A5022178171- Lymphoma Diagnosis and Treatment
- Cancer Genomics and Diagnostics
- Chronic Lymphocytic Leukemia Research
- Redox biology and oxidative stress
- Multiple Myeloma Research and Treatments
- RNA modifications and cancer
- Retinal Development and Disorders
- Alzheimer's disease research and treatments
- Bioinformatics and Genomic Networks
- HER2/EGFR in Cancer Research
- Neuroinflammation and Neurodegeneration Mechanisms
- Ubiquitin and proteasome pathways
- Lung Cancer Treatments and Mutations
- Gene expression and cancer classification
- CNS Lymphoma Diagnosis and Treatment
- Cancer, Hypoxia, and Metabolism
- Genetic factors in colorectal cancer
- Cancer-related molecular mechanisms research
- Protein Degradation and Inhibitors
- Molecular Biology Techniques and Applications
- Glycosylation and Glycoproteins Research
- Colorectal Cancer Treatments and Studies
- Metabolism, Diabetes, and Cancer
- bioluminescence and chemiluminescence research
- Genetic Associations and Epidemiology
Mayo Clinic in Florida
2016-2025
Jacksonville College
2014-2025
WinnMed
2014-2024
Mayo Clinic
2011-2023
Quantitative BioSciences
2023
Nemours Children’s Clinic
2014-2021
Nemours Children's Clinic
2015-2020
Department of Medical Sciences
2008-2019
University of North Florida
2018
St. Christopher's Hospital for Children
2018
To gain insight into the genomic basis of diffuse large B-cell lymphoma (DLBCL), we performed massively parallel whole-exome sequencing 55 primary tumor samples from patients with DLBCL and matched normal tissue. We identified recurrent mutations in genes that are well known to be functionally relevant DLBCL, including MYD88 , CARD11 EZH2 CREBBP . also somatic for which a functional role has not been previously suspected. These include MEF2B MLL2 BTG1 GNA13 ACTB P2RY8 PCLO TNFRSF14 Further,...
Abstract Previous genome-wide association studies (GWAS), conducted by our group and others, have identified loci that harbor risk variants for neurodegenerative diseases, including Alzheimer's disease (AD). Human are enriched polymorphisms affect gene expression, some known to associate with expression changes in the brain. Postulating many confer via transcriptional regulatory mechanisms, we analyzed levels brain tissue of subjects AD related diseases. Herein, describe collective datasets...
Although the costs of next generation sequencing technology have decreased over past years, there is still a lack simple-to-use applications, for comprehensive analysis RNA data. There no one-stop shop transcriptomic genomics. We developed MAP-RSeq, computational workflow that can be used obtaining genomic features from data, any genome. For optimization tools and parameters, MAP-RSeq was validated using both simulated real datasets. consists six major modules such as alignment reads,...
Human colorectal cancers (CRCs) display a large number of genetic and epigenetic alterations, some which are causally involved in tumorigenesis (drivers) others that have little functional impact (passengers). To help distinguish between these two classes we used transposon-based screen mice to identify candidate genes for CRC. Mice harboring mutagenic Sleeping Beauty (SB) transposons were crossed with expressing SB transposase gastrointestinal tract epithelium. Most the offspring developed...
Advanced cholangiocarcinoma continues to harbor a difficult prognosis and therapeutic options have been limited. During the course of clinical trial whole genomic sequencing seeking druggable targets, we examined six patients with advanced cholangiocarcinoma. Integrated genome-wide transcriptome sequence analyses were performed on tumors from advanced, sporadic intrahepatic (SIC) identify potential therapeutically actionable events. Among somatic events captured in our analysis, uncovered...
Abstract APOE4 is the strongest genetic risk factor associated with late-onset Alzheimer’s disease (AD). To address underlying mechanism, we develop cerebral organoid models using induced pluripotent stem cells (iPSCs) APOE ε3/ε3 or ε4/ε4 genotype from individuals either normal cognition AD dementia. Cerebral organoids patients carrying show greater apoptosis and decreased synaptic integrity. While patient-derived have increased levels of Aβ phosphorylated tau compared to healthy...
