Cancer Burden Is Controlled by Mural Cell-ß3-Integrin Regulated Crosstalk with Tumor Cells.

Enhanced blood vessel (BV) formation is thought to drive tumor growth through elevated nutrient delivery. However, this observation has overlooked potential roles for mural cells in directly affecting tumor growth independent of BV function. Here we provide clinical data correlating high percentages of mural-ß3-integrin-negative tumor BVs with increased tumor sizes but no effect on BV numbers. Mural-ß3-integrin loss also enhances tumor growth in implanted and autochthonous mouse tumor models with no detectable effects on BV numbers or function. At a molecular level, mural-cell ß3-integrin loss enhances signaling via FAK-p-HGFR-p-Akt-p-p65, driving CXCL1, CCL2, and TIMP-1 production. In particular, mural-cell-derived CCL2 stimulates tumor cell MEK1-ERK1/2-ROCK2-dependent signaling and enhances tumor cell survival and tumor growth. Overall, our data indicate that mural cells can control tumor growth via paracrine signals regulated by ß3-integrin, providing a previously unrecognized mechanism of cancer growth control.

Mosaic RBD nanoparticles induce intergenus cross-reactive antibodies and protect against SARS-CoV-2 challenge.

Recurrent spillovers of α- and ß-coronaviruses (CoV) such as severe acute respiratory syndrome (SARS)-CoV, Middle East respiratory syndrome-CoV, SARS-CoV-2, and possibly human CoV have caused serious morbidity and mortality worldwide. In this study, six receptor-binding domains (RBDs) derived from α- and ß-CoV that are considered to have originated from animals and cross-infected humans were linked to a heterotrimeric scaffold, proliferating cell nuclear antigen (PCNA) subunits, PCNA1, PCNA2, and PCNA3. They assemble to create a stable mosaic multivalent nanoparticle, 6RBD-np, displaying a ring-shaped disk with six protruding antigens, like jewels in a crown. Prime-boost immunizations with 6RBD-np in mice induced significantly high Ab titers against RBD antigens derived from α- and ß-CoV and increased interferon (IFN-γ) production, with full protection against the SARS-CoV-2 wild type and Delta challenges. The mosaic 6RBD-np has the potential to induce intergenus cross-reactivity and to be developed as a pan-CoV vaccine against future CoV spillovers.

ERG activity is regulated by endothelial FAK coupling with TRIM25/USP9x in vascular patterning.

Precise vascular patterning is crucial for normal growth and development. The ERG transcription factor drives Delta-like ligand 4 (DLL4)/Notch signalling and is thought to act as a pivotal regulator of endothelial cell (EC) dynamics and developmental angiogenesis. However, molecular regulation of ERG activity remains obscure. Using a series of EC-specific focal adhesion kinase (FAK)-knockout (KO) and point-mutant FAK-knock-in mice, we show that loss of ECFAK, its kinase activity or phosphorylation at FAK-Y397, but not FAK-Y861, reduces ERG and DLL4 expression levels together with concomitant aberrations in vascular patterning. Rapid immunoprecipitation mass spectrometry of endogenous proteins identified that endothelial nuclear-FAK interacts with the deubiquitinase USP9x and the ubiquitin ligase TRIM25. Further in silico analysis confirms that ERG interacts with USP9x and TRIM25. Moreover, ERG levels are reduced in FAKKO ECs via a ubiquitin-mediated post-translational modification programme involving USP9x and TRIM25. Re-expression of ERG in vivo and in vitro rescues the aberrant vessel-sprouting defects observed in the absence of ECFAK. Our findings identify ECFAK as a regulator of retinal vascular patterning by controlling ERG protein degradation via TRIM25/USP9x.

Divergent evolution of extreme production of variant plant monounsaturated fatty acids.

