KinasePhos 3.0:Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites

The purpose of this work is to enhance KinasePhos,a machine learning-based kinasespecific phosphorylation site prediction tool.Experimentally verified kinase-specific phosphorylation data were collected from PhosphoSitePlus,UniProtKB,the GPS 5.0,and Phospho.ELM.In total,41,421 experimentally verified kinase-specific phosphorylation sites were identified.A total of 1380 unique kinases were identified,including 753 with existing classification information from KinBase and the remaining 627 annotated by building a phylogenetic tree.Based on this kinase classification,a total of 771 predictive models were built at the individual,family,and group levels,using at least 15 experimentally verified substrate sites in positive training datasets.The improved models demonstrated their effectiveness compared with other prediction tools.For example,the prediction of sites phosphorylated by the protein kinase B,casein kinase 2,and protein kinase A families had accuracies of 94.5%,92.5%,and 90.0%,respectively.The average prediction accuracy for all 771 models was 87.2%.For enhancing interpretability,the SHapley Additive exPlanations(SHAP)method was employed to assess feature importance.The web interface of KinasePhos 3.0 has been redesigned to provide comprehensive annotations of kinase-specific phosphorylation sites on multiple proteins.Additionally,considering the large scale of phosphoproteomic data,a downloadable prediction tool is available at https://awi.cuhk.edu.cn/KinasePhos/download.html or https://github.com/tom-209/KinasePhos-3.0-executable-file.

Kinectin 1 promotes the growth of triple-negative breast cancer via directly co-activating NF-kappaB/p65 and enhancing its transcriptional activity

Triple-negative breast cancer(TNBC)is the most challenging subtype of breast cancer.Various endeavor has been made to explore the molecular biology basis of TNBC.Herein,we reported a novel function of factor Kinectin 1(KTN1)as a carcinogenic promoter in TNBC.KTN1 expression in TNBC was increased compared with adjacent tissues or luminal or Her2 subtypes of breast cancer,and TNBC patients with high KTN1 expression have poor prognosis.In functional studies,knockdown of KTN1 inhibited the proliferation and invasiveness of TNBC both in vitro and in vivo,while overexpression of KTN1 promoted cancer cell proliferation and invasiveness.RNA-seq analysis revealed that the interaction of cytokine-cytokine receptor,particularly CXCL8 gene,was upregulated by KTN1,which was supported by the further experiments.CXCL8 depletion inhibited the tumorigenesis and progression of TNBC.Additionally,rescue experiments validated that KTN1-mediated cell growth acceleration in TNBC was dependent on CXCL8 both in vitro and in vivo.Furthermore,it was found that KTN1 enhanced the phosphorylation of NF-κB/p65 protein at Ser536 site,and specifically bound to NF-κB/p65 protein in the nucleus and cytoplasm of cells.Moreover,the transcription of CXCL8 gene was directly upregulated by the complex of KTN1 and NF-κB/p65 protein.Taken together,our results elucidated a novel mechanism of KTN1 gene in TNBC tumorigenesis and progression.KTN1 may be a potential molecular target for the development of TNBC treatment.