Proteomic discovery of chemical probes that perturb protein complexes in human cells.

Most human proteins lack chemical probes, and several large-scale and generalizable small-molecule binding assays have been introduced to address this problem. How compounds discovered in such "binding-first" assays affect protein function, nonetheless, often remains unclear. Here, we describe a "function-first" proteomic strategy that uses size exclusion chromatography (SEC) to assess the global impact of electrophilic compounds on protein complexes in human cells. Integrating the SEC data with cysteine-directed activity-based protein profiling identifies changes in protein-protein interactions that are caused by site-specific liganding events, including the stereoselective engagement of cysteines in PSME1 and SF3B1 that disrupt the PA28 proteasome regulatory complex and stabilize a dynamic state of the spliceosome, respectively. Our findings thus show how multidimensional proteomic analysis of focused libraries of electrophilic compounds can expedite the discovery of chemical probes with site-specific functional effects on protein complexes in human cells.

TMEM164 is an acyltransferase that forms ferroptotic C20:4 ether phospholipids.

Ferroptosis is an iron-dependent form of cell death driven by oxidation of polyunsaturated fatty acid (PUFA) phospholipids. Large-scale genetic screens have uncovered a specialized role for PUFA ether phospholipids (ePLs) in promoting ferroptosis. Understanding of the enzymes involved in PUFA-ePL production, however, remains incomplete. Here we show, using a combination of pathway mining of genetic dependency maps, AlphaFold-guided structure predictions and targeted lipidomics, that the uncharacterized transmembrane protein TMEM164-the genetic ablation of which has been shown to protect cells from ferroptosis-is a cysteine active center enzyme that selectively transfers C20:4 acyl chains from phosphatidylcholine to lyso-ePLs to produce PUFA ePLs. Genetic deletion of TMEM164 across a set of ferroptosis-sensitive cancer cell lines caused selective reductions in C20:4 ePLs with minimal effects on C20:4 diacyl PLs, and this lipid profile produced a variable range of protection from ferroptosis, supportive of an important but contextualized role for C20:4 ePLs in this form of cell death.

Remodeling oncogenic transcriptomes by small molecules targeting NONO.

Much of the human proteome is involved in mRNA homeostasis, but most RNA-binding proteins lack chemical probes. Here we identify electrophilic small molecules that rapidly and stereoselectively decrease the expression of transcripts encoding the androgen receptor and its splice variants in prostate cancer cells. We show by chemical proteomics that the compounds engage C145 of the RNA-binding protein NONO. Broader profiling revealed that covalent NONO ligands suppress an array of cancer-relevant genes and impair cancer cell proliferation. Surprisingly, these effects were not observed in cells genetically disrupted for NONO, which were instead resistant to NONO ligands. Reintroduction of wild-type NONO, but not a C145S mutant, restored ligand sensitivity in NONO-disrupted cells. The ligands promoted NONO accumulation in nuclear foci and stabilized NONO-RNA interactions, supporting a trapping mechanism that may prevent compensatory action of paralog proteins PSPC1 and SFPQ. These findings show that NONO can be co-opted by covalent small molecules to suppress protumorigenic transcriptional networks.

Assigning functionality to cysteines by base editing of cancer dependency genes.

Covalent chemistry represents an attractive strategy for expanding the ligandability of the proteome, and chemical proteomics has revealed numerous electrophile-reactive cysteines on diverse human proteins. Determining which of these covalent binding events affect protein function, however, remains challenging. Here we describe a base-editing strategy to infer the functionality of cysteines by quantifying the impact of their missense mutation on cancer cell proliferation. The resulting atlas, which covers more than 13,800 cysteines on more than 1,750 cancer dependency proteins, confirms the essentiality of cysteines targeted by covalent drugs and, when integrated with chemical proteomic data, identifies essential, ligandable cysteines in more than 160 cancer dependency proteins. We further show that a stereoselective and site-specific ligand targeting an essential cysteine in TOE1 inhibits the nuclease activity of this protein through an apparent allosteric mechanism. Our findings thus describe a versatile method and valuable resource to prioritize the pursuit of small-molecule probes with high function-perturbing potential.

Next-generation characterization of the Cancer Cell Line Encyclopedia.

