Identification of Regulatory Networks in HSCs and Their Immediate Progeny via Integrated Proteome, Transcriptome, and DNA Methylome Analysis

• Published in: Cell stem cell 2014-10, Vol.15 (4), p.507-522
• Main Authors: Cabezas-Wallscheid, Nina, Klimmeck, Daniel, Hansson, Jenny, Lipka, Daniel B., Reyes, Alejandro, Wang, Qi, Weichenhan, Dieter, Lier, Amelie, von Paleske, Lisa, Renders, Simon, Wünsche, Peer, Zeisberger, Petra, Brocks, David, Gu, Lei, Herrmann, Carl, Haas, Simon, Essers, Marieke A.G., Brors, Benedikt, Eils, Roland, Huber, Wolfgang, Milsom, Michael D., Plass, Christoph, Krijgsveld, Jeroen, Trumpp, Andreas
• Format: Article
• Language: English
• Subjects: Adult; Cell Differentiation - genetics; Cell Lineage - genetics; Cluster Analysis; DNA Methylation - genetics; Epigenesis, Genetic; Gene Expression Profiling; Gene Regulatory Networks; Genome, Human - genetics; Genomic Imprinting; Hematopoietic Stem Cells - cytology; Hematopoietic Stem Cells - metabolism; Humans; Molecular Sequence Data; Protein Isoforms - genetics; Protein Isoforms - metabolism; Proteome - metabolism; RNA, Long Noncoding - genetics; Transcription Factors - genetics; Transcription Factors - metabolism; Transcriptome - genetics
• ISSN: 1934-5909; 1875-9777
• DOI: 10.1016/j.stem.2014.07.005

In this study, we present integrated quantitative proteome, transcriptome, and methylome analyses of hematopoietic stem cells (HSCs) and four multipotent progenitor (MPP) populations. From the characterization of more than 6,000 proteins, 27,000 transcripts, and 15,000 differentially methylated regions (DMRs), we identified coordinated changes associated with early differentiation steps. DMRs show continuous gain or loss of methylation during differentiation, and the overall change in DNA methylation correlates inversely with gene expression at key loci. Our data reveal the differential expression landscape of 493 transcription factors and 682 lncRNAs and highlight specific expression clusters operating in HSCs. We also found an unexpectedly dynamic pattern of transcript isoform regulation, suggesting a critical regulatory role during HSC differentiation, and a cell cycle/DNA repair signature associated with multipotency in MPP2 cells. This study provides a comprehensive genome-wide resource for the functional exploration of molecular, cellular, and epigenetic regulation at the top of the hematopoietic hierarchy. [Display omitted] •Analysis identifies 6,000 proteins, 27,000 transcripts, and 15,000 DMRs in HSCs/MPPs•Core signaling, regulatory networks, and lncRNAs are central nodes in HSCs•Differentiation-associated changes include shifts in alternative transcript isoforms•DNA methylation correlates inversely with gene expression in HSCs and their progeny This study identifies regulatory networks of primary mouse HSCs and four downstream MPPs by combining proteome, transcriptome, and DNA methylome analyses with in vitro and in vivo functional assays.