Biology subjects

Biber, K.

Publications and source records attributed to Biber, K..

6 recordsLinked to original sources

bioRxiv2024

Exploring the Abeta Plaque Microenvironment in Alzheimer's Disease Mice by Multimodal Lipid-Protein-Histology Imaging on a Benchtop Mass Spectrometer

Amyloid-{beta} (A{beta}) plaque deposits in the brain are a hallmark of Alzheimers disease (AD) neuropathology. Plaques consist of complex mixtures of peptides like A{beta}1-42, characteristic lipids such as gangliosides, and they are targeted by reactive microglia and astrocytes. In pharmaceutical research and development it is therefore a formidable challenge to contextualize different biomolecular classes and cell types of the A{beta} plaque microenvironment in a coherent experimental workflow on a single tissue section and on a benchtop imaging reader. Here, we developed such a workflow that combines lipid MALDI mass spectrometry imaging using a vacuum-stable matrix with histopathology stains and with MALDI HiPLEX-immunohistochemistry of plaques and multiple protein markers on a bench-top imaging mass spectrometer. The three data layers consisting of lipid, protein markers, and histology can be co-registered and evaluated together. Multimodal data analysis suggests extensive co-localization of A{beta} plaques with the peptide precursor protein, with a defined subset of lipids and with reactive glia cells on a single brain section of APP/PS1 AD model mice. Plaque-associated lipids like ganglioside GM2 and phosphatidylinositol PI38:4 isoforms were readily identified using the tandem MS-capabilities of the mass spectrometer. Taken together, our data suggests that complex pathology involving multiple lipids, proteins and cell types can be interrogated by this spatial multiomics workflow on an easy-to-use benchtop mass spectrometer.

neuroscience↗

bioRxiv2023

Distinct Transcriptomic Responses to A beta plaques, Neurofibrillary Tangles, and APOE in Alzheimer's Disease

INTRODUCTIONOmics studies have revealed that various brain cell types undergo profound molecular changes in Alzheimers disease (AD) but the spatial relationships with plaques and tangles and APOE-linked differences remain unclear. METHODSWe performed laser capture microdissection of A{beta} plaques, the 50m halo around them, tangles with the 50m halo around them, and areas distant (>50m) from plaques and tangles in the temporal cortex of AD and control donors, followed by RNA-sequencing. RESULTSA{beta} plaques exhibited upregulated microglial (neuroinflammation/phagocytosis) and downregulated neuronal (neurotransmission/energy metabolism) genes, whereas tangles had mostly downregulated neuronal genes. A{beta} plaques had more differentially expressed genes than tangles. We identified a gradient A{beta} plaque>peri-plaque>tangle>distant for these changes. AD APOE{varepsilon}4 homozygotes had greater changes than APOE{varepsilon}3 across locations, especially within A{beta} plaques. DISCUSSIONTranscriptomic changes in AD consist primarily of neuroinflammation and neuronal dysfunction, are spatially associated mainly with A{beta} plaques, and are exacerbated by the APOE{varepsilon}4 allele.

neuroscience↗

bioRxiv2023

Endothelial Cells are Heterogeneous in Different Brain Regions and are Dramatically Altered in Alzheimer's Disease

Vascular endothelial cells play an important role in maintaining brain health, but their contribution to Alzheimers disease (AD) is obscured by limited understanding of the cellular heterogeneity in normal aged brain and in disease. To address this, we performed single nucleus RNAseq on tissue from 32 AD and non-AD donors each with five cortical regions: entorhinal cortex, inferior temporal gyrus, prefrontal cortex, visual association cortex and primary visual cortex. Analysis of 51,586 endothelial cells revealed unique gene expression patterns across the five regions in non-AD donors. Alzheimers brain endothelial cells were characterized by upregulated protein folding genes and distinct transcriptomic differences in response to amyloid beta plaques and cerebral amyloid angiopathy (CAA). This dataset demonstrates previously unrecognized regional heterogeneity in the endothelial cell transcriptome in both aged non-AD and AD brain. Significance StatementIn this work, we show that vascular endothelial cells collected from five different brain regions display surprising variability in gene expression. In the presence of Alzheimers disease pathology, endothelial cell gene expression is dramatically altered with clear differences in regional and temporal changes. These findings help explain why certain brain regions appear to differ in susceptibility to disease-related vascular remodeling events that may impact blood flow.

