sample-preparation-for-metabolic-profiling-using-maldi-mass

Sample Preparation for Metabolic Profiling using MALDI Mass Spectrometry Imaging

Metabolomics, the study to identify and quantify small molecules and metabolites present in an experimental sample, has emerged as an important tool to ...

The City University of New York

Oligodendrocytes (OLs) and myelin are critical for normal brain function and have been implicated in neurodegeneration. Several lines of evidence including neuroimaging and neuropathological data suggest that Alzheimer's disease (AD) may be associated with dysmyelination and a breakdown of OL-axon communication.

Multiscale network modeling of oligodendrocytes reveals molecular components of myelin dysregulation in Alzheimer's disease.

Elucidating brain cell type specific gene expression patterns is critical towards a better understanding of how cell-cell communications may influence brain functions and dysfunctions. We set out to compare and contrast five human and murine cell type-specific transcriptome-wide RNA expression data sets that were generated within the past several years. We defined three measures of brain cell type-relative expression including specificity, enrichment, and absolute expression and identified corresponding consensus brain cell "signatures," which were well conserved across data sets. We validated that the relative expression of top cell type markers are associated with proxies for cell type proportions in bulk RNA expression data from postmortem human brain samples. We further validated novel marker genes using an orthogonal ATAC-seq dataset. We performed multiscale coexpression network analysis of the single cell data sets and identified robust cell-specific gene modules. To facilitate the use of the cell type-specific genes for cell type proportion estimation and deconvolution from bulk brain gene expression data, we developed an R package, BRETIGEA. In summary, we identified a set of novel brain cell consensus signatures and robust networks from the integration of multiple datasets and therefore transcend limitations related to technical issues characteristic of each individual study.

Brain Cell Type Specific Gene Expression and Co-expression Network Architectures.

Oligodendrocyte precursor cells (OPCs), also known as NG2 glia, arise from neural progenitor cells in the embryonic ganglionic eminences that also generate inhibitory neurons. They are ubiquitously distributed in the central nervous system, remain proliferative through life, and generate oligodendrocytes in both gray and white matter. OPCs exhibit some lineage plasticity, and attempts have been made to reprogram them into neurons, with varying degrees of success. However, little is known about how epigenetic mechanisms affect the ability of OPCs to undergo fate switch and whether OPCs have a unique chromatin environment around neuronal genes that might contribute to their lineage plasticity. Our bioinformatic analysis of histone posttranslational modifications at interneuron genes in OPCs revealed that OPCs had significantly fewer bivalent and repressive histone marks at interneuron genes compared to astrocytes or fibroblasts. Conversely, OPCs had a greater degree of deposition of active histone modifications at bivalently marked interneuron genes than other cell types, and this was correlated with higher expression levels of these genes in OPCs. Furthermore, a significantly higher proportion of interneuron genes in OPCs than in other cell types lacked the histone posttranslational modifications examined. These genes had a moderately high level of expression, suggesting that the "no mark" interneuron genes could be in a transcriptionally "poised" or "transitional" state. Thus, our findings suggest that OPCs have a unique histone code at their interneuron genes that may obviate the need for erasure of repressive marks during their fate switch to inhibitory neurons.

The Chromatin Environment Around Interneuron Genes in Oligodendrocyte Precursor Cells and Their Potential for Interneuron Reprograming.

Emerging concepts in neuroscience research: 2019 highlights.

Differentiation of oligodendrocytes (OL) from progenitor cells (OPC) is the result of a unique program of gene expression, which is further regulated by the formation of topological domains of association with the nuclear lamina. In this study, we show that cultured OPC were characterized by progressively declining levels of endogenous Lamin B1 (LMNB1) during differentiation into OL. We then identify the genes dynamically associated to the nuclear lamina component LMNB1 during this transition, using a well established technique called DamID, which is based on the ability of a bacterially-derived deoxyadenosine methylase (Dam), to modify genomic regions in close proximity. We expressed a fusion protein containing Dam and LMNB1 in OPC (OPC) and either kept them proliferating or differentiated them into OL (OL) and identified genes that were dynamically associated to LMNB1 with differentiation. Importantly, we identified Lss, the gene encoding for lanosterol synthase, a key enzyme in cholesterol synthesis, as associated to the nuclear lamina in OL. This finding could at least in part explain the lipid dysregulation previously reported for mouse models of ADLD characterized by persistent LMNB1 expression in oligodendrocytes.

Dynamic Lamin B1-Gene Association During Oligodendrocyte Progenitor Differentiation.