Metabolic extremes provide opportunities to understand enzymatic and metabolic plasticity and biotechnological tools for novel biomaterial production. We discovered that seed oils of many Thunbergia species contain up to 92% of the unusual monounsaturated petroselinic acid (18:1Δ6), one of the highest reported levels for a single fatty acid in plants. Supporting the biosynthetic origin of petroselinic acid, we identified a Δ6-stearoyl-acyl carrier protein (18:0-ACP) desaturase from Thunbergia laurifolia, closely related to a previously identified Δ6-palmitoyl-ACP desaturase that produces sapienic acid (16:1Δ6)-rich oils in Thunbergia alata seeds. Guided by a T. laurifolia desaturase crystal structure obtained in this study, enzyme mutagenesis identified key amino acids for functional divergence of Δ6 desaturases from the archetypal Δ9-18:0-ACP desaturase and mutations that result in nonnative enzyme regiospecificity. Furthermore, we demonstrate the utility of the T. laurifolia desaturase for the production of unusual monounsaturated fatty acids in engineered plant and bacterial hosts. Through stepwise metabolic engineering, we provide evidence that divergent evolution of extreme petroselinic acid and sapienic acid production arises from biosynthetic and metabolic functional specialization and enhanced expression of specific enzymes to accommodate metabolism of atypical substrates.

Boc Protection for Diamine-Appended MOF Adsorbents to Enhance CO2 Recyclability under Realistic Humid Conditions.

Among the various metal-organic framework (MOF) adsorbents, diamine-functionalized Mg2(dobpdc) (dobpdc4- = 4,4-dioxidobiphenyl-3,3'-dicarboxylate) shows remarkable carbon dioxide removal performance. However, applying diamine-functionalized Mg2(dobpdc) in practical applications is premature because it shows persistent performance degradation under real flue gas conditions containing water vapor owing to diamine loss during wet cycles. To address this issue, we employed hydrophobic carbonate compounds to protect diamine groups in een-Mg2(dobpdc) (een-MOF, een = N-ethylethylenediamine). tert-Butyl dicarbonate (Boc) reacted rapidly with diamines at the pore openings of MOF particles to form dense secondary and tertiary hydrophobic amines, effectively preventing moisture ingress. The Boc-protected een-MOF-Boc1 maintained excellent CO2 adsorption even under simulated flue gas conditions containing 10% H2O. This observation indicates that Boc protection renders een groups intact during repeated wet cycles, suggesting that Boc-protected een groups are resistant to replacement by water molecules. To increase the practicability of the MOF adsorbent, we fabricated een-MOF/PAN-Boc1 composite beads by shaping MOF particles with polyacrylonitrile (PAN). Notably, the composite beads maintained their CO2 adsorption performance even after repeating the temperature swing adsorption process more than 150 times in 10% water vapor. Furthermore, breakthrough tests showed that the dynamic CO2 separation performance was retained under humid conditions. These results demonstrate that Boc protection provides an easy and effective way to develop promising adsorbents with high CO2 adsorption capacity, long-term durability, and the properties required for postcombustion applications.

Extended MOF-74-Type Variant with an Azine Linkage: Efficient Direct Air Capture and One-Pot Synthesis.

Direct air capture (DAC) shows considerable promise for the effective removal of CO2; however, materials applicable to DAC are lacking. Among metal-organic framework (MOF) adsorbents, diamine-Mg2(dobpdc) (dobpdc4- = 4,4-dioxidobiphenyl-3,3'-dicarboxylate) effectively removes low-pressure CO2, but the synthesis of the organic ligand requires high temperature, high pressure, and a toxic solvent. Besides, it is necessary to isolate the ligand for utilization in the synthesis of the framework. In this study, we synthesized a new variant of extended MOF-74-type frameworks, M2(hob) (M = Mg2+, Co2+, Ni2+, and Zn2+; hob4- = 5,5'-(hydrazine-1,2-diylidenebis(methanylylidene))bis(2-oxidobenzoate)), constructed from an azine-bonded organic ligand obtained through a facile condensation reaction at room temperature. Functionalization of Mg2(hob) with N-methylethylenediamine, N-ethylethylenediamine, and N,N'-dimethylethylenediamine (mmen) enables strong interactions with low-pressure CO2, resulting in top-tier adsorption capacities of 2.60, 2.49, and 2.91 mmol g-1 at 400 ppm of CO2, respectively. Under humid conditions, the CO2 capacity was higher than under dry conditions due to the presence of water molecules that aid in the formation of bicarbonate species. A composite material combining mmen-Mg2(hob) and polyvinylidene fluoride, a hydrophobic polymer, retained its excellent adsorption performance even after 7 days of exposure to 40% relative humidity. In addition, the one-pot synthesis of Mg2(hob) from a mixture of the corresponding monomers is achieved without separate ligand synthesis steps; thus, this framework is suitable for facile large-scale production. This work underscores that the newly synthesized Mg2(hob) and its composites demonstrate significant potential for DAC applications.

