A5041036600- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Genomics and Chromatin Dynamics
- MicroRNA in disease regulation
- Chronic Obstructive Pulmonary Disease (COPD) Research
- RNA Research and Splicing
- Cancer Genomics and Diagnostics
- Genetic factors in colorectal cancer
- Glioma Diagnosis and Treatment
- CRISPR and Genetic Engineering
- Protein Tyrosine Phosphatases
- Pancreatic and Hepatic Oncology Research
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Brain Metastases and Treatment
- Advanced biosensing and bioanalysis techniques
- Medical and Biological Ozone Research
- Ferroptosis and cancer prognosis
- Molecular Biology Techniques and Applications
- RNA and protein synthesis mechanisms
- Epigenetics and DNA Methylation
- Ocular Oncology and Treatments
- Genetics and Neurodevelopmental Disorders
- Protein Kinase Regulation and GTPase Signaling
- Hydrogen's biological and therapeutic effects
Duke Medical Center
2021-2025
Duke University
2024
Duke University Hospital
2021-2023
University of Alabama at Birmingham
2015-2022
HudsonAlpha Institute for Biotechnology
2015-2020
Oxford University Press (United Kingdom)
2020
St. Luke's-Roosevelt Hospital Center
2012-2013
Psychiatric disorders are multigenic diseases with complex etiology that contribute significantly to human morbidity and mortality. Although clinically distinct, several share many symptoms, suggesting common underlying molecular changes exist may implicate important regulators of pathogenesis provide new therapeutic targets. We performed RNA sequencing on tissue from the anterior cingulate cortex, dorsolateral prefrontal nucleus accumbens three groups 24 patients each diagnosed...
Abstract Transcription factors are DNA-binding proteins that have key roles in gene regulation 1,2 . Genome-wide occupancy maps of transcriptional regulators important for understanding and its effects on diverse biological processes 3–6 However, only a minority the more than 1,600 transcription encoded human genome has been assayed. Here we present, as part ENCODE (Encyclopedia DNA Elements) project, data analyses from chromatin immunoprecipitation followed by high-throughput sequencing...
Section:ChooseTop of pageAbstract <<Materials and MethodsResultsDiscussionReferencesCITING ARTICLES
Rationale Though matrix metalloproteinases (MMPs) are critical in the pathogenesis of COPD, their utility as a disease biomarker remains uncertain. This study aimed to determine whether bronchoalveolar lavage (BALF) or plasma MMP measurements correlated with severity functional decline emphysema. Methods Enzyme-linked immunosorbent assay and luminex assays measured MMP-1, -9, -12 tissue inhibitor metalloproteinase-1 BALF non-smokers, smokers normal lung function moderate-to-severe emphysema...
Rationale Biomass is the energy source for cooking and heating billions of people worldwide. Despite their prevalent use potential impact on global health, effects these fuels lung biology function remain poorly understood. Methods We exposed human small airway epithelial cells C57BL/6 mice to dung biomass smoke or cigarette compare how exposures impacted signaling inflammatory proteolytic responses that have been linked with disease pathogenesis. Results The in vitro exposure siRNA studies...
Protein phosphatase 2A (PP2A) is the primary serine-threonine of eukaryotic cells, and changes in its activity have been linked to neoplastic neurodegenerative diseases. However, role PP2A noncancerous lung diseases such as chronic obstructive pulmonary disease (COPD) has not previously examined. This study determined that was significantly increased lungs advanced emphysema subjects compared with age-matched controls. Furthermore, we found cigarette smoke exposure increases mouse vivo human...
INTRODUCTION: Recent evidence suggests epigenetic heterogeneity may be the primary driver of cell phenotype and treatment resistance in glioblastoma. Epigenetic is defined by alterations chromatin histone modifications with activating marks such as H3K27 acetylation repressive trimethylation. Combinations these govern activity functional genomic elements enhancers or promoters. Single-cell ("sc-") technologies have only recently been adapted to study states significant technical challenges...
Abstract Glioblastoma (GBM) is an aggressive and heterogeneous brain tumor characterized by extensive plasticity, which contributes to resistance against conventional therapies. To address this challenge, we generated a unique single nuclei RNA sequencing atlas, integrating GBM, normal tissue, developmental datasets. Utilizing single-cell (scRNA-seq) analysis methods, comprehensively GBM heterogeneity focusing on identifying homogeneous cell surface antigens suitable for chimeric antigen...
