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qPCR results after ASO (5717 and 5608) treatment of 2 lncRNAs in caki-2 and 786-O cell lines.Three or six PCR by-wells were prepared for each sample. NC, negative control.

Supplementary Figure 1. An overview of the study workflow; Supplementary Figure 2. The principal components analyses (PCA) of samples in the discovery stage and reference samples from the 1000 Genomes Project data. Supplementary Figure 3. Manhattan plots of the genome-wide P values from the association tests on HBV-related HCC. Supplementary Figure 4. Quantile-quantile plots of the observed P values from the association tests on HBV-related HCC. Supplementary Figure 5. Forest plots for rs10272859 across all studies. Supplementary Figure 6. Expression levels of CDK14 mRNA were significantly higher in HCC tissues compared with adjacent non-tumor liver tissues. Supplementary Figure 7. The at-risk G allele of rs10272859 was significantly associated with higher mRNA levels of CDK14 in liver tissues based on the TCGA data. Supplementary Figure 8. The SNPs at 7q21.13 interact physically with the promoter region of CDK14 in GM12878 cells. Supplementary Figure 9. Kaplan-Meier estimates of the overall survival time for the HCC patients stratified by CDK14 mRNA expression levels. Supplementary Figure 10. Kaplan-Meier estimates of disease-free survival time for patients with HBV-related HCC stratified by genotypes of rs10272859. Supplementary Table 1. Summary description of the populations used in this study. Supplementary Table 2. Summary of the quality controls in proband-parent trios. Supplementary Table 3. Summary of SNP imputation in the discovery stage. Supplementary Table 4. The amount of SNPs with various P values in TDT for the 189 trios in the discovery stage. Supplementary Table 5. Summary of the SNPs that have been reported significantly associated with HBV-related HCC in previous GWASs. Supplementary Table 6. Summary of SNPs that have been reported to be significantly associated with HBV-related phenotypes in previous GWASs. Supplementary Table 6. Summary of SNPs that have been reported to be significantly associated with HBV-related phenotypes in previous GWASs (Continued). Supplementary Table 7. Summary of the top 15 SNPs in the discovery stage. Supplementary Table 8. Primers and probes used in this study. Supplementary Table 9. Summary of the replication studies for the 14 SNPs newly identified in the discovery stage. Supplementary Table 10. Stratification analyses of rs10272859 by gender and age. Supplementary Table 11. The associations between genotypes of rs10272859 and mRNA levels of nearby genes. Supplementary Table 12. The predicted functional relevance of rs10272859 and the other 74 SNPs in strong linkage disequilibrium with rs10272859 at the ~110 Kb region of 7q21.13. Supplementary Table 13. Details for the genotypes of rs10272859 and the prognosis of patients with HBV-related HCC. Supplementary Table 14. Multivariate analyses of overall survival time and disease-free survival time of patients with HBV-related HCC. Supplementary Table 15. Genotype distribution of rs10272859 across TNM stages in patients with HBV-related HCC. Supplementary Table 16. Powers for various genetic effects and various minor allele frequencies. Supplementary Table 17. The allele and genotype frequencies of rs10272859 in different populations.

Table S3, S5-S7, S10-S18, S21

Association between gene expression and dependency

Supplementary Figures and Figure Legends

Clear cell renal cell carcinoma (ccRCC) frequently features a high level of tumor heterogeneity. Elucidating the chromatin landscape of ccRCC at the single-cell level could provide a deeper understanding of the functional states and regulatory dynamics underlying the disease. Here, we performed single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) on 19 ccRCC samples, and whole-exome sequencing was used to understand the heterogeneity between individuals. Single-cell transcriptome and chromatin accessibility maps of ccRCC were constructed to reveal the regulatory characteristics of different tumor cell subtypes in ccRCC. Two long noncoding RNAs (RP11-661C8.2 and CTB-164N12.1) were identified that promoted the invasion and migration of ccRCC, which was validated with in vitro experiments. Taken together, this study comprehensively characterized the gene expression and DNA regulation landscape of ccRCC, which could provide new insights into the biology and treatment of ccRCC.Significance:A comprehensive analysis of gene expression and DNA regulation in ccRCC using scATAC-seq and scRNA-seq reveals the DNA regulatory programs of ccRCC at the single-cell level.

