A5102922674- Cancer-related molecular mechanisms research
- CRISPR and Genetic Engineering
- Cervical Cancer and HPV Research
- Virus-based gene therapy research
- Hepatitis B Virus Studies
- Plant Virus Research Studies
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Viral-associated cancers and disorders
- Molecular Biology Techniques and Applications
- Herpesvirus Infections and Treatments
- Hepatitis C virus research
- RNA Interference and Gene Delivery
- Cancer Genomics and Diagnostics
- Genital Health and Disease
- Gestational Diabetes Research and Management
- BRCA gene mutations in cancer
- Ovarian cancer diagnosis and treatment
- Fungal and yeast genetics research
- AI in cancer detection
- RNA regulation and disease
- Advanced Software Engineering Methodologies
- Chromosomal and Genetic Variations
- Vector-Borne Animal Diseases
- Gut microbiota and health
- Reproductive System and Pregnancy
Peking University First Hospital
2024
Peking University
2024
The First Affiliated Hospital, Sun Yat-sen University
2019-2023
Sun Yat-sen University
2019-2023
Abstract Human papillomavirus (HPV) integration is a critical step in cervical cancer development; however, the oncogenic mechanism at genome-wide transcriptional level still poorly understood. In this study, we employed integrative analysis on multi-omics data of six HPV-positive and three HPV-negative cell lines. Through HPV detection, super-enhancer (SE) identification, SE-associated gene expression extrachromosomal DNA (ecDNA) investigation, aimed to explore influence integration. We...
Abstract Gestational diabetes mellitus (GDM) is characterized by insulin resistance and low-grade inflammation, most studies have demonstrated gut dysbiosis in GDM pregnancies. Overall, they were manifested as a reduction microbiome diversity richness, depleted short chain fatty acid (SCFA)-producing genera dominant of Gram-negative pathogens releasing lipopolysaccharide (LPS). The SCFAs functioned energy substance or signaling molecules to interact with host locally beyond the gut. LPS...
Abstract Genome editing technologies hold tremendous potential in biomedical research and drug development. Therefore, it is imperative to discover gene tools with superior cutting efficiency, good fidelity, fewer genomic restrictions. Here, we report a CRISPR/Cas9 from Faecalibaculum rodentium , which characterized by simple PAM (5′-NNTA-3′) guide RNA length of 21–22 bp. We find that FrCas9 could achieve comparable efficiency specificity SpCas9. Interestingly, the presents palindromic...
Zinc-finger nucleases (ZFNs), transcription activator-like endonucleases (TALENs), and CRISPR-associated Cas9 are three major generations of genome editing tools. However, no parallel comparison about the efficiencies off-target activity has been reported, which is critical for final clinical decision. We first time developed genome-wide unbiased identification double-stranded breaks enabled by sequencing (GUIDE-seq) method in ZFNs TALENs with novel bioinformatics algorithms to evaluate...
A genome editing tool targeting the high-risk human papillomavirus (HPV) oncogene is a promising therapeutic strategy to treat HPV-related cervical cancer. To improve gene knockout efficiency, we developed chain reaction (GKCR) method for continually generating mutagenic disruptions and used this disrupt HPV18 E6 E7 genes. We verified that GKCR Cas9/guide RNA (gRNA) cassettes could integrated into targeted loci via homology-independent insertion (HITI). The qPCR results revealed enabled...
From initial human papillomavirus (HPV) infection and precursor stages, the development of cervical cancer takes decades. High-sensitivity HPV DNA testing is currently recommended as primary screening method for cancer, whereas better triage methodologies are encouraged to provide accurate risk management HPV-positive women. Given that virus-driven genomic variation accumulates during carcinogenesis, we designed a 39 Mb custom capture panel targeting 17 types 522 mutant genes related cancer....
Gene therapy has held promises for treating specific genetic diseases. However, the key to clinical application depends on effective gene delivery.
Neoadjuvant chemotherapy (NACT) remains an attractive alternative for controlling locally advanced cervical cancer. However, approximately 15-34% of women do not respond to induction therapy. To develop a risk stratification tool, 56 patients with stage IB-IIB cancer are included in 2 research centers from the discovery cohort. Patient-specific somatic mutations led NACT non-responsiveness identified by whole-exome sequencing. Next, CRISPR/Cas9-based library screenings performed based on...
