A5100782183- RNA modifications and cancer
- Gene expression and cancer classification
- Epigenetics and DNA Methylation
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- Genetic factors in colorectal cancer
- Colorectal Cancer Treatments and Studies
- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Ferroptosis and cancer prognosis
- MicroRNA in disease regulation
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Colorectal Cancer Screening and Detection
- Bladder and Urothelial Cancer Treatments
- Cancer Research and Treatments
- Immune Cell Function and Interaction
- Heme Oxygenase-1 and Carbon Monoxide
- Cancer Immunotherapy and Biomarkers
- Phagocytosis and Immune Regulation
- Gastric Cancer Management and Outcomes
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Cancer Cells and Metastasis
- Redox biology and oxidative stress
- Macrophage Migration Inhibitory Factor
University of South China
2009-2025
Fujian Medical University
2016-2025
Zhejiang Hospital
2019-2025
Second Affiliated Hospital of Zhejiang University
2025
Dalian Medical University
2025
Chongqing Medical University
2025
Second Affiliated Hospital of Chongqing Medical University
2025
University of Hong Kong
2024
Soochow University
2016-2024
First Affiliated Hospital of Soochow University
2016-2024
Abstract Establishing an RNA-associated interaction repository facilitates the system-level understanding of RNA functions. However, as these interactions are distributed throughout various resources, essential prerequisite for effectively applying data requires that they deposited together and annotated with confidence scores. Hence, we have updated database RNAInter (RNA Interactome Database) to version 4.0, which is freely accessible at http://www.rnainter.org or...
Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable resource for clinical researches.However, FFPE are usually considered an unreliable source gene expression analysis due to the partial RNA degradation.In this study, through comparing profiles between and paired fresh-frozen (FF) three cancer types, we firstly showed that measurements of thousands genes had at least two-fold change in compared with FF samples.Therefore, transcriptional signature based on risk scores...
It is often difficult to obtain sufficient quantity of RNA molecules for gene expression profiling under many practical situations. Amplification from low-input samples may induce artificial signals. We compared the measurements mRNA samples, 25 pg 1000 mRNA, which were amplified and profiled by Smart-seq, DP-seq CEL-seq techniques using Illumina HiSeq 2000 platform, with those paired high-input (50 ng) samples. Even input, we found that thousands genes had at least 2 folds-change levels in...
Abstract Lung squamous cell carcinoma (SQCC) accounts for about 30% of all lung cancer cases. Understanding mutational landscape this subtype in Chinese patients is currently limited. We performed whole exome sequencing samples from 100 with SQCCs to search somatic mutations and the subsequent target capture another 98 validation. identified 20 significantly mutated genes, including TP53 , CDH10 NFE2L2 PTEN . Pathways frequently genes included those cell-cell adhesion/Wnt/Hippo 76%,...
Due to experimental batch effects, the application of a quantitative transcriptional signature for disease diagnoses commonly requires inter-sample data normalization, which would be hardly applicable under common clinical settings. Many cancers might have qualitative differences with non-cancer states in gene expression pattern. Therefore, it is reasonable explore power diagnostic signatures are robust against effects and other random factors. Firstly, using technical replicate samples from...
ABSTRACT The immune response to Mycoplasma pneumoniae infection plays a key role in clinical symptoms. Previous investigations focused on the pro-inflammatory effects of leukocytes and pivotal epithelial cell metabolic status finely modulating inflammatory have been neglected. Herein, we examined how glycolysis airway cells is affected by M. an vitro model. Additionally, investigated contribution ATP pulmonary inflammation. Metabolic analysis revealed marked shift bronchial during infection,...
Abstract This research demonstrates that DCC-2036 (Rebastinib), a potent third-generation tyrosine kinase inhibitor (TKI), effectively suppresses tumor growth in colorectal cancer (CRC) models with functional immune systems. The findings underscore the capacity of to enhance both activation and cytotoxic functionality CD8 + T cells, which are crucial for facilitating anti-tumor responses. Through comprehensive multi-omics investigations, significant shifts gene protein expression profiles...
Background Septic shock (SS) is a syndrome with high mortality. Early forewarning and diagnosis of SS, which are critical in reducing mortality, still challenging clinical management. Objective We propose simple fast risk-stratified model for SS to help physicians recognize patients time. Moreover, further insights can be gained from the application improve our understanding SS. Methods A total 5125 sepsis Medical Information Mart Intensive Care-IV (MIMIC-IV) database were divided into...
Thyroid cancer treatments often impact patients' quality of life (QOL). The transoral endoscopic thyroidectomy vestibular approach (TOETVA) gets lot attention as a scarless alternative, but its influence on postoperative QOL remains unclear. This study compares TOETVA and open surgery outcomes regarding QOL, scar satisfaction, mental health in thyroid patients to inform surgical decision-making. We retrospectively analyzed 221 treated between January 2017 September 2024: 136 underwent...
Perforator flap transplantation is an important technique in reconstructive surgery, but necrosis limits its clinical effectiveness. Thymoquinone (TQ), a natural bioactive plant quinone found black seed, exhibits anti-inflammatory, angiogenic, and antimicrobial properties. This study investigates the therapeutic effects of TQ perforator model through vivo vitro experiments. Human umbilical vein endothelial cells (HUVECs) were treated with Tert-butyl Hydroperoxide (TBHP) to simulate then TQ....
