The microRNA-205-5p is correlated to metastatic potential of 21T series: A breast cancer progression model

MicroRNA is a class of noncoding RNAs able to base pair with complementary messenger RNA sequences, inhibiting their expression. These regulatory molecules play important roles in key cellular processes including cell proliferation, differentiation and response to DNA damage; changes in miRNA expression are a common feature of human cancers. To gain insights into the mechanisms involved in breast cancer progression we conducted a microRNA global expression analysis on a 21T series of cell lines obtained from the same patient during different stages of breast cancer progression. These stages are represented by cell lines derived from normal epithelial (H16N2), atypical ductal hyperplasia (21PT), primary in situ ductal carcinoma (21NT) and pleural effusion of a lung metastasis (21MT-1 and 21MT-2). In a global microRNA expression analysis, miR-205-5p was the only miRNA to display an important downregulation in the metastatic cell lines (21MT-1; 21MT-2) when compared to the non-invasive cells (21PT and 21NT). The lower amounts of miR-205-5p found also correlated with high histological grades biopsies and with higher invasion rates in a Boyden chamber assay. This work pinpoints miR-205-5p as a potential player in breast tumor invasiveness.

A common variant in RAB27A gene is associated with fractional exhaled nitric oxide levels in adults

BACKGROUND

Exhaled nitric oxide (FeNO) is a biomarker for eosinophilic inflammation in the airways and for responsiveness to corticosteroids in asthmatics.

OBJECTIVE

We sought to identify in adults the genetic determinants of fractional exhaled nitric oxide (FeNO) levels and to assess whether environmental and disease-related factors influence these associations.

METHODS

We performed a genome-wide association study of FeNO through meta-analysis of two independent discovery samples of European ancestry: the outbred EGEA study (French Epidemiological study on the Genetics and Environment of Asthma, N = 610 adults) and the Hutterites (N = 601 adults), a founder population living on communal farms. Replication of main findings was assessed in adults from an isolated village in Sardinia (Talana study, N = 450). We then investigated the influence of asthma, atopy and tobacco smoke exposure on these genetic associations, and whether they were also associated with FeNO values in children of the EAGLE (EArly Genetics & Lifecourse Epidemiology, N = 8858) consortium.

RESULTS

We detected a common variant in RAB27A (rs2444043) associated with FeNO that reached the genome-wide significant level (P = 1.6 × 10(-7) ) in the combined discovery and replication adult data sets. This SNP belongs to member of RAS oncogene family (RAB27A) and was associated with an expression quantitative trait locus for RAB27A in lymphoblastoid cell lines from asthmatics. A second suggestive locus (rs2194437, P = 8.9 × 10(-7) ) located nearby the sodium/calcium exchanger 1 (SLC8A1) was mainly detected in atopic subjects and influenced by inhaled corticosteroid use. These two loci were not associated with childhood FeNO values.

CONCLUSIONS AND CLINICAL RELEVANCE

This study identified a common variant located in RAB27A gene influencing FeNO levels specifically in adults and with a biological relevance to the regulation of FeNO levels. This study provides new insight into the biological mechanisms underlying FeNO levels in adults.

Developmental changes in human megakaryopoiesis

BACKGROUND

The molecular bases of the cellular changes that occur during human megakaryocyte (MK) ontogeny remain unknown, and may be important for understanding the significance of MK differentiation from human embryonic stem cells (hESCs)

METHODS

We optimized the differentiation of MKs from hESCs, and compared these with MKs obtained from primary human hematopoietic tissues at different stages of development.

RESULTS

Transcriptome analyses revealed a close relationship between hESC-derived and fetal liver-derived MKs, and between neonate-derived and adult-derived MKs. Major changes in the expression profiles of cell cycle and transcription factors (TFs), including MYC and LIN28b, and MK-specific regulators indicated that MK maturation progresses during ontogeny towards an increase in MK ploidy and a platelet-forming function. Important genes, including CXCR4, were regulated by an on-off mechanism during development.

DISCUSSION

Our analysis of the pattern of TF network and signaling pathways was consistent with a growing specialization of MKs towards hemostasis during ontogeny, and support the idea that MKs derived from hESCs reflect primitive hematopoiesis.

Thrombocytopenia induced by the histone deacetylase inhibitor abexinostat involves p53-dependent and -independent mechanisms

Abexinostat is a pan histone deacetylase inhibitor (HDACi) that demonstrates efficacy in malignancy treatment. Like other HDACi, this drug induces a profound thrombocytopenia whose mechanism is only partially understood. We have analyzed its effect at doses reached in patient plasma on in vitro megakaryopoiesis derived from human CD34⁺ cells. When added at day 0 in culture, abexinostat inhibited CFU-MK growth, megakaryocyte (MK) proliferation and differentiation. These effects required only a short incubation period. Decreased proliferation was due to induction of apoptosis and was not related to a defect in TPO/MPL/JAK2/STAT signaling. When added later (day 8), the compound induced a dose-dependent decrease (up to 10-fold) in proplatelet (PPT) formation. Gene profiling from MK revealed a silencing in the expression of DNA repair genes with a marked RAD51 decrease at protein level. DNA double-strand breaks were increased as attested by elevated γH2AX phosphorylation level. Moreover, ATM was phosphorylated leading to p53 stabilization and increased BAX and p21 expression. The use of a p53 shRNA rescued apoptosis, and only partially the defect in PPT formation. These results suggest that HDACi induces a thrombocytopenia by a p53-dependent mechanism along MK differentiation and a p53-dependent and -independent mechanism for PPT formation.

P5-01-07: Identification of SORBS2 as a Candidate Marker To Predict Metastatic Relapse in Breast Cancer

Background

Elucidation of promising cancer biomarkers from gene expression data can provide important insight into the relationship between signaling networks and cancer. SORBS2, sorbin and SH3 domain containing 2, is a multi-adapter protein involved in signal transduction associated to the cytoskeleton and was reported to be strongly repressed in pancreatic and cervical cancers.

