Targeted protein degradation(TPD)has rapidly emerged as a therapeutic modality to eliminate previously undruggable proteins by repurposing the cell's endogenous protein degrada-tion machinery.However,the susceptibility of proteins for targeting by TPD approaches,termed"degradability",is largely unknown.Here,we developed a machine learning model,model-free anal-ysis of protein degradability(MAPD),to predict degradability from features intrinsic to protein tar-gets.MAPD shows accurate performance in predicting kinases that are degradable by TPD compounds[with an area under the precision-recall curve(AUPRC)of 0.759 and an area under the receiver operating characteristic curve(AUROC)of 0.775]and is likely generalizable to inde-pendent non-kinase proteins.We found five features with statistical significance to achieve optimal prediction,with ubiquitination potential being the most predictive.By structural modeling,we found that E2-accessible ubiquitination sites,but not lysine residues in general,are particularly associated with kinase degradability.Finally,we extended MAPD predictions to the entire proteome to find 964 disease-causing proteins(including proteins encoded by 278 cancer genes)that may be tractable to TPD drug development.

Chromatin immunoprecipitation sequencing (ChIP-seq) and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) have become essential technologies to effectively measure protein–DNA interactions and chromatin accessibility. However, there is a need for a scalable and reproducible pipeline that incorporates proper normalization between samples, correction of copy number variations, and integration of new downstream analysis tools. Here we present Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis (CoBRA), a modularized computational workflow which quantifies ChIP-seq and ATAC-seq peak regions and performs unsupervised and supervised analyses. CoBRA provides a comprehensive state-of-the-art ChIP-seq and ATAC-seq analysis pipeline that can be used by scientists with limited computational experience. This enables researchers to gain rapid insight into protein–DNA interactions and chromatin accessibility through sample clustering, differential peak calling, motif enrichment, comparison of sites to a reference database, and pathway analysis. CoBRA is publicly available online at https://bitbucket. org/cfce/cobra.

To investigate the freshness, high molecular weight substances, the determination of polypeptide, haemolysis and agglomeration, biological activity of Cervus and Cucumis polypeptide injection; to provide the direction for improving the quality of products for enterprises; furthermore, to provide reference for the revision of the quality standards of Cervus and Cucumis polypeptide injection. Firstly, we investigated the factors affecting the freshness of the injection, including biogenic amines, aflatoxins, the acid value and peroxide value of the melon seeds. The method of dansyl chloride pre-column derivatization-HPLC was used to determine the content of 8 biogenic amines in Cervus and Cucumis polypeptide injection. The method validation results showed good specificity, precision, linearity and recovery rates, which was suitable for the determination of biogenic amines in Cervus and Cucumis polypeptide injection. The results of sample determination showed that relatively higher concentrations of cadaverine were detected in the products from company B. The results of aflatoxins, acid value and peroxide value showed that the melon seeds from some companies had rancidity, mildew and other problems, indicating that the quality standards of multi-component biochemical drugs containing animal- and plant-derived components should be controlled in terms of freshness. Secondly, the methods for the determination of high molecular weight substances and polypeptides in the quality standard were improved. Tricine-SDS-PAGE electrophoresis was used instead of gel chromatography to determine the high molecular weight substances, which improved the accuracy of determination. The kits were used instead of folin-phenol for the determination of peptide content, which is easy to operate, specific and suitable for high-throughput sample determination. Finally, the haemolysis, agglomeration, and biological activity of Cervus and Cucumis polypeptide injection were studied. The results showed that no haemolysis and agglomeration were found in all samples, and the inhibitory effect of samples on THP-1 proliferation in vitro from different companies was different to some extent. In conclusion, the optimized quality standard is more suitable for the detection of Cervus and Cucumis polypeptide injection, and can lay the foundation for improving the safety of multi-component biochemical drugs.

Objective To identify gene mutations in the BCS1L gene in a patient with Bj(o)rnstad syndrome mainly manifesting as congenital pili torti and sensorineural hearing loss.Methods Clinical data were collected and DNA was extracted from the peripheral blood of the patient and her parents.All the exons and their flanking sequences of the BCS1L gene were amplified by PCR followed by Sanger sequencing,and the sequencing results were compared with the normal sequences.A few hairs were collected from the patient,and examined by the scanning electron microscope.Results There were two mutations in BCS1L gene in the patient,i.e.,a heterozygous nonsense mutation in exon 4 and a heterozygous missense mutation in exon 8.The nonsense mutation in exon 4,which caused a change from CGA to TGA at position 144 and resulted in the substitution of arginine by termination codon (p.R144*),was a novel mutation in the BCS1L gene causing Bj(o)rnstad syndrome,and had never been repotted in the literature.The missense mutation in exon 8 led to a change from CGC to CAC at position 306 and resulted in the substitution of arginine by histidine (p.R306H).The patient's mother only carried a heterozygous mutation c.430 C＞T (p.R144*) in exon 4 of the BCS1L gene,and her father only carried a heterozygous mutation c.917 G＞A (p.R306H) in exon 8 of the BCS1L gene.Scanning electron microscopy showed that flats,grooves and longitudinal twisting irregu larly appeared at intervals on the surface of hair shafts.Conclusions A novel mutation in the BCS1L gene,which causes a change from CGA to TGA at position 144 in the BCS1L gene and results in a premature termination codon,is firstly reported in a patient with Bj(o)rnstad syndrome,and the compound heterozygous mutations c.430 C＞T and c.917 G＞A in the BCS1L gene are associated with the clinical manifestations of the patient.Genetic analvsis is helpful for the diagnosis of Bj(o)rnstad syndrome.

