MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data.

MOTIVATION: Microsatellite instability (MSI) is a promising biomarker for cancer prognosis and chemosensitivity. Techniques are rapidly evolving for the detection of MSI from tumor-normal paired or tumor-only sequencing data. However, tumor tissues are often insufficient, unavailable, or otherwise difficult to procure. Increasing clinical evidence indicates the enormous potential of plasma circulating cell-free DNA (cfNDA) technology as a noninvasive MSI detection approach. RESULTS: We developed MSIsensor-ct, a bioinformatics tool based on a machine learning protocol, dedicated to detecting MSI status using cfDNA sequencing data with a potential stable MSIscore threshold of 20%. Evaluation of MSIsensor-ct on independent testing datasets with various levels of circulating tumor DNA (ctDNA) and sequencing depth showed 100% accuracy within the limit of detection (LOD) of 0.05% ctDNA content. MSIsensor-ct requires only BAM files as input, rendering it user-friendly and readily integrated into next generation sequencing (NGS) analysis pipelines. AVAILABILITY: MSIsensor-ct is freely available at https://github.com/niu-lab/MSIsensor-ct. SUPPLEMENTARY INFORMATION: Supplementary data are available at Briefings in Bioinformatics online.

Comprehensive review and evaluation of computational methods for identifying FLT3-internal tandem duplication in acute myeloid leukaemia.

Internal tandem duplication (ITD) of FMS-like tyrosine kinase 3 (FLT3-ITD) constitutes an independent indicator of poor prognosis in acute myeloid leukaemia (AML). AML with FLT3-ITD usually presents with poor treatment outcomes, high recurrence rate and short overall survival. Currently, polymerase chain reaction and capillary electrophoresis are widely adopted for the clinical detection of FLT3-ITD, whereas the length and mutation frequency of ITD are evaluated using fragment analysis. With the development of sequencing technology and the high incidence of FLT3-ITD mutations, a multitude of bioinformatics tools and pipelines have been developed to detect FLT3-ITD using next-generation sequencing data. However, systematic comparison and evaluation of the methods or software have not been performed. In this study, we provided a comprehensive review of the principles, functionality and limitations of the existing methods for detecting FLT3-ITD. We further compared the qualitative and quantitative detection capabilities of six representative tools using simulated and biological data. Our results will provide practical guidance for researchers and clinicians to select the appropriate FLT3-ITD detection tools and highlight the direction of future developments in this field. Availability: A Docker image with several programs pre-installed is available at https://github.com/niu-lab/docker-flt3-itd to facilitate the application of FLT3-ITD detection tools.

Engineering Bimetallic NiFe-Based Hydroxides/Selenides Heterostructure Nanosheet Arrays for Highly-Efficient Oxygen Evolution Reaction.

Developing cost-effective and high-efficiency electrocatalysts toward alkaline oxygen evolution reaction (OER) is crucial for water splitting. Amorphous bimetallic NiFe-based (oxy)hydroxides have excellent OER activity under alkaline media, but their poorly electrical conductivity impedes the further improvement of their catalytic performance. Herein, a bimetallic NiFe-based heterostructure electrocatalyst that is composed of amorphous NiFe(OH)x and crystalline pyrite (Ni, Fe)Se2 nanosheet arrays is designed and constructed. The catalyst exhibits an outstanding OER performance, only requiring low overpotentials of 180, 220, and 230 mV at the current density of 10, 100, and 300 mA cm-2 and a low Tafel slope of 42 mV dec-1 in 1 m KOH, which is among the state-of-the-art OER catalysts. Based on the experimental and theoretical results, the electronic coupling at the interface that leads to the increased electrical conductivity and the optimized adsorption free energies of the oxygen-contained intermediates plays a crucial role in enhancing the OER activities. This work focusing on improving the OER performance via engineering amorphous-crystalline bimetallic heterostructure may provide some inspiration for reasonably designing advanced electrocatalysts.

Small Nucleolar RNAs as Diagnostic and Prognostic Biomarkers in Cancer: A Systematic Review and Meta-Analysis.

