Search

Author(s): The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I & II Team*; FANTOM Consortium:; Y. Okazaki [1, 2]; M. Furuno [1]; T. Kasukawa [1, 3]; J. [...]

Abstract Background In this paper we present a method for the statistical assessment of cancer predictors which make use of gene expression profiles. The methodology is applied to a new data set of microarray gene expression data collected in Casa Sollievo della Sofferenza Hospital, Foggia – Italy. The data set is made up of normal (22) and tumor (25) specimens extracted from 25 patients affected by colon cancer. We propose to give answers to some questions which are relevant for the automatic diagnosis of cancer such as: Is the size of the available data set sufficient to build accurate classifiers? What is the statistical significance of the associated error rates? In what ways can accuracy be considered dependant on the adopted classification scheme? How many genes are correlated with the pathology and how many are sufficient for an accurate colon cancer classification? The method we propose answers these questions whilst avoiding the potential pitfalls hidden in the analysis and interpretation of microarray data. Results We estimate the generalization error, evaluated through the Leave-K-Out Cross Validation error, for three different classification schemes by varying the number of training examples and the number of the genes used. The statistical significance of the error rate is measured by using a permutation test. We provide a statistical analysis in terms of the frequencies of the genes involved in the classification. Using the whole set of genes, we found that the Weighted Voting Algorithm (WVA) classifier learns the distinction between normal and tumor specimens with 25 training examples, providing e = 21% (p = 0.045) as an error rate. This remains constant even when the number of examples increases. Moreover, Regularized Least Squares (RLS) and Support Vector Machines (SVM) classifiers can learn with only 15 training examples, with an error rate of e = 19% (p = 0.035) and e = 18% (p = 0.037) respectively. Moreover, the error rate decreases as the training set size increases, reaching its best performances with 35 training examples. In this case, RLS and SVM have error rates of e = 14% (p = 0.027) and e = 11% (p = 0.019). Concerning the number of genes, we found about 6000 genes (p < 0.05) correlated with the pathology, resulting from the signal-to-noise statistic. Moreover the performances of RLS and SVM classifiers do not change when 74% of genes is used. They progressively reduce up to e = 16% (p < 0.05) when only 2 genes are employed. The biological relevance of a set of genes determined by our statistical analysis and the major roles they play in colorectal tumorigenesis is discussed. Conclusions The method proposed provides statistically significant answers to precise questions relevant for the diagnosis and prognosis of cancer. We found that, with as few as 15 examples, it is possible to train statistically significant classifiers for colon cancer diagnosis. As for the definition of the number of genes sufficient for a reliable classification of colon cancer, our results suggest that it depends on the accuracy required.

Summary: Background: Children born small for gestational age (SGA) are at increased risk of metabolic dysfunction. Dysregulation of specific microRNAs (miRNAs) contributes to aberrant gene expression patterns underlying metabolic dysfunction. Objective: We aimed to determine and compare circulating miRNA (c‐miRNA) profile of SGA and appropriate for gestational age (AGA) children with obesity and with normal weight, in order to identify biomarkers for early detection of increased risk of developing metabolic dysfunction in SGA and AGA children with obesity. Methods: Small non‐coding RNAs from serum of 15 SGA children with obesity (OB‐SGA), 10 SGA children with normal weight (NW‐SGA), 17 AGA children with obesity (OB‐AGA) and 12 AGA children with normal weight (NW‐AGA) (mean age 11.2 ± 2.6) have been extracted and sequenced in order to detect and quantify miRNA expression profiles. Results: RNA‐seq analyses showed 28 miRNAs dysregulated in OB‐SGA vs. NW‐SGA and 19 miRNAs dysregulated in OB‐AGA vs. NW‐AGA. Among these, miR‐92a‐3p, miR‐122‐5p, miR‐423‐5p, miR‐484, miR‐486‐3p and miR‐532‐5p were up regulated, and miR‐181b‐5p was down regulated in both OB‐SGA and OB‐AGA compared with normal weight counterparts. Pathway analysis and miRNA target prediction suggested that these miRNAs were particularly involved in insulin signalling, glucose transport, insulin resistance, cholesterol and lipid metabolism. Conclusion: We identified a specific profile of c‐miRNAs in SGA and AGA children with obesity compared with SGA and AGA children with normal weight. These c‐miRNAs could represent specific biomarkers for early detection of increased risk of developing metabolic dysfunction in SGA and AGA children with obesity. [ABSTRACT FROM AUTHOR]

