Transcriptome and epigenome analysis of hematopoietic stem cells and their progeny (2014)

Bioinformatics has become an essential component of biology. With the advent of high throughput technologies, interdisciplinary research areas such as life science informatics/computational biology and system biology have emerged. The development in these disciplines fundamentally transformed the way we study molecular biology. Analysis of microarray and next generation sequencing (NGS) data is a trending topic in the area. It requires more computational power and expertise than conventional techniques. Therefore, data analysis and bioinformatics are integral parts of every microarray/NGS base-study. In this thesis, I focused on developing and performing integrative bioinformatic approaches to mine microarray and NGS data in the hematopoietic system. Haematopoiesis, the formation of blood cells from hematopoietic stem cells (HSC), is a well-studied differentiation system. However, the molecular mechanisms underlying the development and differentiation of antigen presenting dendritic cells (DC) remain unclear. To investigate the molecular events in the course of HSC differentiation into DC, comparative analysis of DNA microarray data of HSC, DC progenitor and DC were performed to characterize the lineage-specific transcription programs. Accordingly, many known and novel DC specific genes were identified. This study also uncovered that common DC progenitors (CDP) acquire a DC-primed expression profile. In addition, the analysis of transforming growth factor beta 1 (TGF-beta1) signaling reveals that TGF-beta1 acts on DC bifurcation point and directs conventional DC (cDC) subset specification, at the expense of plasmacytoid DC (pDC) development. Epigenetic modifications and transcription factor binding control gene expression. To understand the regulatory mechanism in DC fate decision, a comprehensive genome-wide chromatin map of DC development was generated by chromatin immunoprecipitation sequencing (ChIP-seq), including PU.1, H3K4me3, H3K9me3, H3K27me3. A stage-to-stage epigenetic regulatory framework (MPP-CDP-cDC/pDC), which drives DC commitment and specification, was constructed and thoroughly examined. Furthermore, an integrative approach was developed to determine the DC regulatory circuitry that elucidate the basic architecture and dynamics of transcriptional regulation during DC development. DNA methylation (DNAm) plays a crucial role in hematopoietic differentiation and aging of organisms. It also provides a new perspective for biomarker selection. In this thesis, a computational approach was developed to analyze a large collection of publicly available genome-wide DNAm profiles of blood samples. A panel of age related CpG sites was identified, that allows to predict human age. An Epigenetic-Aging-Signature was further developed and verified, which only requires measurement of DNAm levels at three CpG sites for age prediction. The DNA de novo methyltransferase DNMT3A establishes the pattern of DNA methylation. Many patients with acute myeloid leukemia (AML) have mutations in the genetic sequence of DNMT3A, leading to a poor prognosis. To understand the epigenetic modification of DNMT3A, a systematic analysis was conducted on the basis of publicly available AML patient dataset from the Cancer Genome Atlas Research Network (TCGA). Several aberrant hypermethylation regions at an internal promoter region of DNMT3A were identified. These epimutations in DNMT3A were observed in AML patients with significantly shorter event-free survival and overall survival, indicating epigenetic modifications in the DNAm pattern mimic genetic mutations and can be used as biomarkers.