Methods: With the purpose of identifying genes involved in metastatic process, we compared gene expression profiling of 19 invasive ovarian cancers and 24 borderline tumors. Prognostic value of the selected genes was then tested in a gene expression array database that includes 1659 patients with early breast cancer (Gyorffy B et al. 2010). Upon isolation of SORBS2 as a predictor, its involvement in cell migration and tumor progression was investigated in vitro. Small interfering RNA targeting SORBS2 was used to downregulate its expression in T47D and Hela, two cell lines overexpressing SORBS2. Functional effect of siRNA-induced knockdown of SORBS2 on cell viability was determined by WST-1 assay and Trypan Blue exclusion test. Effect on cell migration was evaluated by wound-healing and transwell assays. Western blot analyses were also performed to examine the expressions of proteins involved in cell survival, death and migration.

Results: High-throughput analyses of genes that are differentially expressed between borderline ovarian tumors and invasive carcinoma demonstrated that SORBS2 is significantly downregulated in invasive carcinoma (FDR<10e-10). Moreover, SORBS2 loss was a strong predictor of relapse in a gene expression array dataset of 1659 patients presenting an early breast cancer (HR=0.62, 0.52−0.72, p=6.4e-10). In vitro studies showed that SORBS2 specific downregulation stimulated cell proliferation, by an average of 40%, in T47D and Hela cell lines. SORBS2 knockdown had no effect on either cell migration rate or protein expressions of p-FAK and p-Paxillin, two focal adhesion proteins which are critical to cell adhesion and migration. No significant variations in protein expressions of Akt/mTOR pro-survival or caspases activation pathways were observed. Gene expression profiling before and after SORBS2 dowregulation is ongoing in the two cell lines.

Conclusion: This study is the first to provide evidence for an antiproliferative activity of SORBS2 with no effect on cell migration in breast cancer cells. Our clinical and in vitro data suggest that SORBS2 is a candidate marker to predict relapse in patients with early breast cancer. Molecular mechanisms mediating the antiproliferative effect of SORBS2 are currently being investigated.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-01-07.

OT1-03-02: SAFIR01: A Molecular Screening Trial for Metastatic Breast Cancer Patients

Background: High number of new drugs are targeting molecular alterations that occur in a few number of patients. Molecular screening that consists in the assessment of single molecular alteration during the screening phase of the therapeutic trial is not suitable. Indeed, this modality of screening is associated with a high rate of screen failure due to the low incidence of the molecular alteration. In order to optimize molecular screening, we have launched a clinical trial that aims at performing array CGH and hot spot mutations in patients with metastatic breast cancer.

Patients and Methods. The trial plans to include 400 patients with metastatic breast cancer and included the first patient in may 2011. This trial is being sponsored by French federation of Cancer centers (UNICANCER) and involves 20 centers. Biopsy is being performed on metastatic site. Both frozen and FFPE samples are obtained. DNA extraction is being performed in the investigation center after control for the % of cancer cells. Array CGH and PIK3CA/AKT mutations (SANGE method) are being performed in four genomic platforms. A pilot study that included 106 patients has shown the feasibility of such technologies in the context of daily practice. Data from array CGH are being sent to a bioinformatician who forward the results on both pre-selected targets, DNA instability and some targets of interest selected based on log2(ratio) and function. Recommendations for trials are then being sent to each investigator. There is no limitation for previous lines and it is recommended to perform biopsy in patients who do not present progressive disease. This trial is being funded by French NCI (750 000 euros)

Conclusion: SAFIR01 is a trial that aims at using high throughput technologies in order to drive patients with molecular alterations to specific therapeutic trials. Further amendments are being planned including implementation of high throughput sequencing and performance of functional testing. Further trial will compare this high throughput approach to standard methods for target identification.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr OT1-03-02.

A syncytin-like endogenous retrovirus envelope gene of the guinea pig specifically expressed in the placenta junctional zone and conserved in Caviomorpha

Syncytins are genes of retroviral origin that have been co-opted by mammalian hosts for a function in placentation. Two such genes have already been identified in simians, as well as two distinct, unrelated ones in Muridae and a fifth in the rabbit. Here we searched for similar genes in the guinea pig, which belongs to the Caviomorpha lineage within the Hystricognathi suborder of rodents and displays a placental structural organization with several characteristic features comparable to those of the human organ, including deep trophoblast invasion of maternal tissues. An in silico search for envelope (env) genes with full coding capacity identified a candidate gene that showed specific expression in the placenta, as revealed by RT-qPCR using RNAs from a large panel of tissues. This gene belongs to an endogenous retroviral element present at a single-copy in the guinea pig genome, still displaying a retroviral organization - with a degenerate gag and pol, but an intact env gene. In situ hybridization of guinea pig placenta sections demonstrated specific expression at the level of the invasive trophoblast-containing junctional zone, as observed in humans for syncytin-1 and consistent with a role in invasion of the maternal uterine tissues. The identified gene displays a conserved open reading frame in the Caviomorpha, consistent with an entry date >30 million years, and sequence analyses showed purifying selection of the gene. Conclusively, despite the absence of a demonstrated fusogenic activity, it is likely that the identified env gene - that we named syncytin-like env-Cav1 - exerts a physiological function possibly related to trophoblast invasion, in the course of caviomorph placentation.

A brain-specific isoform of mitochondrial apoptosis-inducing factor: AIF2

Apoptosis-inducing factor (AIF) has important supportive as well as potentially lethal roles in neurons. Under normal physiological conditions, AIF is a vital redox-active mitochondrial enzyme, whereas in pathological situations, it translocates from mitochondria to the nuclei of injured neurons and mediates apoptotic chromatin condensation and cell death. In this study, we reveal the existence of a brain-specific isoform of AIF, AIF2, whose expression increases as neuronal precursor cells differentiate. AIF2 arises from the utilization of the alternative exon 2b, yet uses the same remaining 15 exons as the ubiquitous AIF1 isoform. AIF1 and AIF2 are similarly imported to mitochondria in which they anchor to the inner membrane facing the intermembrane space. However, the mitochondrial inner membrane sorting signal encoded in the exon 2b of AIF2 is more hydrophobic than that of AIF1, indicating a stronger membrane anchorage of AIF2 than AIF1. AIF2 is more difficult to be desorbed from mitochondria than AIF1 on exposure to non-ionic detergents or basic pH. Furthermore, AIF2 dimerizes with AIF1, thereby preventing its release from mitochondria. Conversely, it is conceivable that a neuron-specific AIF isoform, AIF2, may have been 'designed' to be retained in mitochondria and to minimize its potential neurotoxic activity.

