PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “transcriptomic analysis”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12Linked to original sources
PubMed2005

Transcriptome analysis of the Mg2+-responsive PhoP regulator in Yersinia pestis.

PhoP was previously shown to be important for Yersinia pestis survival in macrophage and under macrophage-induced stresses. In this work, a phoP disruptant of Y. pestis 201 was generated using the Red cloning procedure. The transcription profile of the wild-type Y. pestis was then compared with that of the phoP mutant under Mg2+-limiting conditions. It was revealed that PhoP/PhoQ governed a wide set of cellular pathways in Y. pestis, especially including the positive regulation of many metabolic processes, Mg2+ transport, peptidoglycan remodeling, lipopolysaccharide (LPS) modification and various stress-protective functions. The Mg2+ transport system regulated by PhoP may make Y. pestis to maintain the magnesium homeostasis under low Mg2+ environments. The PhoP-controlled stress-protective functions likely constitute the molecular basis for the observation that mutation of the phoP gene rendered the bacteria more sensitive to various macrophage-induced stresses. Modification of LPS mediated by PhoP is hypothesized to not only neutralize negative charges as normally done by Mg2+ ions, but also mediate the resistance of Y. pestis to antimicrobial peptides. The microarray results provide a population of candidate genes or pathways, and further biochemical experiments are needed to elucidate the PhoP-dependent mechanisms by which Y. pestis survives the antibacterial strategies employed by host macrophages.

Animals↗
PubMed2006

Transcriptome analysis of the salivary glands of Dermacentor andersoni Stiles (Acari: Ixodidae).

Amongst blood-feeding arthropods, ticks of the family Ixodidae (hard ticks) are vectors and reservoirs of a greater variety of infectious agents than any other ectoparasite. Salivary glands of ixodid ticks secrete a large number of pharmacologically active molecules that not only facilitate feeding but also promote establishment of infectious agents. Genomic, proteomic and immunologic characterization of bioactive salivary gland molecules are, therefore, important as they offer new insights into molecular events occurring at the tick-host interface and they have implications for development of novel control strategies. The present work uses complementary DNA (cDNA) sequence analysis to identify salivary gland transcripts expressed by the Rocky Mountain wood tick, Dermacentor andersoni, a vector of the human pathogens causing Rocky Mountain spotted fever, Colorado tick fever, tularemia, and Powassan encephalitis as well as the veterinary pathogen Anaplasma marginale. Dermacentor andersoni is also capable of inducing tick paralysis. Automated single-pass DNA sequencing was conducted on 1440 randomly selected cDNA clones from the salivary glands of adult female D. andersoni collected during the early stages of feeding (18-24h). Analysis of the expressed sequence tags (ESTs) resulted in 544 singletons and 218 clusters with more than one quality read and attempts were made to assign putative functions to tick genes based on amino acid identity to published protein databases. Approximately 25.6% (195) of the sequences showed limited or no homology to previously identified gene products. A number of novel sequences were identified which presented significant sequence similarity to mammalian genes normally associated with extracellular matrix (ECM), regulation of immune responses, tumor suppression, and wound healing. Several coding sequences possessed various degrees of homology to previously described proteins from other tick species. Preliminary nucleotide variation analysis of these and other tick sequences suggests extensive nucleotide diversity, which has implications for evolution of tick feeding. Intra-species diversity studies can be a promising tool for identifying sequence variations potentially associated with phenotypic traits affecting vector-host-pathogen interactions.

Amino Acid Sequence↗
PubMed2005

Transcriptome analysis of Anopheles stephensi-Plasmodium berghei interactions.