Large panels of comprehensively characterized human cancer models, including the Cancer Cell Line Encyclopedia (CCLE), have provided a rigorous framework with which to study genetic variants, candidate targets, and small-molecule and biological therapeutics and to identify new marker-driven cancer dependencies. To improve our understanding of the molecular features that contribute to cancer phenotypes, including drug responses, here we have expanded the characterizations of cancer cell lines to include genetic, RNA splicing, DNA methylation, histone H3 modification, microRNA expression and reverse-phase protein array data for 1,072 cell lines from individuals of various lineages and ethnicities. Integration of these data with functional characterizations such as drug-sensitivity, short hairpin RNA knockdown and CRISPR-Cas9 knockout data reveals potential targets for cancer drugs and associated biomarkers. Together, this dataset and an accompanying public data portal provide a resource for the acceleration of cancer research using model cancer cell lines.

Proteomic Ligandability Maps of Spirocycle Acrylamide Stereoprobes Identify Covalent ERCC3 Degraders.

Covalent chemistry coupled with activity-based protein profiling (ABPP) offers a versatile way to discover ligands for proteins in native biological systems. Here, we describe a set of stereo- and regiochemically defined spirocycle acrylamides and the analysis of these electrophilic "stereoprobes" in human cancer cells by cysteine-directed ABPP. Despite showing attenuated reactivity compared to structurally related azetidine acrylamide stereoprobes, the spirocycle acrylamides preferentially liganded specific cysteines on diverse protein classes. One compound termed ZL-12A promoted the degradation of the TFIIH helicase ERCC3. Interestingly, ZL-12A reacts with the same cysteine (C342) in ERCC3 as the natural product triptolide, which did not lead to ERCC3 degradation but instead causes collateral loss of RNA polymerases. ZL-12A and triptolide cross-antagonized one another's protein degradation profiles. Finally, we provide evidence that the antihypertension drug spironolactone─previously found to promote ERCC3 degradation through an enigmatic mechanism─also reacts with ERCC3_C342. Our findings thus describe monofunctional degraders of ERCC3 and highlight how covalent ligands targeting the same cysteine can produce strikingly different functional outcomes.

Epidemiological characteristics of neuroendocrine neoplasms in Beijing: a population-based retrospective study.

BACKGROUND: The incidence of neuroendocrine neoplasms (NENs) is rising rapidly worldwide. However, there are few reports on these heterogeneous diseases in China. Our study aimed to explore the epidemiological characteristics of NENs in Beijing. METHODS: We conducted a retrospective cohort study using population-based cancer surveillance data in Beijing, China. All data were extracted from the Beijing Cancer Registry with incidence dates from 1 January 1998 to 31 December 2018; the follow-up period was through 31 December 2021. Segi's world standard population was used to estimate the age-standardized rate. Survival was estimated using the Kaplan-Meier method. RESULTS: From 1998 to 2018, the incidence of NENs in Beijing initially showed a significant increasing trend, from 1.07/100,000 to 3.53/100,000; this began to plateau after 2013. The age-specific incidence rate increased with age and peaked in the age group 70-74 years. The incidence in men was significantly higher than that in women (4.41/100,000 vs. 1.69/100,000). The most common sites of NENs were the lung (2.38/100,000) and rectum (0.14/100,000). Most NENs were diagnosed at a late stage. We found that NENs originating from the lung had worse overall survival than extrapulmonary NENs, and male patients had worse survival than female patients. CONCLUSIONS: This study retrospectively analyzed the epidemiological characteristics of NENs in Beijing from 1998 to 2018. Our findings provide a reference regarding the epidemiological statistics of NENs in Beijing to contribute to the prevention, diagnosis, and treatment of these specific tumors.

Phospholipase Cγ2 regulates endocannabinoid and eicosanoid networks in innate immune cells.