Synergistic proapoptotic effects of the two tyrosine kinase inhibitors pazopanib and lapatinib on multiple carcinoma cell lines

Pazopanib and lapatinib are two tyrosine kinase inhibitors that have been designed to inhibit the VEGF tyrosine kinase receptors 1, 2 and 3 (pazopanib), and the HER1 and HER2 receptors in a dual manner (lapatinib). Pazopanib has also been reported to mediate inhibitory effect on a selected panel of additional tyrosine kinases such as PDGFR and c-kit. Here, we report that pazopanib and lapatinib act synergistically to induce apoptosis of A549 non-small-cell lung cancer cells. Systematic assessment of the kinome revealed that both pazopanib and lapatinib inhibited dozens of different tyrosine kinases and that their combination could suppress the activity of some tyrosine kinases (such as c-Met) that were not or only partially affected by either of the two agents alone. We also found that pazopanib and lapatinib induced selective changes in the transcriptome of A549 cells, some of which were specific for the combination of both agents. Analysis of a panel of unrelated human carcinoma cell lines revealed a signature of 52 genes whose up- or downregulation reflected the combined action of pazopanib and lapatinib. Indeed, pazopanib and lapatinib exerted synergistic cytotoxic effects on several distinct non-small-cell lung cancer cells as well as on unrelated carcinomas. Altogether, these results support the contention that combinations of tyrosine kinase inhibitors should be evaluated for synergistic antitumor effects. Such combinations may lead to a 'collapse' of pro-survival signal transduction pathways that leads to apoptotic cell death.

Functional pathways analyses to identify candidate therapeutic targets in triple-negative breast cancer

569

Background: In the present study, we have analyzed dysregulated pathways in triple-negative breast cancers. Methods: Two datasets of cDNA arrays were used to identify differentially expressed genes between triple negative breast cancer and either normal/benign breast tissue or other molecular classes. The first dataset (I) was included 165 samples. The second data set (II) included 148 samples. Pathway analyses (gene set) were done based using BRB array tool and a software developed in house (SBIME). Results: Fifteen and 27 patients presented a triple negative breast cancer in the dataset I and II respectively. Ten and eleven pathways were significantly different between triple negative and other molecular classes in dataset I and II respectively (LS permutation p value<0.01). Six pathways were common between the two datasets (p53, cyclin E, E2F1, p27 phosphorylation, Ran, cycle regulation). We then focused the analyses on differential pathways between triple negative and normal/benign tissue. In the dataset I, targetable pathways were identified (hotelling t-test <10–7) including VEGF signalling pathway, proteasome, Hedgehog and Notch pathway. In addition, an enrichment of histone overexpression was observed in triple negative breast cancer (3% of overexpressed genes, ratio expression >2). In the dataset II, histone (p = 2x10–6), chromosome organization (p = 2x10–4) gene sets were enriched in triple negative breast cancer. We then assessed whether such pathway dysregulations could be linked to genomic aberration enriched in triple negative breast cancer. Using high resolution CGH arrays (Agilent, 4*44K) on 53 triple negative breast cancers, we detected that 31% of triple negative tumors presented a gene gain in 6p21 and 6p22, two regions that contain VEGFA gene (6p21) and a cluster of histones (6p22). Conclusions: Triple negative breast cancers present dysregulation of targetable pathways, including VEGF signaling and chromosome organization. Dysregulation of these two pathways could be related to gene gains in 6p21–22 regions observed in 30% of triple negative breast cancer.

No significant financial relationships to disclose.

Two populations of double minute chromosomes harbor distinct amplicons, the MYC locus at 8q24.2 and a 0.43-Mb region at 14q24.1, in the SW613-S human carcinoma cell line

High-level amplifications observed in tumor cells are usually indicative of genes involved in oncogenesis. We report here a high resolution characterization of a new amplified region in the SW613-S carcinoma cell line. This cell line contains tumorigenic cells displaying high-level MYC amplification in the form of double minutes (DM(+) cells) and non tumorigenic cells exhibiting low-level MYC amplification in the form of homogeneously staining regions (DM(-) cells). Both cell types were studied at genomic and functional levels. The DM(+) cells display a second amplification, corresponding to the 14q24.1 region, in a distinct population of DMs. The 0.43-Mb amplified and overexpressed region contains the PLEK2, PIGH, ARG2, VTI1B, RDH11, and ZFYVE26 genes. Both amplicons were stably maintained upon in vitro and in vivo propagation. However, the 14q24.1 amplicon was not found in cells with high-level MYC amplification in the form of HSRs, either obtained after spontaneous integration of endogenous DM MYC copies or after transfection of DM(-) cells with a MYC gene expression vector. These HSR-bearing cells are highly tumorigenic. The 14q24.1 amplification may not play a role in malignancy per se but might contribute to maintaining the amplification in the form of DMs.

An exonic expression profile for breast cancer diagnosis of fine needle aspiration biopsies

Abstract #2029

Background: Fine needle aspiration (FNA) for breast cancer diagnosis, a simple, quick and cheap procedure, is limited by a significant number of inconclusive exams. In the present study, we have analyzed whether the expression of a set of exonic probes could accurately diagnose breast cancer of FNA biopsies.&#x2028; Patients and methods: cDNA from 165 breast lesions (120 cancers), obtained by FNA in 2006-2007, and for which RIN score was &gt; 6, was hybridized on splice arrayTM in two separate series (training/validation)(data set Andre et al SABCS 2008). We focused on 703 680 evidenced probe sets. The actual diagnosis of breast cancer was established by pathological examination at surgery. Associations between exonic probes and diagnosis were assessed by correlation coefficients (using t-tests) and a nearest centroid prediction rule was determined on the training set of 94 samples (70 cancers) in order to classify lesions as malignant or benign. Using the validation set of 71 samples (50 cancers), the performance of the prediction rule was evaluated and the proportion of explained variation (PEV) estimated in a logistic regression model (including only variables significant by a likelihood ratio test).&#x2028; &#x2028; Results: In a leave-one-out cross-validation analysis, the nearest prediction rule based on the expression of 1228 exonic probes (all probes with p&lt;10e-9) accurately classified all samples from the training set. In the validation set, 68 out of 71 samples were accurately classified (96%) by this exonic expression profile of 1228 probes. Sensitivity and specificity were 96% (exact 95% CI: 86-100%) and 95% (76-100%). The cytological exam failed to provide a definitive diagnosis in 5 out of 71 patients. Four out of these 5 lesions were accurately classified by the nearest prediction rule. The PEV obtained by a clinical model (age and BI-RADS classification) was 75% (bootstrap standard error +/-8%) and the PEV by the exonic profile alone 81% (+/- 10%) in the validation set. When the clinical model and the exonic profile were combined, the PEV was 87% (+/-7%).&#x2028; Conclusion: We have developed a profile based on the expression of 1228 exonic probes for breast cancer diagnosis using FNA samples. This exonic profile could be a complementary tool to clinical variables and to the cytologic exam to decide about surgery in post-screening programs.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2029.