Evaluation of prognostic potential of ß-catenin and L1CAM expression according to endometrial cancer risk group.

OBJECTIVE: We investigate the prognostic role of ß-catenin and L1 neuronal cell-adhesion molecule (L1CAM) according to risk groups in endometrial carcinomas (EC). METHODS: A total of 335 EC patients were classified according to the Proactive Molecular Risk Classifier for Endometrial Cancer. We evaluated the expression of ß-catenin and L1CAM using immunohistochemistry, and their association with clinicopathological characteristics and survival. RESULTS: The expressions of ß-catenin and L1CAM were observed in 10.4% of all patients, respectively, and showed mutually exclusive pattern. While ß-catenin expression was associated with endometrioid histology (p = 0.035) and low tumor grade (p = 0.045), L1CAM expression was associated with non-endometrioid histology (p < 0.001), high tumor grade (p < 0.001), lymphovascular space invasion (p = 0.006), and advanced International Federation of Gynecology and Obstetrics (FIGO) stage (p = 0.001). ß-catenin expression was most frequent in the no specific molecular (NSMP) group (26/35, 74.3%), followed by the DNA polymerase-ε-mutated (POLE-mut) (6/35, 17.1%), and mismatch repair-deficiency (dMMR) (3/35, 8.6%). L1CAM expression was most frequent in the p53-abnormal group (22/35, 62.9%), followed by the NSMP (6/35, 17.1%), dMMR (4/35, 11.4%), and POLE-mut (3/35, 8.6%). Although both markers did not show statistical significance in multivariate analysis for both progression-free survival (PFS) and overall survival in entire cohort, ß-catenin positivity was identified as the sole factor associated with worse PFS in the high-intermediate risk subgroup (p = 0.001). CONCLUSION: The expression of nuclear ß-catenin may serve as a potential biomarker for predicting recurrence and guiding therapeutic strategies in high-intermediate risk EC patients.

Identification and characterization of a marine bacterium extract from Mameliella sp. M20D2D8 with antiviral effects against influenza A and B viruses.

Despite significant improvements in vaccines and chemotherapeutic drugs, pathogenic RNA viruses continue to have a profound impact on the global economy and pose a serious threat to animal and human health through emerging and re-emerging outbreaks of diseases. To overcome the challenge of viral adaptation and evolution, increased vigilance is required. Particularly, antiviral drugs derived from new, natural sources provide an attractive strategy for controlling problematic viral diseases. In this antiviral study, we discovered a previously unknown bacterium, Mameliella sp. M20D2D8, by conducting an antiviral screening of marine microorganisms. An extract from M20D2D8 exhibited antiviral activity with low cytotoxicity and was found to be effective in vitro against multiple influenza virus strains: A/PR8 (IC50 = 2.93 µg/mL, SI = 294.85), A/Phil82 (IC50 = 1.42 µg/mL, SI = 608.38), and B/Yamagata (IC50 = 1.59 µg/mL, SI = 543.33). The antiviral action was found to occur in the post-entry stages of viral replication and to suppress viral replication by inducing apoptosis in infected cells. Moreover, it efficiently suppressed viral genome replication, protein synthesis, and infectivity in MDCK and A549 cells. Our findings highlight the antiviral capabilities of a novel marine bacterium, which could potentially be useful in the development of drugs for controlling viral diseases.