Human genetic studies have pointed to a prominent role for innate immunity and lipid pathways in immunological and neurodegenerative disorders. Our understanding of the composition and function of immunomodulatory lipid networks in innate immune cells, however, remains incomplete. Here, we show that phospholipase Cγ2 (PLCγ2 or PLCG2)-mutations in which are associated with autoinflammatory disorders and Alzheimer's disease-serves as a principal source of diacylglycerol (DAG) pools that are converted into a cascade of bioactive endocannabinoid and eicosanoid lipids by DAG lipase (DAGL) and monoacylglycerol lipase (MGLL) enzymes in innate immune cells. We show that this lipid network is tonically stimulated by disease-relevant human mutations in PLCγ2, as well as Fc receptor activation in primary human and mouse macrophages. Genetic disruption of PLCγ2 in mouse microglia suppressed DAGL/MGLL-mediated endocannabinoid-eicosanoid cross-talk and also caused widespread transcriptional and proteomic changes, including the reorganization of immune-relevant lipid pathways reflected in reductions in DAGLB and elevations in PLA2G4A. Despite these changes, Plcg2-/- mice showed generally normal proinflammatory cytokine and chemokine responses to lipopolysaccharide treatment, instead displaying a more restricted deficit in microglial activation that included impairments in prostaglandin production and CD68 expression. Our findings enhance the understanding of PLCγ2 function in innate immune cells, delineating a role in cross-talk with endocannabinoid/eicosanoid pathways and modulation of subsets of cellular responses to inflammatory stimuli.

Past dynamics and future prediction of the impacts of land use cover change and climate change on landscape ecological risk across the Mongolian plateau.

Land use/land cover (LULC) change and climate change are interconnected factors that affect the ecological environment. However, there is a lack of quantification of the impacts of LULC change and climate change on landscape ecological risk under different shared socioeconomic pathways and representative concentration pathways (SSP-RCP) on the Mongolian Plateau (MP). To fill this knowledge gap and understand the current and future challenges facing the MP's land ecological system, we conducted an evaluation and prediction of the effects of LULC change and climate change on landscape ecological risk using the landscape loss index model and random forest method, considering eight SSP-RCP coupling scenarios. Firstly, we selected MCD12Q1 as the optimal LULC product for studying landscape changes on the MP, comparing it with four other LULC products. We analyzed the diverging patterns of LULC change over the past two decades and observed significant differences between Mongolia and Inner Mongolia. The latter experienced more intense and extensive LULC change during this period, despite similar climate changes. Secondly, we assessed changes in landscape ecological risk and identified the main drivers of these changes over the past two decades using a landscape index model and random forest method. The highest-risk zone has gradually expanded, with a 30% increase compared to 2001. Lastly, we investigated different characteristics of LULC change under different scenarios by examining future LULC products simulated by the FLUS model. We also simulated the dynamics of landscape ecological risks under these scenarios and proposed an adaptive development strategy to promote sustainable development in the MP. In terms of the impact of climate change on landscape ecological risk, we found that under the same SSP scenario, increasing RCP emission concentrations significantly increased the areas with high landscape ecological risk while decreasing areas with low risk. By integrating quantitative assessments and scenario-based modeling, our study provides valuable insights for informing sustainable land management and policy decisions in the region.

Green and sustainable extraction of lignin by deep eutectic solvent, its antioxidant activity, and applications in the food industry.

Lignin, an amorphous biomacromolecule abundantly distributed in the plant kingdom, has gained considerable attention due to its intrinsic bioactivities and renewable nature. Owing to its polyphenolic structure, lignin has a variety of human health activities, including antioxidant, antimicrobial, antidiabetic, antitumor, and other activities. The extraction of lignin from various sources in a green and sustainable manner is critical in the food industry. Deep eutectic solvent (DES) has recently been recognized as a class of safe and environmentally friendly media capable of efficiently extracting lignin. This article comprehensively reviews the recent advances in lignin extraction using DES, discusses the influential factors on the antioxidant activity of lignin, interprets the relationship between antioxidant activity and lignin structure, and overviews the applications of lignin in the food industry. We aim to highlight the advantages of DES in lignin extraction and valorization from the nutrition and food views.

Performance of different colorectal cancer screening strategies: a long-term passive follow-up population-based screening program in Beijing, China.