Summary: Shotgun metagenomics by high-throughput sequencing may allow deep and accurate characterization of host-associated total microbiomes, including bacteria, viruses, protists and fungi. However, the analysis of such sequencing data is still extremely challenging in terms of both overall accuracy and computational efficiency, and current methodologies show substantial variability in misclassification rate and resolution at lower taxonomic ranks or are limited to specific life domains (e.g. only bacteria). We present here MetaShot, a workflow for assessing the total microbiome composition from host-associated shotgun sequence data, and show its overall optimal accuracy performance by analyzing both simulated and real datasets. [ABSTRACT FROM AUTHOR]

The 67-kDa laminin receptor (67LR) is a nonintegrin cell surface receptor that mediates high-affinity interactions between cells and laminin. Overexpression of this protein in tumor cells has been related to tumor invasion and metastasis. Thus far, only a full-length gene encoding a 37-kDa precursor protein (37LRP) has been isolated. The finding that the cDNA for the 37LRP is virtually identical to a cDNA encoding the ribosomal protein p40 has suggested that 37LRP is actually a component of the translational machinery, with no laminin-binding activity. On the other hand, a peptide of 20 amino acids deduced from the sequence of 37LR/p40 was shown to exhibit high laminin-binding activity. The evolutionary relationship between 23 sequences of 37LRP/p40 proteins was analyzed. This phylogenetic analysis indicated that all of the protein sequences derive from orthologous genes and that the 37LRP is indeed a ribosomal protein that acquired the novel function of laminin receptor during evolution. The evolutionary analysis of the sequence identified as the laminin-binding site in the human protein suggested that the acquisition of the laminin-binding capability is linked to the palindromic sequence LMWWML, which appeared during evolution concomitantly with laminin. [ABSTRACT FROM PUBLISHER]

The base composition of 25 complete mammalian mitochondrial (mt) genomes has been analyzed taking into account all three codon positions (P1230 and fourfold degenerate sites (P4FD) of H-strand genes. In the nontranscribed L strand, G is the less represented base and A is the most represented one in all cases, while C and T differ among species. H-strand protein-coding genes show an asymmetric distribution of the four bases between the two strands. The asymmetry indexes AT and GC skews on P4FD are much higher than those on P123, suggesting the existence of asymmetrical directional mutation pressure. Relationships between the compositional features and transcription of replication processes have been investigated in order to find a possible mechanism that could explain the origin of this asymmetry. AT and GC skews, the base composition in fourfold degenerate sites, and the number of variable sites for each gene are significantly correlated with the duration of single-stranded state of the H-stranded genes during replication. We tested different replication-related hypotheses, such as the existence of biased dNTP pools, gamma DNA polymerase mispairing, and the asymmetric replication itself. Most of them failed to explain the observed results, hydrolytic deaminations being the only one in agreement with our data. Thus, we hypothesize that one of the crucial processes for the origin of asymmetric and biased base composition of mammalian mitochondrial genomes is the spontaneous deamination of C and A in the H strand during replication. [ABSTRACT FROM PUBLISHER]

The complete mitochondrial genome of the fat dormouse, Glis glis, has been sequenced (16,602 bp). A total of 23 complete mitochondrial mammalian genomes have been taken into account for phylogenetic reconstruction. Phylogenetic analyses were performed with parsimony, distance (stationary Markov model), and maximum-likelihood methods. In all cases, data strongly support the paraphyly of rodents, with dormouse and guinea pig in a different clade from rat and mouse, reaching bootstrap values of 95%. Rodent monophyly and the existence of Glires (Rodentia and Lagomorpha) are weakly supported, with maximum bootstrap values of 11% and 8.6%, respectively. This result agrees with the analyses of isochore patterns in the nuclear genome and the B2 and B2-like retroposons, which show a close relationship between dormice and guinea pigs rather than between dormice and rats and mice. [ABSTRACT FROM PUBLISHER]

We studied two polymorphic forms of mtDNA extracted from A. lixula eggs. In order to compare and to quantitate the variability, we sequenced specific regions of the two molecules. In this way, we obtained a precise measurement of the variability within two haplotypes. We also obtained a direct demonstration that some differences in nucleotide sequence can escape detection when restriction endonuclease analysis is used. Our results underline the unreliability of the use of restriction mapping to estimate divergence between relatively short and closely related DNA sequences. [ABSTRACT FROM AUTHOR]

