Integrating Multi-Omics for Uncovering the Architecture of Cross-Talking Pathways in Breast Cancer

Cross-talk among abnormal pathways widely occurs in human cancer and generally leads to insensitivity to cancer treatment. Moreover, alterations in the abnormal pathways are not limited to single molecular level. Therefore, we proposed a strategy that integrates a large number of biological sources at multiple levels for systematic identification of cross-talk among risk pathways in cancer by random walk on protein interaction network. We applied the method to multi-Omics breast cancer data from The Cancer Genome Atlas (TCGA), including somatic mutation, DNA copy number, DNA methylation and gene expression profiles. We identified close cross-talk among many known cancer-related pathways with complex change patterns. Furthermore, we identified key genes (linkers) bridging these cross-talks and showed that these genes carried out consistent biological functions with the linked cross-talking pathways. Through identification of leader genes in each pathway, the architecture of cross-talking pathways was built. Notably, we observed that linkers cooperated with leaders to form the fundamentation of cross-talk of pathways which play core roles in deterioration of breast cancer. As an example, we observed that KRAS showed a direct connection to numerous cancer-related pathways, such as MAPK signaling pathway, suggesting that it may be a central communication hub. In summary, we offer an effective way to characterize complex cross-talk among disease pathways, which can be applied to other diseases and provide useful information for the treatment of cancer.     

拟南芥不定芽发生早期的数字基因表达谱分析

目前,有关不定芽发生的研究主要集中在单基因的调控方面,缺乏转录组方面的系统研究.利用RNA-seq高通量测序技术在全基因组范围内检测了不定芽发生早期的基因表达谱,共检测到2457个差异表达基因.这些基因参与了激素代谢和信号转导、愈伤组织和侧根的形成、茎顶端分生组织的发育和光合作用等过程.进一步的途径富集分析表明,不定芽发生早期苯丙氨酸代谢和苯丙胺素合成等途径相关的基因显著富集.并且苯丙氨酸可以显著抑制不定芽的发生,暗示了苯丙氨酸代谢和苯丙胺素的合成可能在不定芽发生过程起着重要的作用.     

桤木属7种植物的核型分析

利用改良去壁低渗法对分布于欧美地区的桦木科(Betulaceae)桤木属(Alnus Mill.)7种植物进行染色体数目与核型分析。结果显示:所有材料染色体形态比较一致,多为由中部(m)及近中部(sm)着丝点染色体组成。意大利桤木(A.cordata)为六倍体,体细胞染色体数为2n=6x=42,核型公式为2n=6x=42=36m+6sm;绿桤木(A.viridis)为八倍体,体细胞染色体数为2n=8x=56,核型公式为2n=8x=56=46m+10sm(SAT);薄叶桤木(A.tenuifolia)、灰桤木(A.incana)、欧洲桤木(A.glutinosa)、裂叶桤木(A.sinuata)和红桤木(A.rubra)均为四倍体,体细胞染色体数均为2n=4x=28,其核型公式分别为2n=4x=28=16m(1SAT)+12sm、2n=4x=28=22m+6sm、2n=4x=28=24m+4sm、2n=4x=28=24m+4sm、2n=4x=28=26m+2sm。其中红桤木(A.rubra)的核型属于1B型,其余均为2B型。     

Gamma‐amino butyric acid and the A‐type receptor suppress decidualization of mouse uterine stromal cells by down‐regulating cyclin D3

