The Landscape of Malignant Transition: Unraveling Cancer Cell-of-Origin and Heterogeneous Tissue Microenvironment.

Understanding disease progression and sophisticated tumor ecosystems is imperative for investigating tumorigenesis mechanisms and developing novel prevention strategies. Here, we dissected heterogeneous microenvironments during malignant transitions by leveraging data from 1396 samples spanning 13 major tissues. Within transitional stem-like subpopulations highly enriched in precancers and cancers, we identified 30 recurring cellular states strongly linked to malignancy, including hypoxia and epithelial senescence, revealing a high degree of plasticity in epithelial stem cells.

Bedtime music therapy for college students with insomnia: A randomized assessor-blinded controlled trial.

Background: Insomnia, a prevalent sleep disorder in contemporary society, frequently coexists with other mental health conditions such as depression, schizophrenia, and obsessive-compulsive disorder. Sleep disorders can compromise daytime functioning and overall quality of life. While music has been explored as an adjunct therapy for insomnia, its efficacy in improving insomnia among students remains unclear.

Single-cell Landscape of Malignant Transition: Unraveling Cancer Cell-of-Origin and Heterogeneous Tissue Microenvironment.

Understanding disease progression and sophisticated tumor ecosystems is imperative for investigating tumorigenesis mechanisms and developing novel prevention strategies. Here, we dissected heterogeneous microenvironments during malignant transitions by leveraging data from 1396 samples spanning 13 major tissues. Within transitional stem-like subpopulations highly enriched in precancers and cancers, we identified 30 recurring cellular states strongly linked to malignancy, including hypoxia and epithelial senescence, revealing a high degree of plasticity in epithelial stem cells.

StemDriver: a knowledgebase of gene functions for hematopoietic stem cell fate determination.

StemDriver is a comprehensive knowledgebase dedicated to the functional annotation of genes participating in the determination of hematopoietic stem cell fate, available at http://biomedbdc.wchscu.cn/StemDriver/.

FusionNeoAntigen: a resource of fusion gene-specific neoantigens.

Among the diverse sources of neoantigens (i.e. single-nucleotide variants (SNVs), insertions or deletions (Indels) and fusion genes), fusion gene-derived neoantigens are generally more immunogenic, have multiple targets per mutation and are more widely distributed across various cancer types.

Systematic investigation of the homology sequences around the human fusion gene breakpoints in pan-cancer - bioinformatics study for a potential link to MMEJ.

Microhomology-mediated end joining (MMEJ), an error-prone DNA damage repair mechanism, frequently leads to chromosomal rearrangements due to its ability to engage in promiscuous end joining of genomic instability and also leads to increasing mutational load at the sequences flanking the breakpoints (BPs). In this study, we systematically investigated the homology sequences around the genomic breakpoint area of human fusion genes, which were formed by the chromosomal rearrangements initiated by DNA double-strand breakage. Since the RNA-seq data is the typical data set to check the fusion genes, for the known exon junction fusion breakpoints identified from RNA-seq data, we have to infer the high chance of genomic breakpoint regions.

A novel integrated approach to predicting cancer immunotherapy efficacy.

Immunotherapies have revolutionized cancer treatment modalities; however, predicting clinical response accurately and reliably remains challenging. Neoantigen load is considered as a fundamental genetic determinant of therapeutic response. However, only a few predicted neoantigens are highly immunogenic, with little focus on intratumor heterogeneity (ITH) in the neoantigen landscape and its link with different features in the tumor microenvironment.

BarleyExpDB: an integrative gene expression database for barley.

Background: RNA-sequencing (RNA-seq) has been widely used to study the dynamic expression patterns of transcribed genes, which can lead to new biological insights. However, processing and analyzing these huge amounts of histological data remains a great challenge for wet labs and field researchers who lack bioinformatics experience and computational resources.

Results: We present BarleyExpDB, an easy-to-operate, free, and web-accessible database that integrates transcriptional profiles of barley at different growth and developmental stages, tissues, and stress conditions, as well as differential expression of mutants and populations to build a platform for barley expression and visualization.

Integrated mRNA sequence optimization using deep learning.

The coronavirus disease of 2019 pandemic has catalyzed the rapid development of mRNA vaccines, whereas, how to optimize the mRNA sequence of exogenous gene such as severe acute respiratory syndrome coronavirus 2 spike to fit human cells remains a critical challenge. A new algorithm, iDRO (integrated deep-learning-based mRNA optimization), is developed to optimize multiple components of mRNA sequences based on given amino acid sequences of target protein. Considering the biological constraints, we divided iDRO into two steps: open reading frame (ORF) optimization and 5' untranslated region (UTR) and 3'UTR generation.

The barley gene family: An expanded gene family that is involved in stress responses.

Gene family expansion plays a central role in adaptive divergence and, ultimately, speciation is influenced by phenotypic diversity in different environments. Barley () is the fourth most important cereal crop in the world and is used for brewing purposes, animal feed, and human food. Systematic characterization of expanded gene families is instrumental in the research of the evolutionary history of barley and understanding of the molecular function of their gene products.

BGFD: an integrated multi-omics database of barley gene families.

