Protein-Protein Interaction Sites Prediction Using Batch Normalization Based CNNs and Oversampling Method Borderline-SMOTE.

The recognition of protein-protein interaction sites (PPIs) is beneficial for the interpretation of protein functions and the development of new drugs. Traditional biological experiments to identify PPI sites are expensive and inefficient, leading to the generation of various computational methods to predict PPIs. However, the accurate prediction of PPI sites remains a big challenge due to the existence of the sample imbalance issue. In this work, we design a novel model that combines convolutional neural networks (CNNs) with Batch Normalization to predict PPI sites, and employ an oversampling technique Borderline-SMOTE to address the sample imbalance issue. In particular, to better characterize the amino acid residues on the protein chains, we employ a sliding window approach for feature extraction of target residues and their contextual residues. We verify the effectiveness of our method by comparing our method with the existing state-of-the-art schemes. The performance validations of our method on three public datasets achieve accuracies of 88.6%, 89.9%, and 86.7%, respectively, all showing improved accuracies compared with the existing schemes. Moreover, the ablation experiment results suggest that Batch Normalization can greatly improve the generalization and the prediction stability of our model.

Homeobox D9 drives the malignant phenotypes and enhances the Programmed death ligand-1 expression in non-small cell lung cancer cells via binding to Angiopoietin-2 promoter.

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death worldwide. Homeobox D9 (HOXD9), a member of the HOX family of transcription factors, plays a driver role in development of multiple cancers. Angiopoietin-2 (ANGPT2) is reportedly to facilitate angiogenesis, growth and metastasis in various cancers, including lung cancer. In addition, blocking ANGPT2 can effectively improve cancer immunotherapy via downregulation of Programmed death ligand-1 (PD-L1). The purpose of this study was to elucidate the role of HOXD9 in NSCLC and whether ANGPT2 is required for HOXD9-mediated malignant behaviors of NSCLC cells. By performing a series of in vitro functional experiments, we found that knockdown of HOXD9 induced proliferative inhibition, cell cycle G1 arrest, apoptosis, migratory suppression and invasive repression of NSCLC cells. Reduced PD-L1 expression in NSCLC cells was observed after HOXD9 silencing. Besides, HOXD9 deletion decreased the expression of ANGPT2 in NSCLC cells. In line with this, HOXD9 overexpression led to opposite alteration in NSCLC cells. Mechanistically, ANGPT2 was transcriptionally activated by HOXD9. Forced expression of ANGPT2 significantly regulated HOXD9-mediated malignant phenotypes, and enhanced PD-L1 expression of NSCLC cells. Our results expressing HOXD9 may function as an oncogene in NSCLC via trans-activation of ANGPT2.

Prognostic significance of PD-L1 expression on cell-surface vimentin-positive circulating tumor cells in gastric cancer patients.

Although circulating tumor cells (CTCs) have shown promise as potential biomarkers for diagnostic and prognostic assessment in gastric cancer (GC), determining the predictive and prognostic value of programmed death-ligand 1 (PD-L1)-positive CTCs in patients with GC is a challenge. Here, we identified that the expression of total vimentin (VIM) protein was positively correlated with PD-L1 and inhibited CD8+ T-cell activation in patients with GC according to bioinformatics analysis. Notably, coexpression of PD-L1 and cell-surface VIM (CSV) was detected by immunofluorescence and immunohistochemistry assay in locally advanced GC tumor specimens and metastatic lymph nodes. Likewise, CSV expression level was significantly decreased after transiently knocking down PD-L1 in GC cell lines. Based on our established CTC detection platform, CTCs were isolated from peripheral blood samples collected from 70 patients (38 resectable and 32 unresectable) with GC using magnetic positive selection and a CSV-specific monoclonal antibody, 84-1. CSV+ PD-L1+ CTCs were observed in 50 of 70 (71%) GC patient samples, ranging from 0 to 261 mL-1 . A higher number of CSV+ PD-L1+ CTCs were significantly associated with a short survival duration and poor therapeutic response. This study demonstrated that detection of PD-L1+ CTCs using a CSV-enrichment method has promising value as a clinically relevant prognostic marker for GC.

Establishment and biological characteristics of acquired gefitinib resistance in cell line NCI-H1975/gefinitib-resistant with epidermal growth factor receptor T790M mutation.

Non­small cell lung cancer (NSCLC) cells harboring mutations in the epidermal growth factor receptor (EGFR) gene initially respond well to EGFR tyrosine kinase inhibitors (TKI), including gefitinib. However the tumor cells will invariably develop acquired resistance to the drug. The EGFR T790M mutation is generally considered to be the molecular genetic basis of acquired TKI resistance. The present study aimed to explore how the T790M mutation induces tumor cells to escape inhibition by TKI treatment. An acquired gefitinib­resistant cell line (NCI­H1975/GR) was generated from the NCI­H1975 human NSCLC cell line, which harbors the sensitive L858R and resistant T790M mutations of EGFR. The resistant cell line was established by exposing the cells intermittently to increasing concentrations of gefitinib. The mechanisms by which NSCLC acquires resistance to TKIs based on the T790M mutation, were investigated by detecting the protein expression levels of the EGFR/Kirsten rat sarcoma viral oncogene homolog (KRAS)/v­Raf murine sarcoma viral oncogene homolog B (BRAF) transduction pathway, and epithelial­mesenchymal transition (EMT) with immunocytochemistry. The resistance of the NCI­H1975/GR cells to gefitinib was 2.009­fold, as compared with the parent cells; however, the protein expression levels of EGFR, KRAS and BRAF were lower in the resistant cells. Some mesenchymal morphology was observed in the NCI­H1975/GR cells, alongside a decreasing E­cadherin expression and increasing vimentin expression. These results suggest that the reactivation of the EGFR/KRAS/BRAF transduction pathway was not detected in the NCI­H1975/GR cells. EMT may have an important role in the development of acquired resistance to EGFR­TKIs in NSCLC cells with sensitivity and resistance mutations.

