Functional Gene Sets Research Articles

Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data.

IntroductionDiverse microarray and sequencing technologies have been widely used to characterise the molecular changes in malignant epithelial cells in breast cancers. Such gene expression studies to identify markers and targets in tumour cells are, however, compromised by the cellular heterogeneity of solid breast tumours and by the lack of appropriate counterparts representing normal breast epithelial cells.MethodsMalignant neoplastic epithelial cells from primary breast cancers and luminal and myoepithelial cells isolated from normal human breast tissue were isolated by immunomagnetic separation methods. Pools of RNA from highly enriched preparations of these cell types were subjected to expression profiling using massively parallel signature sequencing (MPSS) and four different genome wide microarray platforms. Functional related transcripts of the differential tumour epithelial transcriptome were used for gene set enrichment analysis to identify enrichment of luminal and myoepithelial type genes. Clinical pathological validation of a small number of genes was performed on tissue microarrays.ResultsMPSS identified 6,553 differentially expressed genes between the pool of normal luminal cells and that of primary tumours substantially enriched for epithelial cells, of which 98% were represented and 60% were confirmed by microarray profiling. Significant expression level changes between these two samples detected only by microarray technology were shown by 4,149 transcripts, resulting in a combined differential tumour epithelial transcriptome of 8,051 genes. Microarray gene signatures identified a comprehensive list of 907 and 955 transcripts whose expression differed between luminal epithelial cells and myoepithelial cells, respectively. Functional annotation and gene set enrichment analysis highlighted a group of genes related to skeletal development that were associated with the myoepithelial/basal cells and upregulated in the tumour sample. One of the most highly overexpressed genes in this category, that encoding periostin, was analysed immunohistochemically on breast cancer tissue microarrays and its expression in neoplastic cells correlated with poor outcome in a cohort of poor prognosis estrogen receptor-positive tumours.ConclusionUsing highly enriched cell populations in combination with multiplatform gene expression profiling studies, a comprehensive analysis of molecular changes between the normal and malignant breast tissue was established. This study provides a basis for the identification of novel and potentially important targets for diagnosis, prognosis and therapy in breast cancer.

Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana

We present MultiGO, a web-enabled tool for the identification of biologically relevant gene sets from hierarchically clustered gene expression trees (). High-throughput gene expression measuring techniques, such as microarrays, are nowadays often used to monitor the expression of thousands of genes. Since these experiments can produce overwhelming amounts of data, computational methods that assist the data analysis and interpretation are essential. MultiGO is a tool that automatically extracts the biological information for multiple clusters and determines their biological relevance, and hence facilitates the interpretation of the data. Since the entire expression tree is analysed, MultiGO is guaranteed to report all clusters that share a common enriched biological function, as defined by Gene Ontology annotations. The tool also identifies a plausible cluster set, which represents the key biological functions affected by the experiment. The performance is demonstrated by analysing drought-, cold- and abscisic acid-related expression data sets from Arabidopsis thaliana. The analysis not only identified known biological functions, but also brought into focus the less established connections to defense-related gene clusters. Thus, in comparison to analyses of manually selected gene lists, the systematic analysis of every cluster can reveal unexpected biological phenomena and produce much more comprehensive biological insights to the experiment of interest.

Investigation of the molecular profile of basal cell carcinoma using whole genome microarrays

BackgroundSkin cancer accounts for 1/3 of all newly diagnosed cancer. Although seldom fatal, basal cell carcinoma (BCC) is associated with severe disfigurement and morbidity. BCC has a unique interest for researchers, as although it is often locally invasive, it rarely metastasises. This paper, reporting the first whole genome expression microarray analysis of skin cancer, aimed to investigate the molecular profile of BCC in comparison to non-cancerous skin biopsies. RNA from BCC and normal skin specimens was analysed using Affymetrix whole genome microarrays. A Welch t-test was applied to data normalised using dCHIP to identify significant differentially-expressed genes between BCC and normal specimens. Principal component analysis and support vector machine analysis were performed on resulting genelists, Genmapp was used to identify pathways affected, and GOstat aided identification of areas of gene ontology more highly represented on these lists than would be expected by chance.ResultsFollowing normalisation, specimens clustered into groups of BCC specimens and of normal skin specimens. Of the 54,675 gene transcripts/variants analysed, 3,921 were differentially expressed between BCC and normal skin specimens. Of these, 2,108 were significantly up-regulated and 1,813 were statistically significantly down-regulated in BCCs.ConclusionFunctional gene sets differentially expressed include those involved in transcription, proliferation, cell motility, apoptosis and metabolism. As expected, members of the Wnt and hedgehog pathways were found to be significantly different between BCC and normal specimens, as were many previously undescribed changes in gene expression between normal and BCC specimens, including basonuclin2 and mrp9. Quantitative-PCR analysis confirmed our microarray results, identifying novel potential biomarkers for BCC.

