<p>UM-SCC 22B (A, the mt p53) and 1 (B, the wt p53-deficient) cells were transfected with s... more <p>UM-SCC 22B (A, the mt p53) and 1 (B, the wt p53-deficient) cells were transfected with siRNA to <i>RelA</i> or <i>TP53</i> for 48 h or 72 h. Total RNA was isolated, and genes selected from TF-miRNA networks in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073656#pone-0073656-g003" target="_blank">Figure 3</a> were analyzed by real time qRT-PCR. The data were calculated as the mean plus standard deviation from triplicates with normalization by 18S ribosome RNA, and presented as the comparison with the cultured cells transfected with the control siRNA oligos. The open bar represents the cells transfected with control siRNA, and the values have been normalized to 1. The fold changes of the target genes were presented when compared with those transfected with control siRNA. The black bar represents cells transfected with siRNA targeting TP53, while the blue bar represents cells transfected with siRNA targeting NF-κB subunit, RelA/p65. * refers to statistical significance (t test, <i>P</i><0.05).</p
The coordinated and dynamic modulation or interaction of genes or proteins acts as an important m... more The coordinated and dynamic modulation or interaction of genes or proteins acts as an important mechanism used by a cell in functional regulation. Recent studies have shown that many transcriptional networks exhibit a scale-free topology and hierarchical modular architecture. It has also been shown that transcriptional networks or pathways are dynamic and behave only in certain ways and controlled manners in response to disease development, changing cellular conditions, and different environmental factors. Moreover, evolutionarily conserved and divergent transcriptional modules underline fundamental and species-specific molecular mechanisms controlling disease development or cellular phenotypes. Various computational algorithms have been developed to explore transcriptional networks and modules from gene expression data. In silico studies have also been made to mimic the dynamic behavior of regulatory networks, analyzing how disease or cellular phenotypes arise from the connectivity...
Human embryonic stem (ES) cells hold great promise for medicine and science. The transcriptome of... more Human embryonic stem (ES) cells hold great promise for medicine and science. The transcriptome of human ES cells has been studied in detail in recent years. However, no systematic analysis has yet addressed whether gene expression in human ES cells may be regulated in chromosomal domains, and no chromosomal domains of coexpression have been identified. We report the first transcriptome coexpression map of the human ES cell and the earliest stage of ES differentiation, the embryoid body (EB), for the analysis of how transcriptional regulation interacts with genomic structure during ES self-renewal and differentiation. We determined the gene expression profiles from multiple ES and EB samples and identified chromosomal domains showing coexpression of adjacent genes on the genome. The coexpression domains were not random, with significant enrichment in chromosomes 8, 11, 16, 17, 19, and Y in the ES state, and 6, 11, 17, 19 and 20 in the EB state. The domains were significantly associat...
Proceedings of the National Academy of Sciences, 2004
HuR, a protein that binds to specific mRNA subsets, is increasingly recognized as a pivotal postt... more HuR, a protein that binds to specific mRNA subsets, is increasingly recognized as a pivotal posttranscriptional regulator of gene expression. Here, HuR was immunoprecipitated under conditions that preserved HuR-RNA interactions, and HuR-bound target mRNAs were identified by cDNA array hybridization. Analysis of primary sequences and secondary structures shared among HuR targets led to the identification of a 17- to 20-base-long RNA motif rich in uracils. This HuR motif was found in almost all mRNAs previously reported to be HuR targets, was located preferentially within 3′ untranslated regions of all unigene transcripts examined, and was conserved in >50% of human and mouse homologous genes. Importantly, the HuR motif allowed the successful prediction and subsequent validation of novel HuR targets from gene databases. This study describes an HuR target RNA motif and presents a general strategy for identifying target motifs for RNA-binding proteins.
Proceedings of the National Academy of Sciences of the United States of America, Jan 17, 2014
We previously described a gene signature for breast cancer stem cells (BCSCs) derived from patien... more We previously described a gene signature for breast cancer stem cells (BCSCs) derived from patient biopsies. Selective shRNA knockdown identified ribosomal protein L39 (RPL39) and myeloid leukemia factor 2 (MLF2) as the top candidates that affect BCSC self-renewal. Knockdown of RPL39 and MLF2 by specific siRNA nanoparticles in patient-derived and human cancer xenografts reduced tumor volume and lung metastases with a concomitant decrease in BCSCs. RNA deep sequencing identified damaging mutations in both genes. These mutations were confirmed in patient lung metastases (n = 53) and were statistically associated with shorter median time to pulmonary metastasis. Both genes affect the nitric oxide synthase pathway and are altered by hypoxia. These findings support that extensive tumor heterogeneity exists within primary cancers; distinct subpopulations associated with stem-like properties have increased metastatic potential.
