Antonis Kourtidis | Medical University of South Carolina (original) (raw)

Papers by Antonis Kourtidis

Research paper thumbnail of VEGF and Angiopoietin-1 exert opposing effects on cell junctions by regulating the Rho GEF Syx

Research paper thumbnail of VEGF and Angiopoietin-1 exert opposing effects on cell junctions by regulating the Rho GEF Syx

The Journal of Cell Biology, 2012

Research paper thumbnail of Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

E-cadherin and p120 catenin (p120) are essential for epithelial homeostasis, but can also exert p... more E-cadherin and p120 catenin (p120) are essential for epithelial homeostasis, but can also exert pro-tumorigenic activities. Here, we resolve this apparent paradox by identifying two spatially and functionally distinct junctional complexes in non-transformed polarized epithelial cells: one growth suppressing at the apical zonula adherens (ZA), defined by the p120 partner PLEKHA7 and a non-nuclear subset of the core microprocessor components DROSHA and DGCR8, and one growth promoting at basolateral areas of cell-cell contact containing tyrosine-phosphorylated p120 and active Src. Recruitment of DROSHA and DGCR8 to the ZA is PLEKHA7 dependent. The PLEKHA7-microprocessor complex co-precipitates with primary microRNAs (pri-miRNAs) and possesses pri-miRNA processing activity. PLEKHA7 regulates the levels of select miRNAs, in particular processing of miR-30b, to suppress expression of cell transforming markers promoted by the basolateral complex, including SNAI1, MYC and CCND1. Our work identifies a mechanism through which adhesion complexes regulate cellular behaviour and reveals their surprising association with the microprocessor.

Research paper thumbnail of Pro-Tumorigenic Phosphorylation of p120 Catenin in Renal and Breast Cancer

Altered protein expression and phosphorylation are common events during malignant transformation.... more Altered protein expression and phosphorylation are common events during malignant transformation. These perturbations have been widely explored in the context of E-cadherin cell-cell adhesion complexes, which are central in the maintenance of the normal epithelial phenotype. A major component of these complexes is p120 catenin (p120), which binds and stabilizes E-cadherin to promote its adhesive and tumor suppressing function. However, p120 is also an essential mediator of pro-tumorigenic signals driven by oncogenes, such as Src, and can be phosphorylated at multiple sites. Although alterations in p120 expression have been extensively studied by immunohistochemistry (IHC) in the context of tumor progression, little is known about the status and role of p120 phosphorylation in cancer. Here we show that tyrosine and threonine phosphorylation of p120 in two sites, Y228 and T916, is elevated in renal and breast tumor tissue samples. We also show that tyrosine phosphorylation of p120 at its N-terminus, including at the Y228 site is required for its pro-tumorigenic potential. In contrast, phosphorylation of p120 at T916 does not affect this p120 function. However, phosphorylation of p120 at T916 interferes with epitope recognition of the most commonly used p120 antibody, namely pp120. As a result, this antibody selectively underrepresents p120 levels in tumor tissues, where p120 is phosphorylated. Overall, our data support a role of p120 phosphorylation as a marker and mediator of tumor transformation. Importantly, they also argue that the level and localization of p120 in human cancer tissues immunostained with pp120 needs to be re-evaluated

Research paper thumbnail of Adhesion signaling in tumor progression

Research paper thumbnail of Peroxisome proliferator-activated receptor-gamma protects ERBB2-positive breast cancer cells from palmitate toxicity

Breast Cancer Reseacrh, 2009

Research paper thumbnail of The spindle assembly checkpoint is satisfied in the absence of interkinetochore tension during mitosis with unreplicated genomes

The Journal of Cell Biology, 2008

Research paper thumbnail of The Cystic Fibrosis Conductance Regulator (CFTR) controls c-Src tyrosine kinase signaling and regulates innate immunity and epithelial polarity in cholangiocytes

Research paper thumbnail of VEGF and Angiopoietin-1 exert opposing effects on cell junctions by regulating the Rho GEF Syx

