The development of high-throughput sequencing technologies has advanced our understanding of cancer. However, characterizing somatic structural variants in tumor genomes is still challenging because current strategies depend on the initial alignment of reads to a reference genome. Here, we describe SMUFIN (somatic mutation finder), a single program that directly compares sequence reads from normal and tumor genomes to accurately identify and characterize a range of somatic sequence variation, from single-nucleotide variants (SNV) to large structural variants at base pair resolution. Performance tests on modeled tumor genomes showed average sensitivity of 92% and 74% for SNVs and structural variants, with specificities of 95% and 91%, respectively. Analyses of aggressive forms of solid and hematological tumors revealed that SMUFIN identifies breakpoints associated with chromothripsis and chromoplexy with high specificity. SMUFIN provides an integrated solution for the accurate, fast and comprehensive characterization of somatic sequence variation in cancer.The recent development of high-throughput sequencing technologies has made possible the sequencing of genomes at an unprecedented speed, allowing the identification of the genetic basis of numerous diseases. These advances have been particularly important in the study of cancer, providing information on thousands of tumor genomes and a large catalog of genomic alteration associated with oncogenesis 1 .The characterization of somatic variation in tumor samples is, therefore, rapidly becoming a standard practice in biomedicine 2 . In a large fraction of biomedical studies that rely on high-throughput sequencing, the production of genome sequence data exceeds available computer resources and the capabilities of analytic protocols. This is particularly pertinent in the field of cancer genomics, where the increasing sequencing of tumor genomes calls for faster and more accurate analyses.The identification of somatic variants associated with cancer typically requires sequencing tumor and normal genome samples from the same patient, followed by multiple sequence comparisons. Normal and pathological reads are aligned to a reference genome, and the alignment is used to identify sequence changes to isolate the somatic fraction of variants (i.e., those detected only in the tumor). In principle, this simple strategy can be used to detect single-nucleotide variants (SNVs) and structural variants. Existing methods for the detection of somatic SNVs show high sensitivity and specificity 3,4 , but identifying structural variants is still challenging and remains largely unsolved. The need for a reference sequence is particularly limiting. Reads carrying variations, such as those covering somatic changes in the tumor, are more difficult to align to the reference genome 5 , and corresponding variants might become undetectable. Moreover, reference-based methods also must discriminate germline changes from somatic variants. In addition to these limitations at detection level, this a...

The aryl hydrocarbon receptor (AhR) is involved in various processes such as cytochrome P450 (P450) 1A induction after xenobiotic exposure. It is also considered to play a major role in cell proliferation and differentiation. Recent evidences have suggested a cross-talk between AhR functions and the mitogen-activated protein kinase (MAPK) cascade. We now report that 1,4-diamino-2,3-dicyano-1,4-bis[2-aminophenylthio]butadiene (U0126), a specific inhibitor of MAPK kinase (MEK) MEK1/2, elicits a marked increase in CYP1A1 expression at both mRNA and protein levels associated with a significant increase of enzyme activity in primary rat hepatocytes and a human hepatoma cell line. This induction occurred independently of MEK/extracellular signal-regulated kinase (ERK) activation and in the absence of ERK1 and ERK2 expression. The effect of U0126 was mediated by its ability to transactivate xenobiotic responsive element (XRE)-driven genes, as demonstrated by transfection assays with an XRE-driven luciferase construct in the human B16A2 hepatoma cell line. CYP1A1 modulation was abolished by a cotreatment with resveratrol, an established AhR antagonist, arguing for AhR activation by U0126. Such an effect was demonstrated by direct in vitro ligand binding competition assays using rabbit liver cytosol, showing that this compound binds AhR with an EC 50 ϭ 25 ϫ 10 Ϫ6 M. Moreover, we demonstrated that U0126 is a substrate for several P450s including human CYP1A2, -1A1, and -1B1. We conclude that the widely used specific inhibitor of MEK/ ERK, U0126, also acts as a potent AhR activator and an inducer of related genes. Such effects on the AhR may have an impact on biological functions attributed previously to MAPK inhibition.2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) and polycyclic aromatic hydrocarbons (PAH) are potent inducers of several genes, including some encoding "Phase I" and "Phase II" xenobiotic-metabolizing enzymes. These enzymes include cytochrome P450 (P450), glutathione transferases, NADPH: quinone reductases, and UDP-glucuronosyl transferases.TCDD and PAH effects are mediated by activation of the aryl hydrocarbon receptor (AhR), a cytosolic protein that forms complexes with two 90-kDa heat shock proteins and some other proteins. After ligand binding, the AhR is translocated and localized in the nucleus followed by an heterodimerization with the AhR nuclear translocator (Arnt) protein and acts as a transcriptional factor. Several reports have also shown constitutive activation of the AhR in the absence of exogenous ligand under certain conditions (Singh et al

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A novel mouse model reveals that the dynamic behavior of transcription factors can vary considerably between different cells of an organism.