Recent studies have shown a high level of conservation between Drosophila melanogaster and mammal... more Recent studies have shown a high level of conservation between Drosophila melanogaster and mammalian copper homeostasis mechanisms. These studies have also demonstrated the efficiency with which this species can be used to characterize novel genes, at both the cellular and whole organism level. As a versatile and inexpensive model organism, Drosophila is also particularly useful for gene discovery applications and thus has the potential to be extremely useful in identifying novel copper homeostasis genes and putative disease genes. In order to assess the suitability of Drosophila for this purpose, three screening approaches have been investigated. These include an analysis of the global transcriptional response to copper in both adult flies and an embryonic cell line using DNA microarray analysis. Two mutagenesis-based screens were also utilized. Several candidate copper homeostasis genes have been identified through this work. In addition, the results of each screen were carefully analyzed to identify any factors influencing efficiency and sensitivity. These are discussed here with the aim of maximizing the efficiency of future screens and the most suitable approaches are outlined. Building on this information, there is great potential for the further use of Drosophila for copper homeostasis gene discovery.
Journal of proteomics & bioinformatics, Jan 12, 2009
Cross-species comparison of gene expression profiles allows deciphering fundamental and species-s... more Cross-species comparison of gene expression profiles allows deciphering fundamental and species-specific transcriptional programs of cells and offers insight into organization and evolution of the genome and genetic network. Here, we propose an algorithm for comparing microarray data from different species to unravel transcriptional modules that are conserved or divergent through evolution. The proposed algorithm is based on cross-species matrix decomposition that includes a nonlinear independent component analysis followed a generalized probabilistic sparse matrix factorization on microarray data from different species. The proposed algorithm captures transcriptional modularity that might result from highly nonlinear interactions among genes, and partitions genes into mutually non-exclusive transcriptional modules. The conserved transcriptional modules are identified by the latent variables that are associated with predominant biological prototypes shared across species. We illustr...
<p>UM-SCC 22B (A, the mt p53) and 1 (B, the wt p53-deficient) cells were transfected with s... more <p>UM-SCC 22B (A, the mt p53) and 1 (B, the wt p53-deficient) cells were transfected with siRNA to <i>RelA</i> or <i>TP53</i> for 48 h or 72 h. Total RNA was isolated, and genes selected from TF-miRNA networks in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073656#pone-0073656-g003" target="_blank">Figure 3</a> were analyzed by real time qRT-PCR. The data were calculated as the mean plus standard deviation from triplicates with normalization by 18S ribosome RNA, and presented as the comparison with the cultured cells transfected with the control siRNA oligos. The open bar represents the cells transfected with control siRNA, and the values have been normalized to 1. The fold changes of the target genes were presented when compared with those transfected with control siRNA. The black bar represents cells transfected with siRNA targeting TP53, while the blue bar represents cells transfected with siRNA targeting NF-κB subunit, RelA/p65. * refers to statistical significance (t test, <i>P</i><0.05).</p
The coordinated and dynamic modulation or interaction of genes or proteins acts as an important m... more The coordinated and dynamic modulation or interaction of genes or proteins acts as an important mechanism used by a cell in functional regulation. Recent studies have shown that many transcriptional networks exhibit a scale-free topology and hierarchical modular architecture. It has also been shown that transcriptional networks or pathways are dynamic and behave only in certain ways and controlled manners in response to disease development, changing cellular conditions, and different environmental factors. Moreover, evolutionarily conserved and divergent transcriptional modules underline fundamental and species-specific molecular mechanisms controlling disease development or cellular phenotypes. Various computational algorithms have been developed to explore transcriptional networks and modules from gene expression data. In silico studies have also been made to mimic the dynamic behavior of regulatory networks, analyzing how disease or cellular phenotypes arise from the connectivity...