Simultaneous microarray-based transcription analysis of 4987 Anopheles stephensi midgut and Plasmodium berghei infection stage specific cDNAs was done at seven successive time points: 6, 20 and 40h, and 4, 8, 14 and 20 days after ingestion of malaria infected blood. The study reveals the molecular components of several Anopheles processes relating to blood digestion, midgut expansion and response to Plasmodium-infected blood such as digestive enzymes, transporters, cytoskeletal and structural components and stress and immune responsive factors. In parallel, the analysis provide detailed expression patterns of Plasmodium genes encoding essential developmental and metabolic factors and proteins implicated in interaction with the mosquito vector and vertebrate host such as kinases, transcription and translational factors, cytoskeletal components and a variety of surface proteins, some of which are potent vaccine targets. Temporal correlation between transcription profiles of both organisms identifies putative gene clusters of interacting processes, such as Plasmodium invasion of the midgut epithelium, Anopheles immune responses to Plasmodium infection, and apoptosis and expulsion of invaded midgut cells from the epithelium. Intriguing transcription patterns for highly variable Plasmodium surface antigens may indicate parasite strategies to avoid recognition by the mosquito's immune surveillance system.

Animals↗
PubMed2006

Identification of CD36 as a new surface marker of marginal zone B cells by transcriptomic analysis.

Follicular (FO) B cells and marginal zone (MZ) B cells belong to the mature B cell population in spleen of mice. To identify new surface markers of these mature B cell subsets, we compared gene expression profiles of FO and MZ B cells by DNA microarray using FACS-sorted mouse FO and MZ B cells. From 14,000 mouse genes, 27 membrane proteins were expressed mainly in MZ B cells while another 22 membrane proteins expressed largely in FO B cells. Using FACS analysis, we identified that CD36, CD68, and CD49e were expressed on MZ B cells but not on FO B cells. In addition, using semi-quantitative PCR, we found that the mRNA of CD131 were much more abundant in MZ B cells. These results revealed new phenotypic properties of MZ and FO B cells, and would facilitate further studies in the differentiation and functions of these mature B cells.

Animals↗
PubMed2004

Transcriptome analysis in a rat model of L-DOPA-induced dyskinesia.

We have examined the pattern of striatal messenger RNA expression of over 8000 genes in a rat model of levodopa (L-DOPA)-induced dyskinesia and Parkinson disease (PD). 6-Hydroxydopamine (6-OHDA)-lesioned rats were treated with L-DOPA or physiological saline for 22 days and repeatedly tested for antiakinetic response to L-DOPA and the development of abnormal involuntary movements (AIMs). In a comparison of rats that developed a dyskinetic motor response to rats that did not, we found striking differences in gene expression patterns. In rats that developed dyskinesia, GABA neurons had an increased transcriptional activity, and genes involved in Ca2+ homeostasis, in Ca2+ -dependent signaling, and in structural and synaptic plasticity were upregulated. The gene expression patterns implied that the dyskinetic striatum had increased transcriptional, as well as synaptic activity, and decreased capacity for energy production. Some basic maintenance chores such as ribosome protein biosynthesis were downregulated, possibly a response to expended ATP levels.

Animals↗
PubMed2004

Comparative transcriptome analysis of Yersinia pestis in response to hyperosmotic and high-salinity stress.

DNA microarray was used as a tool to investigate genome-wide transcriptional responses of Yersinia pestis to hyperosmotic and high-salinity stress. Hyperosmotic stress specifically upregulated genes responsible for ABC-type transport and the cytoplasmic accumulation of certain polysaccharides, while high-salinity stress induced the transcription of genes encoding partition proteins and several global transcriptional regulators. Genes whose transcription was enhanced by both kinds of stress comprised those encoding osmoprotectant transport systems and a set of virulence determinants. The number of genes downregulated by the two kinds of stress was much lower than that of upregulated genes, suggesting that neither kind of stress severely depresses cellular processes in general. Many differentially regulated genes still exist whose functions remain unknown. Y. pestis recognized high-salinity and hyperosmotic stress as different kinds of environmental stimuli, and different mechanisms enabled acclimation to these two kinds of stress, although Y. pestis still executed common mechanisms to accommodate both types of stress.