The Journal of Cell Biology, 2012

Research paper thumbnail of The Rho Guanine Nucleotide Exchange Factor Syx Regulates the Balance of Dia and ROCK Activities To Promote Polarized-Cancer-Cell Migration

Molecular and Cellular Biology, 2013

The role of RhoA in promoting directed cell migration has been complicated by studies showing tha... more The role of RhoA in promoting directed cell migration has been complicated by studies showing that it is activated both in the front and the rear of migrating cells. We report here that the RhoA-specific guanine nucleotide exchange factor Syx is required for the polarity of actively migrating brain and breast tumor cells. This function of Syx is mediated by the selective activation of the RhoA downstream effector Dia1, the subsequent re-organization of microtubules, and the downregulation of focal adhesions and actin stress fibers. The data argue that directed cell migration requires the precise spatiotemporal regulation of Dia1 and ROCK activities in the cell. The recruitment of Syx to the cell membrane and the subsequent selective activation of Dia1 signaling, coupled with the suppression of ROCK and activation of cofilin-mediated actin reorganization plays a key role in establishing cell polarity during directed cell migration.

Research paper thumbnail of TEM4 is a junctional Rho GEF required for cell-cell adhesion, monolayer integrity and barrier function

Journal of Cell Science, 2013

Signaling events mediated by Rho family GTPases orchestrate cytoskeletal dynamics and cell juncti... more Signaling events mediated by Rho family GTPases orchestrate cytoskeletal dynamics and cell junction formation. The activation of Rho GTPases is tightly regulated by guanine nucleotide exchange-factors (GEFs). In this study, we identified a novel Rhospecific GEF called TEM4 (Tumor Endothelial Marker 4) that associates with multiple members of the cadherin-catenin complex and with several cytoskeleton-associated proteins. Depending on confluence, TEM4 localized to either actin stress fibers, or areas of cell-cell contact. The junctional localization of TEM4 was independent of actin binding. Depletion of endogenous TEM4 by shRNAs impaired Madin-Darby Canine Kidney (MDCK) and Human Umbilical Vein Endothelial Cell (HUVEC) cell junctions, disrupted MDCK acini formation in 3D culture, and negatively affected endothelial barrier function. Together, our findings implicate TEM4 as a novel and critical junctional RhoGEF that regulates cell junction integrity and epithelial and endothelial cell function. . Rho, rac, and cdc42 GTPases regulate the assembly of multimolecular focal complexes associated with actin stress fibers, lamellipodia, and filopodia. Cell 81, 53-62.

Research paper thumbnail of Phosphorylation-mediated 14-3-3 Protein Binding Regulates the Function of the Rho-specific Guanine Nucleotide Exchange Factor (RhoGEF) Syx

Journal of Biological Chemistry, 2013

Syx is a Rho-specific guanine nucleotide exchange factor (GEF) that localizes at cell-cell juncti... more Syx is a Rho-specific guanine nucleotide exchange factor (GEF) that localizes at cell-cell junctions and promotes junction stability by activating RhoA and the downstream effector Diaphanous homolog 1 (Dia1). Previously, we identified several molecules, including 14-3-3 proteins, as Syx-interacting partners. In the present study, we show that 14-3-3 isoforms interact with Syx at both its N- and C-terminal regions in a phosphorylation-dependent manner. We identify the protein kinase D-mediated phosphorylation of serine 92 on Syx, and additional phosphorylation at serine 938, as critical sites for 14-3-3 association. Our data indicate that the binding of 14-3-3 proteins inhibits the GEF activity of Syx. Furthermore, we show that phosphorylation-deficient, 14-3-3-uncoupled Syx exhibits increased junctional targeting and increased GEF activity, resulting in the strengthening of the circumferential junctional actin ring in Madin-Darby canine kidney cells. These findings reveal a novel means of regulating junctional Syx localization and function by phosphorylation-induced 14-3-3 binding and further support the importance of Syx function in maintaining stable cell-cell contacts.