Osteosarcoma is a common bone tumor in adolescents and children, characterized by rapid progression, high malignancy, poor prognosis, tendency for pulmonary metastasis. Despite extensive research efforts, the specific driver gene associated with osteosarcoma remains unidentified, underscoring urgent need novel therapeutic targets targeted treatment options. In vitro studies were conducted to assess effects of DCC-2036 on proliferation, migration, invasion (OS) cell lines, employing cloning...
Abstract We investigated the correspondence between transcriptome and exome alterations in canine bladder cancer these cancer‐driving genes transcriptional human cancer. profiled tumors using mRNA‐seq exome‐seq order to investigate similarity of cancer, humans canines, at levels gene functions, pathways, cytogenetic regions. found that transcriptomes are remarkably similar functional pathway levels. demonstrated involves coordinated differential expression within bands, patterns consistent...
Due to the heterogeneity of cancer, identifying differentially methylated (DM) CpG sites between a set cancer samples and normal cannot tell us which patients have methylation aberrations in particular DM site.We firstly showed that relative methylation-level orderings (RMOs) within individual lung tissues are highly stable but widely disrupted adenocarcinoma tissues. This finding provides basis using RankComp algorithm, previously developed for differential gene expression analysis at...
Liquid-liquid phase separation (LLPS) partitions cellular contents, underlies the formation of membraneless organelles and plays essential biological roles. To date, most research on LLPS has focused proteins, especially RNA-binding proteins. However, accumulating evidence demonstrated that RNAs can also function as 'scaffolds' play roles in seeding or nucleating granules. better utilize knowledge dispersed published literature, we here introduce RNAPhaSep (http://www.rnaphasep.cn), a...
To detect differentially expressed genes (DEGs) in small-scale cell line experiments, usually with only two or three technical replicates for each state, the commonly used statistical methods such as significance analysis of microarrays (SAM), limma and RankProd (RP) lack power, while fold change method lacks any control. In this study, we demonstrated that within-sample relative expression orderings (REOs) gene pairs were highly stable among a but often widely disrupted after certain...
Long noncoding RNAs (lncRNAs) are emerging as vital regulators in various physiological and pathological processes. It was recently found that lncRNA HIF1A-AS2 could play oncogenic roles several cancers. However, the function regulatory mechanism of osteosarcoma (OS) remain largely unclear. In this study, we demonstrated overexpressed OS tissues cells. Downregulation significantly affects multiple biological functions cells, including cell proliferation, cycle progression, apoptosis,...
Abstract Triple-negative breast cancer (TNBC), an aggressive histological subtype of cancer, exhibits a high risk early recurrence rate and poor prognosis, it is primarily associated with the abundance stem cells (CSCs). At present, strategies for effectively eradicating or inhibiting TNBC CSCs are still limited, which makes development novel drugs anti-CSCs function be great value treatment TNBC, especially refractory TNBC. In this study, we found that small-molecule tyrosine kinase...
Abstract Background and Aim Differentially expressed (DE) genes detected at the population‐level through case–control comparison provide no information on dysregulation frequencies of DE in a cancer. In this work, we aimed to identify with universally upregulated or downregulated expressions colorectal cancer (CRC). Methods We firstly clarified that an individual tissue should be disease‐relevant genes, which are dysregulated its own previously normal state. Then, identified level for 2233...
Abstract Currently, using biopsy specimens for the early diagnosis of colorectal cancer (CRC) is not entirely reliable due to insufficient sampling amount and inaccurate location. Thus, it necessary develop a signature that can accurately identify patients with CRC under these clinical scenarios. Based on relative expression orderings genes within individual samples, we developed qualitative transcriptional discriminate tissues, including adjacent normal tissues from non‐CRC individuals. The...
Pluripotent stem cell-derived cardiomyocytes (PSC-CMs) are widely used models for regenerative medicine and disease research. However, PSC-CMs usually immature in morphology functionality the maturity of could not be determined accurately. In order to reasonably interpret experimental results obtained by PSC-CMs, it is necessary evaluate find key genes related maturation. Using gene expression profiles normal adult cardiac tissue embryonic cell (ESC) samples, we identified pairs with...
The Connectivity Map (CMAP) database, an important public data source for drug repositioning, archives gene expression profiles from cancer cell lines treated with and without bioactive small molecules. However, there are only one or two technical replicates each line under treatment condition. For such small-scale data, current fold-changes-based methods lack statistical control in identifying differentially expressed genes (DEGs) cells. Especially, one-to-one comparison may result too many...
Identifying differentially expressed microRNAs (DE miRNAs) between cancer samples and normal controls is a common way to investigate carcinogenesis mechanisms. However, for DE miRNA detected at the population-level, we do not know whether it in particular sample. Here, based on finding that within-sample relative expression orderings of pairs are highly stable type tissues but widely disrupted corresponding tissues, proposed method, called RankMiRNA, identify miRNAs each tissue compared with...