BRAF is a serine/threonine kinase that harbors activating mutations in ∼7% of human malignancies and ∼60% of melanomas. Despite initial clinical responses to BRAF inhibitors, patients frequently develop drug resistance. To identify candidate therapeutic targets for BRAF inhibitor resistant melanoma, we conduct CRISPR screens in melanoma cells harboring an activating BRAF mutation that had also acquired resistance to BRAF inhibitors. To investigate the mechanisms and pathways enabling resistance to BRAF inhibitors in melanomas, we integrate expression, ATAC-seq, and CRISPR screen data. We identify the JUN family transcription factors and the ETS family transcription factor ETV5 as key regulators of CDK6, which together enable resistance to BRAF inhibitors in melanoma cells. Our findings reveal genes contributing to resistance to a selective BRAF inhibitor PLX4720, providing new insights into gene regulation in BRAF inhibitor resistant melanoma cells.

Objective To investigate the significance of Akt in the pathogenesis of psoriasis.Methods Tissue specimens were obtained from involved and uninvolved skin of 30 patients with progressive psoriasis vulgaris and normal skin of 20 human controls.Immunohistochemistry.immunobloting and kinase activity assay were performed to detect the expressions of Akt and phosphorylated Akt as well as Akt activities in these specimens.Immunostaining intensity Was assessed by optical density detection and the results of immunobiot and activity assay by grey scanning.Statistical analyses were performed by variance analysis and student's t test.Results As immunohistochemistry revealed.there was no significant difierence in Akt protein expression among normal epidermis,psoriatic epidermis and uninvolved epidermis(F=0.611,P＞0.05):the level of phosphorylated Akt in psoriatic epidermis was significantly higher than that in normal epidermis and psoriatic uninvolved epidermis(F=19.081.P＜0.01).while no significant difierence was observed between normal epidermis and psoriatic uninvolved epidermis (t=0.624.P＞0.05).Immunoblot showed a significant difierence in phosphorylated Akt(t=237.75.P＜0.01)but not in Akt(t=1.378,P＞0.05)between psoriatic involved epidermis and normal epidermis.In comparison with normal epidermis,the activity of Akt in psoriatic involved epidermis was increased significantly(t=138.44 1.P＜0.0 1).Conclusion The overproliferation of psoriatic keratinocytcs may be associated with increased activation of Akt.

In this study we successfully prepared desmoglein 1 and desmoglein 3 DNA probes by incorporation of Dig-dUTP during PCR amplification. Eleetrophoresis analysis showed that Dig labelled probes moved slower on the gel than PCR products not incorporated with Dig due to the enlargement of probe fragment. The results of Dot-blot showed that the prepared probes can be used for RNA analysis, and both probes have high specificity, The results provided basis for the quantitative and qualitative study of desmoglein gene expression in tissues or cells by means of in situ hybridization and Northern hybridization etc.

Objective To evaluate the production and regulation of platelet derived growth factor (PDGF) in the skin. Methods Normal human keratinocytes (NHKs) and human dermal fibroblasts (HDFs) were cultured, PDGF peptides were measured by ELISA and PDGF B chain mRNA was detected by Northern hybridization. Results The results showed that NHKs constitutively produced PDGF molecules, phorbol 12 myristate 13 acetate (PMA) inhibited PDGF production, while 1, 25 dihydroxyvitamin D 3 enhanced its production. TNF alpha, interferon ? and interleukin 1 alpha all failed to affect PDGF production. On the other hand, HDFs produced no PDGF molecule in spite of a low level of PDGF B chain mRNA expression in Northern hybridization, suggestting a post transcriptional blocking of PDGF production in HDFs. Conclusion The results obtained above indicate that epidermal keratinocytes may be the major PDGF generating cells, whereas dermal fibroblasts the PDGF responsive cells in the skin.

Objective To study the expression and regulation of interleukin 15 (IL 15) in epidermal keratinocytes. Methods The expression of IL 15 mRNA in cultured normal human keratinocytes (NHKs) and human squamous cell carcinoma cell line (HSC 5) was analysed, and the effect of dexamethasone on IL 15 mRNA expression was studied by using RT PCR and Northern blotting technique. Results The results showed that both NHKs and HSC 5 expressed IL 15 constitutively. The level of IL 15 mRNA was significantly decreased after the cells were cultured with 10 -6 M dexamethasone. Conclusion It is suggested that keratinocyte derived IL 15 might be involved in the development of certain inflammatory skin diseases.

Objective To study the expression of endothelin 1 (ET 1) mRNA in keratinocytes in patients with vitiligo. Methods Fourteen patients with progressive vitiligo were measured by hybridization in situ. Results Our results showed that the expression of ET 1 mRNA was markedly decreased. Conclusion The results revealed that decreased ET 1 expression may be associated with the pathogenesis of vitiligo. The cause and role of decreasing of ET 1 expression of keratinocyte in vitiligo lesion need to be studied further.