Research paper thumbnail of An RNA Interference Screen Identifies Metabolic Regulators NR1D1 and PBP as Novel Survival Factors for Breast Cancer Cells with the ERBB2 Signature

Cancer Research, 2010

Overexpression of the adverse prognostic marker ERBB2 occurs in 30% of breast cancers; however, t... more Overexpression of the adverse prognostic marker ERBB2 occurs in 30% of breast cancers; however, therapies targeting this gene have not proved to be as effective as was initially hoped. Transcriptional profiling meta-analyses have shown that there are approximately 150 genes co-overexpressed with ERBB2, suggesting that these genes may represent alternative factors influencing ERBB2-positive tumors. Here we describe an RNA interference-based analysis of these genes that identifies transcriptional regulators of fat synthesis and storage as being critical for the survival of these cells. These transcription factors, nuclear receptor subfamily 1, group D, member 1 (NR1D1) and peroxisome proliferator activated receptor gamma binding protein (PBP), both reside on ERBB2-containing 17q12-21 amplicons and are part of the ERBB2 expression signature. We show that NR1D1 and PBP act through a common pathway in upregulating several genes in the de novo fatty acid synthesis network, which is highly active in ERBB2-positive breast cancer cells. Malate dehydrogenase 1 and malic enzyme 1, enzymes that link glycolysis and fatty acid synthesis, are also regulated by NR1D1. The resulting high-level fat production from increased expression of these genes likely contributes to an abnormal cellular energy metabolism based on aerobic glycolysis. Together, these results show that the cells of this aggressive form of breast cancer are genetically preprogrammed to depend on NR1D1 and PBP for the energy production necessary for survival.

Research paper thumbnail of EURASIP journal on bioinformatics & systems biology Volume:- ISSN: 1687-4145 ISO Abbreviation:- Publication Date: 2007

Research paper thumbnail of MicroRNA Target Detection and Analysis for Genes Related to Breast Cancer Using MDLcompress

EURASIP Journal on Bioinformatics and Systems Biology, 2007

We describe initial results of miRNA sequence analysis with the optimal symbol compression ratio ... more We describe initial results of miRNA sequence analysis with the optimal symbol compression ratio (OSCR) algorithm and recast this grammar inference algorithm as an improved minimum description length (MDL) learning tool: MDLcompress. We apply this tool to explore the relationship between miRNAs, single nucleotide polymorphisms (SNPs), and breast cancer. Our new algorithm outperforms other grammar-based coding methods, such as DNA Sequitur, while retaining a two-part code that highlights biologically significant phrases. The deep recursion of MDLcompress, together with its explicit two-part coding, enables it to identify biologically meaningful sequence without needlessly restrictive priors. The ability to quantify cost in bits for phrases in the MDL model allows prediction of regions where SNPs may have the most impact on biological activity. MDLcompress improves on our previous algorithm in execution time through an innovative data structure, and in specificity of motif detection (compression) through improved heuristics. An MDLcompress analysis of 144 over expressed genes from the breast cancer cell line BT474 has identified novel motifs, including potential microRNA (miRNA) binding sites that are candidates for experimental validation.

Research paper thumbnail of Identification of Several Cytoplasmic HSP70 Genes from the Mediterranean Mussel (Mytilus galloprovincialis) and Their Long-Term Evolution in Mollusca and Metazoa

