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.

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.

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.

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.

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.

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.

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.

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.

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.

RJAfinder: An automated tool for quantification of responding to joint attention behaviors in autism spectrum disorder using eye tracking data.

Deficits in responding to joint attention (RJA) are early symptoms of autism spectrum disorder (ASD). Currently, no automated tools exist for identifying and quantifying RJA behaviors. A few eye tracking studies have investigated RJA in ASD children but have produced conflicting results. In addition, little is known about the trajectory of RJA development through developmental age. Here, a new video was designed including 12 clips of an actor pointing to or looking at an object. Eye tracking technology was used to monitor RJA in three groups: 143 ASD children assessed with the Autism Diagnostic Interview-Revised (ADI-R) and the Autism Diagnostic Observation Schedule (ADOS) (4-7 years old), 113 age- and gender-matched typically developing children (TDC), and 43 typically developing adults (TDA) (19-32 years old). RJAfinder was developed in R and MATLAB to quantify RJA events from the eye tracking data. RJA events were compared among the three groups. Spearman correlation coefficients between total number of RJA events in ASD and the Social Responsiveness Scale (SRS) scores were calculated. A logistic regression model was built using the average valid sampling rate and the total number of RJA events as two predictive variables to classify ASD and TDC groups. ASD children displayed statistically significantly less RJA events than the TDC and TDA groups with medium-to-large-sized effects. ASD and TDC children both displayed more RJA events in response to pointing stimuli than to looking stimuli. Our logistic regression model predicted ASD tendency with 0.76 accuracy in the testing set. RJA ability improved more slowly between the ages of 4-7 years old in the ASD group than in the TDC group. In ASD children, RJA ability showed negative correlation with SRS total T-score as well as the scores of five subdomains. Our study provides an automated tool for quantifying RJA and insights for the study of RJA in ASD children, which may help improve ASD screening, subtyping, and behavior interventions.

Human dietary exposure to bisphenol-diglycidyl ethers in China: Comprehensive assessment through a total diet study.

Despite the widespread use of bisphenol A diglycidyl ether (BADGE) and bisphenol F diglycidyl ether (BFDGE) in various consumer products as protective plasticizer, studies on human dietary exposure to these compounds are scare. In this study, nine bisphenol diglycidyl ethers (BDGEs) including BADGE, BFDGE, and seven of their derivatives were determined in the Chinese adult population based on composite dietary samples collected from the sixth (2016-2019) China total diet study (TDS). Contamination level of nine BDGEs was determined in 288 composite dietary samples from 24 provinces in China. BADGE·2H2O and BADGE are the most frequently detected and BADGE·2H2O presented the highest mean concentration (2.402 µg/kg). The most contaminated food composite is meats, with a mean ∑9BDGEs of 8.203 µg/kg, followed by aquatic products (4.255 µg/kg), eggs (4.045 µg/kg), and dairy products (3.256 µg/kg). The estimated daily intake (EDI) of ∑9BDGEs based on the mean and 95th percentile concentrations are 121.27 ng/kg bw/day and 249.71 ng/kg bw/day. Meats, eggs, and aquatic products are the main source of dietary exposure. Notably, beverages and water, alcohols were the main contributors of dietary exposure to BADGE and BADGE·2H2O, followed by animal-derived foods. Dietary exposure assessment demonstrated that human dietary BDGEs do not pose risks to general population based on the mean and 95th percentile hazard index with < 1. This is the first comprehensive national dietary exposure assessment of BDGEs in Chinese general population.

Mapping the research trends of astrocytes in stroke: A bibliometric analysis.

Background: Stroke, including ischemic stroke and hemorrhagic stroke, possesses complex pathological mechanisms such as neuroinflammation, oxidative stress and blood-brain barrier damage. Astrocyte functions have been reported during injury, neuroprotection and cell crosstalk. It plays a key role in exacerbating stroke injury, promoting neurological repair and enhancing neuroregeneration. Aim: This holistic bibliometric analysis aimed to provide a general overview of the recent advancement and the hotspots in the field of stroke and astrocyte from 2001 to 2021. Materials and methods: Publications between 2001 and 2021, related to stroke and astrocyte were retrieved from the Web of Science (WOS) and analyzed in Gephi and VOSviewer. Results: In total, 3789 documents were extracted from the WOS databases. The publications showed stable growth since 2001. The United States and China were the most prolific countries and University of California San Francisco and Oakland University were the most influential institutes. The top four most productive journals were Brain Research, Journal of Cerebral Blood Flow and Metabolism, Glia and Journal of Neuroinflammation. Keywords frequency and co-occurrence analysis revealed that the topics related to "micro-RNA", "toll like receptor", "neuroinflammation", "autophagy" and "interleukin" were research frontiers. The field of stroke and astrocyte focused on several aspects, such as the role of astrocytes in the treatment of stroke, metabolic changes in astrocytes, the protective role of apoptosis in astrocytes after oxidative stress injury and neurovascular units. Conclusion: This comprehensive bibliometric study provides an updated perspective on the trend of research associated with stroke and astrocyte. It will benefit scientific community to identify the important issues, future directions and provide a novel understanding of stroke pathophysiology, hotspots and frontiers to facilitate future research direction.