Life‐like self‐reproducers

AbstractIn order to understand the interplay among information, genetic instructions, and phenotypic variations, self‐reproducers discovered in two‐dimensional cellular automata are considered as proto‐organisms, which undergo to mutations as they were in a real environmental situation. We realized a computational model through which we have been able to discover the genetic map of the self‐reproducers and the networks they use. Identifying in these maps sets of different functional genes, we found that mutations in the genetic sequences could affect both external shapes and behavior of the self‐reproducers, thus realizing different life‐like strategies in the evolution process. The results highlight that some strategies evolution uses in selecting organisms that are fitting with changing environmental situations maintain the self‐reproducing function, whereas other variations create new self‐reproducers. These self‐reproducers in turn realize different genetic networks, which can be very different from the basic ancestors pools. The mutations that are disruptive bring self‐reproducers to disappear, while other proto‐organisms are generated. © 2004 Wiley Periodicals, Inc. Complexity 9: 38–55, 2004

Identification of V1R-like putative pheromone receptor sequences in non-human primates. Characterization of V1R pseudogenes in marmoset, a primate species that possesses an intact vomeronasal organ.

The vomeronasal organ (VNO) is responsible in terrestrial vertebrates for the sensory perception of some pheromones, chemicals that elicit characteristic behaviors among individuals of the same species. Two multigene families (V1R, V2R) that encode proteins with seven putative transmembrane domains that are expressed selectively in different neuron subsets of the VNO have been described in rodents. Pheromone-induced behaviors and a functional VNO have been described in a number of mammals, but this sensory organ seems absent in adult catarrhines and apes, including humans. Until now, only pseudogenes have been isolated in humans, except one putative V1R (hV1RL1) sequence expressed in the main olfactory epithelium. We sought to isolate V1R-like genes in a New World monkey species, the marmoset Callithrix jacchus, that possesses an intact VNO and for which pheromone-induced behavior has been well documented. Using library screening approaches, we have identified five different sequences that exhibit characteristic features of V1R sequences, but that are non-functional pseudogenes. In an attempt to sort out functional V1R genes, we next cloned by polymerase chain reaction (PCR) the primate orthologues of hV1RL1. This approach was successful for gorilla, chimpanzee and orangutan, but not for the other species, including marmoset, probably because these species are too divergent from humans. Chimpanzee and orangutan V1RL1 genes are pseudogenes, whereas the gorilla counterpart is potentially functional. These observations raise the possibility that the V1R family has evolved in such a manner in mammals that every species that relies on a VNO-mediated sensory function possesses its own set of functional vomeronasal genes.

Bacterial chemotaxis: Rhodobacter sphaeroides and Sinorhizobium meliloti--variations on a theme?

We are only beginning to understand the mechanisms involved in tactic sensing in the alpha-subgroup of bacteria. It is clear, however, from recent developments that although the central chemosensory pathways are related to those identified in enteric species, the primary signals and the effect on flagellar behaviour are very different. The expression of chemoreceptors is under environmental control, and the strength of a response depends on the metabolic state of the cell. This is very different from enteric species which always respond to MCP-dependent chemoeffectors, and in which the expression of the receptors is constitutive. Chemotaxis in R. sphaeroides and S. meliloti is therefore more directly linked to the environment in which a cell finds itself. The integration of chemosensory pathways dependent on growth state may be much more suited to the fluctuating environment of these soil and water bacteria. There is still a great deal that needs to be understood about the mechanisms involved in motor control. The presence of at least two CheY homologues and the finding that the swimming speed of these bacteria can vary, and, in the case of S. meliloti, vary with chemosensory stimulation, suggests a different control mechanism at the flagellar motor where speed can be altered, or the motor stopped, with a full delta p still present. Why R. sphaeroides should have at least two functional sets of genes encoding homologues of the enteric chemosensory pathway remains to be determined. The major differences in sensory behaviour between the two alpha-subgroup species so far studied in detail and the differences from the enteric species suggests that many more variations of the chemosensory pathways will be found as more species are studied.

The Optimum Recombination Rate That Realizes the Fastest Evolution of a Novel Functional Combination of Many Genes

The effect of genetic recombination (or crossover) by sexual reproduction on the time until a novel set of genes performing a combined function appears, spreads, and becomes fixed is studied. First, we study a haploid finite population with many binary loci, in which only one sequence (called a functional gene set) is significantly advantageous over the others. The time for evolution of the function (Td) is defined as the mean number of generations until the advantageous sequence dominates in an initially random population. When the sequence diversity is initially stored sufficiently, the evolution timeTdis roughly the product of the waiting time until the appearance of the advantageous sequence (creation timeTc) and the average number of appearances of the advantageous sequence from its absence until its fixation (destruction numberNd). Mutation and crossover reduce the former but enlarge the latter. If the mutation rate is low, there is an intermediate optimal rate of crossover that achieves the minimumTd. In contrast, if the mutation rate is sufficiently high,Tdis smallest without crossover. Second, the breakdown of established functions by recurrent deleterious mutation in an infinite population is examined. The number of functional genes maintained decreases monotonically with the recurrent deleterious mutation rate. Thus in higher organisms having many functional sets of genes in the genome, the mutation rate must be kept very low to preserve them, and hence a high crossover rate made possible by sexual reproduction is important in accelerating the evolution of novel functional sets of genes. Implications of this long-term advantage of recombination in the maintenance of sexual reproduction in higher organisms are discussed.