Metabolomics profiling for diagnosis of acute renal failure after cardiopulmonary bypass.

RATIONALE: Acute renal failure (ARF) is one of the most serious complications of cardiopulmonary bypass (CPB) surgery. Serum creatinine level is a key compound examined to understand whether renal function is normal. However, its level may vary based on age, gender, race, muscle mass, nutrition, and drugs taken by an individual. In addition, it may not be detected without a 50% reduction in renal function and may lead to delays in treatment. New markers are needed for early diagnosis of ARF. They were determined for early diagnosis of ARF after CPB. Metabolic differences in plasma samples of individuals who developed and did not develop ARF after cardiopulmonary bypass were determined. METHODS: This study was the first to perform an untargeted metabolomics analysis for early diagnosis of ARF after CPB surgery. Plasma samples were taken from 105 patients (9 ARF patients) at five time points to identify the time at which a more accurate ARF diagnosis can be made. A total of 687 samples, including quality control samples, were analyzed. RESULTS: Two hundred twenty-six metabolites were identified using retention index libraries. Based on the statistical evaluations, tryptophan, threonine, and methionine were found in lower concentrations in patients with ARF compared to the control group at all time points. Whereas gluconic acid, hypoxanthine, and lactic acid showed a decreasing trend over time, longitudinal analysis showed that cysteine, hippuric acid, and uric acid levels increased over time in the ARF group. CONCLUSIONS: These metabolites are candidate biomarkers for early diagnosis of ARF as well as biomarkers for tracking the recovery of ARF patients.

Exploiting epigenetic targets to overcome taxane resistance in prostate cancer.

The development of taxane resistance remains a major challenge for castration resistant prostate cancer (CR-PCa), despite the effectiveness of taxanes in prolonging patient survival. To uncover novel targets, we performed an epigenetic drug screen on taxane (docetaxel and cabazitaxel) resistant CR-PCa cells. We identified BRPF reader proteins, along with several epigenetic groups (CBP/p300, Menin-MLL, PRMT5 and SIRT1) that act as targets effectively reversing the resistance mediated by ABCB1. Targeting BRPFs specifically resulted in the resensitization of resistant cells, while no such effect was observed on the sensitive compartment. These cells were successfully arrested at the G2/M phase of cell cycle and underwent apoptosis upon BRPF inhibition, confirming the restoration of taxane susceptibility. Pharmacological inhibition of BRPFs reduced ABCB1 activity, indicating that BRPFs may be involved in an efflux-related mechanism. Indeed, ChIP-qPCR analysis confirmed binding of BRPF1 to the ABCB1 promoter suggesting direct regulation of the ABCB1 gene at the transcriptional level. RNA-seq analysis revealed that BRPF1 knockdown affects the genes enriched in mTORC1 and UPR signaling pathways, revealing potential mechanisms underlying its functional impact, which is further supported by the enhancement of taxane response through the combined inhibition of ABCB1 and mTOR pathways, providing evidence for the involvement of multiple BRPF1-regulated pathways. Beyond clinical attributes (Gleason score, tumor stage, therapy outcome, recurrence), metastatic PCa databases further supported the significance of BRPF1 in taxane resistance, as evidenced by its upregulation in taxane-exposed PCa patients.

Vocal fold cryptococcal granuloma: A rare occurrence in immunocompetent patient.

INTRODUCTION AND IMPORTANCE: Cryptoccous infection or cryptococcosis is a severe opportunistic infection occurring mainly in immunocompromised patients. Laryngeal cryptococcus infection is rare. In an immunocompetent patient, inhaled corticosteroid was reported to be a possible risk factor. CASE PRESENTATION: We discuss a case of right vocal fold cryptococcus infection in a healthy, immunocompetent 71-year-old man with no history of inhaled corticosteroid, presented with hoarseness and intermittent aspiration symptom for 1 year duration. Further examination showed right anterior vocal fold mass with presence of right vallecular cyst. CLINICAL DISCUSSION: Patient underwent direct laryngoscopy, excision of right vocal fold mass and marsupialization of vallecular cyst. Histopathological examination revealed cryptococcal infection. Patient subsequently treated with oral fluconazole 400 mg daily for 6 months. To date, hoarseness and aspiration symptoms have resolved. CONCLUSION: We are sharing our experience in managing laryngeal cryptococcus infection in an immunocompetent patient where the associated risk factors discussed in previous literatures are absent.

