Antisense-mediated splicing correction as a therapeutic approach for p53 K120R mutation.

The TP53 c.359A＞G mutation significantly disrupts the expression of the major TP53 transcript variant encoding p53 K120R by generating a new splice donor site. An antisense morpholino oligomer (AMO) targeting this mutation successfully restored normal splicing and the expression of the major TP53 variant. Given that p53 exerts its tumor suppressor function by regulating target genes responsible for growth arrest or apoptosis, the p53 K120R protein enhanced by AMO exhibits impaired transcriptional regulation of CDKN1A, a key growth arrest gene, while maintaining normal induction of the pro-apoptotic BBC3 gene. As a result, the mutant p53 K120R protein shows a defective cell growth arrest phenotype but retains apoptotic function, suggesting that it may still possess some tumor suppressor activity. Furthermore, lysine 120, known to provide a critical acetylation site for p53 activation, highlights the relevance of acetylation in tumor suppression through studies of the p53 K120R mutant. However, our findings demonstrate that targeting mutant TP53 mRNA with AMO is essential for restoring p53 function. In conclusion, this study emphasizes the potential of AMO-mediated splice correction as a therapeutic approach for TP53 mutations.

Protective Effects of Purple Corn (Zea mays L.) Byproduct Extract on Blue Light-Induced Retinal Damage in A2E-Accumulated ARPE-19 Cells.

This study investigated the antioxidative characteristics of Zea mays L. purple corn cob and husk extract (PCHE) and its potential protective effects against blue light (BL)-induced damage in N-retinylidene-N-retinylethanolamine (A2E)-accumulated ARPE-19 retinal pigment epithelial cells. PCHE had a 2,2-diphenyl-1-picrylhydrazyl radical-scavenging capacity and Trolox equivalent antioxidant capacity of 1.28±0.43 mM Trolox equivalents (TE)/g and 2,545.41±34.13 mM TE/g, respectively. Total content of anthocyanins, polyphenols, and flavonoids in the PCHE was 11.13±0.10 mg cyanidin-3-glucoside equivalents/100 g, 227.90±7.38 mg gallic acid equivalents/g, and 117.75±2.46 mg catechin equivalents/g, respectively. PCHE suppressed the accumulation of A2E and the photooxidation caused by BL in a dose-dependent manner. After initial treatment with 25 µM/mL A2E and BL, ARPE-19 cells showed increased cell viability following additional treatment with 15 µg/mL PCHE while the expression of the p62 sequestosome 1 decreased, whereas that of heme oxygenase-1 protein increased compared with that in cells without PCHE treatment. This suggests that PCHE may slow the autophagy induced by BL exposure in A2E-accumulated retinal cells and protect them against oxidative stress.

Exploring the complex link between obesity and intelligence: Evidence from systematic review, updated meta-analysis, and Mendelian randomization.

Obesity is a major public health concern associated with a higher risk of various comorbidities. Some studies have explored the impact of obesity on cognitive function and, conversely, how lower intelligence might increase the risk of later obesity. The aim of this study is to analyze a complex relationship between body mass index (BMI) and intelligence quotient (IQ), employing a comprehensive approach, including a systematic review, meta-analysis, and Mendelian randomization (MR). We extracted the data from Medline and Embase to identify relevant studies published since June 22, 2009. MR analysis relied on genetic databases such as the Genome-Wide Association Study (GWAS) and the Genetic Investigation of Anthropometric Traits (GIANT) to explore potential causal relationships. The systematic review and meta-analysis encompassed 34 and 17 studies, respectively. They revealed a substantial correlation between obesity and reduced IQ, particularly notable among school-age children (mean difference -5.26; 95% CI: -7.44 to -3.09). Notably, within the IQ subgroup, verbal IQ also exhibited a significant association with a mean difference of -7.73 (95% CI: -14.70 to -0.77) in school-age children. In contrast, the MR did not unveil a significant causal relationship between BMI and IQ, both in childhood and adulthood. This comprehensive analysis underscores a significant correlation between BMI and IQ, particularly in school-age children. However, the MR analysis implies a potentially weaker causal relationship. Future large-scale cohort studies should address potential confounding factors to provide further insights into the BMI-IQ relationship.

