A5100620673- MicroRNA in disease regulation
- RNA modifications and cancer
- Lung Cancer Treatments and Mutations
- Biomedical Text Mining and Ontologies
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- Bioinformatics and Genomic Networks
- Genomics and Rare Diseases
- Epigenetics and DNA Methylation
- Lung Cancer Diagnosis and Treatment
- Cancer Genomics and Diagnostics
- Ferroptosis and cancer prognosis
- Lung Cancer Research Studies
- DNA Repair Mechanisms
- Topic Modeling
- Radiomics and Machine Learning in Medical Imaging
- Autism Spectrum Disorder Research
- Advanced Radiotherapy Techniques
- Acute Lymphoblastic Leukemia research
- Gene expression and cancer classification
- Pancreatic function and diabetes
- Amino Acid Enzymes and Metabolism
- Esophageal Cancer Research and Treatment
- PARP inhibition in cancer therapy
- Cancer-related gene regulation
Air Force Medical University
2016-2025
Fox Chase Cancer Center
2023-2024
Children's Hospital of Philadelphia
2020-2023
University of Mississippi Medical Center
2016-2020
Jackson Memorial Hospital
2016-2020
University of Pennsylvania
2020
Southwestern Medical Center
2015-2019
The University of Texas Southwestern Medical Center
2015-2019
University of Mississippi
2017-2019
Xijing Hospital
2016
Tumor cells can engage in a process called collective invasion, which cohesive groups of invade through interstitial tissue. Here, we identified an epigenetically distinct subpopulation breast tumor that have enhanced capacity to collectively invade. Analysis spheroid invasion organotypic culture system revealed these "trailblazer" are capable initiating and promote non-trailblazer cell indicating commensal relationship among subpopulations within heterogenous tumors. Canonical mesenchymal...
Pancreatic ductal adenocarcinomas (PDA) activate a glutamine-dependent pathway of cytosolic nicotinamide adenine dinucleotide phosphate (NADPH) production to maintain redox homeostasis and support proliferation. Enzymes involved in this (GLS1 (mitochondrial glutaminase 1), GOT1 (cytoplasmic glutamate oxaloacetate transaminase GOT2 2)) are highly upregulated PDA, among these, inhibitors GLS1 were recently deployed clinical trials target anabolic glutamine metabolism. However, single-agent...
Abstract Tumours frequently activate genes whose expression is otherwise biased to the testis, collectively known as cancer–testis antigens (CTAs). The extent which CTA represents epiphenomena or confers tumorigenic traits unknown. In this study, address this, we implemented a multidimensional functional genomics approach that incorporates 7 different phenotypic assays in 11 distinct disease settings. We identify 26 CTAs are essential for tumor cell viability and/or pathological drivers of...
Although non-small cell lung cancer (NSCLC) patients benefit from standard taxane-platin chemotherapy, many relapse, developing drug resistance. We established preclinical taxane-platin-chemoresistance models and identified a 35-gene resistance signature, which was associated with poor recurrence-free survival in neoadjuvant-treated NSCLC included upregulation of the JumonjiC lysine demethylase KDM3B. In fact, multi-drug-resistant cells progressively increased expression demethylases, had...
Several knowledgebases are manually curated to support clinical interpretations of thousands hotspot somatic mutations in cancer. However, discrepancies or even conflicting observed among these databases. Furthermore, many previously undocumented may have functional impacts on cancer but not systematically interpreted by existing knowledgebases. To address challenges, we developed CancerVar facilitate automated and standardized for 13 million based the AMP/ASCO/CAP 2017 guidelines. We...
To enhance phenotype recognition in clinical notes of genetic diseases, we developed two models - PhenoBCBERT and PhenoGPT for expanding the vocabularies Human Phenotype Ontology (HPO) terms. While HPO offers a standardized vocabulary phenotypes, existing tools often fail to capture full scope due limitations from traditional heuristic or rule-based approaches. Our leverage large language (LLMs) automate detection terms, including those not current HPO. We compared these PhenoTagger, another...
The new 8th American Joint Committee on Cancer (AJCC)/International Union for Control (UICC) lung cancer staging system was developed and internally validated using the International Association Study of Lung (IASLC) database, but external validation is needed. goal this study to validate discriminatory ability prognostic performance in a larger, independent non-small cell (NSCLC) cohort with greater emphasis North patients.A total 858,909 NSCLC cases one malignant primary tumor collected...
Abstract Previous studies have reported that the aberrantly expressed AKR1B10 is associated with many cancer development, however functional roles of and its regulatory mechanisms in hepatocellular carcinoma (HCC) been limited studied. In this project, we identified as an oncogene HCC through tumor/normal human tissue comparison from both GEO microarray TCGA RNAseq dataset. Further experimental validations three cell lines (SMMC-7721, HePG2 HeP3B) also suggested ontogenetic functions tumor...