Activation of transcription factors is a key driver event in cancer. We and others have recently reported that the Krüppel-like transcription factor KLF5 is activated in multiple epithelial cancer types including squamous cancer and gastrointestinal adenocarcinoma, yet the functional consequences and the underlying mechanisms of this activation remain largely unknown. Here we demonstrate that activation of KLF5 results in strongly selective KLF5 dependency for these cancer types. KLF5 bound lineage-specific regulatory elements and activated gene expression programs essential to cancer cells. HiChIP analysis revealed that multiple distal KLF5 binding events cluster and synergize to activate individual target genes. Immunoprecipitation-mass spectrometry assays showed that KLF5 interacts with other transcription factors such as TP63 and YAP1, as well as the CBP/EP300 acetyltransferase complex. Furthermore, KLF5 guided the CBP/EP300 complex to increase acetylation of H3K27, which in turn enhanced recruitment of the bromodomain protein BRD4 to chromatin. The 3D chromatin architecture aggregated KLF5-dependent BRD4 binding to activate polymerase II elongation at KLF5 target genes, which conferred a transcriptional vulnerability to proteolysis-targeting chimera–induced degradation of BRD4. Our study demonstrates that KLF5 plays an essential role in multiple epithelial cancers by activating cancer-related genes through 3D chromatin loops, providing an evidence-based rationale for targeting the KLF5 pathway.Significance:An integrative 3D genomics methodology delineates mechanisms underlying the function of KLF5 in multiple epithelial cancers and suggests potential strategies to target cancers with aberrantly activated KLF5.

Details of each sample

Purpose: Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. In China, chronic hepatitis B virus (HBV) infection remains the major risk factor for HCC. In this study, we performed a genome-wide association study (GWAS) among Chinese populations to identify novel genetic loci contributing to susceptibility to HBV-related HCC.Experimental Design: GWAS scan is performed in a collection of 205 HBV-related HCC trios (each trio includes an affected proband and his/her both parents), and 355 chronic HBV carriers with HCC (cases) and 360 chronic HBV carriers without HCC (controls), followed by two rounds of replication studies totally consisting of 3,796 cases and 2,544 controls.Results: We identified a novel association signal within the CDK14 gene at 7q21.13 (index rs10272859, OR = 1.28, P = 9.46 × 10−10). Furthermore, we observed that the at-risk rs10272859[G] allele was significantly associated with higher mRNA expression levels of CDK14 in liver tissues. Chromosome conformation capture assays in liver cells confirmed that a physical interaction exists between the promoter region of CDK14 and the risk-associated SNPs in strong linkage disequilibrium with the index rs10272859 at 7q21.13. This index rs10272859 also showed significant association with the survival of HCC patients.Conclusions: Our findings highlight a novel locus at 7q21.13 conferring both susceptibility and prognosis to HBV-related HCC, and suggest the CDK14 gene to be the functional target of the 7q21.13 locus. Clin Cancer Res; 24(4); 906–15. ©2017 AACR.

Clear cell renal cell carcinoma (ccRCC) frequently features a high level of tumor heterogeneity. Elucidating the chromatin landscape of ccRCC at the single-cell level could provide a deeper understanding of the functional states and regulatory dynamics underlying the disease. Here, we performed single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) on 19 ccRCC samples, and whole-exome sequencing was used to understand the heterogeneity between individuals. Single-cell transcriptome and chromatin accessibility maps of ccRCC were constructed to reveal the regulatory characteristics of different tumor cell subtypes in ccRCC. Two long noncoding RNAs (RP11-661C8.2 and CTB-164N12.1) were identified that promoted the invasion and migration of ccRCC, which was validated with in vitro experiments. Taken together, this study comprehensively characterized the gene expression and DNA regulation landscape of ccRCC, which could provide new insights into the biology and treatment of ccRCC.Significance:A comprehensive analysis of gene expression and DNA regulation in ccRCC using scATAC-seq and scRNA-seq reveals the DNA regulatory programs of ccRCC at the single-cell level.

