Proteogenomic characterization of pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 normal pancreatic ductal tissues. Proteomic, phosphoproteomic, and glycoproteomic analyses were used to characterize proteins and their modifications. In addition, whole-genome sequencing, whole-exome sequencing, methylation, RNA sequencing (RNA-seq), and microRNA sequencing (miRNA-seq) were performed on the same tissues to facilitate an integrated proteogenomic analysis and determine the impact of genomic alterations on protein expression, signaling pathways, and post-translational modifications. To ensure robust downstream analyses, tumor neoplastic cellularity was assessed via multiple orthogonal strategies using molecular features and verified via pathological estimation of tumor cellularity based on histological review. This integrated proteogenomic characterization of PDAC will serve as a valuable resource for the community, paving the way for early detection and identification of novel therapeutic targets.

Proteogenomic Characterization of Endometrial Carcinoma.

We undertook a comprehensive proteogenomic characterization of 95 prospectively collected endometrial carcinomas, comprising 83 endometrioid and 12 serous tumors. This analysis revealed possible new consequences of perturbations to the p53 and Wnt/ß-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new information about proteomic markers of clinical and genomic tumor subgroups, including relationships to known druggable pathways. An extensive genome-wide acetylation survey yielded insights into regulatory mechanisms linking Wnt signaling and histone acetylation. We also characterized aspects of the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, identify new molecular associations of potential mechanistic significance in the development of endometrial cancers, and suggest novel approaches for identifying potential therapeutic targets.

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.

To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration of proteogenomic measurements uniquely identified protein dysregulation of cellular mechanisms impacted by genomic alterations, including oxidative phosphorylation-related metabolism, protein translation processes, and phospho-signaling modules. To assess the degree of immune infiltration in individual tumors, we identified microenvironment cell signatures that delineated four immune-based ccRCC subtypes characterized by distinct cellular pathways. This study reports a large-scale proteogenomic analysis of ccRCC to discern the functional impact of genomic alterations and provides evidence for rational treatment selection stemming from ccRCC pathobiology.

Pathogenic Germline Variants in 10,389 Adult Cancers.

We conducted the largest investigation of predisposition variants in cancer to date, discovering 853 pathogenic or likely pathogenic variants in 8% of 10,389 cases from 33 cancer types. Twenty-one genes showed single or cross-cancer associations, including novel associations of SDHA in melanoma and PALB2 in stomach adenocarcinoma. The 659 predisposition variants and 18 additional large deletions in tumor suppressors, including ATM, BRCA1, and NF1, showed low gene expression and frequent (43%) loss of heterozygosity or biallelic two-hit events. We also discovered 33 such variants in oncogenes, including missenses in MET, RET, and PTPN11 associated with high gene expression. We nominated 47 additional predisposition variants from prioritized VUSs supported by multiple evidences involving case-control frequency, loss of heterozygosity, expression effect, and co-localization with mutations and modified residues. Our integrative approach links rare predisposition variants to functional consequences, informing future guidelines of variant classification and germline genetic testing in cancer.

Comprehensive transcriptomic profiling of T-2 toxin-induced nephrotoxicity in mice.

T-2 toxin, a trichothecene mycotoxin, is an important environmental pollutant that poses a threat globally to the health of humans and animals. It has been found to induce nephrotoxicity; however, the precise molecular mechanism involved remains unclear. In this study, mice were administered at a single dose of 2 mg/kg body weight T-2 toxin intraperitoneally, and kidney function and ultrastructural observations were assessed after 1 d, 3 d, and 7 d. Histopathological findings revealed that exposure to T-2 toxin caused noticeable tubular degeneration, necrosis and epithelial cell shedding in mouse kidneys. Transmission electron microscopy indicated that exposure to T-2 toxin caused mitochondrial swelling and vacuolization. Transcriptomic data revealed significant differences in the expression of 1122, 58, and 391 genes in kidney tissues 1 d, 3 d, or 7 d after T-2 toxin exposure, respectively. Moreover, after 1 d, the downregulated differentially expressed genes (DEGs) were found to be involved in the cell cycle, p53 signaling, and cellular senescence pathways, while the upregulated DEGs were found to be associated with the ribosomal pathway. Temporal changes in gene expression patterns (i.e., after 3 d and 7 d) and disturbances in cellular metabolism during the recovery period (7 d) were detected in mouse kidneys after exposure to T-2 toxin. In conclusion, this study is the first to provide a comprehensive comparative transcriptomic analysis of T-2 toxin exposure-induced nephrotoxicity-related gene regulation at different time points and to investigate the mechanism underlying the nephrotoxicity of T-2 toxin at the mRNA expression level.