Background: A gene family comprises a group of genes with similar functional domains that play various roles in plant growth, development, and responses to environmental stimuli. Barley (Hordeum vulgare L.) is the fourth most cultivated cereal crop worldwide, and it is an important model species for genetic studies.

Genomic insights into positive selection during barley domestication.

Background: Cultivated barley (Hordeum vulgare) is widely used in animal feed, beverages, and foods and has become a model crop for molecular evolutionary studies. Few studies have examined the evolutionary fates of different types of genes in barley during the domestication process.

Results: The rates of nonsynonymous substitution (Ka) to synonymous substitution (Ks) were calculated by comparing orthologous genes in different barley groups (wild vs.

Genome-wide identification, expression analysis and evolutionary relationships of the IQ67-domain gene family in common wheat (Triticum aestivum L.) and its progenitors.

Background: The plant-specific IQ67-domain (IQD) gene family plays an important role in plant development and stress responses. However, little is known about the IQD family in common wheat (Triticum aestivum L), an agriculturally important crop that provides more than 20% of the calories and protein consumed in the modern human diet.

Results: We identified 125 IQDs in the wheat genome and divided them into four subgroups by phylogenetic analysis.

Identification of genetic variations associated with drug resistance in non-small cell lung cancer patients undergoing systemic treatment.

Non-small cell lung cancer (NSCLC) is characterized by relatively rapid response to systemic treatments yet inevitable resistance and predisposed to distant metastasis. We thus aimed at performing sequencing analysis to determine genomic events and underlying mechanisms concerning drug resistance in NSCLC. We performed targeted sequencing of 40 medication-relevant genes on plasma samples from 98 NSCLC patients and analyzed impact of genetic alterations on clinical presentation as well as response to systemic treatments.

Identification of potential oncogenes in triple-negative breast cancer based on bioinformatics analyses.

Triple-negative breast cancer (TNBC) is a subtype with high rates of metastasis, poor prognosis and limited therapeutic options. The present study aimed to identify the potential pivotal genes for prognosis and treatment in TNBC. A total of two microarray expression datasets, GSE38959 and GSE65212, were downloaded from the Gene Expression Omnibus database, and RNA-sequencing data of breast cancer from The Cancer Genome Atlas database were analyzed to screen out differentially expressed genes (DEGs) between TNBC tissues and normal tissues.

Identifying CpG methylation signature as a promising biomarker for recurrence and immunotherapy in non-small-cell lung carcinoma.

Epigenetic alterations are crucial to oncogenesis and regulation of gene expression in non-small-cell lung carcinoma (NSCLC). DNA methylation (DNAm) biomarkers may provide molecular-level prediction of relapse risk in cancer. Identification of optimal treatment is warranted for improving clinical management of NSCLC patients.

Direct Transformation of Glycerol to Propanal using Zirconium Phosphate-Supported Bimetallic Catalysts.

Selective transformation of glycerol to propanal (PA) provides a feasible route towards the sustainable synthesis of high value-added chemicals. In this work, zirconium phosphate (ZrP) was studied as support and Ru and Co as metal sites for glycerol hydrogenolysis in a continuous-flow reactor. It was found that ZrP-supported Co-O species had a moderate selectivity to PA (49.

Identification of MFI2-AS1, a Novel Pivotal lncRNA for Prognosis of Stage III/IV Colorectal Cancer.

Background: Long noncoding RNAs (lncRNAs) have been shown to play pivotal role in pathogenesis and prognosis of cancers. Identification of novel clinical biomarkers in advanced stage colorectal cancer (CRC) is warranted.

Aims: To identify potential lncRNAs associated with progression of stage III/IV CRC and illuminate regulatory mechanisms.

Multi-omics analysis reveals epithelial-mesenchymal transition-related gene FOXM1 as a novel prognostic biomarker in clear cell renal carcinoma.

Identification of novel clinical biomarker in clear cell renal carcinoma (ccRCC) is warranted. Integrating transcriptome (n=1669), DNA methylation (n=577) and copy number data (n=832), we developed a method to identify driver biomarkers by analyzing the omics-level dynamics of Epithelial-Mesenchymal Transition (EMT)-related genes in ccRCC. We first identified 504 expression dynamic changed genes involved in ccRCC-associated key pathways such as EMT, cell cycle, EGFR and PI3K/AKT signaling.

A seven-DNA methylation signature as a novel prognostic biomarker in breast cancer.

Background: Breast cancer (BC) is a common malignant tumor and its incidence and mortality rates are ranked first among female cancers. So far, there has been no effective biomarkers for BC prognosis.

Methods: The DNA methylation data of BC was downloaded from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus, and Functional ANnoTation of The Mammalian Genome databases.

Transmembrane Channel-Like 5 (TMC5) promotes prostate cancer cell proliferation through cell cycle regulation.

Background: In this study, we aimed to investigate the biological functions of Transmembrane Channel-Like 5 (TMC5) by bioinformatics and molecular biology methods in prostate cancer (PCa).

Methods: We assessed the mRNA expression level of TMC5 in PCa with public database the Cancer Genome Atlas (TCGA) and Oncomine. The biological functions were demonstrated by bioinformatics methods and siRNA mediated knockdown experiments.