Journal of Molecular Evolution, 2006

The HSP70 protein family consists one of the most conserved and important systems for cellular ho... more The HSP70 protein family consists one of the most conserved and important systems for cellular homeostasis under both stress and physiological conditions. The genes of this family are poorly studied in Mollusca, which is the second largest metazoan phylum. To study these genes in Mollusca, we have isolated and identified five HSP70 genes from Mytilus galloprovincialis (Mediterranean mussel) and investigated their short-term evolution within Mollusca and their long-term evolution within Metazoa. Both sequence and phylogenetic analyses suggested that the isolated genes belong to the cytoplasmic (CYT) group of the HSP70 genes. Two of these genes probably represent cognates, whereas the remaining probably represent heat-inducible genes. Phylogenetic analysis including several molluscan CYT HSP70s reveals that the cognate genes in two species have very similar sequences and form intraspecies phylogenetic clades, differently from most metazoan cognate genes studied thus far, implying either recent gene duplications or concerted evolution. The M. galloprovincialis heat-inducible genes show intraspecies phylogenetic clustering, which in combination with the higher amino acid than nucleotide identity suggests that both gene conversion and purifying selection should be responsible for their sequence homogenization. Phylogenetic analysis including several metazoan HSP70s suggests that at least two types of CYT genes were present in the common ancestor of vertebrates and invertebrates, the first giving birth to the heat-inducible genes of invertebrates, whereas the other to both the heat-inducible genes of vertebrates and the cognate genes of all metazoans. These analyses also suggest that inducible and cognate genes seem to undergo divergent evolution.

Research paper thumbnail of Abstract 1894: The lipogenic phenotype of HER2/neu-positive breast cancer cells

Research paper thumbnail of RNAi Applications in Target Validation

Ernst Schering Research Foundation Workshop, 2007

The emergence of systems biology is certain to transform the identification and validation of the... more The emergence of systems biology is certain to transform the identification and validation of therapeutic targets in modern drug discovery. A relatively recent systems biology approach is functional genomics, which identifies the molecular mechanisms responsible for a specific phenotype by interrogating the activity of all of an organism's genes. Initially undertaken in model organisms such as Caenorhabditis elegans, Saccharomyces cerevisiae, and Drosophila melanogaster, functional genomics has now moved into the realm of mammalian cells both in vitro and in vivo due to the development of RNA interference. RNA interference is a conserved biological process that has evolved to specifically and efficiently silence genes. Genome-wide screens using RNA interference have proven powerful in elucidating components of functionally related pathways and have therefore become integral for the development of new and improved therapeutic targets. This article provides an overview of many of the systems biology approaches taken, using RNA interference, in order to demonstrate how it may be used today for drug discovery and tomorrow as a targeted therapy.

Research paper thumbnail of An Improved Minimum Description Length Learning Algorithm for Nucleotide Sequence Analysis

Asilomar Conference on Signals, Systems & Computers, 2006

We present an improved minimum description length (MDL) learning algorithm - MDLCompress - for nu... more We present an improved minimum description length (MDL) learning algorithm - MDLCompress - for nucleotide sequence analysis that outperforms the compression of other Grammar Based Coding methods such as DNA Sequitur while retaining a two-part code that highlights biologically significant phrases. Phrases are recursively added to the MDLCompress model that are not necessarily the longest matches, or the most often

Research paper thumbnail of Isolation and characterization of two cytoplasmic hsp90s from Mytilus galloprovincialis (Mollusca: Bivalvia) that contain a complex promoter with a p53 binding site

Gene, 2009

The commercially important marine bivalve Mytilus galloprovincialis (Mediterranean mussel) is con... more The commercially important marine bivalve Mytilus galloprovincialis (Mediterranean mussel) is considered a valuable bioindicator, due to its exposure to various pollutants and extreme environmental conditions. Environmental responsive genes, such as the hsp90s, protect the structure and function of cells and accomplish a significant task in cellular homeostasis. To study the hsp90s in M. galloprovincialis a genomic library was screened and two hsp90s were isolated. Sequence analysis revealed that the two genes exhibit great similarities in both the 5′ non-coding and the coding region but differ in the 3′ non-coding region, as well as in three introns, due to the presence of repeated sequences. Few synonymous substitutions in the coding region of the genes result to an identical predicted polypeptide, which belongs to the cytoplasmic HSP90 subfamily. The 5′ non-coding region contains a non-translated exon and multiple binding sites for various transcription factors. The presence of a p53 binding site in the promoter of the isolated genes raises questions about the possible implication of hsp90s in the molluscan leukemia.