Establishment of canine mammary gland tumor cell lines harboring PI3K/Akt activation as a therapeutic target.

Canine mammary gland tumors (MGT) have a poor prognosis in intact female canines, posing a clinical challenge. This study aimed to establish novel canine mammary cancer cell lines from primary tumors and characterize their cellular and molecular features to find potential therapeutic drugs. The MGT cell lines demonstrated rapid cell proliferation and colony formation in an anchorage-independent manner. Vimentin and α-SMA levels were significantly elevated in MGT cell lines compared to normal canine kidney (MDCK) cells, while CDH1 expression was either significantly lower or not detected at all, based on quantitative real-time PCR (qRT-PCR) analysis. Functional annotation and enrichment analysis revealed that epithelial-mesenchymal transition (EMT) phenotypes and tumor-associated pathways, particularly the PI3K/Akt signaling pathway, were upregulated in MGT cells. BYL719 (Alpelisib), a PI3K inhibitor, was also examined for cytotoxicity on the MGT cell lines. The results show that BYL719 can significantly inhibit the proliferation of MGT cell lines in vitro. Overall, our findings suggest that the MGT cell lines may be valuable for future studies on the development, progression, metastasis, and management of tumors.

From temperament to YouTube: exploring the link between childhood temperament, YouTube usage patterns, and emotional/behavioral problems among children.

BACKGROUND: YouTube is a widely used video sharing and social networking platform among children and adolescents. However, research on YouTube usage among this population remains scarce. Specifically, studies on factors that influence children and adolescents' usage are clinically significant but largely lacking. Additionally, few studies have examined the association between usage and emotional/behavioral problems, which is fundamental to smartphone research. Therefore, this study explored the relationship between early childhood temperament, subsequent YouTube usage patterns, and emotional/behavioral problems. METHODS: The Kids Cohort for Understanding Internet Addiction Risk Factors in Early Childhood (K-CURE) is the first long-term prospective cohort study in Korea aimed at understanding the long-term effects of media exposure on young children. The study included 195 children aged 8-11 years enrolled in the K-CURE study. Caregivers, predominantly mothers, who voluntarily participated during their visits to community centers for children's mental health in Korea's major cities, completed a detailed self-administered survey. Childhood temperament was measured in 2018 when the children were 5-8 years old. Subsequent YouTube usage patterns and emotional/behavioral problems were assessed in 2021. Data were analyzed using frequency analysis, correlation analysis, and multiple linear regression. RESULTS: The study found that 21.0% of children started using YouTube before age 4, with the most common onset age being 8-9 years (30.3%). These children used YouTube on average 4.8 days per week for 68.5 min per day. Early childhood persistence was negatively associated with the subsequent YouTube usage duration, and the age at first YouTube use was negatively correlated with subsequent usage frequency. Furthermore, a younger age at first YouTube use and higher usage frequency were significantly associated with increased emotional/behavioral problems. CONCLUSIONS: In the YouTube environment, where content is automatically recommended based on user preferences, traits related to usage patterns may be associated with persistence, which is linked to self-regulation. Considering the current trend where children use smartphones, contents frequently for very short durations, our findings highlight the importance of self-regulation in the media usage of children who are still developing. Additionally, our results provide fundamental information for future YouTube studies and illustrate similarities and differences between smartphone and YouTube research.

Investigation of Laser-Induced Graphene (LIG) on a Flexible Substrate and Its Functionalization by Metal Doping for Gas-Sensing Applications.