Gene Expression Regulation, Bacterial↗
PubMed2026

Integrated single-cell and bulk transcriptomic analysis identifies a novel senescent fibroblast subtype associated with poor prognosis in acral melanoma.

BACKGROUND: Acral melanoma (AM) exhibits significant intratumoral heterogeneity, but its tumor microenvironment (TME) and immune regulation remain unclear. This study aims to dissect TME heterogeneity and establish a prognostic model based on key cell subpopulations. METHODS: We collected AM single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data from the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA). Unsupervised clustering, CellChat, and Scissor analysis were performed to characterize cellular heterogeneity, cell-cell communication, and prognosis-related cell subpopulations. Kaplan-Meier analysis was used to assess the prognostic value of key genes, which were further validated by multiplex immunohistochemistry (mIHC). RESULTS: In AM, Mel_C2, C7, and C9 with high SEMA6A and KIT expression were strongly linked to poor prognosis. We further identified a senescent fibroblast subpopulation (sCAF_CDKN2A) characterized by high fibroblast senescence signature (FSS) scores. Integrating Scissor analysis of fibroblast subtypes with bulk prognostic data, we identified COL3A1, VCAN, and KIT as prognosis-associated genes upregulated in poor-outcome-related fibroblast subsets. Cell-cell communication analysis revealed that sCAF_CDKN2A engages in an immunosuppressive network, interacting with regulatory T cells (Tregs) via MIF signaling and receiving signals from exhausted CD8+ T cells through PPIA-BSG interactions. Using transcription factor expression patterns from these fibroblast subtypes, we constructed a prognostic model that effectively stratified patients into distinct risk groups with significant differences in overall survival (OS). mIHC confirmed significantly higher protein levels of SEMA6A and COL3A1 in tumor tissues compared to matched normal tissues. CONCLUSIONS: We established a novel prognostic model for AM and identified sCAF_CDKN2A as an immunosuppressive senescent fibroblast subpopulation driving poor prognosis.

Acral melanoma↗
PubMed2006

Effect of textile wastewaters on Saccharomyces cerevisiae using DNA microarray as a tool for genome-wide transcriptomics analysis.

Textile mill effluents (TMEs) discharged from the textile industry can be considered as one class of hypothetical toxicants in the environment. To investigate the potential toxicity of TMEs, we applied cDNA microarray technology to examine the genome-wide expression profiles in model eukaryote, Saccharomyces cerevisiae. The results revealed a rich source of genetic information for the yeast cells that were exposed to the untreated and treated TMEs. Among the 5956 valid genes, 275 genes were up-regulated and 40 genes were down-regulated for the untreated TMEs. On the other hand, only 90 genes were up-regulated, and 29 genes were down-regulated upon exposure to the treated TMEs. The changes in gene expression were also confirmed by RT-PCR. The potent up- and down-regulation of genes suggest that yeast cells undergo genome-wide changes in mRNA expression, indicative of a stress response. Additionally, a classification into specific functional gene categories indicated that untreated and even treated TMEs still had toxicity. Especially, the genes related to oxidative stress, such as AHP1, ATX1, GRX1, TRX1 and TRX2, were up-regulated in treated TMEs that can directly reach to surface and ground waters, and sediments.

Down-Regulation↗
PubMed2004

Comprehensive transcriptome analysis of differentiation of embryonic stem cells into midbrain and hindbrain neurons.