The nucleotide excision repair (NER) pathway and its leading gene excision-repair cross-complementary 1 (ERCC1) have been shown to be up-regulated in hepatocellular carcinomas even in the absence of treatment with chemotherapeutics. The aim of this study was to determine the mechanism involved in NER regulation during the liver cell growth observed in hepatocellular carcinoma. Both NER activity and ERCC1 expression were increased after exposure to the epidermal growth factor (EGF) in cultured normal and tumoral human hepatocytes. These increases correlated with the activation of the kinase signaling pathway mitogen-activated protein/extracellular signalregulated kinase (ERK) kinase (MEK)/ERK that is known to be a key regulator in the G 1 phase of the hepatocyte cell cycle. Moreover, EGF-mediated activation of ERCC1 was specifically inhibited by either the addition of U0126, a MEK/ERK inhibitor or small interfering RNA-mediated knockdown of ERK2. Basal expression of ERCC1 was decreased in the presence of the phosphoinositide-3-kinase (PI3K) inhibitor and small hairpin RNA (shRNA) against the PI3K pathway kinase FKBP12-rapamycin-associated protein or mammalian target of rapamycin. Transient transfection of human hepatocytes with constructs containing different sizes of the 5 ¶-flanking region of the ERCC1 gene upstream of the luciferase reporter gene showed an increase in luciferase activity in EGF-treated cells, which correlated with the presence of the nuclear transcription factor GATA-1 recognition sequence. The recruitment of GATA-1 was confirmed by chromatin immunoprecipitation assay. In conclusion, these results represent the first demonstration of an up-regulation of NER and ERCC1 in EGFstimulated proliferating hepatocytes. The transcription factor GATA-1 plays an essential role in the induction of ERCC1 through the mitogen-activated protein kinase (MAPK) pathway, whereas the PI3K signaling pathway contributes to ERCC1 basal expression. [Cancer Res 2007;67(5):2114-23]

Phenotypic changes in injured livers involve complex network of genes whose interplays may lead to fibrosis and cirrhosis, a major risk of hepatocellular carcinoma. Gene expression profiles in fibrotic livers were analyzed by using cDNA microarray, hierarchical clustering and gene ontology. Analyses of a major cluster of upregulated genes in cirrhosis identified a new set of genes involved in DNA repair and damage. The upregulation of DNA repair genes was confirmed by real-time quantitative polymerase chain reaction and associated with necroinflammatory activity (P < 0.001). Increased DNA repair activity in cirrhosis with inflammatory activity may reflect increased DNA damages as a consequence of chronic liver injury.

Increasing numbers of human diseases are being linked to genetic variants, but our understanding of the mechanistic links leading from DNA sequence to disease phenotype is limited. The majority of disease-causing nucleotide variants fall within the non-protein-coding portion of the genome, making it likely that they act by altering gene regulatory sequences. We hypothesised that SNPs within the binding sites of the transcriptional repressor REST alter the degree of repression of target genes. Given that changes in the effective concentration of REST contribute to several pathologies—various cancers, Huntington's disease, cardiac hypertrophy, vascular smooth muscle proliferation—these SNPs should alter disease-susceptibility in carriers. We devised a strategy to identify SNPs that affect the recruitment of REST to target genes through the alteration of its DNA recognition element, the RE1. A multi-step screen combining genetic, genomic, and experimental filters yielded 56 polymorphic RE1 sequences with robust and statistically significant differences of affinity between alleles. These SNPs have a considerable effect on the the functional recruitment of REST to DNA in a range of in vitro, reporter gene, and in vivo analyses. Furthermore, we observe allele-specific biases in deeply sequenced chromatin immunoprecipitation data, consistent with predicted differenes in RE1 affinity. Amongst the targets of polymorphic RE1 elements are important disease genes including NPPA, PTPRT, and CDH4. Thus, considerable genetic variation exists in the DNA motifs that connect gene regulatory networks. Recently available ChIP–seq data allow the annotation of human genetic polymorphisms with regulatory information to generate prior hypotheses about their disease-causing mechanism.

Starting with the assumption that they are dead copies of genes lacking functionality, and hence that they are not subjected to selective pressure, pseudogenes can be distinguished from protein-coding genes using neutrality and its measure. Here, we describe the different methods that allow to estimate neutral evolution by calculating the ratio between non-synonymous (i.e., causing an amino-acidic change) and synonymous (silent) substitutions and we discuss their application to the identification of pseudogenes.