OBJECTIVES: Small nucleolar RNAs (snoRNAs) form clusters within the genome, representing a mysterious category of small non-coding RNAs. Research has demonstrated that aberrant snoRNAs can contribute to the development of various types of cancers. Recent studies have identified snoRNAs as potentially valuable biomarkers for the diagnosis or/and prognosis of cancers. However, there has been a lack of comprehensive reviews on prognostic and diagnostic snoRNAs across different types of cancers. METHODS: We conducted a systematic search of various databases including Google Scholar, Medline, Cochrane, Scopus, PubMed, Embase, ScienceDirect, Ovid-Medline, Chinese National Knowledge Infrastructure, WanFang, and SinoMed with a time frame reception to December 30, 2022. A total of 49 relevant articles were included in our analysis, consisting of 21 articles focusing on diagnostic aspects and 41 articles focusing on prognostic aspects. Pooled odds ratio, 95% confidence intervals (CIs), and hazard ratio (HR) were utilized to evaluate clinical parameters and overall survival (OS), respectively. RESULT: The findings indicated that area under the curve, sensitivity, and specificity were 0.85, 75%, and 80% in cancer, respectively. There was a possibility that snoRNAs had a positive impact on the diagnosis (risk ratio, RR = 2.95, 95% CI: 2.75-3.16, P = 0.000) and OS (HR = 1) in cancer. Additionally, abnormally expressed snoRNAs were associated with a positive impact on OS time for chronic lymphocytic leukemia (HR: 0.88, 95%Cl: 0.69-1.11, P < 0.00001), colon adenocarcinoma (HR: 0.97, 95%Cl: 0.91-1.03, P < 0.0001), and ovarian cancer (HR: 0.98, 95%Cl: 0.98-0.99, P < 0.00001). However, dysregulated snoRNAs of colon cancer and colorectal cancer had a negative impact on OS time (HR = 3.01 and 1.01 respectively, P < 0.0001). CONCLUSION: The results strongly suggested that snoRNAs could serve as potential novel indicators for prognosis and diagnosis in cancers. This systematic review followed the guidelines of the Transparent Reporting of Systematic Review and Meta-Analyses (PROSPERO register: CRD42020209096).

Deciphering the comprehensive knowledgebase landscape featuring infertility with IDDB Xtra.

Infertility affects ∼15% of couples globally and half of cases are related to genetic disorders. Despite growing data and unprecedented improvements in high-throughput sequencing technologies, accumulated fertility-related issues concerning genetic diagnosis and potential treatment are urgent to be solved. However, there is a lack of comprehensive platforms that characterise various infertility-related records to provide research applications for exploring infertility in-depth and genetic counselling of infertility couple. To solve this problem, we provide IDDB Xtra by further integrating phenotypic manifestations, genomic datasets, epigenetics, modulators in collaboration with numerous interactive tools into our previous infertility database, IDDB. IDDB Xtra houses manually-curated 2369 genes of human and nine model organisms, 273 chromosomal abnormalities, 884 phenotypes, 60 genomic datasets, 464 epigenetic records, 1144 modulators relevant to infertility diagnosis and treatment. Additionally, IDDB Xtra incorporated customized graphical applications for researchers and clinicians to decipher in-depth disease mechanisms from the perspectives of developmental atlas, mutation effects, and clinical manifestations. Users can browse genes across developmental stages of human and mouse, filter candidate genes, mine potential variants and retrieve infertility biomedical network in an intuitive web interface. In summary, IDDB Xtra not only captures valuable research and data, but also provides useful applications to facilitate the genetic counselling and drug discovery of infertility. IDDB Xtra is freely available at https://mdl.shsmu.edu.cn/IDDB/and http://www.allostery.net/IDDB.

Intercultural sensitivity as a mediator in the relationship between implicit intercultural identification and emotional disturbance-An exploratory study of international high school students.

Background: Intercultural adaptation is always associated with emotional disturbances. Intercultural communication competence, as an important competence of intercultural adaptation, involves implicit intercultural identification and intercultural sensitivity. Competence in these areas promotes the process of intercultural adaptation. Little is known about the relationship between intercultural communication competence and emotional disturbances in new students attending international high schools. The intercultural adaptation process of this population requires attention because of the increasing number of high school students attending international schools, and the fact that most of these teenagers are immersed in intercultural contexts for the first time. Objective: This study aimed to investigate the prevalence of emotional disturbance in new students in an international high school and confirm the relationship among implicit intercultural identification, intercultural sensitivity, and emotional disturbances. Methods: Study 1 was an investigation of the prevalence of emotional disturbance in 105 students in their 1st year at an international high school using the Self-rating Depression Scale and Self-rating Anxiety Scale. Of these students, 34 were invited to participate in Study 2 to further explore the relationship between intercultural sensitivity, implicit intercultural identification, and emotional disturbances using the Intercultural Sensitivity Scale and Single Category Implicit Association procedure. Results: Study 1 indicated that 15.24% of students were affected by apparent depression and 10.48% had anxiety symptoms. Study 2 revealed that emotional disturbances significantly correlated with intercultural sensitivity (p < 0.01) and implicit intercultural identification (p < 0.01). The openness factor from intercultural sensitivity mediated the relationship between implicit intercultural identification and depression (ratio of indirect effect = 41.04%, p < 0.05) and anxiety symptoms (ratio of indirect effect = 34.65%, p < 0.05). Conclusion: The study revealed that a significant proportion of students in the 1st year of international high school are affected by emotional difficulties. However, intercultural communication competence is a protective factor. Enhancing the international communication competence of senior students in international high schools is important to mitigate mental health challenges.

Identification and characterization of differentially expressed circRNA in 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced cleft palate.