Topical Therapy for Atopic Dermatitis: What is New and the New Paradigm.

Atopic dermatitis (AD) is a chronic inflammatory skin disorder that requires a complex management strategy, which often involves multiple and diverse topicals and systemic treatment regimens. While topical steroids and more recently calcineurin inhibitors have been the mainstay therapy for mild-to-moderate disease, recent advances in the understanding of AD pathogenesis have led to the development of different new targets, rapidly widening our therapeutic armamentarium. This review summarizes their efficacy and safety data. We also review topical optimization strategies, including the recently published topical volume calculator, to maximize long-term disease control, especially when using multiple agents at the same time.

Effects of gamification on academic motivation and confidence of undergraduate nursing students: A systematic review and meta-analysis.

OBJECTIVES: This review aimed to evaluate the effects of gamification on academic motivation and confidence among undergraduate nursing students and identify the game design elements contributing to these effects. DESIGN: Systematic review and meta-analysis. DATA SOURCES: Comprehensive systematic searches were conducted to retrieve randomized controlled trials (RCTs) and quasi-experimental studies (QES) with control groups published in English and Korean from inception to January 31, 2024, using PubMed, Embase, CINAHL Plus, ERIC, ProQuest Central, Cochrane Library, and RISS. REVIEW METHODS: Eligible studies, including grey literature, were selected. The quality of the selected studies was evaluated using the Joanna Briggs Institute Critical Tool. Meta-analyses based on a random-effects model were conducted to estimate the standardized pooled effects (SMD). Subgroup analyses were conducted to identify the effect size moderators and game design elements that contributed to the effect size. The grading of recommendations, assessment, development, and evaluation approach (GRADE) was used to evaluate the certainty of evidence. RESULTS: A total of 22 studies were selected for the systematic review, and 18 studies were included in the meta-analysis. The SMD for academic motivation (SMD of RCTs = 0.86, 95 % CI [0.27, 1.45]; SMD of QES = 1.22, 95 % CI [0.17, 2.26]) and confidence (SMD of RCTs = 1.11, 95 % CI [0.54, 1.68]; SMD of QES = 0.79, 95 % CI [0.40, 1.19]) revealed moderate-to-large effects. The subgroup analysis revealed significant differences in effect sizes across academic years, measurement scales, study areas, study quality, game duration, and game design elements. GRADE assessments for academic motivation and confidence were rated as moderate and low, respectively. CONCLUSION: This review provides convincing evidence for the positive effects of gamification interventions on academic motivation and confidence among undergraduate nursing students. However, the limited number of RCTs and moderate-to-low certainty of the evidence underscore the need for additional research.

Impact of Quorum Sensing on the Virulence and Survival Traits of Burkholderia plantarii.

Quorum sensing (QS) is a mechanism by which bacteria detect and respond to cell density, regulating collective behaviors. Burkholderia plantarii, the causal agent of rice seedling blight, employs the LuxIR-type QS system, common among Gram-negative bacteria, where LuxI-type synthase produces QS signals recognized by LuxR-type regulators to control gene expression. This study aimed to elucidate the QS mechanism in B. plantarii KACC18965. Through whole-genome analysis and autoinducer assays, the plaI gene, responsible for QS signal production, was identified. Motility assays confirmed that C8-homoserine lactone (C8-HSL) serves as the QS signal. Physiological experiments revealed that the QS-defective mutant exhibited reduced virulence, impaired swarming motility, and delayed biofilm formation compared to the wild type. Additionally, the QS mutant demonstrated weakened antibacterial activity against Escherichia coli and decreased phosphate solubilization. These findings indicate that QS in B. plantarii significantly influences various pathogenicity and survival traits, including motility, biofilm formation, antibacterial activity, and nutrient acquisition, highlighting the critical role of QS in pathogen virulence and adaptability.

Immunogenicity and Neutralization of Recombinant Vaccine Candidates Expressing F and G Glycoproteins against Nipah Virus.