Knockdown of Dual Oxidase 1 (DUOX1) Promotes Wound Healing by Regulating Reactive Oxygen Species (ROS) by Activation of Nuclear Kactor kappa B (NF-κB) Signaling.

BACKGROUND The aim of this study was to evaluate the potential role of dual oxidase 1 (DUOX1) in wound healing. MATERIAL AND METHODS Primary fibroblasts were isolated from wound granulation tissue. Fibroblasts cell lines were established using DUOX1 overexpression and interference. Cell proliferation and reactive oxygen species (ROS) production were measured and compared among the groups. RESULTS DUOX1 expression was highest in the slow-healing tissues (P<0.05). Knockdown of DUOX1 significantly increased cell proliferation and inhibited ROS production and cell apoptosis (P<0.01). Moreover, expression of malondialdehyde (MDA) was significantly reduced, while expression of superoxide dismutase (SOD) expression was significantly increased (P<0.01). In addition, DUOX1 silencing significantly upregulated collagen I, collagen III, and NF-kappaB protein levels in the cytoplasm, and inhibited the protein levels of P21, P16, and NF-kappaB in the nucleus (P<0.01). Overexpression of DUOX1 caused a reverse reaction mediated by knockdown of DUOX1. When DUOX1-overexpressing cells were treated with the ROS inhibitor N-acetyl-L-cysteine (NAC), the protein levels that were increased by DUOX1 overexpression were reversed. CONCLUSIONS These results suggest that knockdown of DUOX1 significantly benefits wound healing, likely by the regulation of oxidative stress via NF-kappaB pathway activation.

Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability.

Aberrant phospho-signaling is a hallmark of cancer. We investigated kinase-substrate regulation of 33,239 phosphorylation sites (phosphosites) in 77 breast tumors and 24 breast cancer xenografts. Our search discovered 2134 quantitatively correlated kinase-phosphosite pairs, enriching for and extending experimental or binding-motif predictions. Among the 91 kinases with auto-phosphorylation, elevated EGFR, ERBB2, PRKG1, and WNK1 phosphosignaling were enriched in basal, HER2-E, Luminal A, and Luminal B breast cancers, respectively, revealing subtype-specific regulation. CDKs, MAPKs, and ataxia-telangiectasia proteins were dominant, master regulators of substrate-phosphorylation, whose activities are not captured by genomic evidence. We unveiled phospho-signaling and druggable targets from 113 kinase-substrate pairs and cascades downstream of kinases, including AKT1, BRAF and EGFR. We further identified kinase-substrate-pairs associated with clinical or immune signatures and experimentally validated activated phosphosites of ERBB2, EIF4EBP1, and EGFR. Overall, kinase-substrate regulation revealed by the largest unbiased global phosphorylation data to date connects driver events to their signaling effects.

A Self-Categorization Perspective of Idiosyncratic Deals and Creativity: Mediating Role of Perceived Insider Status and Moderating Role of Psychological Safety.

Purpose: Idiosyncratic deals (I-deals), a novel human resource management implement, has significantly contributed to attracting, retaining and motivating personnel to enhance creativity. Building upon self-categorization theory, this study investigates the impact of I-deals on creativity and the moderating role of psychological safety in this process by perceived insider status. Participants and Methods: To mitigate common method bias and causal lag effects, this study was conducted in three phases with a half-month interval for data collection. In this study, a total of 331 employees from six enterprises in China were selected to test the hypotheses using Bootstrap and Johnson-Neyman methods. Results: Results show that I-deals have a positive influence on creativity. Perceived insider status acts as intermediary between I-deals and creativity; Psychological safety strengthens the influence of I-deals on perceived insider status and further enhances the indirect influence of I-deals on creativity through perceived insider status. Conclusion: This study demonstrates that organizations can leverage the unique characteristics of I-deals to fully showcase the diverse talents of their personnel, while simultaneously enhancing their psychological security. This, in turn, empowers employees to confidently propose new ideas and methods, thus catalyzing the generation of creativity.

Consumer Perception of the Performance of Online Catering Food Safety Regulations: The Case of Shanghai, China.