Graphene materials synthesized using direct laser writing (laser-induced graphene; LIG) make favorable sensor materials because of their large surface area, ease of fabrication, and cost-effectiveness. In particular, LIG decorated with metal nanoparticles (NPs) has been used in various sensors, including chemical sensors and electronic and electrochemical biosensors. However, the effect of metal decoration on LIG sensors remains controversial; hypotheses based on computational simulations do not always match the experimental results, and even the experimental results reported by different researchers have not been consistent. In the present study, we explored the effects of metal decorations on LIG gas sensors, with NO2 and NH3 gases as the representative oxidizing and reducing agents, respectively. To eliminate the unwanted side effects arising from metal salt residues, metal NPs were directly deposited via vacuum evaporation. Although the gas sensitivities of the sensors deteriorate upon metal decoration irrespective of the metal work function, in the case of NO2 gas, they improve upon metal decoration in the case of NH3 exposure. A careful investigation of the chemical structure and morphology of the metal NPs in the LIG sensors shows that the spontaneous oxidation of metal NPs with a low work function changes the behavior of the LIG gas sensors and that the sensors' behaviors under NO2 and NH3 gases follow different principles.

Profiling of endogenous metabolites and changes in intestinal microbiota distribution after GEN-001 (Lactococcus lactis) administration.

This study aimed to identify metabolic biomarkers and investigate changes in intestinal microbiota in the feces of healthy participants following administration of Lactococcus lactis GEN-001. GEN-001 is a single-strain L. lactis strain isolated from the gut of a healthy human volunteer. The study was conducted as a parallel, randomized, phase 1, open design trial. Twenty healthy Korean males were divided into five groups according to the GEN-001 dosage and dietary control. Groups A, B, C, and D1 received 1, 3, 6, and 9 GEN-001 capsules (1 × 1011 colony forming units), respectively, without dietary adjustment, whereas group D2 received 9 GEN-001 capsules with dietary adjustment. All groups received a single dose. Fecal samples were collected 2 days before GEN-001 administration to 7 days after for untargeted metabolomics and gut microbial metagenomic analyses; blood samples were collected simultaneously for immunogenicity analysis. Levels of phenylalanine, tyrosine, cholic acid, deoxycholic acid, and tryptophan were significantly increased at 5-6 days after GEN-001 administration when compared with predose levels. Compared with predose, the relative abundance (%) of Parabacteroides and Alistipes significantly decreased, whereas that of Lactobacillus and Lactococcus increased; Lactobacillus and tryptophan levels were negatively correlated. A single administration of GEN-001 shifted the gut microbiota in healthy volunteers to a more balanced state as evidenced by an increased abundance of beneficial bacteria, including Lactobacillus, and higher levels of the metabolites that have immunogenic properties.

Postsynthetically Modified Alkoxide-Exchanged Ni2(OR)2BTDD: Synergistic Interactions of CO2 with Open Metal Sites and Functional Groups.

Postsynthetic modifications (PSMs) of metal-organic frameworks (MOFs) play a crucial role in enhancing material performance through open metal site (OMS) functionalization or ligand exchange. However, a significant challenge persists in preserving open metal sites during ligand exchange, as these sites are inherently bound by incoming ligands. In this study, for the first time, we introduced alkoxides by exchanging bridging chloride in Ni2Cl2BTDD (BTDD=bis (1H-1,2,3,-triazolo [4,5-b],-[4',5'-i]) dibenzo[1,4]dioxin) through PSM. Rietveld refinement of synchrotron X-ray diffraction data indicated that the alkoxide oxygen atom bridges Ni(II) centers while the OMSs of the MOF are preserved. Due to the synergy of the existing OMS and introduced functional group, the alkoxide-exchanged MOFs showed CO2 uptakes superior to the pristine MOF. Remarkably, the tert-butoxide-substituted Ni_T exhibited a nearly threefold and twofold increase in CO2 uptake compared to Ni2Cl2BTDD at 0.15 and 1 bar, respectively, as well as high water stability relative to the other exchanged frameworks. Furthermore, the Grand Canonical Monte Carlo simulations for Ni_T suggested that CO2 interacts with the OMS and the surrounding methyl groups of tert-butoxide groups, which is responsible for the enhanced CO2 capacity. This work provides a facile and unique synthetic strategy for realizing a desirable OMS-incorporating MOF platform through bridging ligand exchange.

