Oxysterol-binding proteins: functions in cell regulation beyond lipid metabolism

Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation

MOTIVATION

Functional relationship networks, which summarize the probability of co-functionality between any two genes in the genome, could complement the reductionist focus of modern biology for understanding diverse biological processes in an organism. One major limitation of the current networks is that they are static, while one might expect functional relationships to consistently reprogram during the differentiation of a cell lineage. To address this potential limitation, we developed a novel algorithm that leverages both differentiation stage-specific expression data and large-scale heterogeneous functional genomic data to model such dynamic changes. We then applied this algorithm to the time-course RNA-Seq data we collected for ex vivo human erythroid cell differentiation.

RESULTS

Through computational cross-validation and literature validation, we show that the resulting networks correctly predict the (de)-activated functional connections between genes during erythropoiesis. We identified known critical genes, such as HBD and GATA1, and functional connections during erythropoiesis using these dynamic networks, while the traditional static network was not able to provide such information. Furthermore, by comparing the static and the dynamic networks, we identified novel genes (such as OSBP2 and PDZK1IP1) that are potential drivers of erythroid cell differentiation. This novel method of modeling dynamic networks is applicable to other differentiation processes where time-course genome-scale expression data are available, and should assist in generating greater understanding of the functional dynamics at play across the genome during development.

AVAILABILITY AND IMPLEMENTATION

The network described in this article is available at http://guanlab.ccmb.med.umich.edu/stageSpecificNetwork.

Organelle biogenesis and interorganellar connections: Better in contact than in isolation

Membrane contact sites (MCSs) allow the exchange of molecules and information between organelles, even when their membranes cannot fuse directly. In recent years, a number of functions have been attributed to these contacts, highlighting their critical role in cell homeostasis. Although inter-organellar connections typically involve the endoplasmic reticulum (ER), we recently reported the presence of a novel MCSs between melanosomes and mitochondria. Melanosome-mitochondrion contacts appear mediated by fibrillar bridges resembling the protein tethers linking mitochondria and the ER, both for their ultrastructural features and the involvement of Mitofusin 2. The frequency of these connections correlates spatially and timely with melanosome biogenesis, suggesting a functional link between the 2 processes and in general that organelle biogenesis in the secretory pathway requires interorganellar crosstalks at multiple steps. Here, we summarize the different functions attributed to MCSs, and discuss their possible relevance for the newly identified melanosome-mitochondrion liaison.

Cross-talk between liver and intestine in control of cholesterol and energy homeostasis

A major hurdle for organisms to dispose of cholesterol is the inability to degrade the sterol nucleus which constitutes the central part of the molecule. Synthesis of the sterol nucleus requires a complex, energy costly, metabolic pathway but also generates a diverse array of intermediates serving crucial roles in cellular energy metabolism and signal transduction. This may be the reason why this complex pathway has survived evolutionary pressure. The only way to get rid of substantial amounts of cholesterol is conversion into bile acid or direct excretion of the sterol in the feces. The lack of versatility in disposal mechanisms causes a lack of flexibility to regulate cholesterol homeostasis which may underlie the considerable human pathology linked to cholesterol removal from the body. Export of cholesterol from the body requires an intricate communication between intestine and the liver. The last decade this inter-organ cross talk has been focus of intense research leading to considerable new insight. This novel information on particular the cross-talk between liver and intestine and role of bile acids as signal transducing molecules forms the focus of this review.