BACKGROUND: We aimed to assess the performance of the risk assessment questionnaire and fecal immunochemical test (FIT) in a population-based colorectal cancer (CRC) screening program to provide timely evidence for tailored screening strategies in China. METHODS: This analysis was conducted using data from Beijing Cancer Screening Prospective Cohort Study (BCSPCS). A risk assessment questionnaire and FIT were selected as the primary screening methods, and participants with any positive results were referred to undergo a diagnostic colonoscopy. RESULTS: From 2015 to 2020, 148,636 Beijing residents aged 40-69 years were invited from designated communities, with 147,807 finishing the risk assessment questionnaire and 115,606 (78.2%) completing the FIT. Among the 42,969 (29.1%) high-risk CRC participants, 23,824 (55.4%) underwent colonoscopy. One year after enrollment, all subjects were linked to the Beijing Cancer Registry (BCR) database and 241 cases of CRC were confirmed. The CRC incidence rate was 58.2/100,000 for the low-risk arm and 418.9/100,000 for the high-risk arm. For participants who underwent colonoscopy, 91 CRC cases were detected, with a detection rate of 91.9% and 63.7% of them were early-stage cases. Furthermore, the sensitivities of utilizing the risk assessment questionnaire alone, FIT alone, combined risk assessment questionnaire and FIT were 75.7%, 50.1%, and 95.1%, and the specificities were 75.3%, 87.3%, and 70.7%, respectively. CONCLUSION: The Beijing CRC screening program can effectively detect early-onset CRC; however, the compliance with colonoscopy still needs to be improved.

DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products.

Microbial natural products represent a rich resource of evolved chemistry that forms the basis for the majority of pharmacotherapeutics. Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a particularly interesting class of natural products noted for their unique mode of biosynthesis and biological activities. Analyses of sequenced microbial genomes have revealed an enormous number of biosynthetic loci encoding RiPPs but whose products remain cryptic. In parallel, analyses of bacterial metabolomes typically assign chemical structures to only a minority of detected metabolites. Aligning these 2 disparate sources of data could provide a comprehensive strategy for natural product discovery. Here we present DeepRiPP, an integrated genomic and metabolomic platform that employs machine learning to automate the selective discovery and isolation of novel RiPPs. DeepRiPP includes 3 modules. The first, NLPPrecursor, identifies RiPPs independent of genomic context and neighboring biosynthetic genes. The second module, BARLEY, prioritizes loci that encode novel compounds, while the third, CLAMS, automates the isolation of their corresponding products from complex bacterial extracts. DeepRiPP pinpoints target metabolites using large-scale comparative metabolomics analysis across a database of 10,498 extracts generated from 463 strains. We apply the DeepRiPP platform to expand the landscape of novel RiPPs encoded within sequenced genomes and to discover 3 novel RiPPs, whose structures are exactly as predicted by our platform. By building on advances in machine learning technologies, DeepRiPP integrates genomic and metabolomic data to guide the isolation of novel RiPPs in an automated manner.

Green Extraction of Polyphenols via Deep Eutectic Solvents and Assisted Technologies from Agri-Food By-Products.

Polyphenols are the largest group of phytochemicals with important biological properties. Their presence in conveniently available low-cost sources, such as agri-food by-products, has gained considerable attention in their recovery and further exploitation. Retrieving polyphenols in a green and sustainable way is crucial. Recently, deep eutectic solvents (DESs) have been identified as a safe and environmentally benign medium capable of extracting polyphenols efficiently. This review encompasses the current knowledge and applications of DESs and assisted technologies to extract polyphenols from agri-food by-products. Particular attention has been paid to fundamental mechanisms and potential applications in the food, cosmetic, and pharmaceutical industries. In this way, DESs and DESs-assisted with advanced techniques offer promising opportunities to recover polyphenols from agri-food by-products efficiently, contributing to a circular and sustainable economy.

Cytochrome P450 oxidoreductase contributes to phospholipid peroxidation in ferroptosis.

Ferroptosis is widely involved in degenerative diseases in various tissues including kidney, liver and brain, and is a targetable vulnerability in multiple primary and therapy-resistant cancers. Accumulation of phospholipid hydroperoxides in cellular membranes is the hallmark and rate-limiting step of ferroptosis; however, the enzymes contributing to lipid peroxidation remain poorly characterized. Using genome-wide, CRISPR-Cas9-mediated suppressor screens, we identify cytochrome P450 oxidoreductase (POR) as necessary for ferroptotic cell death in cancer cells exhibiting inherent and induced susceptibility to ferroptosis. By genetic depletion of POR in cancer cells, we reveal that POR contributes to ferroptosis across a wide range of lineages and cell states, and in response to distinct mechanisms of ferroptosis induction. Using systematic lipidomic profiling, we further map POR's activity to the lipid peroxidation step in ferroptosis. Hence, our work suggests that POR is a key mediator of ferroptosis and potential druggable target for developing antiferroptosis therapeutics.