A Bibliometric Analysis for Global Trends and Full View of the Autophagy in Ischemic Stroke from 2006 to 2022.

Autophagy plays a key role in ischemic stroke, but its mechanism remains to be elucidated. In order to explore the effect of autophagy on ischemic stroke, bibliometric analysis and view tools are used to identify the directions of the global research trends and construct full view of the autophagy in ischemic stroke from 2006 to 2022. The research hotspots of autophagy related to ischemic stroke are visually analyzed and generated various visual maps to display publications, authors, sources, countries, organizations, and keywords. By bibliometric analysis, it can be seen that the investigations of autophagy in ischemic stroke is focused on both brain injury and neuroprotection. The impact of a variety of inflammatory factors and signaling pathways on autophagy following an ischemic stroke is also studied. Autophagy plays an important role in all phases of ischemic stroke. It is of great significance to guide the development of treatment plans for ischemic stroke.

Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer.

Pancreatic ductal adenocarcinoma is a lethal disease with limited treatment options and poor survival. We studied 83 spatial samples from 31 patients (11 treatment-naïve and 20 treated) using single-cell/nucleus RNA sequencing, bulk-proteogenomics, spatial transcriptomics and cellular imaging. Subpopulations of tumor cells exhibited signatures of proliferation, KRAS signaling, cell stress and epithelial-to-mesenchymal transition. Mapping mutations and copy number events distinguished tumor populations from normal and transitional cells, including acinar-to-ductal metaplasia and pancreatic intraepithelial neoplasia. Pathology-assisted deconvolution of spatial transcriptomic data identified tumor and transitional subpopulations with distinct histological features. We showed coordinated expression of TIGIT in exhausted and regulatory T cells and Nectin in tumor cells. Chemo-resistant samples contain a threefold enrichment of inflammatory cancer-associated fibroblasts that upregulate metallothioneins. Our study reveals a deeper understanding of the intricate substructure of pancreatic ductal adenocarcinoma tumors that could help improve therapy for patients with this disease.

[Effect of acupuncture and moxibustion on skin barrier function in guinea pigs with eczema of skin damp-heat accumulation].

OBJECTIVE: To observe the effect of acupuncture and moxibustion on the water content of stratum corneum (WCSC), expression of serum inflammatory factors and aquaporin 3 (AQP3) in skin, lung and rectum in guinea pigs with eczema of skin damp-heat accumulation, and to explore the possible mechanism of acupuncture and moxibustion for regulating skin barrier function. METHODS: A total of 24 male albino guinea pigs were randomly divided into a blank group (n=6) and a modeling group (n=18). The guinea pigs in the modeling group were induced by 2,4-dinitrochlorobenzene (DNCB) to establish the eczema model of skin damp-heat accumulation. The guinea pigs with successful modeling were further randomly divided into a model group, a medication group and an acupuncture-moxibustion group, 6 guinea pigs in each group. The guinea pigs in the medication group were treated with loratadine tablets (0.8 mg/kg) by gavage, once a day for 7 days; the guinea pigs in the acupuncture-moxibustion group were treated with acupuncture at "Feishu" (BL 13), "Pishu" (BL 20), "Quchi" (LI 11), "Zusanli" (ST 36) and "Xuehai" (SP 10); at the same time, moxibustion was applied at "Feishu" (BL 13) and "Zusanli" (ST 36), moxibustion intervention for 10 min and needle retaining for 15 min at each acupoint, once a day for 7 days. The eczema area and severity index (EASI) score was evaluated before and After intervention, and WCSC and trans-epidermal water loss (TEWL) were measured by skin tester. After intervention, The HE staining was used to observe the changes of skin histomorphology in each group; ELISA was used to measure the contents of serum immunoglobulin E (IgE), interleukin (IL)-4 and IL-17; Western blot was used to measure the protein expression of AQP3 in skin, lung and rectum. RESULTS: Before the intervention, compared with the blank group, the EASI scores and TEWL were increased in the remaining groups (P<0.01), and the WCSC was decreased (P<0.01). After the intervention, compared with the model group, the EASI scores and TEWL were decreased (P<0.05, P<0.01), and WCSC was increased (P<0.01) in the medication group and the acupuncture-moxibustion group. The epidermal structure in the blank group was complete and the fibers in the dermis were arranged orderly; in the model group, epidermal hyperkeratosis, proliferation of granular layer, spinous cell layer and basal layer, and disordered arrangement of dermal fibers and infiltration of inflammatory cells were observed. The morphological performance in the medication group and the acupuncture-moxibustion group was better than that in the model group. Compared with the blank group, the contents of serum IgE and IL-17 were increased (P<0.01), and the content of serum IL-4 and the protein expression of AQP3 in skin, lung and rectum were decreased in the model group (P<0.01, P<0.05). Compared with the model group, the contents of serum IgE and IL-17 were decreased and the contents of serum IL-4 were increased in the medication group and the acupuncture-moxibustion group (P<0.01), and the protein expression of AQP3 in skin, lung and rectum in the acupuncture- moxibustion group were increased (P<0.05). Compared with the medication group, the contents of serum IgE and IL-17 were increased (P<0.01), and the content of serum IL-4 was decreased (P<0.01) in the acupuncture-moxibustion group. CONCLUSION: Acupuncture and moxibustion could improve the epidermal water metabolism and skin tissue morphology in guinea pigs with eczema of skin damp-heat accumulation. Its mechanism may be related to regulating inflammatory factors, up-regulating the expression of AQP3, and then repairing the skin barrier function.

