Therapeutic SHPRH-146aa encoded by circ-SHPRH dynamically upregulates P21 to inhibit CDKs in neuroblastoma.

Recent research has underscored the significance of circular RNAs (circRNAs) in various cancers, including neuroblastoma (NB). Specifically, circ-SHPRH, a unique circRNA, has been revealed to inhibit tumor growth by sequestering miRNAs or producing the SHPRH-146aa protein. To explore circ-SHPRH's involvement in NB and its potential application in gene therapy, this study examined circ-SHPRH expression in 94 NB tissues and cell lines (SK-N-BE(2), SH-SY5Y) using real-time PCR and fluorescence in situ hybridization (FISH).

Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project.

Accurate indel calling plays an important role in precision medicine. A benchmarking indel set is essential for thoroughly evaluating the indel calling performance of bioinformatics pipelines. A reference sample with a set of known-positive variants was developed in the FDA-led Sequencing Quality Control Phase 2 (SEQC2) project, but the known indels in the known-positive set were limited.

Landscape of global urban environmental resistome and its association with local socioeconomic and medical status.

Antimicrobial resistance (AMR) poses a critical threat to global health and development, with environmental factors-particularly in urban areas-contributing significantly to the spread of antibiotic resistance genes (ARGs). However, most research to date has been conducted at a local level, leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments. To address this issue, we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples, which were collected by the MetaSUB International Consortium involving diverse urban environments in 60 cities of 27 countries, utilizing a deep-learning based methodology.

Pharmacological boosting of cGAS activation sensitizes chemotherapy by enhancing antitumor immunity.

Enhancing chemosensitivity is one of the largest unmet medical needs in cancer therapy. Cyclic GMP-AMP synthase (cGAS) connects genome instability caused by platinum-based chemotherapeutics to type I interferon (IFN) response. Here, by using a high-throughput small-molecule microarray-based screening of cGAS interacting compounds, we identify brivanib, known as a dual inhibitor of vascular endothelial growth factor receptor and fibroblast growth factor receptor, as a cGAS modulator.

Inhibition of GPR39 restores defects in endothelial cell-mediated neovascularization under the duress of chronic hyperglycemia: Evidence for regulatory roles of the sonic hedgehog signaling axis.

Impaired endothelial cell (EC)-mediated angiogenesis contributes to critical limb ischemia in diabetic patients. The sonic hedgehog (SHH) pathway participates in angiogenesis but is repressed in hyperglycemia by obscure mechanisms. We investigated the orphan G protein-coupled receptor GPR39 on SHH pathway activation in ECs and ischemia-induced angiogenesis in animals with chronic hyperglycemia.

MagMD: Database summarizing the metabolic action of gut microbiota to drugs.

Unlabelled: An increasing number of studies have reported that microbiome can affect drug response by altering pharmacokinetics and pharmacodynamics of formation of toxic metabolites. With the development of metagenomic sequencing, gut microbial composition as well as the metabolic function are drawing more and more attention for the patient stratification. The established microbiota databases provide useful information about the gut microbe-drug interactions.

A Novel Risk-Score Model With Eight MiRNA Signatures for Overall Survival of Patients With Lung Adenocarcinoma.

Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer with heterogeneous outcomes and diverse therapeutic responses. To classify patients into different groups and facilitate the suitable therapeutic strategy, we first selected eight microRNA (miRNA) signatures in The Cancer Genome Atlas (TCGA)-LUAD cohort based on multi-strategy combination, including differential expression analysis, regulatory relationship, univariate survival analysis, importance clustering, and multivariate combinations analysis. Using the eight miRNA signatures, we further built novel risk scores based on the predefined cutoff and beta coefficients and divided the patients into high-risk and low-risk groups with significantly different overall survival time (-value < 2 e-16).

Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association.

In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than half of unclassified reads. Here we uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium.

X-CNV: genome-wide prediction of the pathogenicity of copy number variations.

Background: Gene copy number variations (CNVs) contribute to genetic diversity and disease prevalence across populations. Substantial efforts have been made to decipher the relationship between CNVs and pathogenesis but with limited success.

Results: We have developed a novel computational framework X-CNV ( www.

The Cardamine enshiensis genome reveals whole genome duplication and insight into selenium hyperaccumulation and tolerance.

Cardamine enshiensis is a well-known selenium (Se)-hyperaccumulating plant. Se is an essential trace element associated with many health benefits. Despite its critical importance, genomic information of this species is limited.

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.

Background: Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S.

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology.

Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples.

Inhibitory investigation of niacin derivatives on metalloenzyme indoleamine 2,3-dioxygenase 1 for its immunomodulatory function.