To identify hepatocellular carcinoma (HCC)-implicated long noncoding RNAs (lncRNAs), we performed an integrative omics analysis by integrating mRNA and lncRNA expression profiles in HCC tissues. We identified a collection of candidate HCC-implicated lncRNAs. Among them, we demonstrated that an lncRNA, which is named as p53-stabilizing and activating RNA (PSTAR), inhibits HCC cell proliferation and tumorigenicity through inducing p53-mediated cell cycle arrest. We further revealed that PSTAR can bind to heterogeneous nuclear ribonucleoprotein K (hnRNP K) and enhance its SUMOylation and thereby strengthen the interaction between hnRNP K and p53, which ultimately leads to the accumulation and transactivation of p53. PSTAR is down-regulated in HCC tissues, and the low PSTAR expression predicts poor prognosis in patients with HCC, especially those with wild-type p53. Conclusion: This study sheds light on the tumor suppressor role of lncRNA PSTAR, a modulator of the p53 pathway, in HCC.

A recent study in Nature (Szczerba et al. 2019;566:553–557) reports that the association of neutrophils with circulating tumor cells (CTCs) in the blood of patients with breast cancer can promote CTC proliferation and metastasis. These findings reveal a new mechanism by which the innate immune system may be co-opted to drive tumor progression.

Objective— To investigate the dietary characteristics and nutritional health status of cadets in air force youth aviation school. Methods— The 24-h dietary survey was used to investigate the dietary structure. The body composition index and blood biochemical indexes were measured to evaluate their health status. Results— According to the dietary guidelines for Chinese residents, the intake of fruits was seriously insufficient, reaching only 53.48%–80.23%. The intakes of sodium, potassium and phosphorus were high, calcium, iron, zinc and iodine were low. Folic acid intake reached 50.58% of the recommended amount of Chinese residents. The energy supply for breakfast was 23.97%, which was lower than the recommended amount, while the dinner was higher. Carbohydrate provided 1163.6 kcal (39.80%), which was lower than standard recommended. The proportion of protein intake from animal origin was slightly higher than the upper limit (50%) recommended by military standard. Among the blood biochemical indexes, only VD (25-OH) was low. Conclusions— The dietary structure of the cadets is not reasonable, and the intake of minerals and the energy supply ratio of the three nutrients are unbalanced. The overall nutritional health status was good, individual students had malnutrition.

More efficient biomarkers are needed to facilitate the early detection of hepatocellular carcinoma (HCC). We aimed to identify candidate biomarkers for HCC detection by proteomic analysis. First, we performed a global proteomic analysis of 10 paired HCC and non-tumor tissues. Then, we validated the top-ranked proteins by targeted proteomic analyses in another tissue cohort. At last, we used enzyme-linked immunosorbent assays to validate the candidate biomarkers in multiple serum cohorts including HCC cases (HCCs), cirrhosis cases (LCs), and normal controls (NCs). We identified and validated 33 up-regulated proteins in HCC tissues. Among them, eight secretory or membrane proteins were further evaluated in serum, revealing that aldo–keto reductase family 1 member B10 (AKR1B10) and cathepsin A (CTSA) can distinguish HCCs from LCs and NCs. The area under the curves (AUCs) were 0.891 and 0.894 for AKR1B10 and CTSA, respectively, greater than that of alpha-fetoprotein (AFP; 0.831). Notably, combining the three proteins reached an AUC of 0.969, which outperformed AFP alone (P