Intragenic breakpoints localized by array CGH in a t(2;6) familial translocation

A 244K genome-wide array based comparative genomic hybridization study was carried out in a familial translocation t(2;6)(p25;p21) balanced in the mother and unbalanced in her daughter. In the past, this translocation has allowed us to localize the HLA multigene cluster to chromosome 6. With microarray technology, confirmation of the chromosome localization of the HLA system was easily obtained, showing that such approach may be applied to the breakpoint localizations of other familial structural changes when they are unbalanced. The disruption of genes at the translocation breakpoints that did not have any phenotypic consequences in the parent will allow the generation of a map of 'haplotolerant genes'. In addition, many genomic variants were detected with this technology, enlarging the possibility of analyzing their possible contribution to phenotypic diversity.

Oligonucleotide microarray analysis of estrogen receptor alpha-positive postmenopausal breast carcinomas: identification of HRPAP20 and TIMELESS as outstanding candidate markers to predict the response to tamoxifen

The estrogen receptor alpha (ER alpha) status of breast tumors is used to identify patients who may respond to endocrine agents such as tamoxifen. However, ER alpha status alone is not perfectly predictive, and there is a pressing need for more reliable markers of endocrine responsiveness. In this aim, we used a two-step strategy. We first screened genes of interest by a pangenomic 44 K oligonucleotide microarray in a series of ten ER alpha-positive tumors from five tamoxifen-treated postmenopausal patients who relapsed (distant metastasis) and five tamoxifen-treated postmenopausal patients who did not relapse, matched with respect to age, Scarff-Bloom-Richardson grade, lymph node status, and macroscopic tumor size. Genes of interest (n=24) were then investigated in an independent well-characterized series of ER alpha-positive unilateral invasive primary breast tumors from postmenopausal women who received tamoxifen alone as adjuvant hormone therapy after primary surgery. We identified four genes (HRPAP20, TIMELESS, PTPLB, and MGC29814) for which high mRNA levels were significantly associated with shorter relapse-free survival (log-rank test). We also showed that hormone-regulated proliferation-associated 20 kDa protein (HRPAP20) and TIMELESS are 17beta-estradiol-regulated in vitro and are ectopically expressed in OH-Tam-resistant cell lines. In conclusion, these findings point to HRPAP20 and TIMELESS as promising markers of tamoxifen resistance in women with ER alpha-positive breast tumors.

High expression of DNA repair pathways is associated with metastasis in melanoma patients

We have identified a gene-profile signature for human primary malignant melanoma associated with metastasis to distant sites and poor prognosis. We analyse the differential gene expression by looking at whole biological pathways rather than individual genes. Among the most significant pathways associated with progression to metastasis, we found the DNA replication (P=10(-14)) and the DNA repair pathways (P=10(-16)). We concentrated our analysis on DNA repair and found that 48 genes of this category, among a list of 234 genes, are associated with metastatic progression. These genes belong essentially to the pathways allowing recovery of stalled replication forks due to spontaneous blockage or induced DNA lesions. Because almost all these differentially expressed repair genes were overexpressed in primary tumors with bad prognosis, we speculate that primary melanoma cells that will metastasize try to replicate in a fast and error-free mode. In contrast to the progression from melanocytes to primary melanoma, genetic stability appears to be necessary for a melanoma cell to give rise to distant metastasis. This overexpression of repair genes explains nicely the extraordinary resistance of metastatic melanoma to chemo- and radio-therapy. Our results may open a new avenue for the discovery of drugs active on human metastatic melanoma.

Identification of novel candidate genes for ependymoma progression in chromosomal regions over-represented at recurrence and detected by CGH array

2008

Background: The biology and genetics of ependymomas remain poorly understood. As opposed to other pediatric tumors, few recurrent chromosomal abnormalities or relevant pathways have been identified. Method: In order to gain new insight into the molecular mechanisms involved in ependymoma progression, we performed BAC array-based comparative genomic hybridization (aCGH) in a series of 59 tumors at diagnosis and at relapse (42 posterior fossa and 17 supratentorial). Specific chromosomal imbalances were confirmed by FISH. Expression of candidate genes was evaluated by RT-PCR and immunohistochemistry. Results: As compared to CGH (Cancer Genet Cytogenet 2002), aCGH detected more abnormalities since 18/33 samples at diagnosis and 22/26 at recurrence showed chromosomal imbalances. Three distinct patterns were observed : no imbalance (15 at diagnosis, 4 at relapse), large and numerous imbalances (7 at diagnosis, 12 at relapse) and small and rare imbalances (11 at diagnosis, 10 at relapse). At diagnosis, absence of chromosomal imbalance was correlated with young age (p=0.034) and shorter progression-free survival (p=0.014). At relapse, patients with large and numerous imbalances had a shorter survival (p=0.026). Specific chromosomal imbalances were significantly more frequent at recurrence: 9 qter gain (54% vs 21%), 1q gain (12% vs 0%) and 6q loss (27% vs 6%). Samples were available both at diagnosis and relapse for 16 patients. Whole genome changes were towards increase of genomic abnormalities (n=10) but also simplification (n=6), the former being associated with a higher risk of death from disease (Fisher exact, p=0.03). A candidate gene strategy was focussed on the frequently gained 9qter locus. Significant overexpression compared to normal brain was identified for Tenascin-C (median 35 fold, max 220 fold, p<0.0001) and Notch1 (median 6 fold, max 45 fold, p<0.0001). Notch pathway analysis by RT-PCR revealed potential regulatory loops between JAG1/2 or DLL1/3 and Notch1/2. Conclusion: aCGH pattern may identify subgroups of ependymomas with respect to prognosis. Notch pathway and Tenascin-C are important regulatory genes in ependymoma progression and may represent interesting new targets for therapy.

