6801 Emmett F Lowry Expy
Texas City TX 77591
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Primary Epithelioid Angiosarcoma of Bone with Robust Cell Cycle Progression and High Expression of SPARC: A Case Report and Review of the Literature. - Annals of clinical and laboratory science
Epithelioid angiosarcoma of bone is a rare entity. Secreted protein acidic and rich in cysteine (SPARC), or osteonectin, is a secreted glycoprotein that has been implicated in tumorigenesis. We report a case of epithelioid angiosarcoma involving the long bones of the lower extremity showing diffuse and strong expression for SPARC immunohistochemistry in tumor cells. Ki-67 was positive in ~50% of tumor cell nuclei and the accompanying mitotic index was 19 mitotic figures/10 high power fields.Expression of SPARC in tumors has been correlated with sensitivity to nanoparticle albumin-bound paclitaxel (Nab-paclitaxel), particularly in the context of robust cell cycle progression into the mitotic phase. This finding could suggest new therapeutic options for further consideration.Â© 2015 by the Association of Clinical Scientists, Inc.
Developing discriminate model and comparative analysis of differentially expressed genes and pathways for bloodstream samples of diabetes mellitus type 2. - BMC bioinformatics
Diabetes mellitus of type 2 (T2D), also known as noninsulin-dependent diabetes mellitus (NIDDM) or adult-onset diabetes, is a common disease. It is estimated that more than 300 million people worldwide suffer from T2D. In this study, we investigated the T2D, pre-diabetic and healthy human (no diabetes) bloodstream samples using genomic, genealogical, and phonemic information. We identified differentially expressed genes and pathways. The study has provided deeper insights into the development of T2D, and provided useful information for further effective prevention and treatment of the disease.A total of 142 bloodstream samples were collected, including 47 healthy humans, 22 pre-diabetic and 73 T2D patients. Whole genome scale gene expression profiles were obtained using the Agilent Oligo chips that contain over 20,000 human genes. We identified 79 significantly differentially expressed genes that have fold change â‰¥ 2. We mapped those genes and pinpointed locations of those genes on human chromosomes. Amongst them, 3 genes were not mapped well on the human genome, but the rest of 76 differentially expressed genes were well mapped on the human genome. We found that most abundant differentially expressed genes are on chromosome one, which contains 9 of those genes, followed by chromosome two that contains 7 of the 76 differentially expressed genes. We performed gene ontology (GO) functional analysis of those 79 differentially expressed genes and found that genes involve in the regulation of cell proliferation were among most common pathways related to T2D. The expression of the 79 genes was combined with clinical information that includes age, sex, and race to construct an optimal discriminant model. The overall performance of the model reached 95.1% accuracy, with 91.5% accuracy on identifying healthy humans, 100% accuracy on pre-diabetic patients and 95.9% accuract on T2D patients. The higher performance on identifying pre-diabetic patients was resulted from more significant changes of gene expressions among this particular group of humans, which implicated that patients were having profound genetic changes towards disease development.Differentially expressed genes were distributed across chromosomes, and are more abundant on chromosomes 1 and 2 than the rest of the human genome. We found that regulation of cell proliferation actually plays an important role in the T2D disease development. The predictive model developed in this study has utilized the 79 significant genes in combination with age, sex, and racial information to distinguish pre-diabetic, T2D, and healthy humans. The study not only has provided deeper understanding of the disease molecular mechanisms but also useful information for pathway analysis and effective drug target identification.
A new statistical approach to combining p-values using gamma distribution and its application to genome-wide association study. - BMC bioinformatics
Combining information from different studies is an important and useful practice in bioinformatics, including genome-wide association study, rare variant data analysis and other set-based analyses. Many statistical methods have been proposed to combine p-values from independent studies. However, it is known that there is no uniformly most powerful test under all conditions; therefore, finding a powerful test in specific situation is important and desirable.In this paper, we propose a new statistical approach to combining p-values based on gamma distribution, which uses the inverse of the p-value as the shape parameter in the gamma distribution.Simulation study and real data application demonstrate that the proposed method has good performance under some situations.