Epigenetic-focused CRISPR/Cas9 screen identifies (absent, small, or homeotic)2-like protein (ASH2L) as a regulator of glioblastoma cell survival.

BACKGROUND: Glioblastoma is the most common and aggressive primary brain tumor with extremely poor prognosis, highlighting an urgent need for developing novel treatment options. Identifying epigenetic vulnerabilities of cancer cells can provide excellent therapeutic intervention points for various types of cancers. METHOD: In this study, we investigated epigenetic regulators of glioblastoma cell survival through CRISPR/Cas9 based genetic ablation screens using a customized sgRNA library EpiDoKOL, which targets critical functional domains of chromatin modifiers. RESULTS: Screens conducted in multiple cell lines revealed ASH2L, a histone lysine methyltransferase complex subunit, as a major regulator of glioblastoma cell viability. ASH2L depletion led to cell cycle arrest and apoptosis. RNA sequencing and greenCUT&RUN together identified a set of cell cycle regulatory genes, such as TRA2B, BARD1, KIF20B, ARID4A and SMARCC1 that were downregulated upon ASH2L depletion. Mass spectrometry analysis revealed the interaction partners of ASH2L in glioblastoma cell lines as SET1/MLL family members including SETD1A, SETD1B, MLL1 and MLL2. We further showed that glioblastoma cells had a differential dependency on expression of SET1/MLL family members for survival. The growth of ASH2L-depleted glioblastoma cells was markedly slower than controls in orthotopic in vivo models. TCGA analysis showed high ASH2L expression in glioblastoma compared to low grade gliomas and immunohistochemical analysis revealed significant ASH2L expression in glioblastoma tissues, attesting to its clinical relevance. Therefore, high throughput, robust and affordable screens with focused libraries, such as EpiDoKOL, holds great promise to enable rapid discovery of novel epigenetic regulators of cancer cell survival, such as ASH2L. CONCLUSION: Together, we suggest that targeting ASH2L could serve as a new therapeutic opportunity for glioblastoma. Video Abstract.

Meta-Analysis Assessing Efficacy and Safety of Vitamin K Antagonists Versus Direct Oral Anticoagulants for Atrial Fibrillation After Transcatheter Aortic Valve Implantation.

Patients who underwent transcatheter aortic valve implantation (TAVI) with concomitant atrial fibrillation (AF) are at a higher risk for thromboembolic and bleeding events. The optimal antithrombotic strategy for patients with AF after TAVI remains unclear. We sought to determine the comparative efficacy and safety of direct oral anticoagulants (DOAC) versus oral vitamin K antagonists (VKAs) in these patients. Electronic databases such as PubMed, Cochrane, and Embase databases were searched till January 31, 2023, for relevant studies evaluating clinical outcomes of VKA versus DOAC in patients with AF after TAVI. Outcomes assessed were (1) all-cause mortality, (2) stroke, (3) major/life-threatening bleeding, and (4) any bleeding. Hazard ratios (HRs) were pooled in meta-analysis using random effect model. Nine studies (2 randomized and 7 observational) were included in systematic review, and 8 studies with 25,769 patients were eligible to be included in the meta-analysis. The mean age of the patients was 82.1 years, and 48.3% were male. Pooled analysis using random-effects model showed no statistically significant difference in all-cause mortality (HR 0.91, 95% confidence interval [CI] 0.76 to 1.10, p = 0.33), stroke (HR 0.96, 95% CI 0.80 to 1.16, p = 0.70), and major/life-threatening bleeding (HR 1.05, 95% CI 0.82 to 1.35, p = 0.70) in patients that received DOAC compared with oral VKA. Risk of any bleeding was lower in the DOAC group compared with oral VKA (HR 0.83, 95% CI 0.76 to 0.91, p = 0.0001). In patients with AF, DOACs appear to be a safe alternative oral anticoagulation strategy to oral VKA after TAVI. Further randomized studies are required to confirm the role of DOACs in those patients.