Abstract In the present study we report the identification of a sul3 -associated class 1 integron containing the dfrA12 -orfF -aadA2 - cmlA1 - aadA1 - qacH array embedded in a Tn 21 -derived element that is part of a conjugative FII plasmid named pST1007-1A. The plasmid was identified in the Salmonella Typhimurium strain ST1007, a member of a clinically relevant clonal MDR lineage diffuse in Italy. ST1007 exhibited resistance to ampicillin, chloramphenicol, streptomycin, sulphamethoxazole, tetracycline and trimethoprim encoded by bla TEM-1 , cmlA1 , (aadA1 , aadA2 , strAB), (sul2 , sul3), tet (B) and dfrA12 genes, respectively. Apart from pST1007-1A, ST1007 also harbours two chromosome-integrated resistance units RU1 (bla TEM-1 - sul2 - strAB) and RU2 (tet (B)), flanked by IS 26 elements. RU1 and RU2 were able to move as translocatable units, respectively TU1 and TU2, and integrate via IS 26 mediated recombination into pST1007-1A. A family of conjugative plasmids, harbouring different sets of antimicrobial resistance genes (ARG) was then generated: pST1007-1B (dfrA12 - aadA2 - cmlA1 - aadA1 - sul3- tet (B)), pST1007-1C (dfrA12 - aadA2 - cmlA1 - aadA1 - sul3-bla TEM-1 -sul2-strAB), pST1007-1D (bla TEM-1 -sul2-strAB), pST1007-1E (tet (B)) and pST1007-1F (dfrA12 - aadA2 - cmlA1 - aadA1 - sul3- tet (B) -bla TEM-1 -sul2-strAB). pST1007-1A is also a mosaic plasmid containing two distinct DNA fragments acquired from I1 plasmids through recombination within the repA4 , rfsF and repeat- 3 sites. This study further highlights the role played by IS 26 in intracellular ARGs shuffling. Moreover, attention has been focused on recombination hot spots that might play a key role in generating mosaic plasmids. Highlights • pST1007-1A is a conjugative FII plasmid detected in a Salmonella Typhimurium strain part of a relevant MDR clonal lineage • pST1007-1A is a FII/I1 mosaic plasmid harbouring a sul3 -associated class 1 integron embedded in a Tn 21 -derived element • Two resistance units RU1 (bla TEM-1 - sul2 - strAB) and RU2 (tet (B)), flanked by IS 26 , were chromosome-integrated • RU1 and RU2 can move respectively as translocatable units TU1 and TU2 and integrate, via IS 26 , into pST1007-1A • ST1007 can act as donor to spread different sets of ARGs [ABSTRACT FROM AUTHOR]

The IncQ is a group of non-conjugative but mobilisable plasmids that are found and stably maintained in a wide range of bacteria contributing to the spread of antimicrobial resistance genes and to the insurgence of multidrug resistant bacteria. Here we report the identification, in clinical Salmonella Typhimurium strains, of an IncQ1 plasmid (pNUC) which confers resistance to sulfamethoxazole, streptomycin and tetracycline through the presence of sul2 , strAB and tetA genes, respectively. pNUC was detected in five multidrug resistant S . Typhimurium strains collected in Southern Italy from various hospitals and years of isolation. Bioinformatics analyses highlighted the presence of pNUC-like plasmids in pathogenic bacteria of various Enterobacteriaceae genera or species. Taken as a whole, these plasmids constitute a novel group of IncQ1 plasmids that might have originated through recombination events between a tetR - tetA gene cluster (possibly derived from a Tn 1721 ) and a recipient IncQ1 plasmid related to RSF1010. Our findings raise concerns regarding the possible contribution of the newly identified group of IncQ1 plasmids to the spread of tetracycline resistance. [ABSTRACT FROM AUTHOR]

Abstract: In this work we describe the process that, starting with the production of human full-length-enriched cDNA libraries using the CAP-Trapper method, led us to the discovery of 342 putative new human genes. Twenty-three thousand full-length-enriched clones, obtained from various cell lines and tissues in different developmental stages, were 5′-end sequenced, allowing the identification of a pool of 5300 unique cDNAs. By comparing these sequences to various human and vertebrate nucleotide databases we found that about 40% of our clones extended previously annotated 5′ ends, 662 clones were likely to represent splice variants of known genes, and finally 342 clones remained unknown, with no or poor functional annotation. cDNA-microarray gene expression analysis showed that 260 of 342 unknown clones are expressed in at least one cell line and/or tissue. Further analysis of their sequences and the corresponding genomic locations allowed us to conclude that most of them represent potential novel genes, with only a small fraction having protein-coding potential. [Copyright &y& Elsevier]