Simultaneous Quantification of Apolipoprotein C-III O-Glycoforms by Protein-MRM.

Apolipoprotein C-III (APOC-III) regulates triglyceride levels, associated with a risk of cardiovascular disease. One gene generates several proteoforms, each with a different molecular mass and a unique function. Unlike peptide multiple reaction monitoring (MRM), protein-MRM without digestion is required to analyze clinically relevant individual proteoforms. We developed a protein-MRM method without digestion to individually quantify APOC-III proteoforms in human serum. We optimized the protein-MRM method following 60% acetonitrile extraction with C18 filtration. Bovine serum and myoglobin served as supporting cushions and the internal standard during sample preparation, respectively. Furthermore, we evaluated the LOD, lower limit of quantification, linearity, accuracy, and precision. Good correlation compared with turbidimetric immunoassay (TIA) and peptide-MRM was observed using 30 clinical sera. Individual APOC-III O-glycoforms were identified by top-down proteomics and simultaneously quantified using the protein-MRM method. The sum abundance of APOC-III proteoforms was significantly correlated with TIA and peptide-MRM. Our protein-MRM method provides an affordable and rapid quantification of potential disease-specific proteoforms. Precise quantification of each proteoform allows investigators to identify novel biological roles potentially related to cardiovascular disease or novel biomarkers. We expect our protein-oriented method to be more clinically useful than antibody-based immunoassays and peptide-oriented MRM analysis, especially for quantification of a biomarker proteoform with certain post-translational modifications.

Aminal-Linked Covalent Organic Frameworks with hxl-a and Quasi-hcb Topologies for Efficient C2 H6 /C2 H4 Separation.

In reticular chemistry, topology is a powerful concept for defining the structures of covalent organic frameworks (COFs). However, due to the lack of diversity in the symmetry and reaction stoichiometry of the monomers, only 5% of the two-dimensional topologies have been reported to be COFs. To overcome the limitations of COF connectivity and pursue novel topologies in COF structures, two aminal-linked COFs, KUF-2 and KUF-3, are prepared, with dumbbell-shaped secondary building units. Linear dialdehydes and piperazine are condensed at a ratio of 1:2 to construct an aminal linkage, leading to unreported hxl-a (KUF-2) and quasi-hcb (KUF-3) structures. Notably, KUF-3 displays top-tier C2 H6 /C2 H4 selectivity and C2 H6 uptake at 298 K, outperforming most porous organic materials. The intrinsic aromatic ring-rich and Lewis basic pore environments, and appropriate pore widths enable the selective adsorption of C2 H6 , as confirmed by Grand Canonical Monte Carlo simulations. Dynamic breakthrough curves revealed that C2 H6 can be selectively separated from a gas mixture of C2 H6 and C2 H4 . This study suggests that topology-based design of aminal-COFs is an effective strategy for expanding the field of reticular chemistry and provides the facile integration of strong Lewis basic sites for selective C2 H6 /C2 H4 separation.

Switchable Xe/Kr Selectivity in a Hofmann-Type Metal-Organic Framework via Temperature-Responsive Rotational Dynamics.