Waste-to-Resource Strategy to Fabricate Functionalized MOFs Composite Material Based on Durian Shell Biomass Carbon Fiber and Fe3O4 for Highly Efficient and Recyclable Dye Adsorption.

Recently, metal-organic frameworks (MOFs), which are porous inorganic-organic hybrid materials consisting of metal ions (clusters or secondary building units) and organic ligands through coordination bonds, have attracted wide attention because of their high surface area, huge ordered porosity, uniform structural cavities, and excellent thermal/chemical stability. In this work, durian shell biomass carbon fiber and Fe3O4 functionalized metal-organic framework composite material (durian shell fiber-Fe3O4-MOF, DFM) was synthesized and employed for the adsorption removal of methylene blue (MB) from wastewater. The morphology, structure, and chemical elements of the DFM material were characterized by scanning electron microscope (SEM), X-ray diffraction (XRD), transmission electron microscope (TEM), and X-ray photoelectron spectroscope (XPS) techniques. Adsorption conditions such as pH, adsorption time, and temperature were optimized. The adsorption isotherm and kinetics results show that the adsorption process of DFM material to MB is more in line with the Freundlich model and pseudo-second-order kinetic model. Using these models, the maximum adsorption capacity of 53.31 mg/g was obtained by calculation. In addition, DFM material could be easily reused through an external magnet and the removal rate of MB was still 80% after five adsorption cycles. The obtained results show that DFM composite material, as an economical, environmentally friendly, recyclable new adsorbent, can simply and effectively remove MB from wastewater.

SPIN4 Is a Principal Endogenous Substrate of the E3 Ubiquitin Ligase DCAF16.

DCAF16 is a substrate recognition component of Cullin-RING E3 ubiquitin ligases that can be targeted by electrophilic PROTACs (proteolysis targeting chimeras) to promote the nuclear-restricted degradation of proteins. The endogenous protein substates of DCAF16 remain unknown. In this study, we compared the protein content of DCAF16-wild type and DCAF16-knockout (KO) cells by untargeted mass spectrometry-based proteomics, identifying the Tudor domain-containing protein Spindlin-4 (SPIN4) as a protein with a level that was substantially increased in cells lacking DCAF16. Very few other proteomic changes were found in DCAF16-KO cells, pointing to a specific relationship between DCAF16 and SPIN4. Consistent with this hypothesis, we found that DCAF16 interacts with and ubiquitinates SPIN4, but not other related SPIN proteins, and identified a conserved lysine residue unique to SPIN4 that is involved in DCAF16 binding. Finally, we provide evidence that SPIN4 preferentially binds trimethylated histone H3K4 over other modified histone modifications. These results, taken together, indicate that DCAF16 and SPIN4 form a dedicated E3 ligase-substrate complex that regulates the turnover and presumed functions of SPIN4 in human cells.

The Association Between Age at Initiation of Alcohol Consumption and Type 2 Diabetes Mellitus: A Cohort Study of 0.5 Million Persons in China.

It is well known that alcohol consumption is associated with type 2 diabetes mellitus. However, the association of age at initiation of alcohol consumption and duration of alcohol drinking with type 2 diabetes mellitus among Chinese adults is not fully understood. This study was based on data from the China Kadoorie Biobank, which included 512,712 participants aged 30-79 years who were living in China in 2004-2008. A Cox proportional hazards model was used to estimate the association of AAI and drinking duration with type 2 diabetes. After adjustment for potential covariates, ages at alcohol initiation (AAIs) of 18.1-29.0 years, 29.1-39.0 years, and >39.0 years were associated with 22% (95% confidence interval (CI): 14, 30), 25% (95% CI: 17, 33), and 32% (95% CI: 24, 39) lower hazards of type 2 diabetes compared with abstaining, respectively. Drinking durations of <10.1 years, 10.1-20.0 years, and 20.1-30.0 years were associated with a lower risk of type 2 diabetes, compared with abstaining. Among current (weekly) drinkers, AAI <18.1 years and drinking duration >30.0 years were associated with 18% (95% CI: 4, 33) and 20% (95% CI: 3, 40) higher hazards of type 2 diabetes, compared with AAI 18.1-29.0 years and drinking duration <10.1 years, respectively. In conclusion, late AAI and a short drinking duration were associated with a lower risk of type 2 diabetes in this large prospective cohort study of Chinese adults, but early AAI and long drinking duration were not.