EPIKOL, a chromatin-focused CRISPR/Cas9-based screening platform, to identify cancer-specific epigenetic vulnerabilities.

Dysregulation of the epigenome due to alterations in chromatin modifier proteins commonly contribute to malignant transformation. To interrogate the roles of epigenetic modifiers in cancer cells, we generated an epigenome-wide CRISPR-Cas9 knockout library (EPIKOL) that targets a wide-range of epigenetic modifiers and their cofactors. We conducted eight screens in two different cancer types and showed that EPIKOL performs with high efficiency in terms of sgRNA distribution and depletion of essential genes. We discovered novel epigenetic modifiers that regulate triple-negative breast cancer (TNBC) and prostate cancer cell fitness. We confirmed the growth-regulatory functions of individual candidates, including SS18L2 and members of the NSL complex (KANSL2, KANSL3, KAT8) in TNBC cells. Overall, we show that EPIKOL, a focused sgRNA library targeting ~800 genes, can reveal epigenetic modifiers that are essential for cancer cell fitness under in vitro and in vivo conditions and enable the identification of novel anti-cancer targets. Due to its comprehensive epigenome-wide targets and relatively high number of sgRNAs per gene, EPIKOL will facilitate studies examining functional roles of epigenetic modifiers in a wide range of contexts, such as screens in primary cells, patient-derived xenografts as well as in vivo models.

Mechanical Behaviour of Pin-Reinforced Foam Core Sandwich Panels Subjected to Low Impact Loading.

As a light structure, composite sandwich panels are distinguished by their significant bending stiffness that is rapidly used in the manufacture of aircraft bodies. This study focuses on the mechanical behaviour of through-thickness polymer, pin-reinforced foam core sandwich panels subjected to indentation and low impact loading. Experimental and computational approaches are used to study the global and internal behaviour of the sandwich panel. The samples for experimental testing were made from glass/polyester laminates as the face sheets and polyurethane foam as the foam core. To further reinforce the samples against bending, different sizes of polymeric pins were implemented on the sandwich panels. The sandwich panel was fabricated using the vacuum infusion process. Using the experimental data, a finite element model of the sample was generated in LS-DYNA software, and the effect of pin size and loading rate were examined. Results of the simulation were validated through a proper prediction compared to the test data. The results of the study show that using polymeric pins, the flexural strength of the panel significantly increased under impact loading. In addition, the impact resistance of the pin-reinforced foam core panel increased up to 20%. Moreover, the size of pins has a significant influence on the flexural behaviour while the sample was under a moderate strain rate. To design an optimum pin-reinforced sandwich panel a "design of experiment model" was generated to predict energy absorption and the maximum peak load of proposed sandwich panels. The best design of the panel is recommended with 1.8 mm face sheet thickness and 5 mm pins diameter.

Design and Adoption of Low-Cost Point-of-Care Diagnostic Devices: Syrian Case.

Civil wars produce immense humanitarian crises, causing millions of individuals to seek refuge in other countries. The rate of disease prevalence has inclined among the refugees, increasing the cost of healthcare. Complex medical conditions and high numbers of patients at healthcare centers overwhelm the healthcare system and delay diagnosis and treatment. Point-of-care (PoC) testing can provide efficient solutions to high equipment cost, late diagnosis, and low accessibility of healthcare services. However, the development of PoC devices in developing countries is challenged by several barriers. Such PoC devices may not be adopted due to prejudices about new technologies and the need for special training to use some of these devices. Here, we investigated the concerns of end users regarding PoC devices by surveying healthcare workers and doctors. The tendency to adopt PoC device changes is based on demographic factors such as work sector, education, and technology experience. The most apparent concern about PoC devices was issues regarding low accuracy, according to the surveyed clinicians.