No significant financial relationships to disclose.

Genome-wide expression profiling and tissue array analysis for prediction of recurrences in stage II-III colorectal cancer (CRC)

3572

Background: Despite substantial progress in molecular pathogenesis of colon cancer (CC), no reliable biomarkers of outcome have yet been identified in patients with resected stage II-III CC. Methods: We analyzed genome-wide mRNA expression profiles in 20 stage II or III left side CC from 10 patient who developed metastasis (M+) and 10 disease free patients followed up for at least 4 years (M-) using high-density oligonucleotide microarrays (Agilent technology). RNA from tumor tissue (T) was hybridized against normal tissue (NT) from the same patient and each experiment was replicated 4 times (with 2 dye-swaps). The goal was to select genes both differentially expressed between T and NT and between M+ and M-. A tissu-array was constructed using 212 stage II and III resected CRC (164 CC, 64 rectal cancers) and their matched NT. For survival analysis, immunohistochemistry (IHC) data was dichotomized at the median value. Results: Analysis of microarray data yielded 27 genes that had a 2-fold difference between the expression in T and NT in at least 5 out of 20 patients and for which the average expression was significantly different between M+ and M- (p<0.01, t-test). Among the 6 most differentially expressed genes between M+ and M- in T, 4 of them were found to be involved in interferon γ pathway and could be evaluated by IHC: CXCL9, CXCL13, PPARγ, THSD. In order to assess macrophage and natural killer (NK) cell infiltration, CD68 and CD57 were also analyzed. Intensity was measured by semi-quantitative scores for the first 4 genes and by the number of infiltrating cells for the others. CXCL9, PPARGγ, CXCL13, CD57 and CD68 were significantly underexpressed in T as compared to NT (p<0.0001, paired t-test). The logrank test stratified by cancer site indicated that high IHC expression of CD57 possessed a significantly better recurrence-free survival (RFS) than those low expression (p=0.004). Multivariate Cox analysis identified tumor site (p=0.001), node stage (p<0.001) and CD57 (p=0.002) as independent predictors of RFS. Conclusions: NK cell infiltration within colorectal cancers is associated with prolonged recurrence-free survival in stage II and III CRC.

No significant financial relationships to disclose.

Study of BRAF mutations in melanoma and nevi from patients with germline mutation in the CDKN2A gene

10075

Background: Germline mutations in the CDKN2A tumor suppressor gene is a rare condition associated with a high risk of melanoma. Somatic activating mutations of the BRAF gene are frequently observed in cutaneous melanoma (40–60%) but their occurrence vary according to melanoma subtypes (cutaneous, vs mucosal or uveal) and are less frequent in melanoma located on chronically sun-exposed skin. It is thought that melanomas occurring in patients carrier of a CDKN2A germline mutation are associated a second inactivating genetic event in the tumor, facilitating cellular transformation by loss of function this crucial gatekeeper of the G1-S checkpoint. However, the potential role of the MAP-kinase pathway, and more precisely, the involvement of BRAF activation, in this particular population of patients, are still unknown. Thus, our objective was to evaluate the frequency of BRAF somatic mutations in melanoma and nevi developed by patients carrier of a CDKN2A germline mutation. Methods: DNA was extracted from paraffin-embedded tissues of 36 primary melanomas, 9 metastases and 20 nevi from 31 patients with CDKN2A germline mutation. Ten sporadic melanoma from patients harbouring no CDKN2A mutation were also studied as a control population. BRAF mutations were screened by direct sequencing of exon 11 and 15. Results: BRAF mutations (V599E) were found with a significantly lower frequency of 14% (5/36) in melanomas from patients with proven CDKN2A germline mutation, as compared to a frequency of 55% (5/9) in patients with no genetic predisposition (two-sided Fishers exact test, p=0.02). Frequencies of BRAF mutations in metastases and nevi from patients with CDKN2A germline mutation were 33%(3/9) and 10% (2/20) respectively. Conclusions: BRAF mutations seem to be less frequent in melanoma from patients with familial predisposition harbouring CDKN2A germ line mutation than in sporadic melanoma. These results suggest that CDKN2A loss of function gives rise to tumorigenic pathways where genetic events distinct from BRAF activating mutation can induce cell transformation. Additional biological studies are performed on this rare population of melanoma samples in order to better characterize the specificity of cellular transformation in the context of CDKN2A germ line mutation.

No significant financial relationships to disclose.

Gene expression profiling of primary cutaneous melanoma: Expression of replication origins firing genes predicts clinical outcome

8024

Background: Gene-expression profiling in human cutaneous melanomas is impaired by the difficulty in getting access to a retrospective collection of frozen tumors. Thus, compared to other tumors, gene expression profiling data on human cutaneous melanomas are scarce, and data with prognostic implication are entirely lacking. In order to better understand the progression of this tumor and to identify key genes involved in melanoma prognosis, we correlated gene-expression profiles with clinical outcome in a cohort of 83 patients with primary melanoma. Methods: A class comparison and class prediction analysis was performed to identify genes able to predict 4-years. distant metastasis free-survival in 58 primary melanomas with at least 4-years follow-up or intercurrent distant metastasis or death. Results were also validated at the protein level in an independent population of 176 primary melanomas with a median clinical follow-up of 8.5 years. Results: We identified a set of sequences discriminating between primary melanomas associated with good and poor prognosis. Some of these sequences correspond to key-genes in the regulation of replication origins firing, such as mini-chromosome maintenance genes and geminin. The prognostic value of overexpression of replication origins firing genes is independent from thickness, ulceration, age and sex. Conclusions: This study has identified key-genes associated with in vivo metastatic dissemination of cutaneous melanomas. Some of our data provide new diagnostic tools for the accurate diagnosis of melanoma and shed new light on the molecular mechanisms underlying poor prognosis in melanoma patients. As some of these molecules are currently under study as targets for therapy, our data can have significant impact on the development of new melanoma therapies.

No significant financial relationships to disclose.

