A5076870332- RNA Research and Splicing
- RNA regulation and disease
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- CRISPR and Genetic Engineering
- Lymphoma Diagnosis and Treatment
- Neonatal and Maternal Infections
- Ubiquitin and proteasome pathways
- Streptococcal Infections and Treatments
- SARS-CoV-2 and COVID-19 Research
- Immune Cell Function and Interaction
- Viral-associated cancers and disorders
- Peptidase Inhibition and Analysis
- Plant Reproductive Biology
- Viral gastroenteritis research and epidemiology
- Phagocytosis and Immune Regulation
- Erythropoietin and Anemia Treatment
- Animal Vocal Communication and Behavior
- Nitrogen and Sulfur Effects on Brassica
- Multiple and Secondary Primary Cancers
- Bone health and treatments
- Bone Metabolism and Diseases
- Cancer Mechanisms and Therapy
- Autophagy in Disease and Therapy
University of California, Los Angeles
2018-2025
Zhuzhou Central Hospital
2024
Hangzhou Medical College
2023-2024
University of South China
2014-2019
Wuhan University
2018
Fujian Normal University
2018
Kaohsiung Veterans General Hospital
2018
Kunming Medical University
2018
Ludwig Cancer Research
2014-2015
University of California, San Diego
2015
Abstract Although long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which significantly under-explored. Here, we present an in-depth study detect and analyze sites in RNA-seq. Our new method, L-GIREMI, effectively handles sequencing errors read biases. Applied PacBio data, L-GIREMI affords a high accuracy identification. Additionally, our analysis uncovered...
Understanding the function of rare non-coding variants represents a significant challenge. Using MapUTR, screening method, we studied 3' UTR affecting mRNA abundance post-transcriptionally. Among 17,301 gnomAD variants, an average 24.5% were functional, with 70% in cancer-related genes, many critical cancer pathways. This observation motivated interrogation 11,929 somatic mutations, uncovering 3928 (33%) functional mutations 155 driver genes. Functional MapUTR enriched microRNA- or...
The transport of LDL-derived cholesterol from lysosomes to peroxisomes is facilitated by membrane contacts formed between the lysosomal protein synaptotagmin VII and peroxisomal lipid phosphatidylinositol 4, 5-bisphosphate [PI(4,5)P2]. Here, we used RNA interference search for regulators PI(4,5)P2 study effects altered homeostasis on transport. We found that knockdown 5-phosphate 4-kinase type-2 α (PIP4K2A) reduced levels, decreased lysosome-peroxisome contacts, increased accumulation in...
Abstract Allele-specific protein-RNA binding is an essential aspect that may reveal functional genetic variants (GVs) mediating post-transcriptional regulation. Recently, genome-wide detection of in vivo RNA-binding proteins greatly facilitated by the enhanced crosslinking and immunoprecipitation (eCLIP) method. We developed a new computational approach, called BEAPR, to identify allele-specific (ASB) events eCLIP-Seq data. BEAPR takes into account crosslinking-induced sequence propensity...
RNA editing, the endogenous modification of nucleic acids, is known to be altered in genes with important neurological function schizophrenia (SCZ). However, global profile and molecular functions disease-associated editing remain unclear. Here, we analyzed postmortem brains four SCZ cohorts uncovered a significant reproducible trend hypoediting patients European descent. We report set SCZ-associated sites via WGCNA analysis, shared across cohorts. Using massively parallel reporter assays...
PURPOSE We evaluated the efficacy and safety of roxadustat, a first-in-class hypoxia-inducible factor prolyl hydroxylase inhibitor, for chemotherapy-induced anemia (CIA) in patients with nonmyeloid malignancies receiving multicycle treatments chemotherapy. PATIENTS AND METHODS In this open-label, noninferiority phase III study conducted at 44 sites China, 159 participants age ≥18 years CIA malignancy were randomly assigned (1:1) to oral roxadustat or subcutaneous recombinant human...
RNA editing generates modifications to the sequences, thereby increasing protein diversity and shaping various layers of gene regulation. Recent studies have revealed global shifts in levels across many cancer types, as well a few specific mechanisms implicating individual sites tumorigenesis or metastasis. However, most tumor-associated sites, predominantly noncoding regions, unknown functional relevance.Here, we carry out integrative analysis profiles between epithelial mesenchymal tumors,...
Abstract Myeloid cells undergo large changes to their gene expression profile in response inflammatory stimulation. This includes an increase post-transcriptional modifications carried out by adenosine-to-inosine (A-to-I) and cytosine-to-uracil (C-to-U) RNA editing enzymes. However, the precise targets altered stimulation consequences of on proteome have been understudied. We present a comprehensive analysis stimulated myeloid across three independent cohorts totalling 297 samples, including...
STAT3 is an important molecule in Janus kinase (JAK) signal transducer and activator of transcription (STAT) pathway, facilitates expression various oncogenic genes such as Bcl-2, thus correlated with tumor onset, progression dru
A variety of cellular pathways are regulated by protein modifications with ubiquitin-family proteins. SUMO, the Small Ubiquitin-like MOdifier, is covalently attached to lysine on target proteins via a cascade reaction catalyzed E1, E2, and E3 enzymes. major barrier understanding diverse regulatory roles SUMO has been lack suitable methods identify sumoylation sites. Here we developed mass-spectrometry (MS) based approach combining chemical enzymatic We applied this method analyze...
Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels. Most analyses of scRNA-seq have focused on gene expression profiles, it remains challenging to extract variants isoform-specific information. Here, we present scAllele, an integrative approach that detects single-nucleotide variants, insertions, deletions, their allelic linkage with splicing patterns in scRNA-seq. We demonstrate scAllele achieves better performance identifying...
Streptococcus suis causes disease in both pigs and humans. Many virulence genes, including mrp, ef, sly, gapdh, fbps, hyl, are shown to contribute S. pathogenesis. In this study, the differential expression of key serotype 2 virulence-associated genes was monitored 24 48 h after infection HeLa cells. Gene further investigated bacteria harvested from blood, lungs, brains, synovia swine 24, 48, 72 postintravenous with 2. Bacterial RNA extracted gene using real-time reverse transcriptase-PCR at...
Infection with Epstein-Barr virus (EBV) induces activation and proliferation of B lymphocytes. Detection latent membrane protein (LMP)-1 is used to identify the proliferative ability cells. However, changes in expression levels three LMPs during EBV-induced lymphocyte transformation, have not yet been reported. In present study, LMP-1, LMP-2A LMP-2B were compared between EBV-transformed lymphocytes paired normal Seven lymphoblast cell lines established by EBV infection human vitro. The LMP...
As the understanding of mechanisms SARS-CoV-2 infection continues to grow, researchers have come realize that ACE2 and TMPRSS2 receptors are not only way for virus invade host, there many molecules may serve as potential or cofactors. The functionality these numerous receptors, proposed by different research groups, demands a fast, simple, accurate validation method. To address this issue, we here established DnaE intein-based cell-cell fusion system, key result our study, which enables...
Abstract Using third-generation sequencers, long-read RNA-seq is increasingly applied in transcriptomic studies given its major advantage characterizing full-length transcripts. A number of methods have been developed to analyze this new type data for transcript isoforms and their abundance. Another application, which significantly under-explored, identify single nucleotide variants (SNVs) the RNA. Identification SNVs, such as genetic mutations or RNA editing sites, fundamental many...
PODXL, a protein that is dysregulated in multiple cancers, plays an important role promoting cancer metastasis. In this study, we report RNA editing promotes the inclusion of PODXL alternative exon. The resulting edited long isoform more prone to protease digestion and has strongest effects on reducing cell migration cisplatin chemoresistance among three isoforms (short, unedited long, isoforms). Importantly, level recoding site exon are strongly associated with overall patient survival...
Although the Epstein-Barr virus (EBV) is a well-known human oncogenic virus, its molecular mechanisms involved in transformation of healthy cells remain poorly understood. In this study, lymphocytes were isolated from peripheral blood adults, and transformed vitro by EBV. Agilent whole genome microarrays used to detect differential gene expression profiles EBV-transformed lymphoblasts (PBLs). By constructing functional network EBV-induced lymphocyte transformation, we screened out candidate...
Protein sumoylation is a reversible post‐translational modification that regulates nuclear processes including gene transcription, transport and DNA repair. Like ubiquitin, SUMO attached to the lysine side chains of target proteins via cascade E1‐activating, E2‐conjugating, E3‐ligating enzymes, it removed by SUMO‐specific isopeptidases. Hundreds are known be sumoylated in yeast saccharomyces cerevisiae, however, relatively little about precise site(s) most proteins. This due lack suitable...
Objective: To study the associations of single nucleotide polymorphisms (SNP) myosin heavy chain 6 (MYH6) gene with risk atrial fibrillation (AF) and warfarin anticoagulation therapy. Methods: Sanger sequencing was employed to analyze genotypes MYH6 gene's rs28730771, rs365990, rs2277473 loci in 243 AF patients non-AF (control group) selected according age sex at a 1:1 ratio. A multiple logistic regression analysis used factors AF. SHEsis adopted association between haplotypes susceptibility...
Respiratory infectious viruses, including SARS‐CoV‐2, undergo rapid genetic evolution, resulting in diverse subtypes with complex mutations. Detecting and differentiating these pose significant challenges respiratory virus surveillance. To address challenges, we integrated ARMS‐PCR molecular beacon probes, allowing selective amplification discrimination of based on adjacent mutation sites. The method exhibited high specificity sensitivity, detecting as low 10 4 copies/mL via direct...
Raf-1 Kinase Inhibitory Protein (RKIP) belongs to a new class modulators of signalling cascades involved in maintaining biological balance many living organisms.RKIP targets and inhibits different kinases (Mitogen Activated (MAP) kinase, G-protein coupled receptor (GPCR) kinase nuclear factor kappa B (NF-B) signaling pathways), its loss is associated with progression solid cancers development metastasis.In this study we analyzed RKIP expression follicular, papillary undifferentiated thyroid...