SurvivalGWAS_SV: software for the analysis of genome-wide association studies of imputed genotypes with "time-to-event" outcomes.

BACKGROUND: Analysis of genome-wide association studies (GWAS) with "time to event" outcomes have become increasingly popular, predominantly in the context of pharmacogenetics, where the survival endpoint could be death, disease remission or the occurrence of an adverse drug reaction. However, methodology and software that can efficiently handle the scale and complexity of genetic data from GWAS with time to event outcomes has not been extensively developed. RESULTS: SurvivalGWAS_SV is an easy to use software implemented using C# and run on Linux, Mac OS X & Windows operating systems. SurvivalGWAS_SV is able to handle large scale genome-wide data, allowing for imputed genotypes by modelling time to event outcomes under a dosage model. Either a Cox proportional hazards or Weibull regression model is used for analysis. The software can adjust for multiple covariates and incorporate SNP-covariate interaction effects. CONCLUSIONS: We introduce a new console application analysis tool for the analysis of GWAS with time to event outcomes. SurvivalGWAS_SV is compatible with high performance parallel computing clusters, thereby allowing efficient and effective analysis of large scale GWAS datasets, without incurring memory issues. With its particular relevance to pharmacogenetic GWAS, SurvivalGWAS_SV will aid in the identification of genetic biomarkers of patient response to treatment, with the ultimate goal of personalising therapeutic intervention for an array of diseases.

SurvivalGWAS_Power: a user friendly tool for power calculations in pharmacogenetic studies with "time to event" outcomes.

BACKGROUND: Power calculators are currently available for the design of genetic association studies of binary phenotypes and quantitative traits, but not for "time to event" outcomes, which are of particular relevance in pharmacogenetics. With the rapid emergence of pharmacogenetic association studies of single nucleotide polymorphisms (SNPs), and the complexity of clinical outcomes they consider, there is a need for software to perform power calculations of time to event data over a range of design scenarios and analytical methodologies. RESULTS: We have developed the user friendly software tool SurvivalGWAS_Power to perform power calculations for time to event outcomes over a range of study designs and different analytical approaches. The software calculates the power to detect SNP association with a time to event outcome over a range of study design scenarios. The software enables analyses under a Cox proportional hazards model or Weibull regression model, and can account for treatment and SNP-treatment interaction effects. Simulated data sets can also be generated by SurvivalGWAS_Power to enable analyses with methods that are not currently supported by the power calculator, thereby increasing the flexibility of the software. CONCLUSIONS: SurvivalGWAS_Power addresses the need for flexible and user-friendly software for power calculations for genetic association studies of time to event outcomes, with particular design features of relevance in pharmacogenetics.

Evaluation of methodology for the analysis of 'time-to-event' data in pharmacogenomic genome-wide association studies.

AIM: To evaluate the power to detect associations between SNPs and time-to-event outcomes across a range of pharmacogenomic study designs while comparing alternative regression approaches. MATERIALS & METHODS: Simulations were conducted to compare Cox proportional hazards modeling accounting for censoring and logistic regression modeling of a dichotomized outcome at the end of the study. RESULTS: The Cox proportional hazards model was demonstrated to be more powerful than the logistic regression analysis. The difference in power between the approaches was highly dependent on the rate of censoring. CONCLUSION: Initial evaluation of single-nucleotide polymorphism association signals using computationally efficient software with dichotomized outcomes provides an effective screening tool for some design scenarios, and thus has important implications for the development of analytical protocols in pharmacogenomic studies.

Mucoepidermoid carcinoma of the soft palate salivary gland

Mucoepidermoid carcinoma is a malignant epithelial tumour of glandular tissue, usually of the major salivary glands. However it can present in the minor salivary glands, especially in the soft palate. We report the case of a 72-year-old Malay female after presentation with sore throat, fever and odynophagia, was diagnosed with mucoepidermoid carcinoma of the soft palate.