Early mammalian embryonic development is precisely regulated by spatio-temporally controlled gene expression. It is important for us to understand the molecular mechanisms by which the embryo develops. However, the study of human embryo development, especially the post-implantation human embryo development is scarce. Post-implantation human embryo development consists of gastrulation and organogenesis processes. Defining gene expression profiles during these processes is an essential step for understanding molecular networks that control embryonic development. A large scale of analyzing microarray-based transcriptional profiling has been applied to development biology research, which provides us a great amount of information of temporal and genome-wide gene expression patterns. In this study, we used microarray to detect and analyze gene expression of the post-implantation human embryos at six successive developmental stages from Carnegie stage 9 to 14, spanning the period from the onset of organogenesis to formation of primordia of the most organs. Our analysis categorizes these stages into three major phases: the Phase I containing Stage 9 (S9), the Phase II consisting of Stages 10-12 (S10-12) and the Phase III consisting of Stages 13-14 (S13-14). Our data show that morphological changes occurring within the whole embryo during human post-implantation embryonic development are driven by the corresponding transcriptome changes. Particularly, dramatic changes in transcriptome during the transition from the Phase I to the Phase II underlie the expanding organogenesis observed as the embryo develops, indicating that the Stages 9 to 10 are a pivotal period for organogenesis. Thus, our study establishes the first comprehensive transcriptional database of human organogenesis. Moreover, comparison of disparate genomic data reveals that conserved expression patterns exist during early organogenesis between human and Drosophila as well as between human and mouse. Interestingly, by comparing disparate genomic data in human embryonic stem cells, we find that sequential loss of the stemness-relevant state during human post-implantation development can be implicated, while diversified changes of differentiating potentials may be needed to ensure proper functionality.In addition to the integrating analysis, expression-active protein-protein subnetwork (termed as hPIEDNet) is uncovered to account for the most characteristics during human post-implantation development, which are largely contributed by its inherited stemness-relevant module and other remaining differentiation-relevant module. The bi-module of hPIEDNet allows inspection of multipotent states of human post-implantation development in various model systems. The results implicate that hStemModule gradually loses its functionalities during human post-implantation development, whereas hDiffModule reflects stage-specific developmental potentials. Taken together, both modules are probably integrated into hPIEDNet to function as a Yin-Yang-like cross-talk between general stemness-maintaining programs versus differentiation machineries during early human organogenesis. From the perspective view of biological information, starting with transcriptome profiles in the context of human post-implantation development, integration of network biology and various-omics data allows the success of this study, thus setting as a paradigm for network-like understanding of any biological process.
The bystin-like (Bysl) gene was previously characterized as an accessory protein that participates in early embryo implantation. It is also involved in pre-ribosomal RNA processing. Here, we report that Bysl is required for nucleogenesis and is essential for hepatocarcinoma cell growth. We screened paraffin-embeded hepatectomy specimens of 98 patients with hepatocellular carcinoma by immunohistochemistry using Bysl antibody. This screening identified stronger staining in HCC compared to the adjacent non-cancerous tissues. Further Real-time PCR assay and Western blot assay also found that Bysl was upregulated in HCC sample than the adjacent non-cancerous tissues. Thus, Bysl expression significantly correlates with HCC. Experimental inhibition of Bysl by short hairpin RNA knockdown of Bysl decreased survival of cancer cells in both in vitro and in vivo assays and reduced HCC cell tolerance to serum starvation. To determine the cellular basis for Bysl RNAi-induced cell growth arrest, subcellular localization of Bysl in mitotic and interphase HepG2 cells was examined. It was revealed that Bysl was present in the nucleolus-derived foci (NDF) and perichromosomal region during mitosis; and it translocated from the perichromosomal region to the prenucleolar body (PNB) in telophase and G1 phase. Bysl depletion suppressed NDF and PNBs and disrupted the reformation of the nucleoli after mitosis. Taken together, these data indicate that Bysl is required for nucleolus assembly during cell growth of hepatocarcinoma. Thus, Bysl is potentially a novel target for hepatocarcinoma therapy.