Section:ChooseTop of pageAbstract <<Materials and MethodsResultsDiscussionReferencesCITING ARTICLES
// Ryne C. Ramaker 1, 2, * , Brittany N. Lasseigne Andrew A. Hardigan 2 Laura Palacio 1 David S. Gunther Richard M. Myers Sara J. Cooper HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA Department of Genetics, University Alabama at Birmingham, These authors contributed equally to this work Correspondence to: Myers, email: rmyers@hudsonalpha.org Cooper, sjcooper@hudsonalpha.org Keywords: cell proliferation, cancer, reelin, survival, RNA-seq Received: January 02,...
Pancreatic ductal adenocarcinoma (PDAC) patients suffer poor outcomes, including a five-year survival of below 10%. Poor outcomes result in part from therapeutic resistance that limits the impact cytotoxic first-line therapy. Novel approaches are needed, but currently no targeted therapies exist to treat PDAC.To assess cellular mechanisms common four chemotherapies (gemcitabine, 5-fluorouracil, irinotecan, and oxaliplatin) used PDAC patients, we performed genome-wide CRISPR activation...
Mutations that alter signaling of RAS/MAPK-family proteins give rise to a group Mendelian diseases known as RASopathies. However, among RASopathies, the matrix genotype-phenotype relationships is still incomplete, in part because there are many RAS-related and phenotypic consequences may be variable and/or pleiotropic. Here, we describe cohort ten cases, drawn from six clinical sites over 16,000 sequenced probands, with de novo protein-altering variation RALA, RAS-like small GTPase. All...
The wide range of RNA-seq applications and their high-computational needs require the development pipelines orchestrating entire workflow optimizing usage available computational resources. We present aRNApipe, a project-oriented pipeline for processing data in high-performance cluster environments. aRNApipe is highly modular can be easily migrated to any computing (HPC) environment. current included combine essential primary analyses, including quality control metrics, transcript alignment,...
Purpose: Colorectal cancer is the third most common worldwide, causing approximately 700,000 deaths each year. The majority of colorectal cancers begin as adenomas. Definitive screening for adenomas currently accomplished through colonoscopy but, owing largely to costs and invasiveness, typically limited patient groups at higher risk by virtue age or family history. We sought determine if blood-based small RNA markers could detect adenoma.Experimental Design: applied high-depth sequencing...
In small RNA (smRNA) sequencing studies, highly abundant molecules such as adapter dimer products and tissue-specific microRNAs (miRNAs) inhibit accurate quantification of lowly expressed species. We previously developed a method to selectively deplete miRNAs. However, this does not ligation that, unless removed by gel-separation, comprise most the library. Here, we have adapted modified recently described methods for CRISPR/Cas9-based Depletion Abundant Species Hybridization ('DASH')...
DNA-associated proteins (DAPs) classically regulate gene expression by binding to regulatory loci such as enhancers or promoters. As expanding catalogs of genome-wide DAP maps reveal thousands that, unlike the majority conventional and promoters, associate with dozens different DAPs apparently little regard for motif preference, an understanding association coordination at is essential deciphering how these regions contribute normal development disease. In this study, we aggregated publicly...
Highly abundant microRNAs (miRNAs) in small RNA sequencing libraries make it difficult to obtain efficient measurements of more lowly expressed species. We present a new method that allows for the selective blocking specific, miRNAs during preparation libraries. This technique is specific with little off-target effects and has no impact on reproducibility measurement non-targeted In human plasma samples, we demonstrate highly hsa-miR-16–5p leads improved detection precise differential...
BACKGROUND: The management of intracranial oncological disease remains a significant challenge despite advances in systemic cancer therapy. Laser interstitial thermal therapy (LITT) represents novel treatment for local control brain tumors through photocoagulation with stereotactically implanted laser fiber. Because the use continues to increase within neurosurgery, characterization LITT is necessary improve outcomes. OBJECTIVE: To quantify risk tumor seeding along fiber tract patients...
Abstract The care of patients with both high-grade glioma and low-grade necessitates an interdisciplinary collaboration between neurosurgeons, neuro-oncologists, neurologists other practitioners. In this review, we aim to detail the considerations, approaches advances in neurosurgical gliomas. We describe impact extent-of-resection glioma, particular focus on primary recurrent glioblastoma. address surgical methods adjunct technologies such as intraoperative imaging fluorescence guided...
Large-scale efforts like the ENCODE Project have made tremendous progress in cataloging genomic binding patterns of DNA-associated proteins (DAPs), such as transcription factors (TFs). However, most chromatin immunoprecipitation-sequencing (ChIP-seq) analyses focused on a few immortalized cell lines whose activities and physiology differ important ways from endogenous cells tissues. Consequently, data primary human tissue are essential to improving our understanding vivo gene regulation....