Nipah virus (NiV), of the Paramyxoviridae family, causes highly fatal infections in humans and is associated with severe neurological and respiratory diseases. Currently, no commercial vaccine is available for human use. Here, eight structure-based mammalian-expressed recombinant proteins harboring the NiV surface proteins, fusion glycoprotein (F), and the major attachment glycoprotein (G) were produced. Specifically, prefusion NiV-F and/or NiV-G glycoproteins expressed in monomeric, multimeric (trimeric F and tetra G), or chimeric forms were evaluated for their properties as sub-unit vaccine candidates. The antigenicity of the recombinant NiV glycoproteins was evaluated in intramuscularly immunized mice, and the antibodies in serum were assessed. Predictably, all homologous immunizations exhibited immunogenicity, and neutralizing antibodies to VSV-luciferase-based pseudovirus expressing NiV-GF glycoproteins were found in all groups. Comparatively, neutralizing antibodies were highest in vaccines designed in their multimeric structures and administered as bivalent (GMYtet + GBDtet) and trivalent (Ftri + GMYtet + GBDtet). Additionally, while all adjuvants were able to elicit an immunogenic response in vaccinated groups, bivalent (GMYtet + GBDtet) and trivalent (Ftri + GMYtet + GBDtet) induced more potent neutralizing antibodies when administered with oil-in-water nano-emulsion adjuvant, AddaS03. For all experiments, the bivalent GMYtet + GBDtet was the most immunogenic vaccine candidate. Results from this study highlight the potential use of these mammalian-expressed recombinant NiV as vaccine candidates, deserving further exploration.

The Potential of Percent Agreement as an Adjunctive Diagnostic Tool for Acute Temporomandibular Disorder.

Background/Objectives: It is well established that individuals with chronic temporomandibular disorder (TMD) exhibit differences in their physical and psychosocial characteristics from those with acute TMD. However, few studies have analyzed the physical and psychosocial characteristics of patients with acute TMD. The objective of this cross-sectional study is twofold: first, to ascertain whether there are differences in physical and psychosocial factors among patients with acute TMD based on the percent agreement between patient-reported pain sites and pain sites identified through standardized palpation and, second, to determine the potential of percent agreement as a diagnostic and prognostic factor. Methods: We analyzed physical and psychosocial factors in 309 patients diagnosed with acute TMD. Of these, 171 patients were selected for an analysis of their response to treatment. These patients were divided into three groups based on their percent agreement: Group A (agreement under 80%), Group B (agreement 80-89%), and Group C (agreement 90% or over) in the initial analysis and Group a (agreement under 80%), Group b (agreement 80-89%), and Group c (agreement 90% or over) in the subsequent analysis. This study was approved by the Ethics Committee of Pusan National University Dental Hospital (IRB No. 2023-05-011, 25 May 2023). Results: The lower the percent agreement, the greater the parafunctional oral habits, stress, chronicity, somatization, depression, anxiety, and number of painful sites. A lower percent agreement was associated with poorer treatment outcomes. The percent agreement demonstrated a 41.2% capacity to predict residual pain after treatment. Conclusions: Clinicians can utilize percentage agreement as an adjunctive diagnostic tool to provide more suitable treatments to patients.

The Chronic Toxicity of Endocrine-Disrupting Chemical to Daphnia magna: A Transcriptome and Network Analysis of TNT Exposure.

Endocrine-disrupting chemicals (EDCs) impair growth and development. While EDCs can occur naturally in aquatic ecosystems, they are continuously introduced through anthropogenic activities such as industrial effluents, pharmaceutical production, wastewater, and mining. To elucidate the chronic toxicological effects of endocrine-disrupting chemicals (EDCs) on aquatic organisms, we collected experimental data from a standardized chronic exposure test using Daphnia magna (D. magna), individuals of which were exposed to a potential EDC, trinitrotoluene (TNT). The chronic toxicity effects of this compound were explored through differential gene expression, gene ontology, network construction, and putative adverse outcome pathway (AOP) proposition. Our findings suggest that TNT has detrimental effects on the upstream signaling of Tcf/Lef, potentially adversely impacting oocyte maturation and early development. This study employs diverse bioinformatics approaches to elucidate the gene-level toxicological effects of chronic TNT exposure on aquatic ecosystems. The results provide valuable insights into the molecular mechanisms of the adverse impacts of TNT through network construction and putative AOP proposition.