The development of adsorbents for Kr and Xe separation is essential to meet industrial demands and for energy conservation. Although a number of previous studies have focused on Xe-selective adsorbents, stimuli-responsive Xe/Kr-selective adsorbents still remain underdeveloped. Herein, a Hofmann-type framework Co(DABCO)[Ni(CN)4 ] (referred to as CoNi-DAB; DABCO = 1,4-diazabicyclo[2,2,2]octane) that provides a temperature-dependent switchable Xe/Kr separation performance is reported. CoNi-DAB showed high Kr/Xe (0.8/0.2) selectivity with significant Kr adsorption at 195 K as well as high Xe/Kr (0.2/0.8) selectivity with superior Xe adsorption at 298 K. Such adsorption features are associated with the temperature-dependent rotational configuration of the DABCO ligand, which affects the kinetic gate-opening temperature of Xe and Kr. The packing densities of Xe (2.886 g cm-3 at 298 K) and Kr (2.399 g  cm-3 at 195 K) inside the framework are remarkable and comparable with those of liquid Xe (3.057 g cm-3 ) and liquid Kr (2.413 g cm-3 ), respectively. Breakthrough experiments confirm the temperature-dependent reverse separation performance of CoNi-DAB at 298 K under dry and wet (88% relative humidity) conditions and at 195 K under dry conditions. The unique adsorption behavior is also verified through van der Waals (vdW)-corrected density functional theory (DFT) calculations and nudged elastic band (NEB) simulations.

PSMD1 as a prognostic marker and potential target in oropharyngeal cancer.

BACKGROUND: Despite the diverse genetic mutations in head and neck cancer, the chemotherapy outcome for this cancer has not improved for decades. It is urgent to select prognostic factors and therapeutic targets for oropharyngeal cancer to establish precision medicine. Recent studies have identified PSMD1 as a potential prognostic marker in several cancers. We aimed to assess the prognostic significance of PSMD1 expression in oropharyngeal squamous cell carcinoma (OPSCC) patients using immunohistochemistry. METHODS: We studied 64 individuals with OPSCC tissue from surgery at Seoul National University Bundang Hospital between April 2008 and August 2017. Immunostaining analysis was conducted on the tissue microarray (TMA) sections (4 µm) for p16 and PSMD1. H-score, which scale from 0 to 300, was calculated from each nucleus, cytoplasm, and cellular expression. Clinicopathological data were compared with Chi-squared test, Fisher's exact test, t-test, and logistic regression. Survival data until 2021 were achieved from national statistical office of Korea. Kaplan-Meier method and cox-regression model were used for disease-specific survival (DSS) analysis. RESULTS: H-score of 90 in nucleus was appropriate cutoff value for 'High PSMD1 expression' in OPSCC. Tonsil was more frequent location in low PSMD1 group (42/52, 80.8%) than in high PSMD1 group (4/12, 33.3%; P = .002). Early-stage tumor was more frequent in in low PSMD1 group (45/52, 86.5%) than in high PSMD1 group (6/12, 50%; P = .005). HPV was more positive in low PSMD1 group (43/52, 82.7%) than in high PSMD1 group (5/12, 41.7%; P = .016). Patients with PSMD1 high expression showed poorer DSS than in patients with PSMD1 low expression (P = .006 in log rank test). In multivariate analysis, PSMD1 expression, pathologic T staging, and specimen age were found to be associated with DSS (P = .011, P = .025, P = .029, respectively). CONCLUSIONS: In our study, we established PSMD1 as a negative prognostic factor in oropharyngeal squamous cell carcinoma, indicating its potential as a target for targeted therapy and paving the way for future in vitro studies on drug repositioning.

A differential diagnosis between uterine leiomyoma and leiomyosarcoma using transcriptome analysis.