<h3>Importance</h3> High-risk human papillomavirus (hrHPV) persistent infection is the major etiology of cervical precancer and cancer. Noninvasive self-sampling HPV testing a promising alternative cancer screening for avoiding stigma improving patient willingness to participate. <h3>Objective</h3> To investigate feasibility accuracy menstrual blood (MB) hrHPV capture sequencing in detection. <h3>Design, Setting, Participants</h3> This cohort study collected 137 sanitary pads from 120 women...
Human papillomavirus (HPV) integrating into human genome is the main cause of cervical carcinogenesis. HPV integration selection preference shows strong dependence on local genomic environment. Due to this theory, it possible predict sites. However, a published bioinformatic tool not available date. Thus, we developed an attention-based deep learning model DeepHPV sites by environment features automatically. In total, 3608 known were applied train model, and 584 reviewed used as testing...
Integration of oncogenic DNA viruses into the human genome is a key step in most virus-induced carcinogenesis. Here, we constructed virus integration site (VIS) Atlas database, an extensive collection breakpoints for three prevalent oncoviruses, papillomavirus, hepatitis B virus, and Epstein-Barr based on next-generation sequencing (NGS) data, literature, experimental data. There are 63,179 47,411 junctional sequences with full annotations deposited VIS comprising 47 genotypes 17 disease...
Since human papillomavirus (HPV) DNA testing has been promoted as primary screening strategy, the triage method also evolved from morphological to a molecular biomarker detection improve efficiency. In this study, we investigated performance of three HPV integration hot-spots, HMGA2, LRP1B, and TP63, potential markers in tests.This cross-sectional study was conducted November 2016 December 2017 First Affiliated Hospital Sun Yat-sen University. Immunocytochemistry carried out using residual...
Abstract Background The hepatitis B virus (HBV) is one of the main causes viral and liver cancer. HBV integration key steps in virus-promoted malignant transformation. Results An attention-based deep learning model, DeepHBV, was developed to predict sites. By local genomic features automatically, DeepHBV trained tested using site data from dsVIS database. Initially, showed an AUROC 0.6363 AUPR 0.5471 for dataset. repeat peaks TCGA Pan-Cancer significantly improved model performance, with...
Type 2 diabetes mellitus (T2DM) represents a common complication during pregnancy that affects fetoplacental development. We demonstrated the existence of impaired trophoblast syncytialization under hyperglycemic conditions. However, exact mechanism remains unknown. RNA N6-methyladenosine (m6A) is an emerging regulatory mRNA and participates in various biological processes. described global m6A modification pattern T2DM placenta by combined analysis methylated immunoprecipitation sequencing...
The activity of a gene newly integrated into chromosome depends on the genomic context integration site. This "position effect" has been widely reported, although other side coin, that is, how affects local chromosomal environment, remained largely unexplored, as have mechanism and phenotypic consequences this "externality" position effect. Here, we examined transcriptome profiles approximately 250 Saccharomyces cerevisiae strains, each with GFP different locus wild-type strain. We found in...
Epstein-Barr virus (EBV) is one of the most prevalent DNA oncogenic viruses. The integration EBV into host genome has been reported to play an important role in cancer development. preference showed strong dependence on local genomic environment, which enables prediction sites.An attention-based deep learning model, DeepEBV, was developed predict sites by features automatically. First, DeepEBV trained and tested using data from dsVIS database. results that with sequences plus Repeat peaks...
The current cervical cancer screening strategies based on Papanicolaou (Pap) and Human papillomavirus (HPV) tests receive great achievement but still exhibit many limitations in clinical practice. Exploring new biomarkers as stratified management method HPV primary is becoming the tendency of research.Immunocytochemistry (ICC) FHIT C-MYC were performed exfoliated cells from 197 eligible high-risk positive women. Mann-Whitney U test, Pearson Chi-Square logistic regression analysis receiver...
Gut microbiome dysbiosis is associated with gestational diabetes mellitus (GDM), and its modulation represents a promising approach for enhancing glycemic control. In this study, we aimed to discover specific alterations in the gut through lifestyle management. We performed metagenome sequencing on fecal samples measured short-chain fatty acid (SCFA) plasma from 27 well-controlled GDM pregnancies before after At same time, 38 normal glucose tolerance (NGT) served as controls. Additionally,...
Different method calls may have different contributions to the precision of final application when abstracted into call strings. The existing string based pointer analysis algorithms do not consider such contribution difference and hence often can achieve best cost-effectiveness. To solve problem, this paper firstly proposes a contribution-based stack abstraction which abstracts stacks strings with information under consideration. Then, we apply new AspectJ programs propose concern-sensitive...