Prevalence and Correlates of Suicidal Ideation among Psycho-Oncology Outpatients.

PURPOSE: The characteristics of suicidal ideation among psycho-oncology outpatients remain unexplored. This study determined the prevalence and risk factors of suicidal ideation among patients in a psycho-oncology outpatient clinic. MATERIALS AND METHODS: The prevalence of suicidal ideation during the previous 2 weeks among 545 psycho-oncology outpatients aged 80 years or below was determined using the Patient Health Questionnaire-9 Item 9. Descriptive analyses, including the prevalence of suicidal ideation, were performed. After multiple imputation, multivariable logistic regression was performed using demographic and clinical variables and functional (the Functional Assessment of Cancer Therapy-General) and emotional status (the Hospital Anxiety and Depression Scale and the distress thermometer). RESULTS: There were 252 (46.2%) suicidal ideators. After adjusting for sex and age, active disease [odds ratio (OR)=1.708, 95% confidence interval (CI)=1.049-2.780], lower levels of physical (OR=0.948, 95% CI=0.905-0.992) and emotional well-being (OR=0.925, 95% CI=0.875-0.978), and higher degrees of depressive symptoms (OR=1.126, 95% CI=1.036-1.224) and psychological distress (OR=1.201, 95% CI=1.071-1.347) were associated with suicidal ideation. CONCLUSION: Approximately half of the psycho-oncology outpatients experienced suicidal ideation, emphasizing the importance of identifying and understanding the risk factors of suicidal ideation specific to this group. For those who are under active cancer treatment, show poorer physical and emotional well-being, and report more severe depressive symptoms and psychological distress, a thorough evaluation of suicidal ideation needs to be performed.

AMPK-Mediated Hypolipidemic Effects of a Salvia miltiorrhiza and Paeonia lactiflora Mixed Extract on High-Fat Diet-Induced Liver Triglyceride Accumulation: An In Vivo and In Vitro Study.

BACKGROUND: This study investigates the hypolipidemic effects of a mixed extract of Salvia miltiorrhiza and Paeonia lactiflora (USCP119) in HFD-fed hamsters and in vitro cellular models. METHODS: Over an 8-week period, HFD-fed hamsters were assigned to one of six groups: normal diet, HFD control, HFD with 50 mg/kg USCP119, HFD with 100 mg/kg USCP119, HFD with 50 mg/kg USCP119 twice daily (BID), and HFD with omega-3 fatty acids. Key outcomes assessed included body weight, serum triglycerides (TG), total cholesterol (TC), liver weight, hepatic TG levels, and epididymal fat. In cellular models, the impact of USCP119 on lipid accumulation and adipogenic markers was evaluated. RESULTS: USCP119 treatment at 50 mg/kg BID resulted in the lowest weight gain (15.5%) and the most significant reductions in serum TG and hepatic TG levels compared to the HFD control. The 100 mg/kg dose also led to substantial reductions in serum TG and TC levels and notable decreases in low-density lipoprotein cholesterol. USCP119 at 50 mg/kg once daily reduced TG and TC levels but was less effective than the higher doses. In cellular models, USCP119 was non-toxic up to 400 µg/mL and effectively reduced lipid accumulation, modulated adipogenic markers, and enhanced AMPK signaling, improving lipid metabolism and insulin sensitivity. CONCLUSIONS: All USCP119 treatments demonstrated effectiveness in managing hyperlipidemia and related metabolic disorders, with variations in impact depending on the dosage. The ability of USCP119 to reduce fat accumulation, improve lipid profiles, and enhance insulin sensitivity highlights its potential as a valuable dietary supplement for addressing high-fat diet-induced hyperlipidemia and metabolic disturbances.

Actinidia chinensis Planch Ameliorates Photoaging in UVB-Irradiated NIH-3T3 Cells and SKH-1 Hairless Mice by Controlling the Reactive Oxygen Species/AKT Pathway.