A new genomic approach to describe the natural history of node negative breast cancer patients

10058

Background: Breast cancer is a heterogeneous and complex disease beyond good/bad prognosis groups. Previous studies identified prognostic tools that are undergoing inter-group validation. Our present study aims at better defining pre-malignant vs. malignant lesions and tumors that will give local vs. distant metastases (DM) or early vs. late DM. Methods: We selected 3 groups of patients (pts) in a consecutive series of node-negative breast cancers with a very long follow-up (>10 years (y)) and available frozen tumor samples. Pts who did not receive any adjuvant treatment were selected: 60 with no relapse after 10 y, 29 with early DM before 5 y and 18 with late DM after 5y. Genomic profiling on 44K Agilent pangenomic arrays taking as reference non-relapsing pts (after 10y) or normal breast (Clonetech) allowed us to select specific genes related to DM occurrence or tumorigenesis. Random permutations were performed to assess the statistical significance of our prediction accuracy. Results: 1- we identified a 141 gene-profile and related genes distinguishing tumors with early DM from tumors with late DM (71% prediction accuracy). 2- Similarly, we identified a 285-gene signature for late DM vs. no relapse at 10 y (80% prediction accuracy). Genes were further classified according to family clusters allowing description of genes involved in DM occurrence. 3- a total of 435 genes were also significantly over-expressed in at least 90% of 148 tumours (compared to normal breast). Among those, a selection of the most significant genes were analysed for RT-PC expression throughout the various steps of tumour development (normal breast, benign tumors, in situ carcinomas, invasive carcinomas). Among the 15 most upregulated genes listed, 3 unknown genes appear, that are overexpressed in 98% of the tumors with an average fold change > 11 and are currently explored. Discussion: In this unique series of untreated node-negative breast cancers, identification of molecular profiles of early and late DM could be useful in better early prediction of breast cancer outcome. Based on genomic analysis, a molecular gene based classification of progression from benign tissue to aggressive tumors allows to dissect pathways towards malignancy and to identify early diagnostic markers or targets for prevention.

No significant financial relationships to disclose.

An Atlas on genes and chromosomes in oncology and haematology

The "Atlas of Genetics and Cytogenetics in Oncology and Haematology" http://www.infobiogen.fr/services/chromcancer is a peer-reviewed and free internet database aimed at genes involved in cancer, cytogenetics and clinical entities in cancer, and cancer-prone diseases. It contains concise and updated review articles, a huge portal towards genetics and/or cancer databases, and teaching materials in genetics for the students. This database is made for and by clinicians and researchers, who are encouraged to contribute. The Atlas is part of the genome project. It provides information in cancer epidemiology. It contributes to research, university and post-university teaching, and telemedicine. It contributes to 'meta-medicine', a mediation using new information technology, between the overflowing information provided by the scientific community and the individual practitioner.

Identification, phylogeny, and evolution of retroviral elements based on their envelope genes

Phylogenetic analyses of retroviral elements, including endogenous retroviruses, have relied essentially on the retroviral pol gene expressing the highly conserved reverse transcriptase. This enzyme is essential for the life cycle of all retroid elements, but other genes are also endowed with conserved essential functions. Among them, the transmembrane (TM) subunit of the envelope gene is involved in virus entry through membrane fusion. It has also been reported to contain a domain, named the immunosuppressive domain, that has immunosuppressive properties most probably essential for virus spread within the host. This domain is conserved among a large series of retroviral elements, and we have therefore attempted to generate phylogenetic links between retroviral elements identified from databases following tentative alignments of the immunosuppressive domain and adjacent sequences. This allowed us to unravel a conserved organization among TM domains, also found in the Ebola and Marburg filoviruses, and to identify a large number of human endogenous retroviruses (HERVs) from sequence databases. The latter elements are part of previously identified families of HERVs, and some of them define new families. A general phylogenetic analysis based on the TM proteins of retroelements, and including those with no clearly identified immunosuppressive domain, could then be derived and compared with pol-based phylogenetic trees, providing a comprehensive survey of retroelements and definitive evidence for recombination events in the generation of both the endogenous and the present-day infectious retroviruses.

Paramecium genome survey: a pilot project

A consortium of laboratories undertook a pilot sequencing project to gain insight into the genome of Paramecium. Plasmid-end sequencing of DNA fragments from the somatic nucleus together with similarity searches identified 722 potential protein-coding genes. High gene density and uniform small intron size make random sequencing of somatic chromosomes a cost-effective strategy for gene discovery in this organism.

An element within the 5' untranslated region of human Hsp70 mRNA which acts as a general enhancer of mRNA translation

The untranslated regions of mRNAs encoding heat-shock proteins have been reported to contain elements important to the post-transcriptional regulation of these key components of the stress response. In this report we describe an element from the 5'UTR of human Hsp70 mRNA that increases the efficiency of mRNA translation. Cloning of this region upstream of the coding sequence of two different reporter genes (firefly luciferase and chloramphenicol acetyltransferase) increases expression of the reporter under normal cell culture conditions by up to an order of magnitude. This effect was observed in three different promoter contexts (HSP, SV40 and CMV) and in six cell lines. The increase in protein production is not accompanied by any alteration in mRNA levels, suggesting that the element facilitates translation. 5' or 3' truncated sequences are ineffective in enhancing reporter expression, suggesting that the activity arises from the secondary structure of the element, rather than from some smaller defined motif. Computer analysis of this region revealed that it is able to form stable secondary structures (DeltaG approximately -292.6 kJ x mol(-1)). The Hsp70 element does not seem to act as an internal ribosome entry site. Incorporation of the sequence into plasmids used for DNA vaccination produces increased antibody responses, confirming that the sequence is functional in primary cells. These data suggest that the 5'UTR of human Hsp70 mRNA plays an important role in determining Hsp70 expression levels, and that it contains an element of general utility in enhancing recombinant protein expression systems.

Atlas of Genetics and Cytogenetics in Oncology and Haematology, updated

The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/chromcancer) is an Internet database aimed at genes involved in cancer, cytogenetics and clinical entities in cancer, and cancer-prone diseases. It presents information in concise and updated reviews (cards) or longer texts (deep insights), a (new) case report section, a huge portal towards genetics and/or cancer databases, and teaching items in genetics for students in medicine and the sciences. This database is made for and by clinicians and researchers in the above-mentioned fields, who are encouraged to contribute. It deals with cancer research, genomics and cytogenomics. It is at the crossroads of research, post-university teaching and telemedicine. The Atlas is available at no cost.