Inhibitors of indoleamine 2,3-dioxygenase 1 (IDO1) have received wide attention for their roles in cancer immunotherapy. It highlights the important role of metalloenzymes in performing human physiological functions. Herein, the recombinant human IDO1 was expressed and purified successfully, and the protein molecule was characterized by SDS-PAGE, MALDI-TOF mass spectrometry, and metalloenzymology.

Whole exome sequencing identifies a novel homozygous MECR mutation in a Chinese patient with childhood-onset dystonia and basal ganglia abnormalities, without optic atrophy.

Childhood-onset dystonia with optic atrophy and basal ganglia abnormalities is an extremely rare autosomal recessive mitochondrial disease caused by biallelic mutations in MECR. Using whole-exome sequencing, we identified a novel homozygous MECR mutation (c.910G > T, p.

Comprehensive Characterization of Circular RNAs in Neuroblastoma Cell Lines.

Neuroblastoma (NB) is a rare type of cancer but frequently occurred in children. However, it is still unclear whether circular RNAs (circRNAs) play key roles in NB tumorigenesis or progression. In this study, we identified 39,022 circRNAs across the 39 neuroblastoma and 2 normal cell lines.

Disease spectrum analysis of hospitalized children in China: A study of 18 tertiary children's hospitals.

Importance: Morbidity and mortality of children are important indicators of the performance of the public health system in any country. In China, the children's disease spectrum has gradually changed in recent years. However, the gender- and age-specific disease spectrum for hospitalized children under 15 years old is still unclear.

Genotype-phenotype correlations of Berardinelli-Seip congenital lipodystrophy and novel candidate genes prediction.

Background: Berardinelli-Seip congenital lipodystrophy (BSCL) is a heterogeneous autosomal recessive disorder characterized by an almost total lack of adipose tissue in the body. Mutations in the AGPAT2, BSCL2, CAV1 and PTRF genes define I-IV subtype of BSLC respectively and clinical data indicate that new causative genes remain to be discovered. Here, we retrieved 341 cases from 60 BSCL-related studies worldwide and aimed to explore genotype-phenotype correlations based on mutations of AGPAT2 and BSCL2 genes from 251 cases.

Corrigendum: Genotype-Phenotype Association Analysis Reveals New Pathogenic Factors for Osteogenesis Imperfecta Disease.

[This corrects the article DOI: 10.3389/fphar.2019.

Genotype-Phenotype Association Analysis Reveals New Pathogenic Factors for Osteogenesis Imperfecta Disease.

Osteogenesis imperfecta (OI), mainly caused by structural abnormalities of type I collagen, is a hereditary rare disease characterized by increased bone fragility and reduced bone mass. Clinical manifestations of OI mostly include multiple repeated bone fractures, thin skin, blue sclera, hearing loss, cardiovascular and pulmonary system abnormalities, triangular face, dentinogenesis imperfecta (DI), and walking with assistance. Currently, 20 causative genes with 18 subtypes have been identified for OI, of them, variations in and have been demonstrated to be major causative factors to OI.

DNMIVD: DNA methylation interactive visualization database.

Aberrant DNA methylation plays an important role in cancer progression. However, no resource has been available that comprehensively provides DNA methylation-based diagnostic and prognostic models, expression-methylation quantitative trait loci (emQTL), pathway activity-methylation quantitative trait loci (pathway-meQTL), differentially variable and differentially methylated CpGs, and survival analysis, as well as functional epigenetic modules for different cancers. These provide valuable information for researchers to explore DNA methylation profiles from different aspects in cancer.

Systematically Analyzing the Pathogenic Variations for Acute Intermittent Porphyria.

The rare autosomal dominant disorder acute intermittent porphyria (AIP) is caused by the deficient activity of hydroxymethylbilane synthase (HMBS). The symptoms of AIP are acute neurovisceral attacks which are induced by the dysfunction of heme biosynthesis. To better interpret the underlying mechanism of clinical phenotypes, we collected 117 gene mutations from reported individuals with AIP and evaluated the mutations' impacts on the corresponding protein structure and function.

Natural variations of growth thermo-responsiveness determined by SAUR26/27/28 proteins in Arabidopsis thaliana.

How diversity in growth thermo-responsiveness is generated for local adaptation is a long-standing biological question. We investigated molecular genetic basis of natural variations in thermo-responsiveness of plant architecture in Arabidopsis thaliana. We measured the extent of rosette architecture at 22°C and 28°C in a set of 69 natural accessions and determined their thermo-responsiveness of plant architecture.