In this study, we evaluated the antiphotoaging properties of Actinidia chinensis Planch (ACP) and the molecular mechanisms underlying its ability to prevent UVB-mediated photoaging. Administration of the ethanolic extract of ACP (EEACP) to the dorsal area of hairless mice effectively ameliorated UVB-mediated wrinkle formation, epidermal thickening, and loss of lipid droplets in the epidermis. Additionally, the UVB-induced loss of collagen content in the epidermis was significantly attenuated in mouse skin treated with EEACP. The expression of procollagen type 1 and metalloproteinase-1a, which are related to collagen content in the epidermis, was restored by EEACP treatment in UVB-irradiated mice and NIH-3T3 mouse skin fibroblast cells. Interestingly, EEACP effectively ameliorated UVB-induced reactive oxygen species overproduction. Furthermore, the activation/phosphorylation of AKT, rather than mitogen-activated protein kinases, has been identified as a major target of EEACP in preventing UVB-mediated photoaging. Additionally, N-(1 deoxy-1-fructosyl) valine and phenethylamine glucuronide were identified as analytical indicators of EEACP using high-performance liquid chromatography/mass spectrometry. These results suggest that EEACP can be developed as a functional natural agent capable of preventing photoaging by attenuating UVB-induced activation of the reactive oxygen species/AKT pathway.

Simple Enzymatic Incorporation of 2'OMeU Nucleotide at the End of the Poly-A Tail for Enhancement of the mRNA Stability and Protein Expression.

This study focused on the efficient post-transcriptional incorporation of a modified nucleoside at the end of the poly-A tail of mRNA. The modified mRNA was obtained in high yield and served to enhance protein expression. Utilizing poly-U polymerase, our method successfully enabled a single 2'OMeU residue to be incorporated into mRNA, which unexpectedly provided significant stabilization, even with only a single incorporation, to enhance the resistance of mRNA to degradation by cellular exonuclease. This stabilization effect allowed the mRNA to remain viable within the cell for an extended period to ultimately increase the translation efficiency at least 3-fold. This approach to mRNA modification at the 3' end with a single 2'OMeU residue, by utilizing a straightforward tailing method, surpasses other ligation methods in terms of mRNA modification efficiency. Collectively, our results highlight the potential of this method to significantly advance the development of highly effective mRNA-based therapies in the future.

Cancer Risks of Patients with Graves' Disease Who Received Antithyroid Drugs as Initial Treatment: A Nationwide Population-Based Analysis.

Background: Population-based studies that examine the associations between hyperthyroidism and cancer risk have yielded inconsistent results. It remains unclear whether the risks of different cancers increase in patients with Graves' disease (GD) who received antithyroid drugs (ATDs) as initial treatment. We aimed to determine whether cancer risk increases in patients with GD, compared with controls. Methods: This nationwide retrospective cohort study utilized data from the National Health Information Database of South Korea. We included 29,502 patients aged >20 years with GD, who received ATDs as initial treatment, and 57,173 age- and sex-matched controls. The primary outcome was the incidence of various types of cancers. Hazard ratios (HRs) with confidence intervals (CIs) for cancer risk were estimated using Cox proportional hazards models. We also analyzed HR by follow-up period since the diagnosis of GD, accounting for surveillance effect. Results: The risk of biliary tract and pancreatic cancers (HR: 1.41, CI: 1.24-1.60), thyroid cancer (HR: 15.51, CI: 12.29-19.57), prostate cancer (HR: 1.48, CI: 1.28-1.71), and ovarian cancer (HR: 1.31, CI: 1.13-1.52) was elevated in the GD group than in the control group even after the first year of follow-up was excluded. The increased risk of these cancers persisted after a follow-up period of more than 5 years. The risk of thyroid cancer in patients with GD was higher during the initial follow-up period (1 to <2 years) (HR: 19.35, CI: 7.66-48.87) compared with that in the follow-up period exceeding 2 years. The cancer risk estimates remained significant after excluding patients with GD who underwent subsequent radioactive iodine therapy. Conclusion: In this large-scale population-based study, GD was associated with increased risks of biliary tract and pancreatic, prostate, ovarian, and thyroid cancers. The increased risk of thyroid cancer, particularly during the initial follow-up period, may be a surveillance effect.

ChatGPT vs. sleep disorder specialist responses to common sleep queries: Ratings by experts and laypeople.