To protect the safety of food bought from the online catering sector, the former State Food and Drug Administration of China issued two separate regulations in 2016 and 2017. Independently, the Shanghai government formulated local regulations, including the Shanghai Online Catering Service Supervision and Management Measures, to strengthen food safety supervision in this megacity with the largest catering sector in China. This study explored factors that influence consumer perceptions of the performance of online catering food safety regulations using survey data from 1050 respondents collected in 2019. The results indicate that consumers believe that Shanghai's online catering industry has improved by varying degrees in terms of food freshness, ingredient traceability, foreign matter control, food temperature control, internal packaging hygiene and environmental protection, and satisfaction with food safety. The factors that influenced the listed features include the number and effectiveness of government-issued regulations regarding the online catering sector, effectiveness of ordering platform food safety regulations, employee training frequency, employee food safety awareness, delivery box cleanliness and courier personal hygiene, consumer trust in ordering platform services, and consumer confidence in government supervision. These factors significantly and positively affected the consumers' perceptions of the performance of food safety regulations in the online catering sector.

[Research progress on the pyroptosis mediated by the NLRP3 inflammasome in the pathology of ischemic stroke].

Ischemic stroke is one of the diseases which pose a significant threat to human health. Recent studies have suggested that programmed cell death plays an important role in brain tissues affected by ischemia and hypoxia. Pyroptosis, which is characterized by both apoptosis and necrosis, is mediated by activation of inflammasomes, such as NOD-like receptor family, pyrin domain containing 3 (NLRP3). Pyroptosis, which depends on caspase-1 activation and the release of pro-inflammatory cytokines, such as Interleukin 1ß and Interleukin 18, plays a vital role in regulating cell survival and death following ischemic injury. Previous studies have shown that pyroptosis is closely related to the activation of the NLRP3 inflammasome in ischemic stroke tissues. This distinctive form of cell death mainly occurs in microglia, neurons, astrocytes and endothelial cells. This paper reviews the role of pyroptosis mediated by inflammasomes in ischemic stroke, discussing the targets and substances that affect the activation of the NLRP3 inflammasome, which can provide a new theoretical and experimental basis for the treatment of ischemic stroke.

Association analysis of antibiotic and disinfectant resistome in human and foodborne E. coli in Beijing, China.

The widespread use of chemical disinfectants and antibiotics poses a major threat to food safety and human health. However, the mechanisms of co-transmission of antimicrobial resistance genes (ARGs) and biocides and metal resistance genes (BMRGs) of foodborne pathogens in the food chain is still unclear. This study isolated 343 E. coli strains from animal-derived foods in Beijing and incorporated online data of human-derived E. coli strains from NCBI. Our results demonstrated a relatively uniform distribution of strains from various regions in Beijing, indicating a lack of region-specific clustering. Additionally, predominant sequence types varied between food- and human-derived strains, suggesting a preference for different hosts and environments. Phenotypic association analysis showed that the chlorine disinfectants peroxides had a significant positive correlation with tetracyclines. Many more ARGs and BMRGs were enriched in human-associated E. coli compared with those in chicken- and pork-origin. The quaternary ammonium compounds (QACs) resistance gene qacEΔ1 had a strong correlation with aminoglycoside resistance gene aadA5, folate pathway antagonist resistance gene dfrA17, sul1 and macrolide resistance gene mph(A). The correlation results indicated a significant association between the copper resistance gene cluster pco and the silver resistance gene cluster sil. Coexistence of many resistance genes was observed within the qacEΔ1 gene structure, with qacEΔ1-sul1 being the most common combination. Our findings demonstrated that the epidemiological spread of resistance is affected by a combination of heavy metals, disinfectants and antibiotic use, suggesting that the prevention and control strategies of antimicrobial resistance need to be multifaceted and comprehensive.

A SILAC-based accurate quantification of shrimp allergen tropomyosin in complex food matrices using UPLC-MS/MS.

The carryover of trace allergens in complex food matrices poses challenges for detection techniques. Here, we demonstrate an accurate UPLC-MS/MS quantification assay for the shrimp allergen tropomyosin with a full-length isotope-labelled recombinant tropomyosin (TM-I) internal standard in complex food matrices. The TM-I, expressed based on the SILAC technique, exhibited a high isotope labelling ratio (>99%), purity, and alignment with the natural sequence. This method determined the tropomyosin ranging from 0.2 to 100 ng/mL. Mean recoveries ranged from 89 to 116%, with intra- and inter-day RSDs below 12%, for three signature peptides across three types of commercially processed food matrices. The limits of quantitation were 1 µg/g in pop food and sauce, and 10 µg/g in surimi product, respectively. This study supports the use of recombinant full-length isotope-labelled proteins rather than stable-isotope labelling peptides as internal standards to achieve more accurate quantitation of food allergens as the digestion error is corrected.

Omnidirectional compliance on cross-linked actuator coordination enables simultaneous multi-functions of soft modular robots.