Abstract It is well established that epilepsy and autism spectrum disorder (ASD) commonly co-occur; however, the underlying biological mechanisms of co-occurence from their genetic susceptibility are not understood. Our aim in this study to characterize modules subgroups genes have similar phenotypic manifestations functions. We first integrate a large number expert-compiled well-established epilepsy- ASD-associated multiplex network, where one layer connected through protein–protein...
Abstract Metastasis is a multistep process requiring cancer cell signaling, invasion, migration, survival, and proliferation. These processes require dynamic modulation of surface proteins by endocytosis. Given this functional connection, it has been suggested that endocytosis dysregulated in cancer. To test this, we developed In-Cell ELISA assays to measure three different endocytic pathways: clathrin-mediated endocytosis, caveolae-mediated clathrin-independent compared these activities...
Diffuse gliomas, grades II and III, hereafter called lower-grade gliomas (LGG), have variable, difficult to predict clinical courses, resulting in multiple studies identify prognostic biomarkers. The purpose of this study was assess expression or methylation the homeobox family gene SHOX2 as independent markers for LGG survival.We downloaded publically available glioma datasets methylation. Cancer Genome Atlas (TCGA) (LGG, n=516) used a training set, three other (n=308) (n=320), were...
// Hongmei Wu 1, 7, * , Jiong Bi 8, Yan Peng 2, Lei Huo 3, Xiaobin Yu 1 Zhihui Yang 4 Yunyun Zhou 5, 9 Li Qin Yixiang Xu Lan Liao Xie 5 Orla M. Conneely Jos Jonkers 6 and Jianming Department of Molecular Cellular Biology, Baylor College Medicine, Houston, TX 77030, USA 2 Pathology, UT Southwestern Medical Center, Dallas, 75390, 3 MD Anderson Cancer Institute for School Basic Sciences, Xinan University, Luzhou, Sichuan 646000, China Simmons Comprehensive Netherlands Institute, Antoni van...
Intradialytic hypertension (IH) occurs frequently in some hemodialysis patients and increases mortality risk. We simultaneously compared pre-dialysis, post-dialysis changes extracellular volume hemodynamics recurrent IH controls.We performed a case-control study among prevalent with hypertensive controls. used bioimpedance spectroscopy impedance cardiography to compare post-dialysis, intradialytic change total body water (TBW) (ECW), as well cardiac index (CI) peripheral resistance...
Background: Breast cancer is intrinsically heterogeneous and commonly classified into four main subtypes associated with distinct biological features clinical outcomes. However, currently available data resources methods are limited in identifying molecular subtyping on protein-coding genes, little known about the roles of long non-coding RNAs (lncRNAs), which occupies 98% whole genome. lncRNAs may also play important subgrouping patients phenotypes. Methods: The purpose this project was to...
Abstract In pancreatic ductal adenocarcinoma (PDAC), the fibroblastic stroma constitutes most of tumor mass and is remarkably devoid functional blood vessels. This raises an unresolved question how PDAC cells obtain essential metabolites water-insoluble lipids. We have found a critical role for cancer-associated fibroblasts (CAFs) in obtaining transferring lipids from blood-borne particles to via trogocytosis CAF plasma membranes. also determined that CAF-expressed phospholipid scramblase...
Efficiently learning representations of clinical concepts (i. e., symptoms, lab test, etc.) from unstructured notes electronic health record (EHR) data remain significant challenges, since each patient may have multiple visits at different times and visit contain sequential concepts. Therefore, distributed temporal patterns is an essential step for downstream applications on EHR data. However, existing methods representation can not adequately capture either contextual information per-visit...
Lung cancer is among the major causes of deaths, and survival rate lung patients extremely low. Recent studies have demonstrated that gene CDKN3 related to neoplasia, but in literature severe controversy exists over whether it involved progression or, conversely, tumor inhibition. In this study, we investigated expression its association with prognosis adenocarcinoma (ADC) squamous cell carcinoma (SCC) using datasets Cancer Explorer (LCE; http://qbrc.swmed.edu/lce/ ). We found was...
Ku70-binding protein 5 (Kub5)-Hera (K-H)/RPRD1B maintains genetic integrity by concomitantly minimizing persistent R-loops and promoting repair of DNA double strand breaks (DSBs). We used tandem affinity purification-mass spectrometry, co-immunoprecipitation gel-filtration chromatography to define higher-order complexes containing K-H scaffolding gain insight into its cellular functions. confirmed known partners (Ku70, RNA Pol II, p15RS) discovered several novel associated proteins that...