The reverse effect of X-ray irradiation on acquired gefitinib resistance in non-small cell lung cancer cell line NCI-H1975 in vitro.

The clinical efficacy of gefitinib in the treatment of non-small cell lung cancer (NSCLC) with mutations in exon 18, 19 or 21 of epidermal growth factor receptor (EGFR) is limited by the acquired resistance to the drug. To explore whether X-ray irradiation could reverse the acquired gefitinib resistance in NSCLC cell in vitro. We chose a human NSCLC cell line NCI-H1975 to establish acquired gefitinib-resistant cell line named as NCI-H1975/GR. NCI-H1975/GR was irradiated with X-ray and then named as NCI-H1975/GR/XR. In the three cell lines, subsequently cell growth curves and cell population doubling time were calculated by cell proliferation assay, the changes of cell viability were evaluated by trypan blue dye exclusion method and MTT assay, the cell cycle distribution and apoptosis were investigated by flow cytometry, the expressions of E-cadherin and vimentin used to indicate epithelial-mesenchymal transition (EMT) were determined by western blot analysis, the protein expressions in EGFR/KRAS/BRAF transduction pathway were detected by immunocytochemistry, and the mutations of EGFR, KRAS and BRAF were detected by high resolution melting analysis and direct sequencing. We found that the X-ray irradiation enhanced the growth inhibitory effects of gefitinib on the acquired gefitinib-resistant cell line. Of NCI-H1975/GR/XR following gefitinib treatment, the IC50 decreased significantly, the cell proportion of phase G0/G1 was slightly higher, and the apoptosis cell proportion was significantly higher than those of NCI-H1975/GR. In addition, the reversal of EMT being present in NCI-H1975/GR cells was likely appearing in NCI-H1975/GR/XR cells. These results indicated that the acquired gefitinib resistance could be reversed by X-ray irradiation in NSCLC cell line NCI-H1975 harboring both the L858R and T790M mutation in vitro.

A graphene-based smart catalytic system with superior catalytic performances and temperature responsive catalytic behaviors.

We have successfully developed a unique graphene-based smart catalytic system which consists of the graphene supported Au-Pt bimetallic nanocatalyst with a well-defined core-shell structure and a dextran-based temperature-responsive polymer. The unique catalytic system possesses excellent catalytic performances and the catalytic activities could be readily switched on or off at different temperature windows.

Quadruple-responsive nanocomposite based on dextran-PMAA-PNIPAM, iron oxide nanoparticles, and gold nanorods.

A quadruple-responsive nanocomposite that responds to temperature, pH, magnetic field, and NIR is obtained by incorporating superparamagnetic iron oxide nanoparticles (SPIONs) and gold nanorods (AuNRs) into a dextran-based smart copolymer network. The dual-sensitive copolymer is prepared by sequential RAFT polymerization of methacrylic acid and N-isopropylacrylamide from trithiocarbonate groups linked to dextran in one pot. These functionalized nanocomposites with superior stability can respond to the four stimuli mentioned above well. As evidenced by UV-vis and TEM measurements, the temperature-induced unusual blue-shift in the longitudinal plasmon band is possibly due to the side-to-side assembly of AuNRs.

Temperature- and redox-directed multiple self assembly of poly(N-isopropylacrylamide) grafted dextran nanogels.

Poly(N-isopropylacrylamide) (PNIPAAm) grafted dextran nanogels with dodecyl and thiol end groups have been synthesized by RAFT process. Dodecyl-terminated polymers (DexPNI) can be readily dissolved in water and further self assemble into ordered stable nanostructures through direct noncovalent interactions at room temperature. SEM, AFM and DLS measurements confirm the formation of spherical nanogels at hundred-nanometer scales. The elevation of environment temperature will indirectly result in the formation of collapsed nanostructures due to the LCST phase transition of PNIPAAm side chains. Turbidimetry results show that the phase transition behaviors of DexPNI are greatly dependent on PNIPAAm chain length and polymer concentration: increasing PNIPAAm chain length and polymer concentration both lead to lower LCSTs and sharper phase transitions. Moreover, the dodecyl-terminated polymers can transform into thiol-terminated versions by aminolysis of trithiocarbonate groups, and further into chemical (disulfide) cross-linked versions (SS-DexPNI) by oxidation. SS-DexPNI nanogels have "doubled" chain length of PNIPAAm, and hence sharper phase transitions. In situ DLS measurements of the evolution of hydrodynamic radius attest that the self assembly of SS-DexPNI nanogels can be selectively directed by the change in either external temperature or redox potential. These nanogels thus are promising candidates for triggered intracellular delivery of encapsulated cargo. We can also expect that the polymer can be noncovalently (by dodecyl end groups) or covalently (by thiol end groups) coated on a series of nanomaterials (e.g., carbon nanotubes, graphene, gold nanomaterials) to build a variety of novel smart, and robust nanomaterials.

Gold Nanoparticles Functionalized by a Dextran-Based pH- and Temperature-Sensitive Polymer.

A dextran-based dual-sensitive polymer is employed to endow gold nanoparticles with stability and pH- and temperature-sensitivity. The dual-sensitive polymer is prepared by RAFT polymerization of N-isopropylacrylamide from trithiocarbonate groups linked to dextran and succinoylation of dextran after polymerization. The functionalized nanoparticles show excellent stability under various conditions and can be stored in powder-form. UV and DLS measurements confirm that the temperature-induced optical changes and aggregation behaviors of the particles are strongly dependent on pH.