Earthworms have entirely soft bodies mainly composed of circular and longitudinal muscle bundles but can handle the complexity of unstructured environments with exceptional multifunctionality. Soft robots are naturally appropriate for mimicking soft animal structures thanks to their inherent compliance. Here, we explore the new possibility of using this compliance to coordinate the actuation movements of single-type soft actuators for not only high adaptability but the simultaneous multifunctionality of soft robots. A cross-linked actuator coordination mechanism is proposed and explained with a novel conceptual design of a cross-linked network, characterization of modular coordinated kinematics, and a modular control strategy for multiple functions. We model and analyze the motion patterns for these functions, including grabbing, manipulation, and locomotion. This further enables the combination of simultaneous multi-functions with this very simple actuator network structure. In this way, a soft modular robot is developed with demonstrations of a novel continuous-transportation mode, for which multiple objects could be simultaneously transported in unstructured environments with either mobile manipulation or pick-and-place operation. A comprehensive workflow is presented to elaborate the cross-linked actuator coordination concept, analytical modeling, modular control strategy, experimental validation, and multi-functional applications. Our understanding of actuator coordination inspires new soft robotic designs for wider robotic applications.

Spread of multidrug-resistant Pseudomonas aeruginosa in animal-derived foods in Beijing, China.

Pseudomonas aeruginosa is the most common bacterium occurred in nosocomial infections and is also an important indicator of food spoilage. The worldwide spread of multidrug resistant (MDR) P. aeruginosa is threatening public health. However, the prevalence and spread of MDR P. aeruginosa through the food chain is little referred under the One Health perspective. Here, we collected a total of 259 animal-derived foods (168 chicken and 91 pork) from 16 supermarkets and farmer's markets in six regions of Beijing, China. The prevalence of P. aeruginosa in chicken and pork was 42.1 %. The phenotypic antimicrobial susceptibility testing showed that 69.7 % of isolates were MDR, and isolates from Chaoyang district exhibited a higher resistance rate compared to that from Xicheng district (p < 0.05). P. aeruginosa isolates exhibited high levels of resistance against ß-lactams (91.7 %), cephalosporins (29.4 %), and carbapenems (22.9 %). Interestingly, none of strains showed resistance to amikacin. Whole-genome sequencing showed that all isolates carried various kinds of antimicrobial resistance genes (ARGs) and virulence genes (VGs), especially for blaOXA genes and phz genes. Multilocus sequence typing (MLST) analysis indicated that ST111 (12.8 %) was the most predominant ST. Notably, the emergence of ST697 clones in food-borne P. aeruginosa was firstly reported. In addition, the toxin pyocyanin was detected in 79.8 % of P. aeruginosa strains. These findings help to decipher the prevalence and the strong toxigenic ability of MDR P. aeruginosa from animal-derived foods and highlight the effective supervision of animal-derived food hygiene should be strengthened to prevent the spread of ARGs in a One Health strategy.

Multi-immunoaffinity column for the simultaneous analysis of bisphenol A and its analogues in Chinese foods by liquid chromatography tandem mass spectrometry.

Bisphenol A (BPA) and its four analogues have been receiving considerable attention owing to their potential endocrine disrupting effects. The European Food Safety Authority has proposed 0.04 ng/kg·body weight/day of thetemporary tolerable daily intake for BPA. Therefore, a more sensitive analytical method was urgently needed for the necessity of the risk reassessment of bisphenols (BPs). The matrix effect of Chinese foods is a challenge for the analysis of ultra-trace analytes due to the presence of various spices. A multi-immunoaffinity column (mIAC) was prepared for the purification of BPA, BPB, BPF, BPS, and BPAF in Chinese foods following ultra-high-performance liquid chromatography tandem mass spectrometry detection (UHLPC-MS/MS). The recoveries of each of BPs were ranged from 84.6% to 116.7%, and the intra-day precision and inter-day precision were ranged from 1.6% to 12.4%, and from 4.1% to 14.0%, respectively. This is the first report on the mIACs for simultaneous clean-up and analysis of BPs in complex Chinese foods.

The effects and potential of microglial polarization and crosstalk with other cells of the central nervous system in the treatment of Alzheimer's disease.