Identification of genes and pathways involved in kidney renal clear cell carcinoma. - BMC bioinformatics
Kidney Renal Clear Cell Carcinoma (KIRC) is one of fatal genitourinary diseases and accounts for most malignant kidney tumours. KIRC has been shown resistance to radiotherapy and chemotherapy. Like many types of cancers, there is no curative treatment for metastatic KIRC. Using advanced sequencing technologies, The Cancer Genome Atlas (TCGA) project of NIH/NCI-NHGRI has produced large-scale sequencing data, which provide unprecedented opportunities to reveal new molecular mechanisms of cancer. We combined differentially expressed genes, pathways and network analyses to gain new insights into the underlying molecular mechanisms of the disease development.Followed by the experimental design for obtaining significant genes and pathways, comprehensive analysis of 537 KIRC patients' sequencing data provided by TCGA was performed. Differentially expressed genes were obtained from the RNA-Seq data. Pathway and network analyses were performed. We identified 186 differentially expressed genes with significant p-value and large fold changes (P < 0.01, |log(FC)| > 5). The study not only confirmed a number of identified differentially expressed genes in literature reports, but also provided new findings. We performed hierarchical clustering analysis utilizing the whole genome-wide gene expressions and differentially expressed genes that were identified in this study. We revealed distinct groups of differentially expressed genes that can aid to the identification of subtypes of the cancer. The hierarchical clustering analysis based on gene expression profile and differentially expressed genes suggested four subtypes of the cancer. We found enriched distinct Gene Ontology (GO) terms associated with these groups of genes. Based on these findings, we built a support vector machine based supervised-learning classifier to predict unknown samples, and the classifier achieved high accuracy and robust classification results. In addition, we identified a number of pathways (P < 0.04) that were significantly influenced by the disease. We found that some of the identified pathways have been implicated in cancers from literatures, while others have not been reported in the cancer before. The network analysis leads to the identification of significantly disrupted pathways and associated genes involved in the disease development. Furthermore, this study can provide a viable alternative in identifying effective drug targets.Our study identified a set of differentially expressed genes and pathways in kidney renal clear cell carcinoma, and represents a comprehensive computational approach to analysis large-scale next-generation sequencing data. The pathway and network analyses suggested that information from distinctly expressed genes can be utilized in the identification of aberrant upstream regulators. Identification of distinctly expressed genes and altered pathways are important in effective biomarker identification for early cancer diagnosis and treatment planning. Combining differentially expressed genes with pathway and network analyses using intelligent computational approaches provide an unprecedented opportunity to identify upstream disease causal genes and effective drug targets.
Orthology-driven mapping of bidirectional promoters in human and mouse genomes. - BMC bioinformatics
The presence of bidirectional promoters in all vertebrate species suggests that the promoters may be maintained in orthologous positions. Therefore the identification of the comprehensive orthologous mapping of this type promoter across species can facilitate elucidation of regulatory mechanisms controlling bidirectional gene expression. However, the lack of annotation for many transcribed regions in the genome can impact the orthology designation of these promoters. Human and mouse are among genomes that have been relatively well annotated. Thus we used them as models to study the orthologous patterns of bidirectional promoters.We developed a method to annotate these regulatory regions by confirming the orthology of the genes found on each side of the promoters. In this manuscript we report the cross-species comparisons between human and mouse genomes, where the bidirectional promoter sets regulating UCSC Known Genes and spliced EST annotations were mapped from human to mouse and vice versa. We validate hundreds of orthologous bidirectional promoters through the presence of orthologous flanking gene annotations in the second species. We also show that regulatory activity of these orthologous promoters confers similar gene expression profiles in 21 tissues of human and mouse. In particular, more than one third of human bidirectional promoters annotated from spliced EST annotations regulate ncRNA, of which over 90% are lncRNAs.Although evolutionary conservation shows a weaker signature in promoters than coding regions, our technique of mapping of orthologous genes shows that most bidirectional promoter arrangements are conserved across human and mouse genomes, suggesting a critical function. In addition, the similar expression patterns of the orthologous gene sets indicate that the regulatory mechanisms remain largely conserved as well.
Gene regulation mediated by microRNAs in response to green tea polyphenol EGCG in mouse lung cancer. - BMC genomics
Epigallocatechin-3-gallate (EGCG) has been demonstrated to inhibit cancer in experimental studies through its antioxidant activity and modulations on cellular functions by binding specific proteins. We demonstrated previously that EGCG upregulates the expression of microRNA (i.e. miR-210) by binding HIF-1Î±, resulting in reduced cell proliferation and anchorage-independent growth. However, the binding affinities of EGCG to HIF-1Î± and many other targets are higher than the EGCG plasma peak level in experimental animals administered with high dose of EGCG, raising a concern whether the microRNA regulation by HIF-1Î± is involved in the anti-cancer activity of EGCG in vivo.We employed functional genomic approaches to elucidate the role of microRNA in the EGCG inhibition of tobacco carcinogen-induced lung tumors in A/J mice. By analysing the microRNA profiles, we found modest changes in the expression levels of 21 microRNAs. By correlating these 21 microRNAs with the mRNA expression profiles using the computation methods, we identified 26 potential targeted genes of the 21 microRNAs. Further exploration using pathway analysis revealed that the most impacted pathways of EGCG treatment are the regulatory networks associated to AKT, NF-ÎºB, MAP kinases, and cell cycle, and the identified miRNA targets are involved in the networks of AKT, MAP kinases and cell cycle regulationThese results demonstrate that the miRNA-mediated regulation is actively involved in the major aspects of the anti-cancer activity of EGCG in vivo.
Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms. - BMC bioinformatics
Advances of high-throughput technologies have rapidly produced more and more data from DNAs and RNAs to proteins, especially large volumes of genome-scale data. However, connection of the genomic information to cellular functions and biological behaviours relies on the development of effective approaches at higher systems level. In particular, advances in RNA-Seq technology has helped the studies of transcriptome, RNA expressed from the genome, while systems biology on the other hand provides more comprehensive pictures, from which genes and proteins actively interact to lead to cellular behaviours and physiological phenotypes. As biological interactions mediate many biological processes that are essential for cellular function or disease development, it is important to systematically identify genomic information including genetic mutations from GWAS (genome-wide association study), differentially expressed genes, bidirectional promoters, intrinsic disordered proteins (IDP) and protein interactions to gain deep insights into the underlying mechanisms of gene regulations and networks. Furthermore, bidirectional promoters can co-regulate many biological pathways, where the roles of bidirectional promoters can be studied systematically for identifying co-regulating genes at interactive network level. Combining information from different but related studies can ultimately help revealing the landscape of molecular mechanisms underlying complex diseases such as cancer.
MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity. - BMC genomics
RDX is a well-known pollutant to induce neurotoxicity. MicroRNAs (miRNA) and messenger RNA (mRNA) profiles are useful tools for toxicogenomics studies. It is worthy to integrate MiRNA and mRNA expression data to understand RDX-induced neurotoxicity.Rats were treated with or without RDX for 48 h. Both miRNA and mRNA profiles were conducted using brain tissues. Nine miRNAs were significantly regulated by RDX. Of these, 6 and 3 miRNAs were up- and down-regulated respectively. The putative target genes of RDX-regulated miRNAs were highly nervous system function genes and pathways enriched. Fifteen differentially genes altered by RDX from mRNA profiles were the putative targets of regulated miRNAs. The induction of miR-71, miR-27ab, miR-98, and miR-135a expression by RDX, could reduce the expression of the genes POLE4, C5ORF13, SULF1 and ROCK2, and eventually induce neurotoxicity. Over-expression of miR-27ab, or reduction of the expression of unknown miRNAs by RDX, could up-regulate HMGCR expression and contribute to neurotoxicity. RDX regulated immune and inflammation response miRNAs and genes could contribute to RDX- induced neurotoxicity and other toxicities as well as animal defending reaction response to RDX exposure.Our results demonstrate that integrating miRNA and mRNA profiles is valuable to indentify novel biomarkers and molecular mechanisms for RDX-induced neurological disorder and neurotoxicity.
The emerging genomics and systems biology research lead to systems genomics studies. - BMC genomics
Synergistically integrating multi-layer genomic data at systems level not only can lead to deeper insights into the molecular mechanisms related to disease initiation and progression, but also can guide pathway-based biomarker and drug target identification. With the advent of high-throughput next-generation sequencing technologies, sequencing both DNA and RNA has generated multi-layer genomic data that can provide DNA polymorphism, non-coding RNA, messenger RNA, gene expression, isoform and alternative splicing information. Systems biology on the other hand studies complex biological systems, particularly systematic study of complex molecular interactions within specific cells or organisms. Genomics and molecular systems biology can be merged into the study of genomic profiles and implicated biological functions at cellular or organism level. The prospectively emerging field can be referred to as systems genomics or genomic systems biology. The Mid-South Bioinformatics Centre (MBC) and Joint Bioinformatics Ph.D. Program of University of Arkansas at Little Rock and University of Arkansas for Medical Sciences are particularly interested in promoting education and research advancement in this prospectively emerging field. Based on past investigations and research outcomes, MBC is further utilizing differential gene and isoform/exon expression from RNA-seq and co-regulation from the ChiP-seq specific for different phenotypes in combination with protein-protein interactions, and protein-DNA interactions to construct high-level gene networks for an integrative genome-phoneme investigation at systems biology level.
Ovarian microcystic stromal tumor: report of a new entity with immunohistochemical and ultrastructural studies. - Ultrastructural pathology
Microcystic stromal tumor is a recently described rare subtype of ovarian tumor for which there has been no previously reported ultrastructural study. We report a case with the characteristic histological and immunohistochemical features and the first ultrastructural study. The immunohistochemical findings of strong and diffuse nuclear staining for beta catenin and P27 are suggestive of dysregulation of more than one genetic pathway. The ultrastructural findings are supportive of the previous postulation of an ovarian stromal origin of the neoplastic cells.
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