Research paper thumbnail of VEGF and Angiopoietin-1 exert opposing effects on cell junctions by regulating the Rho GEF Syx

Research paper thumbnail of VEGF and Angiopoietin-1 exert opposing effects on cell junctions by regulating the Rho GEF Syx

The Journal of Cell Biology, 2012

Research paper thumbnail of Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

E-cadherin and p120 catenin (p120) are essential for epithelial homeostasis, but can also exert p... more E-cadherin and p120 catenin (p120) are essential for epithelial homeostasis, but can also exert pro-tumorigenic activities. Here, we resolve this apparent paradox by identifying two spatially and functionally distinct junctional complexes in non-transformed polarized epithelial cells: one growth suppressing at the apical zonula adherens (ZA), defined by the p120 partner PLEKHA7 and a non-nuclear subset of the core microprocessor components DROSHA and DGCR8, and one growth promoting at basolateral areas of cell-cell contact containing tyrosine-phosphorylated p120 and active Src. Recruitment of DROSHA and DGCR8 to the ZA is PLEKHA7 dependent. The PLEKHA7-microprocessor complex co-precipitates with primary microRNAs (pri-miRNAs) and possesses pri-miRNA processing activity. PLEKHA7 regulates the levels of select miRNAs, in particular processing of miR-30b, to suppress expression of cell transforming markers promoted by the basolateral complex, including SNAI1, MYC and CCND1. Our work identifies a mechanism through which adhesion complexes regulate cellular behaviour and reveals their surprising association with the microprocessor.

Research paper thumbnail of Pro-Tumorigenic Phosphorylation of p120 Catenin in Renal and Breast Cancer

Altered protein expression and phosphorylation are common events during malignant transformation.... more Altered protein expression and phosphorylation are common events during malignant transformation. These perturbations have been widely explored in the context of E-cadherin cell-cell adhesion complexes, which are central in the maintenance of the normal epithelial phenotype. A major component of these complexes is p120 catenin (p120), which binds and stabilizes E-cadherin to promote its adhesive and tumor suppressing function. However, p120 is also an essential mediator of pro-tumorigenic signals driven by oncogenes, such as Src, and can be phosphorylated at multiple sites. Although alterations in p120 expression have been extensively studied by immunohistochemistry (IHC) in the context of tumor progression, little is known about the status and role of p120 phosphorylation in cancer. Here we show that tyrosine and threonine phosphorylation of p120 in two sites, Y228 and T916, is elevated in renal and breast tumor tissue samples. We also show that tyrosine phosphorylation of p120 at its N-terminus, including at the Y228 site is required for its pro-tumorigenic potential. In contrast, phosphorylation of p120 at T916 does not affect this p120 function. However, phosphorylation of p120 at T916 interferes with epitope recognition of the most commonly used p120 antibody, namely pp120. As a result, this antibody selectively underrepresents p120 levels in tumor tissues, where p120 is phosphorylated. Overall, our data support a role of p120 phosphorylation as a marker and mediator of tumor transformation. Importantly, they also argue that the level and localization of p120 in human cancer tissues immunostained with pp120 needs to be re-evaluated

Research paper thumbnail of Adhesion signaling in tumor progression

Research paper thumbnail of Peroxisome proliferator-activated receptor-gamma protects ERBB2-positive breast cancer cells from palmitate toxicity

Breast Cancer Reseacrh, 2009

Research paper thumbnail of The spindle assembly checkpoint is satisfied in the absence of interkinetochore tension during mitosis with unreplicated genomes

The Journal of Cell Biology, 2008

Research paper thumbnail of The Cystic Fibrosis Conductance Regulator (CFTR) controls c-Src tyrosine kinase signaling and regulates innate immunity and epithelial polarity in cholangiocytes

Research paper thumbnail of VEGF and Angiopoietin-1 exert opposing effects on cell junctions by regulating the Rho GEF Syx