Primary central nervous system lymphoma (PCNSL) is an aggressive non-Hodgkin confined to the system. Whether there a PCNSL-specific genomic signature and, if so, how it differs from systemic diffuse large B-cell (DLBCL) uncertain.We performed comprehensive study of tumor samples 19 immunocompetent PCNSL patients. Testing comprised array-comparative hybridization and whole exome sequencing.Biallelic inactivation TOX PRKCD was recurrently found in but not DLBCL, suggesting specific role...
Purpose To develop a genomic signature that predicts benefit from trastuzumab in human epidermal growth factor receptor 2–positive breast cancer. Patients and Methods DASL technology was used to quantify mRNA samples 1,282 patients enrolled onto the Combination Chemotherapy With or Without Trastuzumab Treating Women Breast Cancer (North Central Treatment Group N9831 [NCCTG-N9831]) adjuvant trial. Cox proportional hazard ratios (HRs), adjusted for significant clinicopathologic risk factors,...
The human genome contains "dark" gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these may relevant to disease. Here, we identify with few mappable reads call dark by depth, and others have ambiguous alignment, called camouflaged. We assess how well long-read linked-read technologies resolve regions. Based on whole-genome Illumina data, 36,794 in 6054 bodies pathways...
We investigated whether previously reported muscle mitochondrial dysfunction and altered gene transcript levels in type 2 diabetes might be secondary to abnormal blood glucose insulin rather than an intrinsic defect of diabetes. A total 13 diabetic 17 nondiabetic subjects were studied on two separate occasions while maintaining similar both groups by 7-h infusions somatostatin, low- or high-dose (0.25 1.5 mU/kg fat-free mass per min, respectively), glucose. Muscle DNA abundance was not...
Type 2 diabetes has become a global epidemic, and Asian Indians have higher susceptibility to than Europeans. We investigated whether had any metabolic differences compared with Northern European Americans that may render them more susceptible diabetes.We studied 13 diabetic Indians, nondiabetic who were matched for age, BMI, sex. The primary comparisons insulin sensitivity by hyperinsulinemic-euglycemic clamp skeletal muscle mitochondrial capacity oxidative phosphorylation (OXPHOS)...
Many men develop a rising PSA after initial therapy for prostate cancer. While some of these will local or metastatic recurrence that warrants further therapy, others have no evidence disease progression. We hypothesized an expression biomarker panel can predict which with would benefit from therapy.A case-control design was used to test the association gene outcome. Systemic (SYS) progression cases were post-prostatectomy who developed systemic within 5 years recurrence. controls matched...
Abstract Background Massive parallel sequencing has the potential to replace microarrays as method for transcriptome profiling. Currently there are two protocols: full-length RNA (RNA-SEQ) and 3'-tag digital gene expression (DGE). In this preliminary effort, we evaluated 3' DGE approach using reference samples from MicroArray Quality Control Consortium (MAQC). Results Using Brain sample multiple runs, demonstrated that transcript profiles were highly reproducible between technical biological...
We used deep sequencing technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly breast cell lines develop a model for how these genomic features are integrated estrogen receptor positive (ER+) negative cancer. Total mRNA sequence, were carried out using Illumina Genome Analyzer. Sequences mapped human genome obtain digitized expression data, DNA number reference non-tumor line (MCF10A), of 21,570 islands identify...
Changes in miRNA expression are a common feature colon cancer. Those changes occurring the transition from normal to adenoma and carcinoma, however, have not been well defined. Additionally, among tumor subgroups of cancer also adequately evaluated. In this study, we examined global 315 samples that included 52 colonic mucosa, 41 tubulovillous adenomas, 158 adenocarcinomas with proficient DNA mismatch repair (pMMR) selected for stage age onset, 64 defective (dMMR) sporadic (n = 53) inherited...
Abstract Introduction Comparative transcriptome analyses in Alzheimer's disease (AD) and other neurodegenerative proteinopathies can uncover both shared distinct pathways. Methods We analyzed 940 brain transcriptomes including patients with AD, progressive supranuclear palsy (PSP; a primary tauopathy), control subjects. Results identified transcriptional coexpression networks implicated myelination, which were lower PSP temporal cortex (TCX) compared AD. Some of these associations retained...