Various circular RNAs (circRNAs) are novel class of non-coding RNAs, which are pervasively transcribed in the genome. CircRNAs play important roles in human, animals and plants. Up to now, there was no report regarding circRNAs of cleft palate by 2,3,7,8-tetrachlorodibenzo-pdioxin (TCDD) induce. The present study screened identification and characterization of differential expressed-circRNAs in TCDD-induced cleft palate. 6903 circRNAs candidates came from cleft palates. Among them, 3525 circRNAs are up-regulation, and 3378 circRNAs are down-regulation by TCDD induce. The cluster and GO analysis found that circRNAs involved in biological process, cellular component, and molecular function. Through the analysis of KEGG Pathway, circRNAs made functions via classical signaling pathway in cleft palate, such as TGF-beta signaling pathway, BMP signal pathway, MAPK signaling pathway. In addition, we found down-regulated circRNA224, circRNA3302 and up-regulated circRNA5021 targeted tgfbr3, but up-regulated circRNA4451 targeted tgfbr2. circRNA4451 may make functions through TGF-beta signaling pathway. These results suggested that many different circRNAs may make important role in TCDD-induced cleft palate, which provided a theoretical basis for further research.

Myocardin inhibits cellular proliferation by inhibiting NF-kappaB(p65)-dependent cell cycle progression.

We previously reported the importance of the serum response factor (SRF) cofactor myocardin in controlling muscle gene expression as well as the fundamental role for the inflammatory transcription factor NF-kappaB in governing cellular fate. Inactivation of myocardin has been implicated in malignant tumor growth. However, the underlying mechanism of myocardin regulation of cellular growth remains unclear. Here we show that NF-kappaB(p65) represses myocardin activation of cardiac and smooth muscle genes in a CArG-box-dependent manner. Consistent with their functional interaction, p65 directly interacts with myocardin and inhibits the formation of the myocardin/SRF/CArG ternary complex in vitro and in vivo. Conversely, myocardin decreases p65-mediated target gene activation by interfering with p65 DNA binding and abrogates LPS-induced TNF-alpha expression. Importantly, myocardin inhibits cellular proliferation by interfering with NF-kappaB-dependent cell-cycle regulation. Cumulatively, these findings identify a function for myocardin as an SRF-independent transcriptional repressor and cell-cycle regulator and provide a molecular mechanism by which interaction between NF-kappaB and myocardin plays a central role in modulating cellular proliferation and differentiation.

DIVIS: Integrated and Customizable Pipeline for Cancer Genome Sequencing Analysis and Interpretation.

Next-generation sequencing (NGS) has drastically enhanced human cancer research, but diverse sequencing strategies, complicated open-source software, and the identification of massive numbers of mutations have limited the clinical application of NGS. Here, we first presented GPyFlow, a lightweight tool that flexibly customizes, executes, and shares workflows. We then introduced DIVIS, a customizable pipeline based on GPyFlow that integrates read preprocessing, alignment, variant detection, and annotation of whole-genome sequencing, whole-exome sequencing, and gene-panel sequencing. By default, DIVIS screens variants from multiple callers and generates a standard variant-detection format list containing caller evidence for each sample, which is compatible with advanced analyses. Lastly, DIVIS generates a statistical report, including command lines, parameters, quality-control indicators, and mutation summary. DIVIS substantially facilitates complex cancer genome sequencing analyses by means of a single powerful and easy-to-use command. The DIVIS code is freely available at https://github.com/niu-lab/DIVIS, and the docker image can be downloaded from https://hub.docker.com/repository/docker/sunshinerain/divis.

Endoreduplication of human smooth muscle cells induced by 2-methoxyestradiol: a role for cyclin-dependent kinase 2.

Endoreduplication has been suggested to contribute to the development of hypertrophy of smooth muscle cells (SMCs) in hypertension. However, endoreduplication in vascular SMCs and the underlying molecular mechanisms are not clear. Treatment of human SMCs with 10 microM 2-methoxyestradiol (2-ME) for 24 h induces accumulation of cells with > or =4N DNA content, and some polyploid/aneuploid cells actively synthesize their DNA, suggesting the occurrence of endoreduplication. In addition, 2-ME treatment upregulates the expression of cyclin-dependent kinase 2 (Cdk2). The present study was designed to characterize endoreduplication of human SMCs and explore the potential roles of Cdk2 in endoreduplication induced by 2-ME. Treatment with 2-ME (10 microM) for 2-4 days not only caused increases in >4N cells and their reentry into S phase but also induced overduplication of chromosomes. Furthermore, 2-ME increased the kinase activity of Cdk2 and its interaction with cyclin E. Inducible overexpression of dominant-negative Cdk2 in human SMCs inhibited both DNA synthesis of >4N cells and the accumulation of >4N cells induced by 2-ME. We conclude that 2-ME induces endoreduplication of human SMCs and Cdk2 plays an important role in endoreduplication in response to 2-ME.