Targeting an oncogenic kinase/phosphatase signaling network for cancer therapy

Protein kinases and phosphatases signal by phosphorylation and dephosphorylation to precisely control the activities of their individual and common substrates for a coordinated cellular outcome. In many situations, a kinase/phosphatase complex signals dynamically in time and space through their reciprocal regulations and their cooperative actions on a substrate. This complex may be essential for malignant transformation and progression and can therefore be considered as a target for therapeutic intervention. p38 is a unique MAPK family member that contains a PDZ motif at its C-terminus and interacts with a PDZ domain-containing protein tyrosine phosphatase PTPH1. This PDZ-coupled binding is required for both PTPH1 dephosphorylation and inactivation of p38 and for p38 phosphorylation and activation of PTPH1. Moreover, the p38/PTPH1 complex can further regulate their substrates phosphorylation and dephosphorylation, which impacts Ras transformation, malignant growth and progression, and therapeutic response. This review will use the p38/PTPH1 signaling network as an example to discuss the potential of targeting the kinase/phosphatase signaling complex for development of novel targeted cancer therapy.

Comparative Analysis of Human Genes Frequently and Occasionally Regulated by mA Modification / 基因组蛋白质组与生物信息学报·英文版

The mA modification has been implicated as an important epitranscriptomic marker, which plays extensive roles in the regulation of transcript stability, splicing, translation, and localization. Nevertheless, only some genes are repeatedly modified across various conditions and the principle of mA regulation remains elusive. In this study, we performed a systems-level analysis of human genes frequently regulated by mA modification (mAfreq genes) and those occasionally regulated by mA modification (mAocca genes). Compared to the mAocca genes, the mAfreq genes exhibit gene importance-related features, such as lower dN/dS ratio, higher protein-protein interaction network degree, and reduced tissue expression specificity. Signaling network analysis indicates that the mAfreq genes are associated with downstream components of signaling cascades, high-linked signaling adaptors, and specific network motifs like incoherent feed forward loops. Moreover, functional enrichment analysis indicates significant overlaps between the mAfreq genes and genes involved in various layers of gene expression, such as being the microRNA targets and the regulators of RNA processing. Therefore, our findings suggest the potential interplay between mA epitranscriptomic regulation and other gene expression regulatory machineries.

Transduction motif analysis of gastric cancer based on a human signaling network

To investigate signal regulation models of gastric cancer, databases and literature were used to construct the signaling network in humans. Topological characteristics of the network were analyzed by CytoScape. After marking gastric cancer-related genes extracted from the CancerResource, GeneRIF, and COSMIC databases, the FANMOD software was used for the mining of gastric cancer-related motifs in a network with three vertices. The significant motif difference method was adopted to identify significantly different motifs in the normal and cancer states. Finally, we conducted a series of analyses of the significantly different motifs, including gene ontology, function annotation of genes, and model classification. A human signaling network was constructed, with 1643 nodes and 5089 regulating interactions. The network was configured to have the characteristics of other biological networks. There were 57,942 motifs marked with gastric cancer-related genes out of a total of 69,492 motifs, and 264 motifs were selected as significantly different motifs by calculating the significant motif difference (SMD) scores. Genes in significantly different motifs were mainly enriched in functions associated with cancer genesis, such as regulation of cell death, amino acid phosphorylation of proteins, and intracellular signaling cascades. The top five significantly different motifs were mainly cascade and positive feedback types. Almost all genes in the five motifs were cancer related, including EPOR, MAPK14, BCL2L1, KRT18, PTPN6, CASP3, TGFBR2, AR, and CASP7. The development of cancer might be curbed by inhibiting signal transductions upstream and downstream of the selected motifs.

Application of single cell network profiling / 中国药理学通报

SCNP( single cell network profiling) assay can depict the characters of signal pathway network without isolating the dif-ferent cells in advance in complex tissues. It will promote the disease mechanism elucidating, disease classification, diagnosis, and therapeutic regimen at cell level. Drug screening and ration-al personalized treatment will also be improved.

The Important Role of Three Auxiliary Factors of Mammalian Aminoacyl-tRNA Synthetase Complex in The Cellular Signaling Network / 生物化学与生物物理进展

Aminoacyl-tRNA synthetase catalyzing the first reaction of protein biosynthesis. In mammalian cells, eight aminoacyl-tRNA synthetases (aaRSs) and three auxiliary protein factors form a macromolecular aminoacyl-tRNA synthetases complex (aaRS complex). The three nonsynthetase protein factors, namely, p43, p38, and p18 were found to be involved in many other important life activities besides their roles in the complex. The auxiliary factor p43 was the precursor of endothelial monocyte activating polypeptideⅡ (EMAPⅡ), which involved in angiogenesis and apoptosis. The auxiliary factor p38 was crucial for the development of lung, and its abnormal accumulation in neuron would be related to the Parkinson’s disease. The auxiliary factor p38 and p18 could promote the repair of DNA damage via different pathways in a highly organized way. All these breakthroughs enhance our understanding about the interaction between the aaRS complex and the macromolecular signaling network and promote the studies on this field.

Transcription Factors in the Cellular Signaling Network as Prime Targets of Chemopreventive Phytochemicals / Journal of the Korean Cancer Association, 대한암학회지

Accumulating evidence from epidemiologic and laboratory studies support an inverse relationship between a regular consumption of fruits and vegetables and the risk of specific cancers. Numerous phytochemicals derived from edible plants have been reported to possess ability to interfere with a specific stage of carcinogenic process. Multiple mechanisms have been proposed to account for the anti-carcinogenic actions of dietary constituents, but more attention has recently focussed on intracellular signaling cascades as common molecular targets of a wide variety of chemopreventive phytochemicals.