Pollock: fishing for cell states.

Motivation: The use of single-cell methods is expanding at an ever-increasing rate. While there are established algorithms that address cell classification, they are limited in terms of cross platform compatibility, reliance on the availability of a reference dataset and classification interpretability. Here, we introduce Pollock, a suite of algorithms for cell type identification that is compatible with popular single-cell methods and analysis platforms, provides a set of pretrained human cancer reference models, and reports interpretability scores that identify the genes that drive cell type classifications. Results: Pollock performs comparably to existing classification methods, while offering easily deployable pretrained classification models across a wide variety of tissue and data types. Additionally, it demonstrates utility in immune pan-cancer analysis. Availability and implementation: Source code and documentation are available at https://github.com/ding-lab/pollock. Pretrained models and datasets are available for download at https://zenodo.org/record/5895221. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Prevalence of Escherichia coli and Antibiotic Resistance in Animal-Derived Food Samples - Six Districts, Beijing, China, 2020.

WHAT IS ALREADY KNOWN ABOUT THIS TOPIC?: Escherichia coli is an important hygiene indicator for animal-derived foods such as pork and chicken, and the contamination of retail meat is associated with the spread of antimicrobial resistance (AMR) and public health. WHAT IS ADDED BY THIS REPORT?: The prevalence of E. coli in 6 different districts of Beijing was 64.1%. The contamination of chicken was more serious than pork in Beijing. E. coli isolates were highly resistant to sulfonamides (87.4%). TheampC1 and ampC2 genes were the main antibiotic resistance genotype (94.7% and 99.4%). WHAT ARE THE IMPLICATIONS FOR PUBLIC HEALTH PRACTICE?: This study highlights the need to strengthen the surveillance of antibiotic resistance of E. coli in animal-derived foods. A national or regional multicenter study is required to assess the dissemination and evolution of multidrug resistant (MDR) E. coli in clinical medicine and animal production for food.

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.

Spatially interacting phosphorylation sites and mutations in cancer.

Advances in mass-spectrometry have generated increasingly large-scale proteomics datasets containing tens of thousands of phosphorylation sites (phosphosites) that require prioritization. We develop a bioinformatics tool called HotPho and systematically discover 3D co-clustering of phosphosites and cancer mutations on protein structures. HotPho identifies 474 such hybrid clusters containing 1255 co-clustering phosphosites, including RET p.S904/Y928, the conserved HRAS/KRAS p.Y96, and IDH1 p.Y139/IDH2 p.Y179 that are adjacent to recurrent mutations on protein structures not found by linear proximity approaches. Hybrid clusters, enriched in histone and kinase domains, frequently include expression-associated mutations experimentally shown as activating and conferring genetic dependency. Approximately 300 co-clustering phosphosites are verified in patient samples of 5 cancer types or previously implicated in cancer, including CTNNB1 p.S29/Y30, EGFR p.S720, MAPK1 p.S142, and PTPN12 p.S275. In summary, systematic 3D clustering analysis highlights nearly 3,000 likely functional mutations and over 1000 cancer phosphosites for downstream investigation and evaluation of potential clinical relevance.