Harm or reduction of podocytes is estimated for being accountable for about 90% of kidney ailments in people. To date a few hereditary kidney diseases are regarded which might be triggered by mutations in genes associated with the podocyte GBM interface, e. g. Alport syndrome. Hence, the podo cyte GBM interface is of central value in kidney biology and pathology. We constructed a protein interaction network Raf kinase inhibitor from the podocyte GBM interface based on expert awareness. We collected proteins and experimentally nicely described protein protein interactions of the podocyte GBM inter face by a extensive survey on the podocyte literature. The professional network includes 42 nodes and 33 edges. The proteins in the skilled network had been screened for more interaction component ners making use of the STRING database, to lengthen the professional network by even more experimentally verified interac tions involving not less than a single node on the network.
If not however existent during the network, the respective interac tion partners had been also extra. The extended network consists of 124 nodes and 206 edges. Podocyte cell lines really are a frequently employed instrument to study podocyte biology. Nevertheless, it is actually popular that podocyte cell lines are partially selleck inhibitor dedifferentiated as com pared to in vivo podocytes. To extract the primary differ ences involving the podocyte GBM interface of in vivo vs. cultured podocytes, we mapped microarray gene expression information of in vivo and cultured mouse podo cytes onto the extended network shown in Figure four. We implemented publicly available microarray data generated from a podocyte cell line and from in vivo podocytes, which were isolated as podocalyxin constructive cells in a cell suspension of enzymatically digested mouse glomeruli. By condensing a protein interaction network using gene expression data, we implicitly assume that protein abundance is correlated to gene expression.
We log transformed and quantile regular ized these information. By interactive use of ExprEssence we eliminated 94% of

the edges maintaining the 3% quantiles from the most strongly differentially altered interactions concerning in vivo and cultured podocytes. ExprEssence uncovered the interactions of semaphorin three d, fibroblast development component receptor one and Gipc1 PDZ domain containing protein with neuropilin 1 along with the interaction between pinch 2 as well as a parvin are most strongly dimin ished in cultured podocytes as when compared with the in vivo condition. On the flip side, the interac tions of integrin b3 and myelin connected glycoprotein with fibronectin 1 are most strongly up regulated in cultured podocytes. As Mag had up to now not been reported as being a podocyte protein, we analyzed Mag expression by RT PCR in the podocyte cell line.