The Journal of Cell Biology, 2012

Research paper thumbnail of The Rho Guanine Nucleotide Exchange Factor Syx Regulates the Balance of Dia and ROCK Activities To Promote Polarized-Cancer-Cell Migration

Molecular and Cellular Biology, 2013

The role of RhoA in promoting directed cell migration has been complicated by studies showing tha... more The role of RhoA in promoting directed cell migration has been complicated by studies showing that it is activated both in the front and the rear of migrating cells. We report here that the RhoA-specific guanine nucleotide exchange factor Syx is required for the polarity of actively migrating brain and breast tumor cells. This function of Syx is mediated by the selective activation of the RhoA downstream effector Dia1, the subsequent re-organization of microtubules, and the downregulation of focal adhesions and actin stress fibers. The data argue that directed cell migration requires the precise spatiotemporal regulation of Dia1 and ROCK activities in the cell. The recruitment of Syx to the cell membrane and the subsequent selective activation of Dia1 signaling, coupled with the suppression of ROCK and activation of cofilin-mediated actin reorganization plays a key role in establishing cell polarity during directed cell migration.

Research paper thumbnail of TEM4 is a junctional Rho GEF required for cell-cell adhesion, monolayer integrity and barrier function

Journal of Cell Science, 2013

Signaling events mediated by Rho family GTPases orchestrate cytoskeletal dynamics and cell juncti... more Signaling events mediated by Rho family GTPases orchestrate cytoskeletal dynamics and cell junction formation. The activation of Rho GTPases is tightly regulated by guanine nucleotide exchange-factors (GEFs). In this study, we identified a novel Rhospecific GEF called TEM4 (Tumor Endothelial Marker 4) that associates with multiple members of the cadherin-catenin complex and with several cytoskeleton-associated proteins. Depending on confluence, TEM4 localized to either actin stress fibers, or areas of cell-cell contact. The junctional localization of TEM4 was independent of actin binding. Depletion of endogenous TEM4 by shRNAs impaired Madin-Darby Canine Kidney (MDCK) and Human Umbilical Vein Endothelial Cell (HUVEC) cell junctions, disrupted MDCK acini formation in 3D culture, and negatively affected endothelial barrier function. Together, our findings implicate TEM4 as a novel and critical junctional RhoGEF that regulates cell junction integrity and epithelial and endothelial cell function. . Rho, rac, and cdc42 GTPases regulate the assembly of multimolecular focal complexes associated with actin stress fibers, lamellipodia, and filopodia. Cell 81, 53-62.

Research paper thumbnail of Phosphorylation-mediated 14-3-3 Protein Binding Regulates the Function of the Rho-specific Guanine Nucleotide Exchange Factor (RhoGEF) Syx

Journal of Biological Chemistry, 2013

Syx is a Rho-specific guanine nucleotide exchange factor (GEF) that localizes at cell-cell juncti... more Syx is a Rho-specific guanine nucleotide exchange factor (GEF) that localizes at cell-cell junctions and promotes junction stability by activating RhoA and the downstream effector Diaphanous homolog 1 (Dia1). Previously, we identified several molecules, including 14-3-3 proteins, as Syx-interacting partners. In the present study, we show that 14-3-3 isoforms interact with Syx at both its N- and C-terminal regions in a phosphorylation-dependent manner. We identify the protein kinase D-mediated phosphorylation of serine 92 on Syx, and additional phosphorylation at serine 938, as critical sites for 14-3-3 association. Our data indicate that the binding of 14-3-3 proteins inhibits the GEF activity of Syx. Furthermore, we show that phosphorylation-deficient, 14-3-3-uncoupled Syx exhibits increased junctional targeting and increased GEF activity, resulting in the strengthening of the circumferential junctional actin ring in Madin-Darby canine kidney cells. These findings reveal a novel means of regulating junctional Syx localization and function by phosphorylation-induced 14-3-3 binding and further support the importance of Syx function in maintaining stable cell-cell contacts.