Neurogenesis is one of the most complex events in embryonic development. However, little information is available regarding the molecular events that occur during neurogenesis. To identify regulatory genes and underlying mechanisms involved in the differentiation of embryonic stem (ES) cells to neurons, gene expression profiling was performed using cDNA microarrays. In mouse ES cells, we compared the gene expression of each differentiated cell stage using a five-stage lineage selection method. Of 10,368 genes, 1633 (16%) known regulatory genes were differentially expressed at least 2-fold or greater at one or more stages. At stage 3, during which ES cells differentiate into neural stem cells, modulation of nearly 1000 genes was observed. Most of transcription factors (Otx2, Ebf-3, Ptx3, Sox4, 13, 18, engrailed, Irx2, Pax8, and Lim3), signaling molecules (Wnt, TGF, and Shh family members), and extracellular matrix/adhesion molecules (collagens, MAPs, and NCAM) were up-regulated. However, some genes which may play important roles in maintaining the pluripotency of ES cells (Kruppel-like factor 2, 4, 5, 9, myeloblast oncogene like2, ZFP 57, and Esg-1) were down-regulated. The many genes identified with this approach that are modulated during neurogenesis will facilitate studies of the mechanisms underlying ES cell differentiation, neural induction, and neurogenesis.

Animals↗
PubMed2001

The potato tuber transcriptome: analysis of 6077 expressed sequence tags.

This is the first report of the biosynthetic potential of a tuber storage organ investigated by expressed sequence tag sequencing. A cDNA library was generated from the mature tuber of field grown potato (Solanum tuberosum var. Kuras). Partial sequences obtained from 6077 clones were assembled into 828 clusters and 1533 singletons. The average read length was 592 bp, and 2254 clones were full length. 5717 clones showed homology to genes from other organisms. Genes involved in protein synthesis, protein destination and cell defense predominated in tuber compared to stolon, shoot and leaf organs. 1063 clones were unique to tuber. Transcripts of starch metabolizing enzymes showed similar relative levels in tuber and stolon.

Expressed Sequence Tags↗
PubMed2003

The poplar root transcriptome: analysis of 7000 expressed sequence tags.

To date, most poplar expressed sequence tags (ESTs) are from above-ground tissues such as wood, leaf and buds. Here, we present a large-scale production of ESTs from roots of the hybrid cottonwood, Populus trichocarpaxdeltoides. cDNA libraries were generated from the root system of 2-month-old rooted cuttings, and roots of 2.5-month-old cuttings water-stressed for 19 days. Partial sequences obtained from 7013 clones were assembled into 1347 clusters and 3527 singletons. This set of ESTs represents 4874 unique transcripts expressed in roots. Putative functions could be assigned to 3021 (62%) of the transcripts. A significant portion of the ESTs encode proteins of common metabolic pathways; energy and metabolism represented 5% and 8% of total transcripts, respectively. Of specific interest to root functions are the 6% of ESTs involved in signalling pathways and hormone metabolism, and 4% encoding transporters and channels. The current poplar root ESTs and the aspen root ESTs present in public databases represent 6700 unique transcripts. The Unigene set was selected from the ESTs and used to generate nylon microarrays. Changes in aquaporins and transporter transcripts were then studied during adventitious root development.

Aquaporins↗
PubMed2002

Cerebral transcriptome analysis of transgenic mice overexpressing erythropoietin.

Erythropoietin (EPO) and its receptor are expressed in the brain, and one of its roles appears to be neuroprotection. This study investigates whether chronic overexpression of EPO changes brain mRNA expression in the brains of transgenic mice. Therefore, cerebral mRNA expression was investigated in transgenic mice overexpressing EPO. Microarray analysis revealed an upregulation (2.8- to 3.6-fold) of N-acetylglucosamine-6-O-sulfotransferase (prolongation of the EPO effect), a translocase of the inner mitochondrial membrane (mitochondrial matrix import of nuclear encoded proteins), a mitochondrial ribosomal protein (mitochondrial protein translation), and a peroxisomal biogenesis factor (formation of peroxisomes). In conclusion, components of oxidative metabolism pathways were activated at the level of transcription which could be related to neuroprotective effects of EPO or could indicate compromised tissue.

Animals↗
PubMed2004

Transcriptome analysis of early chondrogenesis in ATDC5 cells induced by bone morphogenetic protein 4.