Human embryonic stem (ES) cells hold great promise for medicine and science. The transcriptome of... more Human embryonic stem (ES) cells hold great promise for medicine and science. The transcriptome of human ES cells has been studied in detail in recent years. However, no systematic analysis has yet addressed whether gene expression in human ES cells may be regulated in chromosomal domains, and no chromosomal domains of coexpression have been identified. We report the first transcriptome coexpression map of the human ES cell and the earliest stage of ES differentiation, the embryoid body (EB), for the analysis of how transcriptional regulation interacts with genomic structure during ES self-renewal and differentiation. We determined the gene expression profiles from multiple ES and EB samples and identified chromosomal domains showing coexpression of adjacent genes on the genome. The coexpression domains were not random, with significant enrichment in chromosomes 8, 11, 16, 17, 19, and Y in the ES state, and 6, 11, 17, 19 and 20 in the EB state. The domains were significantly associat...
Proceedings of the National Academy of Sciences, 2004
HuR, a protein that binds to specific mRNA subsets, is increasingly recognized as a pivotal postt... more HuR, a protein that binds to specific mRNA subsets, is increasingly recognized as a pivotal posttranscriptional regulator of gene expression. Here, HuR was immunoprecipitated under conditions that preserved HuR-RNA interactions, and HuR-bound target mRNAs were identified by cDNA array hybridization. Analysis of primary sequences and secondary structures shared among HuR targets led to the identification of a 17- to 20-base-long RNA motif rich in uracils. This HuR motif was found in almost all mRNAs previously reported to be HuR targets, was located preferentially within 3′ untranslated regions of all unigene transcripts examined, and was conserved in >50% of human and mouse homologous genes. Importantly, the HuR motif allowed the successful prediction and subsequent validation of novel HuR targets from gene databases. This study describes an HuR target RNA motif and presents a general strategy for identifying target motifs for RNA-binding proteins.
Proceedings of the National Academy of Sciences of the United States of America, Jan 17, 2014
We previously described a gene signature for breast cancer stem cells (BCSCs) derived from patien... more We previously described a gene signature for breast cancer stem cells (BCSCs) derived from patient biopsies. Selective shRNA knockdown identified ribosomal protein L39 (RPL39) and myeloid leukemia factor 2 (MLF2) as the top candidates that affect BCSC self-renewal. Knockdown of RPL39 and MLF2 by specific siRNA nanoparticles in patient-derived and human cancer xenografts reduced tumor volume and lung metastases with a concomitant decrease in BCSCs. RNA deep sequencing identified damaging mutations in both genes. These mutations were confirmed in patient lung metastases (n = 53) and were statistically associated with shorter median time to pulmonary metastasis. Both genes affect the nitric oxide synthase pathway and are altered by hypoxia. These findings support that extensive tumor heterogeneity exists within primary cancers; distinct subpopulations associated with stem-like properties have increased metastatic potential.
Recent studies have shown a high level of conservation between Drosophila melanogaster and mammal... more Recent studies have shown a high level of conservation between Drosophila melanogaster and mammalian copper homeostasis mechanisms. These studies have also demonstrated the efficiency with which this species can be used to characterize novel genes, at both the cellular and whole organism level. As a versatile and inexpensive model organism, Drosophila is also particularly useful for gene discovery applications and thus has the potential to be extremely useful in identifying novel copper homeostasis genes and putative disease genes. In order to assess the suitability of Drosophila for this purpose, three screening approaches have been investigated. These include an analysis of the global transcriptional response to copper in both adult flies and an embryonic cell line using DNA microarray analysis. Two mutagenesis-based screens were also utilized. Several candidate copper homeostasis genes have been identified through this work. In addition, the results of each screen were carefully analyzed to identify any factors influencing efficiency and sensitivity. These are discussed here with the aim of maximizing the efficiency of future screens and the most suitable approaches are outlined. Building on this information, there is great potential for the further use of Drosophila for copper homeostasis gene discovery.
Journal of proteomics & bioinformatics, Jan 12, 2009
Cross-species comparison of gene expression profiles allows deciphering fundamental and species-s... more Cross-species comparison of gene expression profiles allows deciphering fundamental and species-specific transcriptional programs of cells and offers insight into organization and evolution of the genome and genetic network. Here, we propose an algorithm for comparing microarray data from different species to unravel transcriptional modules that are conserved or divergent through evolution. The proposed algorithm is based on cross-species matrix decomposition that includes a nonlinear independent component analysis followed a generalized probabilistic sparse matrix factorization on microarray data from different species. The proposed algorithm captures transcriptional modularity that might result from highly nonlinear interactions among genes, and partitions genes into mutually non-exclusive transcriptional modules. The conserved transcriptional modules are identified by the latent variables that are associated with predominant biological prototypes shared across species. We illustr...
Uploads