Mastermind proteins are required for transcription of Notch target genes, yet the molecular basis for mastermind function remains incompletely understood. Previous work has shown that Notch can induce transcriptional responses by binding to promoters but more often by binding to enhancers, with HES4 and DTX1 as representative mammalian examples of promoter and enhancer responsiveness, respectively. Here, we show that mastermind dependence of the Notch response at these loci is differentially encoded in Jurkat T-cell acute lymphoblastic leukemia (T-ALL) cells. Knockout of Mastermind-like 1 (MAML1) eliminates Notch-responsive activation of both these genes, and reduced target gene expression is accompanied by a decrease in H3K27 acetylation, consistent with the importance of MAML1 for p300 activity. Add-back of MAML1 variants in knockout cells identifies residues 151 to 350 of MAML1 as essential for expression of either Notch-responsive gene. Fusion of the Notch-binding region of MAML1 to the histone acetyltransferase (HAT) domain of p300 rescues expression of HES4 but not DTX1, suggesting that an additional activity of MAML1 is needed for gene induction at a distance. Together, these studies establish the functional importance of the MAML1 region from residues 151 to 350 for Notch-dependent transcriptional induction and reveal differential requirements for MAML1-dependent recruitment activities at different Notch-responsive loci, highlighting the molecular complexity of Notch-stimulated transcription.

This study focuses the energy distribution of a hydroelectric generating system. Understanding the way energy distribution is important for researchers because it determines many of the macroscopic attributes, such as conversion efficiency, dynamic characteristics, et al. Historically, energy modeling has been split into two directions, focusing on stability analysis and its control, and has not yet been studied from the viewpoint for the stochastic turbine flow. Here we established a novel stochastic model to analyze the energy distribution of the hydroelectric generating system. We verified this model with the monitored data from Nazixia hydropower station of China. We also show how the stochastic turbine flow affects the energy losses of the system. The result shows that the one with the highest influence is the hydraulic impact losses in spiral case (more than 60%), and the hydraulic friction loss first keeps 19% as the stochastic intensity changes from 0.01 to 0.5, then increases to 20% when the stochastic intensity reaches 0.6.

Purpose: Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. In China, chronic hepatitis B virus (HBV) infection remains the major risk factor for HCC. In this study, we performed a genome-wide association study (GWAS) among Chinese populations to identify novel genetic loci contributing to susceptibility to HBV-related HCC. Experimental Design: GWAS scan is performed in a collection of 205 HBV-related HCC trios (each trio includes an affected proband and his/her both parents), and 355 chronic HBV carriers with HCC (cases) and 360 chronic HBV carriers without HCC (controls), followed by two rounds of replication studies totally consisting of 3,796 cases and 2,544 controls. Results: We identified a novel association signal within the CDK14 gene at 7q21.13 (index rs10272859, OR = 1.28, P = 9.46 × 10−10). Furthermore, we observed that the at-risk rs10272859[G] allele was significantly associated with higher mRNA expression levels of CDK14 in liver tissues. Chromosome conformation capture assays in liver cells confirmed that a physical interaction exists between the promoter region of CDK14 and the risk-associated SNPs in strong linkage disequilibrium with the index rs10272859 at 7q21.13. This index rs10272859 also showed significant association with the survival of HCC patients. Conclusions: Our findings highlight a novel locus at 7q21.13 conferring both susceptibility and prognosis to HBV-related HCC, and suggest the CDK14 gene to be the functional target of the 7q21.13 locus. Clin Cancer Res; 24(4); 906–15. ©2017 AACR.