Valyl-tRNA synthetase from Escherichia coli MALDI-MS identification of the binding sites for L-valine or for noncognate amino acids upon qualitative comparative labeling with reactive amino-acid analogs

Bromomethyl ketone derivatives of L-valine (VBMK), L-isoleucine (IBMK), L-norleucine (NleBMK) and L-phenylalanine (FBMK) were synthesized. These reagents were used for qualitative comparative labeling of Escherichia coli valyl-tRNA synthetase (ValRS), an enzyme with Val/Ile editing activity, in order to identify the binding sites for L-valine or noncognate amino acids. Labeling of E. coli ValRS with the substrate analog valyl-bromomethyl ketone (VBMK) resulted in a complete loss of valine-dependent isotopic [32P]PPi-ATP exchange activity. L-Valine protected the enzyme against inactivation. Noncognate amino acids analogs isoleucyl-, norleucyl- and phenylalanyl-bromomethyl ketones (IBMK, NleBMK and FBMK) were also capable of abolishing the activity of ValRS, FBMK being less efficient in inactivating the synthetase. Matrix-assisted laser desorption-ionization mass spectrometry designated cysteines 424 and 829 as the target residues of the substrate analog VBMK on E. coli ValRS, whereas, altogether, IBMK, NleBMK and FBMK labeled His266, Cys275, His282, His433 and Cys829, of which Cys275, His282 and His433 were labeled in common by all three noncognate amino-acid-derived bromomethyl ketones. With the exception of Cys829, which was most likely unspecifically labeled, the amino-acid residues labeled by the reagents derived from noncognate amino acids were distributed between two fragments 259-291 and 419-434 in the primary structure of E. coli ValRS. In fragment 419-434, Cys424 was specifically labeled by the substrate analog VBMK, while His433 was labeled in common by all the used bromomethyl ketone derivatives of noncognate amino acids, suggesting that the synthetic site where aminoacyl adenylate formation takes place on E. coli ValRS is built up of two subsites. One subsite containing Cys424 might represent the catalytic locus of the active center where specific L-valine activation takes place. The second subsite containing His433 might represent the binding site for noncognate amino acids. The fact that Cys275 and His282, fragment 259-291, were labeled by IBMK, NleBMK and FBMK, but not by the substrate analog VBMK, suggests that these residues might be located at or near the editing site of E. coli ValRS. Comparison of fragment 259-291 with all the available ValRS amino-acid sequences revealed that His282 is strictly conserved, with the exception of its replacement by a glycine in a subgroup corresponding to the archaebacteria. Because a nucleophile is needed in the editing site to achieve hydrolysis of an undesired product at the level of the carbonyl group thereof, it is proposed that the conserved His282 of E. coli ValRS is involved in editing.

The "Atlas of genetics and cytogenetics in oncology and haematology" on the internet and a review on infant leukemias

The "Atlas of Genetics and Cytogenetics in Oncology and Haematology" (URL: http://www.infobiogen.fr/services/chromcancer) is a database devoted to chromosome abnormalities in cancer, cancer-prone diseases, and genes involved in cancer. The information is concise and updated. This database is made for and by cytogeneticists, molecular biologists, clinicians in oncology and hematology, and pathologists, who are encouraged to contribute. The database is herein presented, together with an example concerning congenital leukemias.

Sequence and expression of seven new tetraspans

The tetraspans are components of large molecular complexes that include also non-tetraspan molecules, in particular integrins. We have identified and sequenced several new members of the tetraspan superfamily, called NET-1 to NET-7 (new EST tetraspan). Sequence analysis of the NET reveals a structure typical for tetraspans, with the presence of four transmembrane domains delimiting two extracellular regions as well as conserved amino acid residues. The NET are differentially expressed in human cell lines.

The PAUSE software for analysis of translational control over protein targeting: application to E. nidulans membrane proteins

The PAUSE software has been developed as a new tool to study translational control over protein targeting. This makes it possible to correlate the position of clusters of rare codons in a gene, predicted to cause a translational pause, with the position of hydrophobic stretches in the encoded protein, predicted to span a membrane or to act as a cleavable signal for targeting to the secretory pathway. Furthermore, this software gathers these correlations over whole sets of genes. The PAUSE software is described here, and its use is illustrated on a set of membrane proteins from the fungus Emericella nidulans. Preferential distances of about 45 codons and of about 70 codons between putative transmembrane domains and predicted translational pauses were observed. Given that approximately 30 residues are required to span the large ribosomal subunit, the predicted pauses would therefore occur when the hydrophobic domain starts protruding from the ribosome ('+45 pause'), or fully protrudes as a hairpin ('+70 pause'). Thus, these specific pauses might reflect a translational control over membrane protein targeting or early recognition ('+45 pause'), and over insertion or folding ('+70 pause').

Atlas of genetics and cytogenetics in oncology and haematology, an interactive database

The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/chromcancer ) is a database devoted to chromosome abnormalities in cancer, cancer-prone diseases and genes involved in cancer. Information presented in each page is concise and updated. This database is made for and by: cytogeneticists, molecular biologists, clinicians in oncology and in haematology, and pathologists, who are encouraged to contribute.

Virgil database for rich links (1999 update)

With so many databases available for research in the Human Genome Project, it is crucial to efficiently relate information from different resources. For that purpose, we maintain Virgil, a database of rich links for data browsing, data analysis and database interconnection. Virgil current version contains more than 40 000 rich links from five major databases: SWISS-PROT, GenBank, PDB, GDB and OMIM. Materials described in this paper are available from http://www.infobiogen.fr/services/virgil/

A database on cytogenetics in haematology and oncology

The aim of 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/chromcancer) is to present summarized information on chromosome abnormalities in cancer, with extensions to genes involved in cancer and to cancer-prone diseases. Information is to be updated. This database is made for and by cytogeneticists, molecular biologists, clinicians in oncology and in haematology, and pathologists.

The Internet for the medical and scientific community

With the explosion of data coming out from the international scientific community, researchers can now locate and manipulate data of interest quickly and easily on the Internet. The scope of this review is to focus on some of the recent developments of the Internet that are specially relevant to health scientists. The review also provides the medical and scientific community with a selection of sites to visit on the Internet, dealing with clinical and laboratory aspects of science.

