes, we performed a volumetric analysis of phospho-Tau (P-Tau), Amyloid-beta (Abeta), and phospho-alpha-Synuclein (P-Syn) loads, quantified and classified microglia according to distinct morphological phenotypes using high-resolution confocal 3D microscopy of hippocampal CA1, CA3 and DG/CA4 subfields of late-onset AD (n=10) and DLB (n=8) as well as age-matched control samples (n=11). We found that each of the Tau, Abeta and Synuclein pathologies followed a specific subregional distribution, relatively preserved across AD and DLB. P-Tau, Abeta and P-Syn burdens were significantly exacerbated in AD, with Tau pathology being particularly severe in the AD CA1. P-Tau and P-Syn burdens were highly correlated across subfields and conditions (R2Spear = 0.79; P < 0.001) and result from a local co-distribution of P-Tau and P-Syn inclusions in neighbouring neurons, with only a low proportion of double-positive cells. In parallel, we assessed the changes of the microglia responses by measuring 16 morphological features of more than 35,000 individual microglial cells and classifying them into seven-distinct morphological clusters. We found microglia features- and clusters-variations subfield- and condition-dependent. Two of the seven morphological clusters, with more amoeboid and less branched forms, were identified as disease-enriched and found to be further increased in AD. Interestingly, some microglial features or clusters were associated with one but more often with a combination of two pathologies in a subfield-dependent manner. In conclusion, our study shows a multimodal association of the hippocampal microglia responses with the co-occurrence, distribution and severity of AD and DLB pathologies. In DLB hippocampi, pathological imprint and microglia responses follow AD trends but with lesser severity. Our study suggests that the increased pathological burdens of P-Tau and P-Syn and associated microglia alterations are involved in a more severe deterioration of the CA1 in AD as compared to DLB. Competing Interest Statement The authors have declared no competing interest.