// Zhiyu Bao 1, 2, 3, 4, 5, * , Lei Lu 6, * , Xinyi Liu 1, 4, 5, * , Bingqian Guo 1, 4, 5, * , Yun Zhai 1, 4, 5 , Yuanfeng Li 1, 4, 5 , Yahui Wang 1, 4, 5 , Bobo Xie 1, 4, 5 , Qian Ren 1, 4, 5 , Pengbo Cao 1, 4, 5 , Yuqing Han 1, 4, 5 , Weihua Jia 7, 8 , Minshan Chen 9 , Xinqiang Liang 2 , Xuan Wang 6 , Yi-Xin Zeng 7, 8 , Fuchu He 1, 4, 5 , Hongxing Zhang 1, 4, 5 , Ying Cui 2 and Gangqiao Zhou 1, 4, 5, 10 1 State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China 2 Guangxi Medical University, Nanning, China 3 Affiliated Hospital of Jining Medical University, Jining, China 4 National Engineering Research Center for Protein Drugs, Beijing, China 5 National Center for Protein Sciences Beijing, Beijing, China 6 Department of Surgical Oncology, Bayi Hospital Affiliated Nanjing University of Chinese Medicine, Jindu Hospital, Nanjing, China 7 State Key Laboratory of Oncology in Southern China, Guangzhou, China 8 Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, China 9 Department of Hepatobiliary Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China 10 Anhui Medical University, Hefei, Anhui, China * These authors have contributed equally to this work Correspondence to: Gangqiao Zhou, email: zhougq114@126.com Ying Cui, email: cuiying@csco.org.cn Hongxing Zhang, email: zhanghx08@126.com Keywords: hepatocellular carcinoma, hepatitis B virus, AURKA, polymorphism, susceptibility Received: February 17, 2017 Accepted: May 22, 2017 Published: June 27, 2017 ABSTRACT Aurora kinase A (AURKA) is a serine threonine kinase which affects chromosomal separation and mitotic spindle stability through interaction with the centrosome during mitosis. Two functional nonsynonymous polymorphisms of the AURKA gene (Ile31Phe and Val57Ile) have been reported recently. We analyzed the association between the two polymorphisms and risk of the occurrence of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) in the Guangxi population consisting of 348 patients with HCC and 359 control subjects, and then validated the significant association in the Guangdong population consisting of 440 cases and 456 controls. All of the participants were of Chinese origin and HBV carriers. The two polymorphisms were genotyped by polymerase chain reaction-restriction fragment length polymorphism assay or Sequenom MassARRAY iPLEX platform. In the Guangxi population, carriers of the AURKA 31Phe allele (Ile/Phe + Phe/Phe) were significantly associated with decreased susceptibility to HBV-related HCC when compared with noncarriers (Ile/Ile) (odds ratio [OR] = 0.63, 95% confidence interval [CI] = 0.46-0.86, P = 3.4 × 10 -3 ). On the contrary, no significant association was found between Val57Ile and HBV-related HCC occurrence. The association of Ile31Phe with HBV-related HCC occurrence was confirmed in the Guangdong population (OR = 0.64, 95% CI = 0.49-0.83, P = 8.0 × 10 -4 ). The pooled analysis gave a joint P value of 5.5 × 10 -6 (joint OR = 0.63, 95% CI = 0.52-0.77). Our findings suggest that AURKA Ile31Phe may play a role in mediating the susceptibility to HBV-related HCC among Chinese.

Mastermind proteins are required for transcription of Notch target genes, yet the molecular basis for mastermind function remains incompletely understood. Previous work has shown that Notch can induce transcriptional responses by binding to promoters, but more often by binding to enhancers, with HES4 and DTX1 as representative mammalian examples of promoter and enhancer responsiveness, respectively. Here, we show that mastermind dependence of the Notch response at these loci is differentially encoded in Jurkat T-ALL cells. Knockout of Mastermind-like1 (MAML1) eliminates Notch responsive activation of both these genes, and reduced target gene expression is accompanied by a decrease in H3K27 acetylation, consistent with the importance of MAML1 for p300 activity. Add-back of defined MAML1 constructs in knockout cells identifies residues 151-350 of MAML1 as essential for expression of either Notch-responsive gene. Fusion of the Notch-binding region of MAML1 to the HAT domain of p300 rescues expression of HES4 but not DTX1, suggesting that an additional activity of MAML1 is needed for gene induction at a distance. Together, these studies establish the functional importance of the MAML1151-350 region for Notch-dependent transcriptional induction, and reveal differential requirements for MAML1-dependent recruitment activities at different Notch responsive loci, highlighting the molecular complexity of NTC-stimulated transcription.

Small cell lung cancer (SCLC) is a neuroendocrine tumor treated clinically as a single disease with poor outcomes. Distinct SCLC molecular subtypes have been defined based on expression of ASCL1, NEUROD1, POU2F3, or YAP1. Here, we use mouse and human models with a time-series single-cell transcriptome analysis to reveal that MYC drives dynamic evolution of SCLC subtypes. In neuroendocrine cells, MYC activates Notch to dedifferentiate tumor cells, promoting a temporal shift in SCLC from ASCL1+ to NEUROD1+ to YAP1+ states. MYC alternatively promotes POU2F3+ tumors from a distinct cell type. Human SCLC exhibits intratumoral subtype heterogeneity, suggesting that this dynamic evolution occurs in patient tumors. These findings suggest that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.