GenXref. VI: Automatic generation of links between two heterogeneous databases

MOTIVATION

A large proportion of the information found in public databases is not sufficiently cross-referenced. We developed genXref, an automated system for link inference, because embarking on a manual cross-referencing of genome data would require too much expensive human expertise. It uses information retrieval technology to generate links between objects of heterogeneous databases.

RESULTS

GenXref was used to generate links between GDB genes and Genbank human sequences. It resulted in > 10,000 links with a precision of 83% and a recall of approximately 32%.

Further characterisation of the p53 responsive element--identification of new candidate genes for trans-activation by p53

The p53 protein is known to trans-activate a number of genes by specific binding to a consensus sequence containing two decamers of the type: PuPuPuCA/TT/AGPyPyPy. In order to identify new p53 trans-activated genes, we defined a set of criteria for computer search of p53-responsive elements. Based on experimental data, we proposed an extended consensus sequence composed of the two decamers of the El-Deiry consensus sequence flanked by two additional ones. A maximum of 3 bp substitutions was accepted for the two decamers of the El-Deiry consensus sequence, as well as for each additional decamer, except when the two decamers of the El-Deiry consensus sequence are contiguous. In this case, each additional decamer is allowed to bear one base insertion or deletion between the median C and G. This set of criteria was validated by identifying within the promoter region of the IGF-BP3 gene the existence of a novel p53-responsive element whose functional significance was verified. By limiting our computer search to Vertebrate genes involved in cell cycle regulation, cellular adhesion or metastatic processes and to gene families most often found in HOVERGEN database, 7785 gene sequences were first analysed. Among the oncogenes, kinases, proteases and structural proteins, 55 new genes were selected; six of them were retrieved in more than one species.

Intriguing association between disease associated unstable trinucleotide repeat and CpG island

Expansion of (C+G)-rich trinucleotide repeats has been shown to be associated with several autosomal or X-linked genetic diseases and/or fragile sites. By analysing the sequences available in the databases, we found, in a significant proportion of triplet associated genes or fragile sites (11/12), a CpG island close to the trinucleotide repeat. This association led us to assume that flanking regions and chromatin structure near the triplets might play a role in repeat instability.

Structure of the human luteinizing hormone-choriogonadotropin receptor gene: unusual promoter and 5' non-coding regions

The complete organization of the human luteinizing hormone-choriogonadotropin (LH/CG) receptor (LH/CGR) gene and the structure of 1591 bp of its 5' flanking region have been determined. This gene spans over 70 kbp and contains 11 exons. The first ten exons and part of the last exon encode the extracellular domain of the receptor while the transmembrane and intracellular domains are encoded by the remaining part of the last exon. The gene encodes a 701 amino acids long preprotein, contrary to a previous report of 699 amino acids. Primer extension experiments and polymerase chain reaction (PCR) mapping allowed definition of the transcription initiation site, which is located 1085 bp upstream from the initiation codon. The 5' non-coding region is thus unusually long. The promoter region which is different from the murine LH/CG receptor promoter, contains two putative TATA boxes at positions -34 and -47 and a CAAT box consensus sequence at position -89. A consensus sequence corresponding to a cAMP responsive element is found at position -697. Seven API consensus sequences are also found in the 5' flanking region of the gene. Southern blot experiments demonstrated an informative biallelic polymorphism within the human LH/CG receptor gene locus using BglII endonuclease. The cloning of the human LH/CGR gene and the determination of the organization and structure of its 5' flanking region allow the study of its hormonal, developmental and tissue-specific regulation. Primers and PCR conditions are described for the direct genomic sequencing of all the exons of the gene. This information should facilitate the study of pathological mutations of the receptor.

A rapid access motif database (RAMdb) with a search algorithm for the retrieval patterns in nucleic acids or protein databanks

We present here a codification structure, entirely interfaced with the main packages for biomolecule database management, associated with a new search algorithm to retrieve quickly a sequence in a database. This system is derived from a method previously proposed for homology search in databanks with a preprocessed codification of an entire database in which all the overlapping subsequences of a specific length in a sequence were converted into a code and stored in a hash-coding file. This new algorithm is designed for an improved use of the codification. It is based on the recognition of the rarest strings which characterize the query sequence and the intersection of sorted lists read in the codification structure. The system is applicable to both nucleic acid and protein sequences and is used to find patterns in databanks or large sets of sequences. A few examples of applications are given. In addition, the comparison of our method with existing ones shows that this new approach speeds up the search for query patterns in large data sets.

Structure-function relationship of the Lrp-binding region upstream of lysU in Escherichia coli

In Escherichia coli, one of the two genes encoding lysyl-tRNA synthetase, lysU, belongs to the regulon controlled by the leucine-responsive regulatory protein (Lrp). To map the site of Lrp action, mutants escaping regulation in rich medium were generated through random mutagenesis of the lysU promoter region. The mutations showed parallel effects on the strength of Lrp-DNA association, as measured in vitro by gel retardation experiments, and on the degree of repression of lysU expression by Lrp in vivo. In addition, DNase I and hydroxyl radical footprinting experiments indicated that several Lrp molecules bind to a DNA region of over 110 bp in a highly cooperative manner. This region, which encompasses the -35 box of the lysU promoter, was the target of all the mutations affecting the strength of the Lrp-DNA association. These mutations are frequently located in short A + T-rich runs distributed along the Lrp binding region with a periodicity of one helix turn. Because we could find such a regular alternance of A + T runs upstream of several other Lrp-regulated genes, we suggest that this pattern is one feature indicative of the binding of Lrp.

Fast protein sequence verification by matrix assisted laser desorption mass spectrometric analysis of whole enzymatic digests

Matrix assisted laser desorption mass spectrometry provides a very fast and efficient way to check protein sequences by the analysis of whole proteolytic digests. This method has been applied to the sequence verification of E. coli isoleucyl tRNA synthetase, for which two different sequences are found in data banks. The result of this investigation clearly shows that no one of these sequences is correct.

Structure of the human progesterone receptor gene

The complete organization of the human progesterone receptor (hPR) gene has been determined. It spans over 90 kbp and contains eight exons. The first exon encodes the N-terminal part of the receptor. The DNA binding domain is encoded by two exons, each exon corresponding to one zinc finger. The steroid binding domain is encoded by five exons. The nucleotide sequence of 1144 bp of the 5' flanking region has been determined.