BACKGROUND: Many individuals use the Internet, including generative artificial intelligence like ChatGPT, for sleep-related information before consulting medical professionals. This study compared responses from sleep disorder specialists and ChatGPT to common sleep queries, with experts and laypersons evaluating the responses' accuracy and clarity. METHODS: We assessed responses from sleep medicine specialists and ChatGPT-4 to 140 sleep-related questions from the Korean Sleep Research Society's website. In a blinded study design, sleep disorder experts and laypersons rated the medical helpfulness, emotional supportiveness, and sentence comprehensibility of the responses on a 1-5 scale. RESULTS: Laypersons rated ChatGPT higher for medical helpfulness (3.79 ± 0.90 vs. 3.44 ± 0.99, p < .001), emotional supportiveness (3.48 ± 0.79 vs. 3.12 ± 0.98, p < .001), and sentence comprehensibility (4.24 ± 0.79 vs. 4.14 ± 0.96, p = .028). Experts also rated ChatGPT higher for emotional supportiveness (3.33 ± 0.62 vs. 3.01 ± 0.67, p < .001) but preferred specialists' responses for sentence comprehensibility (4.15 ± 0.74 vs. 3.94 ± 0.90, p < .001). When it comes to medical helpfulness, the experts rated the specialists' answers slightly higher than the laypersons did (3.70 ± 0.84 vs. 3.63 ± 0.87, p = .109). Experts slightly preferred specialist responses overall (56.0%), while laypersons favored ChatGPT (54.3%; p < .001). ChatGPT's responses were significantly longer (186.76 ± 39.04 vs. 113.16 ± 95.77 words, p < .001). DISCUSSION: Generative artificial intelligence like ChatGPT may help disseminate sleep-related medical information online. Laypersons appear to prefer ChatGPT's detailed, emotionally supportive responses over those from sleep disorder specialists.

Diagnostic value of a deep learning-based hyoid bone tracking model for aspiration in patients with post-stroke dysphagia.

Objective: Hyoid bone movement is potentially related to aspiration risk in post-stroke dysphagia (PSD) patients but is difficult to assess quantitatively. This study aimed to measure the distance of hyoid bone movement more efficiently and accurately using a deep learning model and determine the clinical usefulness of the model in PSD patients. Methods: This study included 85 patients with PSD within 6 months from onset. Patients were grouped into an aspiration group (n = 35) and a non-aspiration group (n = 50) according to the results of a videofluoroscopic swallowing study. Hyoid bone movement was tracked using a deep learning model constructed with the BiFPN-U-Net(T) architecture. The maximum distance of hyoid bone movement was measured horizontally (H max), vertically (V max), and diagonally (D max). Results: Compared with the non-aspiration group, the aspiration group showed significant decreases in hyoid bone movement in all directions. The area under the curve of V max was highest at 0.715 with a sensitivity of 0.680 and specificity of 0.743. The V max cutoff value for predicting aspiration risk was 1.61 cm. The success of oral feeding at the time of discharge was significantly more frequent when hyoid movement was equal to or larger than the cutoff value although no significant relationship was found between hyoid movement and other clinical characteristics. Conclusion: Hyoid bone movement of PSD patients can be measured quantitatively and efficiently using a deep learning model. Deep learning model-based analysis of hyoid bone movement seems to be useful for predicting aspiration risk and the possibility of resuming oral feeding.

Asymmetrical Functionalization of Polarizable Interface Restructuring Molecules for Rapid and Longer Operative Lithium Metal Batteries.

Lithium metal batteries (LMBs) have been recognized as high-energy storage alternatives; however, problematic surface reactions due to dendritic Li growth are major obstacles to their widespread utilization. Herein, a 3-mercapto-1-propanesulfonic acid sodium salt (MPS) with asymmetrically functionalized thiol and sulfonate groups as polarizable interface-restructuring molecules is proposed to achieve rapid and longer-operating LMBs. Under a harsh condition of 5 mA cm-2, Li-Li symmetric cells employing MPS can be cycled over 1200 cycles, outperforming those employing other molecules symmetrically functionalized by thiol or sulfonate groups. The improved performance of the Li|V2O5 full cell is demonstrated by introducing MPS additives. MPS additives offer advantages by flattening the surface, reconfiguring Li nucleation and growth along the stable (110) plane, and forming a durable and conductive solid-electrolyte interface layer (SEI). This study suggests an effective way to develop a new class of electrolyte additives for LMBs by controlling engineering factors, such as functional groups and polarizable properties.