With polyethylene glycol as a porogen, vinyltrimethoxysilane (VTMS) and tetramethoxysilane (TMOS) as silica precursors, a hybrid silica monolithic material was obtained under the catalysis of acetic acid and thermally decomposed urea. The silica monolithic material was ground by a ballmill, treated with tris(hydroxymethyl)aminomethane (Tris), then washed and dried to obtain silica particles with particle size~3 μm. The effects of different reaction conditions on the particle size, surface morphology and dispersibility of silica particles were investigated. When the volume ratio of TMOS to VTMS was 3:1, it was observed that silica particles with a pore diameter of 7.5 nm and a specific surface area of 245 m2/g were obtained. The resultant silica particles were modified by binding with chlorodimethyloctadecylsilane (C18) and by the thiol-ene click reaction to obtain a mixed-mode type stationary phase. The test results showed that the silica packing materials prepared in this work has certain applicability.

In recent years, nanomaterials have aroused people's interest in the field of biomedicine. Polypyrrole (PPy) has become a research hotspot because of its simple synthesis, excellent photothermal conversion performance, and high biocompatibility. Here, we report the synthesis of PPy nanoparticles (PPy-PVP NPs) using a vapor deposition method, for tumor photothermal therapy. In this method, the slowly produced volatile pyrrole vapor was absorbed by the PVP (polyvinylpyrrolidone)/FeCl3 aqueous solution. This slow vapor production and absorption allows the formation of uniform PPy-PVP NPs at room temperature. Then, the effects of the molecular weight of PVP on the photothermal property and anti-tumor efficiency of PPy-PVP NPs were compared. It was found that the selection of PVP40kDa as the template and surface linker can ensure a better application performance of the synthesized nanomaterials. This work provides a theoretical basis for the rational design of nano-therapy carriers and biomedical applications.

Small cell lung cancer (SCLC) is a highly aggressive neuroendocrine tumor that is treated clinically as a single disease with poor outcomes. However, SCLC is recently recognized to comprise multiple molecular subsets with unique therapeutic vulnerabilities. Four distinct subtypes of SCLC have been defined based on expression of lineage-related transcription factors: ASCL1, NEUROD1, POU2F3 or YAP1. The origins of these subtypes remain unknown. We use mouse and human SCLC models with a time-series analysis of single-cell transcriptome profiling to reveal that the oncogene MYC drives the dynamic evolution of SCLC subtypes by activation of Notch signaling. MYC cooperates with Notch signaling to promote a temporal shift from an ASCL1-to-NEUROD1-to-YAP1-positive state from a neuroendocrine cell of origin, whereas MYC promotes POU2F3+ tumors from a distinct cell type. SCLC molecular subtypes are therefore not distinct, but rather represent dynamic stages of MYC-driven tumor evolution. Treatment-naive human SCLC exhibits intratumoral heterogeneity in SCLC subtypes, suggesting this dynamic evolution occurs in patient tumors. These findings demonstrate that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype. Given the reported unique therapeutic vulnerabilities of each subtype, we postulate that SCLC tumors represent a “moving therapeutic target” that may require more general, combinatorial, or plasticity-directed therapeutic approaches to combat this transcriptional flexibility. We anticipate that molecular subsets of other cancer types may also represent dynamic stages of tumor evolution. Citation Format: Abbie S. Ireland, Alexi M. Micinski, David W. Kastner, Bingqian Guo, Sarah J. Wait, Kyle B. Spainhower, Christopher C. Conley, Opal S. Chen, Matthew R. Guthrie, Danny Soltero, Yi Qiao, Xiaomeng Huang, Szabolcs Tarapcsak, Siddhartha Devarakonda, Milind D. Chalishazar, Jason Gertz, Justin C. Moser, Gabor Marth, Sonam Puri, Benjamin L. Witt, Benjamin T. Spike, Trudy G. Oliver. MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-120.