Multiple Sclerosis (MS) is an autoimmune demyelinating disorder resulting from the interplay of genetic predisposition and environmental variables, including gut microbiota, diet and life style factors. Here, we first discuss the evidence supporting the effect of early life events, diet and body mass index on the composition of the microbiota, and then review studies on gut dysbiosis conducted in MS patients and in animal models. We address the effect of disease, immunomodulatory therapies, diet and probiotics on enrichment or depletion of gut microbial species. Finally, we discuss the ability of gut bacteria to produce toxins and metabolites which serve as signals for the cross-talk between the gut and the brain.

Gut-brain communication in demyelinating disorders.

The disease course of patients with a confirmed diagnosis of primary progressive multiple sclerosis (PPMS) is uncertain. In an attempt to identify potential signaling pathways involved in the evolution of the disease, we conducted an exploratory unbiased lipidomic analysis of plasma from non-diseased controls (n = 8) and patients with primary progressive MS (PPMS, n = 19) and either a rapid (PPMS-P, n = 9) or slow (PPMS-NP, n = 10) disease course based on worsening disability and/or MRI-visible appearance of new T2 lesions over a one-year-assessment. Partial least squares-discriminant analysis of the MS/MS lipidomic dataset, identified lipids driving the clustering of the groups. Among these lipids, sphingomyelin-d18:1/14:0 and mono-hexosylceramide-d18:1/20:0 were differentially abundant in the plasma of PPMS patients compared to controls and their levels correlated with MRI signs of disease progression. Lyso-phosphatidic acid-18:2 (LPA-18:2) was the only lipid with significantly lower abundance in PPMS patients with a rapidly deteriorating disease course, and its levels inversely correlated with the severity of the neurological deficit. Decreased levels of LPA-18:2 were detected in patients with more rapid disease progression, regardless of therapy and these findings were validated in an independent cohort of secondary progressive (SPMS) patients, but not in a third cohorts of relapsing-remitting (RRMS) patients. Collectively, our analysis suggests that sphingomyelin-d18:1/14:0, mono-hexosylceramide-d18:1/20:0, and LPA-18:2 may represent important targets for future studies aimed at understanding disease progression in MS.

Retrospective unbiased plasma lipidomic of progressive multiple sclerosis patients-identifies lipids discriminating those with faster clinical deterioration.

The past decade has seen an important revision of the traditional concept of the role and function of glial cells. From "passive support" for neurons, oligodendrocyte lineage cells are now recognized as metabolic exchangers with neurons, a cellular interface with blood vessels and responders to gut-derived metabolites or changes in the social environment. In the developing brain, the differentiation of neonatal oligodendrocyte progenitors (nOPCs) is required for normal brain function. In adulthood, the differentiation of adult OPCs (aOPCs) serves an important role in learning, behavioral adaptation and response to myelin injury. Here, we propose the concept of OPCs as environmental biosensors, which "sense" chemical and physical stimuli over time and adjust to the new challenges by modifying their epigenome and consequent transcriptome. Because epigenetics defines the ability of the cell to "adapt" gene expression to changes in the environment, we propose a model of OPC differentiation resulting from time-dependent changes of the epigenomic landscape in response to declining mitogens, raising hormone levels, neuronal activity, changes in space constraints or stiffness of the extracellular matrix. We propose that the intrinsically different functional properties of aOPCs compared to nOPCs result from the accrual of "epigenetic memories" of distinct events, which are "recorded" in the nuclei of OPCs as histone and DNA marks, defining a "unique epigenomic landscape" over time.

Article	Year
Multiscale network modeling of oligodendrocytes reveals molecular components of myelin dysregulation in Alzheimer's disease. Molecular neurodegeneration\| PubMed ID: 29110684	2017
Brain Cell Type Specific Gene Expression and Co-expression Network Architectures. Scientific reports\| PubMed ID: 29892006	2018
The Chromatin Environment Around Interneuron Genes in Oligodendrocyte Precursor Cells and Their Potential for Interneuron Reprograming. Frontiers in neuroscience\| PubMed ID: 31440130	2019
Emerging concepts in neuroscience research: 2019 highlights. The Lancet. Neurology\| PubMed ID: 31839244	2020
Dynamic Lamin B1-Gene Association During Oligodendrocyte Progenitor Differentiation. Neurochemical research\| PubMed ID: 32020491	2020
Gut-brain communication in demyelinating disorders. Current opinion in neurobiology\| PubMed ID: 32066076	2020
Retrospective unbiased plasma lipidomic of progressive multiple sclerosis patients-identifies lipids discriminating those with faster clinical deterioration. Scientific reports\| PubMed ID: 32973249	2020
Oligodendrocyte progenitors as environmental biosensors. Seminars in cell & developmental biology\| PubMed ID: 33092959	2020

Patrizia Casaccia

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