Research paper thumbnail of An RNA Interference Screen Identifies Metabolic Regulators NR1D1 and PBP as Novel Survival Factors for Breast Cancer Cells with the ERBB2 Signature

Cancer Research, 2010

Overexpression of the adverse prognostic marker ERBB2 occurs in 30% of breast cancers; however, t... more Overexpression of the adverse prognostic marker ERBB2 occurs in 30% of breast cancers; however, therapies targeting this gene have not proved to be as effective as was initially hoped. Transcriptional profiling meta-analyses have shown that there are approximately 150 genes co-overexpressed with ERBB2, suggesting that these genes may represent alternative factors influencing ERBB2-positive tumors. Here we describe an RNA interference-based analysis of these genes that identifies transcriptional regulators of fat synthesis and storage as being critical for the survival of these cells. These transcription factors, nuclear receptor subfamily 1, group D, member 1 (NR1D1) and peroxisome proliferator activated receptor gamma binding protein (PBP), both reside on ERBB2-containing 17q12-21 amplicons and are part of the ERBB2 expression signature. We show that NR1D1 and PBP act through a common pathway in upregulating several genes in the de novo fatty acid synthesis network, which is highly active in ERBB2-positive breast cancer cells. Malate dehydrogenase 1 and malic enzyme 1, enzymes that link glycolysis and fatty acid synthesis, are also regulated by NR1D1. The resulting high-level fat production from increased expression of these genes likely contributes to an abnormal cellular energy metabolism based on aerobic glycolysis. Together, these results show that the cells of this aggressive form of breast cancer are genetically preprogrammed to depend on NR1D1 and PBP for the energy production necessary for survival.

Research paper thumbnail of EURASIP journal on bioinformatics & systems biology Volume:- ISSN: 1687-4145 ISO Abbreviation:- Publication Date: 2007

Research paper thumbnail of MicroRNA Target Detection and Analysis for Genes Related to Breast Cancer Using MDLcompress

EURASIP Journal on Bioinformatics and Systems Biology, 2007

We describe initial results of miRNA sequence analysis with the optimal symbol compression ratio ... more We describe initial results of miRNA sequence analysis with the optimal symbol compression ratio (OSCR) algorithm and recast this grammar inference algorithm as an improved minimum description length (MDL) learning tool: MDLcompress. We apply this tool to explore the relationship between miRNAs, single nucleotide polymorphisms (SNPs), and breast cancer. Our new algorithm outperforms other grammar-based coding methods, such as DNA Sequitur, while retaining a two-part code that highlights biologically significant phrases. The deep recursion of MDLcompress, together with its explicit two-part coding, enables it to identify biologically meaningful sequence without needlessly restrictive priors. The ability to quantify cost in bits for phrases in the MDL model allows prediction of regions where SNPs may have the most impact on biological activity. MDLcompress improves on our previous algorithm in execution time through an innovative data structure, and in specificity of motif detection (compression) through improved heuristics. An MDLcompress analysis of 144 over expressed genes from the breast cancer cell line BT474 has identified novel motifs, including potential microRNA (miRNA) binding sites that are candidates for experimental validation.

Research paper thumbnail of Identification of Several Cytoplasmic HSP70 Genes from the Mediterranean Mussel (Mytilus galloprovincialis) and Their Long-Term Evolution in Mollusca and Metazoa