Microglia are resident immune cells in the central nervous system. During the pathogenesis of Alzheimer's disease, stimulatory factors continuously act on the microglia causing abnormal activation and unbalanced phenotypic changes; these events have become a significant and promising area of research. In this review, we summarize the effects of microglial polarization and crosstalk with other cells in the central nervous system in the treatment of Alzheimer's disease. Our literature search found that phenotypic changes occur continuously in Alzheimer's disease and that microglia exhibit extensive crosstalk with astrocytes, oligodendrocytes, neurons, and penetrated peripheral innate immune cells via specific signaling pathways and cytokines. Collectively, unlike previous efforts to modulate microglial phenotypes at a single level, targeting the phenotypes of microglia and the crosstalk with other cells in the central nervous system may be more effective in reducing inflammation in the central nervous system in Alzheimer's disease. This would establish a theoretical basis for reducing neuronal death from central nervous system inflammation and provide an appropriate environment to promote neuronal regeneration in the treatment of Alzheimer's disease.

Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness.

Clear cell renal cell carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- and intratumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. To obtain the most comprehensive profile of ccRCC, we perform integrative histopathologic, proteogenomic, and metabolomic analyses on 305 ccRCC tumor segments and 166 paired adjacent normal tissues from 213 cases. Combining histologic and molecular profiles reveals ITH in 90% of ccRCCs, with 50% demonstrating immune signature heterogeneity. High tumor grade, along with BAP1 mutation, genome instability, increased hypermethylation, and a specific protein glycosylation signature define a high-risk disease subset, where UCHL1 expression displays prognostic value. Single-nuclei RNA sequencing of the adverse sarcomatoid and rhabdoid phenotypes uncover gene signatures and potential insights into tumor evolution. In vitro cell line studies confirm the potential of inhibiting identified phosphoproteome targets. This study molecularly stratifies aggressive histopathologic subtypes that may inform more effective treatment strategies.

Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma.

Identifying tumor-cell-specific markers and elucidating their epigenetic regulation and spatial heterogeneity provides mechanistic insights into cancer etiology. Here, we perform snRNA-seq and snATAC-seq in 34 and 28 human clear cell renal cell carcinoma (ccRCC) specimens, respectively, with matched bulk proteogenomics data. By identifying 20 tumor-specific markers through a multi-omics tiered approach, we reveal an association between higher ceruloplasmin (CP) expression and reduced survival. CP knockdown, combined with spatial transcriptomics, suggests a role for CP in regulating hyalinized stroma and tumor-stroma interactions in ccRCC. Intratumoral heterogeneity analysis portrays tumor cell-intrinsic inflammation and epithelial-mesenchymal transition (EMT) as two distinguishing features of tumor subpopulations. Finally, BAP1 mutations are associated with widespread reduction of chromatin accessibility, while PBRM1 mutations generally increase accessibility, with the former affecting five times more accessible peaks than the latter. These integrated analyses reveal the cellular architecture of ccRCC, providing insights into key markers and pathways in ccRCC tumorigenesis.

Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma.

Current treatment approaches for renal cell carcinoma (RCC) face challenges in achieving durable tumor responses due to tumor heterogeneity and drug resistance. Combination therapies that leverage tumor molecular profiles could offer an avenue for enhancing treatment efficacy and addressing the limitations of current therapies. To identify effective strategies for treating RCC, we selected ten drugs guided by tumor biology to test in six RCC patient-derived xenograft (PDX) models. The multitargeted tyrosine kinase inhibitor (TKI) cabozantinib and mTORC1/2 inhibitor sapanisertib emerged as the most effective drugs, particularly when combined. The combination demonstrated favorable tolerability and inhibited tumor growth or induced tumor regression in all models, including two from patients who experienced treatment failure with FDA-approved TKI and immunotherapy combinations. In cabozantinib-treated samples, imaging analysis revealed a significant reduction in vascular density, and single-nucleus RNA sequencing (snRNA-seq) analysis indicated a decreased proportion of endothelial cells in the tumors. SnRNA-seq data further identified a tumor subpopulation enriched with cell-cycle activity that exhibited heightened sensitivity to the cabozantinib and sapanisertib combination. Conversely, activation of the epithelial-mesenchymal transition pathway, detected at the protein level, was associated with drug resistance in residual tumors following combination treatment. The combination effectively restrained ERK phosphorylation and reduced expression of ERK downstream transcription factors and their target genes implicated in cell-cycle control and apoptosis. This study highlights the potential of the cabozantinib plus sapanisertib combination as a promising treatment approach for patients with RCC, particularly those whose tumors progressed on immune checkpoint inhibitors and other TKIs. SIGNIFICANCE: The molecular-guided therapeutic strategy of combining cabozantinib and sapanisertib restrains ERK activity to effectively suppress growth of renal cell carcinomas, including those unresponsive to immune checkpoint inhibitors.