Uterine decidualization, characterized by stromal cell proliferation and differentiation into polyploid decidual cells, is critical to the establishment of pregnancy in mice, although the mechanism underlying this process remains poorly understood. This study is the first to investigate the expression of gamma‐amino butyric acid (GABA) and the GABA A‐type receptor π subunit (GABPR) in the early‐pregnancy mouse uterus and their roles in decidualization. The expression of GABRP was detected from Day 4 to 8 of pregnancy. The effects of GABA and GABA A‐type receptor on cell proliferation and apoptosis were investigated using the Cell Titer 96® AQueous One Solution Cell Proliferation Assay and flow cytometry. The levels of cyclin D3 protein were measured in cultured stromal cells artificially induced to undergo decidualization, and treated with GABA and a GABA A‐type receptor agonist or antagonist, respectively, at the same time. mRNA expression of gabrp in implantation sites was lower than that in inter‐implanted sites. GABA and GABRP protein were localized in the luminal and glandular epithelium, stromal cells, and decidual cells. In vitro, GABPR protein level was decreased in cultured stromal cells during the decidualization process. The addition of GABA and the GABA A‐type receptor agonist Muscimol inhibited stromal cell proliferation, promoted apoptosis, and arrested cells in S‐phase, followed by decreased expression of cyclin D3. These results show that in mice, GABA was actively involved in inhibiting stromal cell proliferation and suppresses decidualization progress through GABA A‐type receptors by down‐regulating cyclin D3 level. Mol. Reprod. Dev. 80: 59–69, 2013. © 2012 Wiley Periodicals, Inc.     

Baculovirus Superinfection: A Probable Restriction Factor on the Surface Display of Proteins for Library Screening

In addition to the expression of recombinant proteins, baculoviruses have been developed as a platform for the display of complex eukaryotic proteins on the surface of virus particles or infected insect cells. Surface display has been used extensively for antigen presentation and targeted gene delivery but is also a candidate for the display of protein libraries for molecular screening. However, although baculovirus gene libraries can be efficiently expressed and displayed on the surface of insect cells, target gene selection is inefficient probably due to super-infection which gives rise to cells expressing more than one protein. In this report baculovirus superinfection of Sf9 cells has been investigated by the use of two recombinant multiple nucleopolyhedrovirus carrying green or red fluorescent proteins under the control of both early and late promoters (vAcBacGFP and vAcBacDsRed). The reporter gene expression was detected 8 hours after the infection of vAcBacGFP and cells in early and late phases of infection could be distinguished by the fluorescence intensity of the expressed protein. Simultaneous infection with vAcBacGFP and vAcBacDsRed viruses each at 0.5 MOI resulted in 80% of infected cells co-expressing the two fluorescent proteins at 48 hours post infection (hpi), and subsequent infection with the two viruses resulted in similar co-infection rate. Most Sf9 cells were re-infectable within the first several hours post infection, but the re-infection rate then decreased to a very low level by 16 hpi. Our data demonstrate that Sf9 cells were easily super-infectable during baculovirus infection, and super-infection could occur simultaneously at the time of the primary infection or subsequently during secondary infection by progeny viruses. The efficiency of super-infection may explain the difficulties of baculovirus display library screening but would benefit the production of complex proteins requiring co-expression of multiple polypeptides.     

Disruption of YPS1 and PEP4 genes reduces proteolytic degradation of secreted HSA/PTH in Pichia pastoris GS115

Human serum albumin (HSA) and human parathyroid hormone (1-34) [PTH (1-34)] fusion protein [HSA/PTH (1-34)] is a promising long-acting form of PTH (1-34) for osteoporosis treatment. Secretory expression of intact HSA/PTH (1-34) in Pichia pastoris GS115 was accompanied by two degradation fragments, with molecular weights around 66 kDa, in addition to the well-known ~45 kDa HSA-truncated fragment, resulting in a low yield of intact protein. In this study, two internal cleavage sites were identified in the PTH (1-34) portion of the fusion protein by Western Blot analysis. To minimize proteolytic cleavages, several protease genes including PEP4 (encoding proteinase A), PRB1 (proteinase B) and seven YPSs genes (yapsin family members) were knocked out respectively by disruption of the individual genes and the selective combinations. Reduced degradation was observed by single disruption of either PEP4 gene or YPS1 gene, and the lowest level of degradation was observed in a pep4△yps1△ double disruptant. After 72 h of induction, more than 80 % of the HSA/PTH (1-34) secreted by the pep4△yps1△ double disruptant remained intact, in comparison to only 30 % with the wild-type strain.