BACKGROUND: The objective of this study was to estimate the accuracy of transcriptome-based classifier in differential diagnosis of uterine leiomyoma and leiomyosarcoma. We manually selected 114 normal uterine tissue and 31 leiomyosarcoma samples from publicly available transcriptome data in UCSC Xena as training/validation sets. We developed pre-processing procedure and gene selection method to sensitively find genes of larger variance in leiomyosarcoma than normal uterine tissues. Through our method, 17 genes were selected to build transcriptome-based classifier. The prediction accuracies of deep feedforward neural network (DNN), support vector machine (SVM), random forest (RF), and gradient boosting (GB) models were examined. We interpret the biological functionality of selected genes via network-based analysis using GeneMANIA. To validate the performance of trained model, we additionally collected 35 clinical samples of leiomyosarcoma and leiomyoma as a test set (18 + 17 as 1st and 2nd test sets). RESULTS: We discovered genes expressed in a highly variable way in leiomyosarcoma while these genes are expressed in a conserved way in normal uterine samples. These genes were mainly associated with DNA replication. As gene selection and model training were made in leiomyosarcoma and uterine normal tissue, proving discriminant of ability between leiomyosarcoma and leiomyoma is necessary. Thus, further validation of trained model was conducted in newly collected clinical samples of leiomyosarcoma and leiomyoma. The DNN classifier performed sensitivity 0.88, 0.77 (8/9, 7/9) while the specificity 1.0 (8/8, 8/8) in two test data set supporting that the selected genes in conjunction with DNN classifier are well discriminating the difference between leiomyosarcoma and leiomyoma in clinical sample. CONCLUSION: The transcriptome-based classifier accurately distinguished uterine leiomyosarcoma from leiomyoma. Our method can be helpful in clinical practice through the biopsy of sample in advance of surgery. Identification of leiomyosarcoma let the doctor avoid of laparoscopic surgery, thus it minimizes un-wanted tumor spread.

Prognostic significance of L1CAM expression in addition to ProMisE in endometrial cancer.

OBJECTIVE: To investigate the prognostic significance of L1 cell-adhesion molecule (L1CAM), ß-catenin, and programmed death-ligand 1 (PD-L1) in endometrial cancer (EC) patients, with a focus on p53 wild-type subgroup, for additional risk stratification. METHODS: This retrospective cohort study included EC patients classified according to Proactive Molecular Risk Classifier for Endometrial Cancer (ProMisE) who underwent primary surgical treatment at the single center between January 2014 and December 2018. Immunohistochemical staining was performed for four mismatch repair (MMR) proteins, p53, L1CAM, ß-catenin, and PD-L1. DNA polymerase epsilon (POLE) mutation was detected by hot spot sequencing via droplet digital polymerase chain reaction. Survival outcome of each subgroup of L1CAM, ß-catenin, and PD-L1 was measured according to their expression. RESULTS: A total of 162 EC patients were included. Endometrioid histologic type and early-stage disease were 140 (86.4%) and 109 (67.3%), respectively. ProMisE classification assigned 48 (29.6%), 16 (9.9%), 72 (44.4%), and 26 (16.0%) patients to MMR-deficient, POLE-mutated, p53 wild-type, and p53 abnormal subgroups, respectively. L1CAM was identified as an independent poor prognostic factor for progression-free survival (PFS; adjusted hazard ratio [aHR], 3.207; 95% confidence interval (CI), 1.432-7.187; P = 0.005), whereas ß-catenin and PD-L1 positivity were not associated with recurrence (P = 0.462 and P = 0.152, respectively). In p53 wild-type subgroup, L1CAM positivity was associated with worse PFS (aHR, 4.906; 95% CI, 1.685-14.287; P = 0.004). CONCLUSION: L1CAM positivity was associated with poor prognosis in EC and further stratified the risk of recurrence in p53 wild-type subgroup, whereas ß-catenin and PD-L1 were not informative for risk stratification.

Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method.

Protein-ligand interactions are essential to drug discovery and drug development efforts. Desirable on-target or multitarget interactions are the first step in finding an effective therapeutic, while undesirable off-target interactions are the first step in assessing safety. In this work, we introduce a novel ligand-based featurization and mapping of human protein pockets to identify closely related protein targets and to project novel drugs into a hybrid protein-ligand feature space to identify their likely protein interactions. Using structure-based template matches from PDB, protein pockets are featured by the ligands that bind to their best co-complex template matches. The simplicity and interpretability of this approach provide a granular characterization of the human proteome at the protein-pocket level instead of the traditional protein-level characterization by family, function, or pathway. We demonstrate the power of this featurization method by clustering a subset of the human proteome and evaluating the predicted cluster associations of over 7000 compounds.