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Reprogramming of somatic cells to induced pluripotent stem cells, by overexpressing certain factors referred to as the reprogramming factors, can revolutionize regenerative medicine. To provide a coherent description of induced pluripotency from the gene regulation perspective, we use 35 microarray datasets to construct a reprogramming gene regulatory network. Comprising 276 nodes and 4471 links, the resulting network is, to the best of our knowledge, the largest gene regulatory network constructed for human fibroblast reprogramming and it is the only one built using a large number of experimental datasets. To build the network, a model that relates the expression profiles of the initial (fibroblast) and final (induced pluripotent stem cell) states is proposed and the model parameters (link strengths) are fitted using the experimental data. Twenty nine additional experimental datasets are collectively used to test the model/network, and good agreement between experimental and predicted gene expression profiles is found. We show that the model in conjunction with the constructed network can make useful predictions. For example, we demonstrate that our approach can incorporate the effect of reprogramming factor stoichiometry and that its predictions are consistent with the experimentally observed trends in reprogramming efficiency when the stoichiometric ratios vary. Using our model/network, we also suggest new (not used in training of the model) candidate sets of reprogramming factors, many of which have already been experimentally verified. These results suggest our model/network can potentially be used in devising new recipes for induced pluripotency with higher efficiencies. Additionally, we classify the links of the network into three classes of different importance, prioritizing them for experimental verification. We show that many of the links in the top ranked class are experimentally known to be important in reprogramming. Finally, comparing with other methods, we show that using our model is advantageous. [ABSTRACT FROM AUTHOR]

Purpose: Ischemia-reperfusion injury (IRI) is associated with significant patient mortality and morbidity. The complex cascade of IRI is incompletely understood, but inflammation is known to be a key mediator. In addition to the predominant innate immune responses, previous research has also indicated that αβ T cells contribute to IRI in various organ models. The aim of this study was to clarify the role αβ T cells play in IRI to the gut. Methods: Adult wild-type (WT) and αβ T cell-deficient mice were subjected to acute intestinal IRI with 30min ischemia followed by 4h reperfusion. The gene expression of pro-inflammatory cytokines was measured by qPCR, and the influx of leukocyte subpopulations in the gut was assessed via flow cytometry and histology. Pro-inflammatory cytokines in the serum were measured, and transaminases were assessed as an indicator of distant organ IRI. Results: Intestinal IRI led to an increased expression of pro-inflammatory cytokines in the gut tissue and an influx of leukocytes that predominantly consisted of neutrophils and macrophages. Furthermore, intestinal IRI increased serum IL-6, TNF-α, and ALT/AST levels. The αβ T cell-deficient mice did not exhibit a more significant increase in pro-inflammatory cytokines in the gut or serum following IR than the WT mice. There was also no difference between WT- and αβ T cell-deficient mice in terms of neutrophil infiltration or macrophage activation. Furthermore, the increase in transaminases was equal in both groups indicating that the level of distant organ injury was comparable. Conclusion: An increasing body of evidence demonstrates that αβ T cells play a key role in IRI. In the gut, however, αβ T cells are not pivotal in the first hours following acute IRI as deficiency does not impact cytokine production, neutrophil recruitment, macrophage activation, or distant organ injury. Thus, αβ T cells may be considered innocent bystanders during the acute phase of intestinal IRI. [ABSTRACT FROM AUTHOR]