Evolutionary dependency of cancer mutations in gene pairs inferred by nonsynonymous-synonymous mutation ratios.

BACKGROUND: Determining the impact of somatic mutations requires understanding the functional relationship of genes acquiring mutations; however, it is largely unknown how mutations in functionally related genes influence each other. METHODS: We employed non-synonymous-to-synonymous or dNdS ratios to evaluate the evolutionary dependency (ED) of gene pairs, assuming a mutation in one gene of a gene pair can affect the evolutionary fitness of mutations in its partner genes as mutation context. We employed PanCancer- and tumor type-specific mutational profiles to infer the ED of gene pairs and evaluated their biological relevance with respect to gene dependency and drug sensitivity. RESULTS: We propose that dNdS ratios of gene pairs and their derived cdNS (context-dependent dNdS) scores as measure of ED distinguishing gene pairs either as synergistic (SYN) or antagonistic (ANT). Mutation contexts can induce substantial changes in the evolutionary fitness of mutations in the paired genes, e.g., IDH1 and IDH2 mutation contexts lead to substantial increase and decrease of dNdS ratios of ATRX indels and IDH1 missense mutations corresponding to SYN and ANT relationship with positive and negative cdNS scores, respectively. The impact of gene silencing or knock-outs on cell viability (genetic dependencies) often depends on ED, suggesting that ED can guide the selection of candidates for synthetic lethality such as TCF7L2-KRAS mutations. Using cell line-based drug sensitivity data, the effects of targeted agents on cell lines are often associated with mutations of genes exhibiting ED with the target genes, informing drug sensitizing or resistant mutations for targeted inhibitors, e.g., PRSS1 and CTCF mutations as resistant mutations to EGFR and BRAF inhibitors for lung adenocarcinomas and melanomas, respectively. CONCLUSIONS: We propose that the ED of gene pairs evaluated by dNdS ratios can advance our understanding of the functional relationship of genes with potential biological and clinical implications.

Mapping Tumor Habitats in IDH-Wild Type Glioblastoma: Integrating MR Imaging, Pathologic, and RNA Data from Ivy Glioblastoma Atlas Project.

BACKGROUND: To spatially validate intratumoral subregions (tumor habitat) using physiologic MRI on pathology of the isocitrate dehydrogenase (IDH)-wildtype whole-glioblastoma sample. METHODS: Data of 20 patients (168 slides) were obtained from the Ivy Glioblastoma Atlas Project. On MRI, tumor habitats were defined using voxel-wise clustering of apparent diffusion coefficient (ADC) and cerebral blood volume (CBV) maps for contrast-enhancing lesion (CEL) and non-enhancing lesion (NEL). On pathology slides, normalized areas of leading edge (LE), infiltrating tumor (IT), cellular tumor (CT), hypervascular lesion (CThypervascular), and perinecrotic lesion (CTperinecrotic) were obtained. Gross specimen was co-registered on MRI and correlation between pathology-MRI habitats was calculated. RNA sequencing of 67 samples was assessed using 4 Neftel subtypes and further correlated with pathology. RESULTS: Six tumor habitats were identified: hypervascular, hypovascular cellular, and hypovascular hypocellular habitats for CEL and NEL. CT was correlated with hypovascular cellular habitat in CEL (r= 0.238, p =.005). IT was correlated with hypovascular cellular habitat in NEL (r= 0.294, p =.017). CThypervascular was correlated with hypervascular habitat in NEL (r= 0.195, p = .023). CTperinecrotic was correlated with imaging necrosis (r= 0.199, p =.005). Astrocyte-like subtypes were correlated with IT (r= 0.256, p <.001), while mesenchymal-like subtypes were correlated with CTperinecrotic area (r= 0.246, p <.001). CONCLUSION: Pathologically matched tumor subregions were cellular tumor with hypovascular cellular habitat in CEL and infiltrative tumor with hypovascular cellular habitat in NEL. Identification of the most aggressive as well as infiltrative tumor portion can be achieved using non-invasive MRI tumor habitats.