Journal of Molecular Evolution, 2006

The HSP70 protein family consists one of the most conserved and important systems for cellular ho... more The HSP70 protein family consists one of the most conserved and important systems for cellular homeostasis under both stress and physiological conditions. The genes of this family are poorly studied in Mollusca, which is the second largest metazoan phylum. To study these genes in Mollusca, we have isolated and identified five HSP70 genes from Mytilus galloprovincialis (Mediterranean mussel) and investigated their short-term evolution within Mollusca and their long-term evolution within Metazoa. Both sequence and phylogenetic analyses suggested that the isolated genes belong to the cytoplasmic (CYT) group of the HSP70 genes. Two of these genes probably represent cognates, whereas the remaining probably represent heat-inducible genes. Phylogenetic analysis including several molluscan CYT HSP70s reveals that the cognate genes in two species have very similar sequences and form intraspecies phylogenetic clades, differently from most metazoan cognate genes studied thus far, implying either recent gene duplications or concerted evolution. The M. galloprovincialis heat-inducible genes show intraspecies phylogenetic clustering, which in combination with the higher amino acid than nucleotide identity suggests that both gene conversion and purifying selection should be responsible for their sequence homogenization. Phylogenetic analysis including several metazoan HSP70s suggests that at least two types of CYT genes were present in the common ancestor of vertebrates and invertebrates, the first giving birth to the heat-inducible genes of invertebrates, whereas the other to both the heat-inducible genes of vertebrates and the cognate genes of all metazoans. These analyses also suggest that inducible and cognate genes seem to undergo divergent evolution.

Research paper thumbnail of Abstract 1894: The lipogenic phenotype of HER2/neu-positive breast cancer cells

Research paper thumbnail of RNAi Applications in Target Validation

Ernst Schering Research Foundation Workshop, 2007

The emergence of systems biology is certain to transform the identification and validation of the... more The emergence of systems biology is certain to transform the identification and validation of therapeutic targets in modern drug discovery. A relatively recent systems biology approach is functional genomics, which identifies the molecular mechanisms responsible for a specific phenotype by interrogating the activity of all of an organism's genes. Initially undertaken in model organisms such as Caenorhabditis elegans, Saccharomyces cerevisiae, and Drosophila melanogaster, functional genomics has now moved into the realm of mammalian cells both in vitro and in vivo due to the development of RNA interference. RNA interference is a conserved biological process that has evolved to specifically and efficiently silence genes. Genome-wide screens using RNA interference have proven powerful in elucidating components of functionally related pathways and have therefore become integral for the development of new and improved therapeutic targets. This article provides an overview of many of the systems biology approaches taken, using RNA interference, in order to demonstrate how it may be used today for drug discovery and tomorrow as a targeted therapy.

Research paper thumbnail of An Improved Minimum Description Length Learning Algorithm for Nucleotide Sequence Analysis

Asilomar Conference on Signals, Systems & Computers, 2006

We present an improved minimum description length (MDL) learning algorithm - MDLCompress - for nu... more We present an improved minimum description length (MDL) learning algorithm - MDLCompress - for nucleotide sequence analysis that outperforms the compression of other Grammar Based Coding methods such as DNA Sequitur while retaining a two-part code that highlights biologically significant phrases. Phrases are recursively added to the MDLCompress model that are not necessarily the longest matches, or the most often

Research paper thumbnail of Isolation and characterization of two cytoplasmic hsp90s from Mytilus galloprovincialis (Mollusca: Bivalvia) that contain a complex promoter with a p53 binding site

Gene, 2009

The commercially important marine bivalve Mytilus galloprovincialis (Mediterranean mussel) is con... more The commercially important marine bivalve Mytilus galloprovincialis (Mediterranean mussel) is considered a valuable bioindicator, due to its exposure to various pollutants and extreme environmental conditions. Environmental responsive genes, such as the hsp90s, protect the structure and function of cells and accomplish a significant task in cellular homeostasis. To study the hsp90s in M. galloprovincialis a genomic library was screened and two hsp90s were isolated. Sequence analysis revealed that the two genes exhibit great similarities in both the 5′ non-coding and the coding region but differ in the 3′ non-coding region, as well as in three introns, due to the presence of repeated sequences. Few synonymous substitutions in the coding region of the genes result to an identical predicted polypeptide, which belongs to the cytoplasmic HSP90 subfamily. The 5′ non-coding region contains a non-translated exon and multiple binding sites for various transcription factors. The presence of a p53 binding site in the promoter of the isolated genes raises questions about the possible implication of hsp90s in the molluscan leukemia.