In this research, a novel nanoenzyme-based theranostic nanoplatform, named PPy@MnO2-BSA (bovine serum albumin (BSA)-modified manganese dioxide (MnO2)/polypyrrole (PPy)) was invented for T1-MRI-guided combined photothermal therapy (PTT) and photodynamic therapy (PDT) of tumors. The materials design was based on the in-situ oxidation and polymerization of pyrrole, using potassium permanganate (KMnO4) as the oxidant. The formed PPy@MnO2-BSA was further used to load with Ce6, via physical absorption. The PPy, with a high absorbance within the near-infrared (NIR) region, endowes the nanoenzyme with outstanding photothermal performance with the photo-to-heat conversion efficiency of 21.05%, while the MnO2, which could reduce the relaxation time of nearby protons, serves to enhance the tumor T1-MRI ability. Moreover, upon exposure to red light, the PPy@MnO2-BSA(Ce6) nanoparticle could produce the cellular toxic reactive oxygen species (ROS, i.e., 1O2) to trigger the tumor PDT. Meanwhile, the nanoparticle could continuously catalyze H2O2 into endogenous oxygen, to not only relieve the hypoxia inside the tumor but also enhance the tumor PDT effect. The in vitro and in vivo experiments both affirmed the great potential of PPy@MnO2-BSA(Ce6) nanoparticle in MRI-guided combined PDT and PTT for tumor. This research lays a solid foundation for the theoretical design and clinical application of theranostic nanoprobe in the future.

With an excellent near-infrared (NIR) light-responsive property, polypyrrole (PPy) nanoparticle has emerged as a promising NIR photothermal transducing agent for tumor photothermal therapy (PTT). Herein, we reported the PVP mediated one-pot synthesis of colloidal stable and biocompatible PPy nanoparticles (PPy-PVP NPs) for combined tumor photothermal-chemotherapy. The influence of molecular weight and PVP concentration on the spectroscopic characteristic, photothermal feature, drug loading performance, and antitumor efficiency of the resultant PPy-PVP NPs was systematically studied. By choosing PVP with a molecular weight of 360 kDa (concentration of 5 mg/mL) as the template and surface modifier during the synthesis, PPy-PVP NPs with optimal spectroscopic characteristic, photothermal feature, drug loading performance, and antitumor efficiency were synthesized. Findings in this study are anticipated to provide an in-depth understanding of the important character of surface engineering in the rational design and biomedical applications of PPy NPs.

The sodium taurocholate cotransporting polypeptide (NTCP) encoded by SLC10A1 was recently demonstrated to be a functional receptor for hepatitis B virus (HBV). The role of SLC10A1 polymorphisms, particularly the Ser267Phe variant (rs2296651) in exon 4, has been frequently investigated in regard to risk of persistent HBV infection. However, these investigations have generated conflicting results. To examine whether common genetic variation at the SLC10A1 locus is associated with risk of persistent HBV infection, haplotype-tagging and imputed single nucleotide polymorphisms (SNPs) were assessed in two case-control sample sets, totally including 2,550 cases (persistently HBV infected subjects, PIs) and 2,124 controls (spontaneously recovered subjects, SRs) of Southern Chinese ancestry. To test whether rare or subpolymorphic SLC10A1 variants are associated with disease risk, the gene’s exons in 244 cases were sequenced. Overall, we found neither SNPs nor haplotypes of SLC10A1 showed significant association in the two sample sets. Furthermore, no significant associations of rare variants or copy number variation covering SLC10A1 were observed. Finally, expression quantitative trait locus analyses revealed that SNPs potentially affecting SLC10A1 expression also showed no significant associations. We conclude that genetic variation at the SLC10A1 locus is not likely a major risk factor of persistent HBV infection among Southern Chinese.