We performed serial analysis of gene expression (SAGE) profiling in mouse chondrogenic ATDC5 cells before and 6 h after the onset of chondrogenesis induced by BMP4. A total of 43,656 SAGE tags (21,875 and 21,781 tags from the uninduced and induced libraries, respectively) were analyzed. Our analysis predicted that 139 transcripts were differentially represented in the two libraries (p < 0.05), including 72 downregulated and 67 upregulated transcripts. Ninety-five of them matched single UniGene entries (77 known genes and 18 ESTs), while 12 tags corresponded to potentially novel genes. Surprisingly, many of these known genes have never been implicated in chondrogenic differentiation. Interestingly, we found that a significant fraction of these genes formed physical linkage groups. This suggests that the transcriptional control by BMP signaling is in part targeted to genes in certain chromosomal domains. Together, our results provide novel insights into molecular events regulated by BMP signaling in chondrogenesis.

Animals↗
PubMed2001

Transcriptome analysis reveals a role of interferon-gamma in human neointima formation.

The most effective immediate cure for coronary stenosis is stent-supported angioplasty. Restenosis due to neointima proliferation represents a major limitation. We investigated the expression of 2435 genes in atherectomy specimens and blood cells of patients with restenosis, normal coronary artery specimens, and cultured human smooth muscle cells (SMCs). Of the 223 differentially expressed genes, 37 genes indicated activation of interferon-gamma (IFN-gamma) signaling in neointimal SMCs. In cultured SMCs, IFN-gamma inhibited apoptosis. Genetic disruption of IFN-gamma signaling in a mouse model of restenosis significantly reduced the vascular proliferative response. Our data suggest an important role of IFN-gamma in the control of neointima proliferation.

Animals↗
PubMedDate not supplied

Proteome and transcriptome analysis of retinoic acid-induced differentiation of human acute promyelocytic leukemia cells, NB4.

Acute promyelocytic leukemia (APL) is characterized by a translocation t(15:17) that fuses the retinoic acid receptor gene with the promyelocytic gene, which blocks differentiation to normal granulocytes. NB4 cells, derived from human acute promyelocytic leukemia, display this genotype and phenotype. All trans-retinoic acid (ATRA) induces differentiation of NB4 cell cultures in vitro and APL in vivo, although resistance to differentiation therapy frequently develops. To identify genes involved in differentiation, we compared gene expression at the mRNA and protein levels using microarray analyses and two-dimensional (2D) difference gel electrophoresis (DIGE), plus MALDI-TOF-TOF mass spectrometry. Differentially expressed transcripts were identified using oligonucleotide-based microarrays with targets representing almost 14 000 genes. Real time PCR was performed on a subset of genes whose products were shown to be differentially expressed using proteomic and/or genomic approaches. Our analyses identified 46 genes that were differentially expressed in NB4 +/- ATRA; 22 were identified using 2D-DIGE and 24 using microarray analysis. All but four of these genes were expressed at higher levels in differentiated cells, and several controlled cell structure (internal and cytoskelatal) or signal transduction. We observed that proteome analysis with DIGE and silver-stained 2D gel electrophoresis analyses revealed significant differences between the two measurement approaches. Furthermore, our data showed significant discordance between gene expression at the protein and transcript levels.

Cell Differentiation↗
PubMed2003

Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni.

Schistosoma mansoni is the primary causative agent of schistosomiasis, which affects 200 million individuals in 74 countries. We generated 163,000 expressed-sequence tags (ESTs) from normalized cDNA libraries from six selected developmental stages of the parasite, resulting in 31,000 assembled sequences and 92% sampling of an estimated 14,000 gene complement. By analyzing automated Gene Ontology assignments, we provide a detailed view of important S. mansoni biological systems, including characterization of metazoa-specific and eukarya-conserved genes. Phylogenetic analysis suggests an early divergence from other metazoa. The data set provides insights into the molecular mechanisms of tissue organization, development, signaling, sexual dimorphism, host interactions and immune evasion and identifies novel proteins to be investigated as vaccine candidates and potential drug targets.

Animals↗