cost-efficient-transcriptomic-based-drug-screening

Cost-Efficient Transcriptomic-Based Drug Screening

Transcriptomics allows&#160;to obtain comprehensive insights into cellular programs and their responses to perturbations. Despite a significant decrease ...

German Center for Neurodegenerative Diseases (DZNE) eV.

DZNE and University of Bonn

The usage of mouse models has been vital for biomedical research over the last decades, yet the generation of these models has been extremely difficult and labor-intensive. The identification and generation of nucleases able to introduce site-specific DNA double-strand breaks, particularly the CRIPSR/Cas system, is a major breakthrough for this field as the endogenous DNA repair machinery can be hijacked to specifically introduce genome modifications at these sites. This allows for the time-efficient and cost-efficient generation of mouse models by delivery of designer nucleases together with donor DNA into fertilized oocytes.

Genetic engineering as a tool for the generation of mouse models to understand disease phenotypes and gene function.

Weighted gene co-expression network analysis (WGCNA) allows for the identification and characterization of cell type-specific gene modules in complex transcriptome datasets. Here, we use a microarray dataset of human macrophages comprising 29 conditions and 299 samples generated by differentiation of CD14 monocytes into macrophages followed by in vitro stimulations to identify stimulation-specific gene modules. These gene modules can be used for experimental validation, as well as further bioinformatic analysis to determine key pathways or upstream transcription factors.

Bioinformatic Assessment of Macrophage Activation by the Innate Immune System.

Regulatory T cells (Treg cells) are important for preventing autoimmunity and maintaining tissue homeostasis, but whether Treg cells can adopt tissue- or immune-context-specific suppressive mechanisms is unclear. Here, we found that the enzyme hydroxyprostaglandin dehydrogenase (HPGD), which catabolizes prostaglandin E (PGE) into the metabolite 15-keto PGE, was highly expressed in Treg cells, particularly those in visceral adipose tissue (VAT). Nuclear receptor peroxisome proliferator-activated receptor-γ (PPARγ)-induced HPGD expression in VAT Treg cells, and consequential Treg-cell-mediated generation of 15-keto PGE suppressed conventional T cell activation and proliferation. Conditional deletion of Hpgd in mouse Treg cells resulted in the accumulation of functionally impaired Treg cells specifically in VAT, causing local inflammation and systemic insulin resistance. Consistent with this mechanism, humans with type 2 diabetes showed decreased HPGD expression in Treg cells. These data indicate that HPGD-mediated suppression is a tissue- and context-dependent suppressive mechanism used by Treg cells to maintain adipose tissue homeostasis.

Enzymatic Activity of HPGD in Treg Cells Suppresses Tconv Cells to Maintain Adipose Tissue Homeostasis and Prevent Metabolic Dysfunction.

What defines regulatory T (Treg) cells in healthy human tissues? In this issue of Immunity, Delacher et al. describe a human follicular helper T cell-like tissue-repair Treg cell signature governed by BATF based on chromatin accessibility data and link this on a transcriptome and protein level to important functional features like CCR8 expression.

ATAC-ing human tissue Treg cells.

The advance of single-cell RNA-sequencing technologies in the past years has enabled unprecedented insights into the complexity and heterogeneity of microglial cell states in the homeostatic and diseased brain. This includes rather complex proteomic, metabolomic, morphological, transcriptomic, and epigenetic adaptations to external stimuli and challenges resulting in a novel concept of core microglia properties and functions. To uncover the regulatory programs facilitating the rapid transcriptomic adaptation in response to changes in the local microenvironment, the accessibility of gene bodies and gene regulatory elements can be assessed. Here, we describe the application of a previously published method for simultaneous high-throughput ATAC and RNA expression with sequencing (SHARE-seq) on microglia nuclei isolated from frozen mouse brain tissue.

Article	Year
Genetic engineering as a tool for the generation of mouse models to understand disease phenotypes and gene function. Current opinion in biotechnology\| PubMed ID: 28704794	2017
Bioinformatic Assessment of Macrophage Activation by the Innate Immune System. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 29177853	2018
Enzymatic Activity of HPGD in Treg Cells Suppresses Tconv Cells to Maintain Adipose Tissue Homeostasis and Prevent Metabolic Dysfunction. Immunity\| PubMed ID: 31027998	2019
ATAC-ing human tissue Treg cells. Immunity\| PubMed ID: 33852825	2021
Combined Analysis of mRNA Expression and Open Chromatin in Microglia. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 37639146	2024

Marc Beyer

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