| Literature DB >> 35099000 |
Ipek Ilgin Gönenc1, Alexander Wolff1, Julia Schmidt1, Arne Zibat1, Christian Müller1, Lukas Cyganek2,3, Loukas Argyriou1, Markus Räschle4, Gökhan Yigit1,3, Bernd Wollnik1,3,5.
Abstract
Bloom syndrome (BS) is an autosomal recessive disease clinically characterized by primary microcephaly, growth deficiency, immunodeficiency and predisposition to cancer. It is mainly caused by biallelic loss-of-function mutations in the BLM gene, which encodes the BLM helicase, acting in DNA replication and repair processes. Here, we describe the gene expression profiles of three BS fibroblast cell lines harboring causative, biallelic truncating mutations obtained by single-cell (sc) transcriptome analysis. We compared the scRNA transcription profiles from three BS patient cell lines to two age-matched wild-type controls and observed specific deregulation of gene sets related to the molecular processes characteristically affected in BS, such as mitosis, chromosome segregation, cell cycle regulation and genomic instability. We also found specific upregulation of genes of the Fanconi anemia pathway, in particular FANCM, FANCD2 and FANCI, which encode known interaction partners of BLM. The significant deregulation of genes associated with inherited forms of primary microcephaly observed in our study might explain in part the molecular pathogenesis of microcephaly in BS, one of the main clinical characteristics in patients. Finally, our data provide first evidence of a novel link between BLM dysfunction and transcriptional changes in condensin complex I and II genes. Overall, our study provides novel insights into gene expression profiles in BS on an sc level, linking specific genes and pathways to BLM dysfunction.Entities:
Mesh:
Substances:
Year: 2022 PMID: 35099000 PMCID: PMC9262399 DOI: 10.1093/hmg/ddab373
Source DB: PubMed Journal: Hum Mol Genet ISSN: 0964-6906 Impact factor: 5.121
Figure 1QC elements obtained from the CogentAP pipeline (Cogent NGS Analysis Pipeline, Takara Bio) reveal a robust sc transcriptome sequencing technique. (A) More than 70% of all reads mapped to exonic reads. (B) After removing cells with <10 000 total reads or <300 genes, the number of reads per cell was around 250K for all samples including two WT (WT1, WT2) and three BS patient fibroblast cell lines (BS1, BS2, BS3). (C) After removing genes with <100 total reads or expressed in fewer than three cells, the overall gene number per cell was between 7000 and 8000 genes for all samples. (D) The UMAP analysis of raw data presents the different gene expression profiles of each cell line originating from healthy and patient cell lines. Clustering between cells from different cell lines can be observed on the UMAP because of differential expression profiles of single cells. The plot was generated using ggplot2 package for R-programming language (72).
Figure 2Barplots of ORA show mainly BS-related terms in the top 20 denominations when the gene expressions of the BS patient fibroblasts and the WT fibroblasts were compared. (A) Top 20 differentially expressed GO terms were obtained via ORA from the R-package clusterProfiler (71). (B) The top 20 MeSH (26) obtained by ORA as in (A). Most of the GO terms and all of the top 20 MeSH nominations were linked to BLM dysfunction and BS pathogenesis. The x-axis shows the number of significantly deregulated genes on each denomination. The adjusted P-value calculation was done by using the Benjamini–Hochberg procedure for each P-value (70).
Figure 3Volcano plot shows differentially expressed genes in BS single cells in comparison to WT single cells. Significantly deregulated genes in the condensin I and II complexes, FA pathway and the genes known to cause microcephaly (42) are highlighted with different colors as the following: condesin I/II complex, red; FA group, black; and genes that are clinically associated with microcephaly, blue. The plot was generated using EnhancedVolcano package from Bioconductor for R programming language. Complete gene list and the corresponding values are given in Supplementary Material, Table S3.