Pluto Bioinformatics

GSE128692: Next-Generation Sequencing Characterization of Hematopoietic Stem and Progenitors Cells in Murine Systemic Lupus Erythematosus

Bulk RNA sequencing

Purpose: Next-generation sequencing (NGS) technology was exploited to map genome-wide expression profile of hematopoietic stem and progenitor cells (HSPCs) in mouse model of Systemic Lupus Erythematosus (SLE).; Methods: Total RNA was extracted as described by manufacturer (NucleoSpin RNA XS) and mRNA libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Single-end 75-bp mRNA sequencing was performed on Illumina NextSeq 500 platform. Quality of sequencing was assessed using FastQC software. Raw reads in fastq format were collected and aligned to the mouse genome (mm10 version) using STAR 2.6 algorithm. Gene quantification was performed using HTSeq and differential expression analysis was performed using edgeR package.; Results: Transcriptomic analysis of F1-L LSK indicates activation as they respond to type I IFN, displayed increased proliferation and replicative stress, and profoundly prefer to differentiate towards myeloid/granulocytic lineage. Gene expression analysis of F1-L CMPs suggests arrest of differentiation at the level of myeloid progenitors as key regulators including Cebpa, Cebpe, Irf8 are suppressed.; Conclusions: Our study suggests deregulation of differentiation at the level of CMPs and priming of LSK cells towards granulocytic branch proposing an alternative granulopoiesis route. This comparison indicates an arrest at the progenitor stage both in murine lupus hematopoiesis as important regulators for terminal differentiation are downregulated. SOURCE: Maria Grigoriou BRFAA