Scaffold-based selective SHP2 inhibitors design using core hopping, molecular docking, biological evaluation and molecular simulation.

PTPN11 (coding the gene of SHP2), a classic non-receptor protein tyrosine phosphatase, is implicated in multiple cell signaling pathway. Abnormal activation of SHP2 has been shown to contribute to a variety of human diseases, including Juvenile myelomonocytic leukemia (JMML), Noonan syndrome and tumors. Thus, the SHP2 inhibitors have important therapeutic value. Here, based on the compound PubChem CID 8,478,960 (IC50 = 45.01 µM), a series of thiophene [2,3-d] pyrimidine derivatives (IC50 = 0.4-37.87 µM) were discovered as novel and efficient inhibitors of SHP2 through powerful "core hopping" and CDOCKER technology. Furthermore, the SHP2-PTP phosphatase activity assay indicated that Comp#5 (IC50 = 0.4 µM) was the most active SHP2 inhibitor. Subsequently, the effects of Comp#5 on the structure and function of SHP2 were investigated through molecular dynamics (MD) simulation and post-kinetic analysis. The result indicated that Comp#5 enhanced the interaction of residues THR357, ARG362, LYS366, PRO424, CYS459, SER460, ALA461, ILE463, ARG465, THR507 and GLN510 with the surrounding residues, improving the stability of the catalytic active region and the entrance of catalytic active region. In particular, the Comp#5 conjugated with residue ARG362, elevating the efficient and selectivity of SHP2 protein. The study here may pave the way for discovering the novel SHP2 inhibitors for suffering cancer patients.

Leakage behavior of toxic substances of naphthalene sulfonate-formaldehyde condensation from cement based materials.

Naphthalene sulfonate-formaldehyde condensatation (NSF) is the main component of the naphthalene based water reducers for cement based materials, as well as an organic substance with potential toxicity. However it is still uncertain whether it can leak from the cement based materials. In this work, the leakage ratio and adsorption behavior of NSF from various cement based materials such as the different water/cement (w/c) ratio, NSF content, types of cementitious materials as well as at different hydration time were evaluated. The product components of the cement based materials cured for different times were also quantified to explore the mechanisms which are responsible for the leakage and adsorption behaviors. The results indicate that more NSF, lower w/c ratio and less mineral admixture decrease the NSF leakage ratio. The leakage ratio of NSF from cement paste mixed 0.3% NSF is up to 50.8% at 0.5 h, and it decreases to 31.0% at 28 d. The leakage ratio of NSF from cement paste decreases as the hydration time prolongs. The lower leakage ratio corresponds to the higher adsorption capacity. Less adsorption capacity and thinner adsorption film imply that lower temperature and mineral admixture decrease the NSF adsorption behavior. When 0.3% NSF is added into the cement paste, the adsorption amount and NSF layer thickness are 5.53 mg/g and 0.98 nm, 5.87 mg/g and 4.7  nm at 0.5 h and 28 d respectively. The result demonstrates that the adsorption behavior of NSF in cement significantly increases at the initial several hours and gradually stabilizes after the first day. The X-ray powder diffractometer (XRD) results show that the contents of tricalcium silicate (C3S) and dicalcium silicate (C2S) continuously decline and the amorphous phases and ettringite (AFt) increase rapidly in the early stage. NSF adsorption and leakage behaviors are closely related to the hydration process of cement. These results indicate that NSF can definitely leak from the cement based materials and thus the NSF potential environmental pollution cannot be ignored. At least, it should be restricted or cautious to produce the water tower and pipe concrete structure with it. These results will sever as a theoretically reference for the pollution control as well as better application of NSF in cement-based materials.