neuroscience↗

bioRxiv2022

Astrocyte transcriptomic changes along the spatiotemporal progression of Alzheimer's disease

Astrocytes play a critical role in brain homeostasis and normal functions but their changes along the spatiotemporal progression of Alzheimers disease (AD) neuropathology remain largely unknown. Here we performed single-nucleus RNA-sequencing on brain regions along the stereotypical progression of AD pathology from donors ranging the entire normal aging-AD continuum comprising 628,943 astrocyte nuclei from 32 donors across 5 brain regions. We discovered temporal gene-expression-trajectories with gene sets differentially activated at various disease stages. Surprisingly, a gene set enriched in proteostasis and energy metabolism, was upregulated in late-stage but unexpectedly returned to baseline levels in end-stage, suggesting exhaustion of response in "burnt-out" astrocytes. The spatial gene-expression-trajectories revealed that astrocytic genes of tripartite synapses are dysregulated in parallel to the stereotypical progression of tangle pathology across regions. We identified astrocyte heterogeneity across brain regions with a continuum from homeostatic to reactive cells through "intermediate" transitional states. These findings suggest complex astrocytic dysfunction in AD neurodegeneration.

neuroscience↗

bioRxiv2020

ABACUS: A flexible UMI counter that leverages intronic reads for single-nucleus RNAseq analysis

Single-nucleus RNA sequencing (sNuc-RNAseq) is an emerging powerful genomics technology that combines droplet microfluidics with next-generation sequencing to interrogate transcriptome changes at single nucleus resolution. Here we developed Abacus, a flexible UMI counter software for sNuc-RNAseq analysis. Abacus draws extra information from sequencing reads mapped to introns of pre-mRNAs (~60% of total data) that are ignored by many single-cell RNAseq analysis pipelines. When applied to our pilot human brain sNuc-RNAseq data, ABACUS nearly doubled the number of nuclei identified by the CellRanger workflow, recovering a large number of nuclei from non-neuronal cells. By incorporating intronic reads into gene expression quantification, we showed that they encoded additional and valid transcription features of individual cells and could be used to improve cluster resolution of different cell types. By separately counting UMIs derived from forward and reverse intronic reads and from exonic reads, Abacus gives users flexibility in representing genes expressed at different abundance levels. In summary, Abacus represents a flexible, improved workflow for sNuc-RNAseq data processing and analysis.

bioinformatics↗

bioRxiv2020

Neurodegeneration and neuroinflammation are linked, but independent of alpha-synuclein inclusions, in a seeding/spreading mouse model of Parkinson disease

A key process of neurodegeneration in Parkinson disease (PD) is the transneuronal spreading of alpha-synuclein. Alpha-synuclein is a presynaptic protein that is implicated in the pathogenesis of PD and other synucleinopathies, where it forms, upon intracellular aggregation, pathological inclusions. Other hallmarks of PD include neurodegeneration and microgliosis in susceptible brain regions. Whether it is primarily transneuronal spreading of alpha-synuclein particles, inclusion formation, or other mechanisms, such as inflammation, that cause neurodegeneration in PD is unclear. We used spreading/aggregation of alpha-synuclein induced by intracerebral injection of alpha-synuclein preformed fibrils into the mouse brain to address this question. We performed quantitative histological analysis for alpha-synuclein inclusions, neurodegeneration, and microgliosis in different brain regions, and a gene expression profiling of the ventral midbrain, at two different timepoints after disease induction. We observed significant neurodegeneration and microgliosis in brain regions not only with, but also without alpha-synuclein inclusions. We also observed prominent microgliosis in injured brain regions that did not correlate with neurodegeneration nor with inclusion load. In longitudinal gene expression profiling experiments, we observed early and unique alterations linked to microglial mediated inflammation that preceded neurodegeneration, indicating an active role of microglia in inducing neurodegeneration. Our observations indicate that alpha-synuclein inclusion formation is not the major driver in the early phases of PD-like neurodegeneration, but that diffusible, oligomeric alpha-synuclein species, which induce unusual microglial reactivity, play a key role in this process. Our findings uncover new features of alpha-synuclein induced pathologies, in particular microgliosis, and point to the necessity of a broader view of the process of prion-like spreading of that protein.

neuroscience↗