NEMO is a scaffolding protein that, together with the catalytic subunits IKKα and IKKβ, plays an essential role in the formation of the IKK complex and in the activation of the canonical NF-κB pathway. Rational drug design targeting the IKK-binding site on NEMO would benefit from structural insight, but to date, the determination of the structure of unliganded NEMO has been hindered by protein size and conformational heterogeneity. Here we show how the utilization of a homodimeric coiled-coil adaptor sequence stabilizes the minimal IKK-binding domain NEMO(44-111) and furthers our understanding of the structural requirements for IKK binding. The engineered constructs incorporating the coiled coil at the N-terminus, C-terminus, or both ends of NEMO(44-111) present high thermal stability and cooperative melting and, most importantly, restore IKKβ binding affinity. We examined the consequences of structural content and stability by circular dichoism and nuclear magnetic resonance (NMR) and measured the binding affinity of each construct for IKKβ(701-745) in a fluorescence anisotropy binding assay, allowing us to correlate structural characteristics and stability to binding affinity. Our results provide a method for engineering short stable NEMO constructs to be suitable for structural characterization by NMR or X-ray crystallography. Meanwhile, the rescuing of the binding affinity implies that a preordered IKK-binding region of NEMO is compatible with IKK binding, and the conformational heterogeneity observed in NEMO(44-111) may be an artifact of the truncation.

The development of next generation of flexible electronic devices requires new materials to replace the glass as transparent windows. Here, flexible, transparent, and very strong cross-linked celluloses have been prepared by cross-linking free cellulose chains with epichlorohydrin (ECH) in its aqueous solution. Atomic force microscopy (AFM), light transmittance, differential thermogravimetric (DTG) thermal analyses, and tensile tests revealed that the as-prepared films are a thickness of about 10 μm with highly optical transparency and mechanical strength. The film also showed a low coefficient of thermal expansion (CTE) of about 6.9 ppm/K, which is superior to that of glass. Then the as-prepared cellulose film was combined with a dried foam ultrathin film of reduced graphene oxide to prepare a new, flexible, transparent, very strong, and electrically conductive thin film.

The Notch signaling pathway has a critical role in cell fate determination and tissue homeostasis in a variety of different lineages. In the context of normal Notch signaling, the Notch receptor of the 'signal-receiving' cell is activated in trans by a Notch ligand from a neighboring 'signal-sending' cell. Genetic studies in several model organisms have established that ubiquitination of the Notch ligand, and its regulated endocytosis, is essential for transmission of this activation signal. In mammals, this ubiquitination step is dependent on the protein Mind bomb 1 (Mib1), a large multi-domain RING-type E3 ligase, and its direct interaction with the intracellular tails of Notch ligand molecules. Here, we discuss our current understanding of Mind bomb structure and mechanism in the context of Notch signaling and beyond.

Recombinant soluble TRAIL and agonistic antibodies against TRAIL receptors (DR4 and DR5) are currently being created for clinical cancer therapy, due to their selective killing of cancer cells and high safety characteristics. However, resistance to TRAIL and other targeted therapies is an important issue facing current cancer research field. An attractive strategy to sensitize resistant malignancies to TRAIL-induced cell death is the design of small molecules that target and promote caspase 8 activation. For the first time, we describe the discovery and characterization of a small molecule that directly binds caspase 8 and enhances its activation when combined with TRAIL, but not alone. The molecule was identified through an in silico chemical screen for compounds with affinity for the caspase 8 homodimer’s interface. The compound was experimentally validated to directly bind caspase 8 and to promote caspase 8 activation and cell death in single living cells or population of cells, upon TRAIL stimulation. Our approach is a proof-of-concept strategy leading to the discovery of a novel small molecule that not only stimulates TRAIL-induced apoptosis in cancer cells, but may also provide insights into the structure-function relationship of caspase 8 homodimers as putative targets in cancer.

We present a versatile method to characterize ATPase and kinase activities and discover new inhibitors of these proteins. The proton NMR-based assay directly monitors ATP turnover and is easy to implement, requires no additional reagents and can potentially be applied to GTP. We validated the method's accuracy, applied it to the monitoring of ATP turnover by actin and to the screening of ATPase inhibitors, and showed that it is also applicable for the monitoring of GTP hydrolysis.