Specific Gene Expression Signature Research Articles

THU0005 Investigating the Plasma Cell Signature in Autoimmune Disease

BackgroundProduction of pathogenic autoantibodies by self-reactive plasma cells (PC) is a hallmark of autoimmune diseases; thus, PC levels could be associated with efficacy of B-cell depleting therapies. Additionally, investigating the...

Visualization of stem cell features in human hepatocellular carcinoma revealsin vivosignificance of tumor-host interaction and clinical course

Hepatocellular carcinoma (HCC) is one of the most aggressive malignancies because of recurrence and/or metastasis even after curative resection. Emerging evidence suggests that tumor metastasis and recurrence might be driven by a small subpopulation of stemness cells, so-called cancer stem cells (CSCs). Previous investigations have revealed that glioma and breast CSCs exhibit intrinsically low proteasome activity and that breast CSCs also reportedly contain a lower reactive oxygen species (ROS) level than corresponding nontumorigenic cells. Here we visualized two stem cell features, low proteasome activity and low intracellular ROS, in HCC cells using two-color fluorescence activated cell sorting to isolate cells with stem cell features. These cells were then analyzed for their division behavior in normoxia and hypoxia, expression of stem cell markers, tumorigenicity, metastatic potential, specific gene expression signatures, and their clinical implications. A visualized small subpopulation of HCC cells demonstrated asymmetric divisions. Their remarkable tumorigenicity in nonobese diabetic/severe combined immunodeficient mice suggested the cancer initiation potential of these HCC CSCs. Comprehensive gene expression analysis revealed that chemokine-related genes were up-regulated in the CSCs subpopulation. Our identified HCC CSCs facilitated the migration of macrophages in vitro and demonstrated metastatic potential by way of recruitment of macrophages in vivo. In patients who undergo curative operation for HCC, the CSC-specific gene signature in the liver microenvironment significantly correlates with recurrence. Based on these findings, the stem cell feature monitoring system proposed here is a promising tool to analyze the in vivo significance of CSC microenvironments in human HCCs.

NGS-based targeted RNA sequencing for expression profiling and relative quantitation of specific gene isoforms and fusions in tumor-specific panels.

11108 Background: Gene expression signatures have become a useful tool for the identification of tumor subtypes and response to specific therapies. Expression of tumor, metastatic and macrophage specific transcripts utilizing alternative promoters and transcriptional start sites can further characterize these tumors . NGS is a powerful tool for gene expression analysis, however larger sample input requirements (>100ng) and excessive sequencing depth requirements (30-40M tags/sample) to detect the expression of rare isoforms or fusions in tumor samples are prohibitive for clinical assay development. We describe the development of a targeted RNA sequencing assay for the relative quantitation of specific gene expression signatures, known splice variants and gene fusions from less than 100 ng of starting material in a single tube universal amplification format. Methods: Primers for 52 genes, isoforms and gene fusion products were designed using the universal amplification strategy. 10 ng of RNA from 5 matched tumor/adjacent normal breast cancer tumor pairs were assayed. Libraries were prepared for sequencing by emPCR and sequenced on Ion Torrent PGM. Data were aligned via TMAP. Relative expression was determined vs. housekeeping genes or wild type transcripts. Results: All gene targets were detected at significant levels in at least one tumor sample. Robust expression profiling (5 log dynamic range) was obtained from FFPE macrodissected tumor and normal samples with as little as 200K reads/sample. Immune specific transcripts demonstrated differential expression (CCL3, AIF, FCGR3A and CSF1) across patients and matched pairs as well as an upregulation of CXCL12, indicative of tumor associated macrophages. Conclusions: Targeted RNAseq demonstrates detection and quantitation of relative expression levels of not only tumor subclass specific gene expression signatures, but immune cell specific transcripts from 10ng of FFPE derived total RNA derived from macrodissected tumor samples. The lower input requirements, quicker turnaround time and incredible sensitivity of targeted RNAseq make this assay a useful tool for clinical assay development.

Abstract 3169: Lentiviral vector-based insertional mutagenesis identifies new clinically relevant liver cancer genes.

Abstract Next generation sequencing approaches are identifying a plethora of mutations in a variety of human cancers. However, the clinical implications of these new findings are still limited, since the identification of cancer driving mutations is hampered by the co-occurrence of several bystander and progression related events. Here we developed a forward genetics approach based on a new lentiviral vector-based insertional mutagen aimed at identifying cancer initiating genes that are relevant in human hepatocarcinogenesis. We generated a replication-defective lentiviral vector (LV) engineered with long terminal repeats carrying hepatospecific enhancers able to deregulate genes upon integration. Differently from retroviruses and transposons, our replication-defective LV provides a single round of integration shortly after the administration, thus tagging mainly early events in carcinogenesis. A single administration of LV in newborn mice was able to induce hepatocellular carcinoma (HCC) in 3 clinically relevant models of hepatocarcinogenesis: in 30% of Cdkn2a deficient mice (P=0.005 Vs untreated), in 27% of liver-specific Pten deficient mice (P=0.04) and in 75% of wild type mice coupled to CCl4 administration (P=0.002). From 30 LV-induced HCCs we retrieved 172 LV integrations that allowed the identification of Braf, Fign, Sos1 and Rtl1 as candidate cancer loci. The causative role of these 4 genes in HCC was experimentally validated in vivo by forced expression in the mouse liver. Whole transcriptome gene expression analysis allowed unveiling the molecular pathways deregulated by the newly identified cancer genes. HCC induced by integration at the paternally expressed gene Rtl1 (mapping within the imprinted Dlk1-Dio3 region) displayed the peculiar upregulation of oxidative phosphorylation genes. Conversely, LV-mediated upregulation of Braf and Fign caused the overexpression of the maternally expressed microRNAs encoded within the Dlk1-Dio3 region in HCCs which display the downregulation of oxidative phosphorylation genes. These findings highlighted a relevant role of Dlk1-Dio3 region in HCCs and in the regulation of metabolism. Additionally, we showed that WNT pathway may represent a target of the new enigmatic oncogene Fign. We then analyzed different human HCCs collections induced by HBV or HCV (N tot of HCC=221). We found that all the newly identified cancer genes were significantly upregulated and amplified or deleted in human HCCs. Moreover, we showed that the expression level of the new liver cancer genes or the specific gene expression signature caused by their upregulation can efficiently distinguish HCC patients characterized by poor survival. Overall, we developed a new insertional mutagen by which we identified new clinically relevant liver cancer genes that may provide novel prognostic markers and therapeutic targets for the diagnosis and treatment of human HCCs. Citation Format: Marco Ranzani, Daniela Cesana, Cynthia C. Bartholomä, Francesca Sanvito, Michela Riba, Mauro Pala, Fabrizio Benedicenti, Pierangela Gallina, Stefano Annunziato, Lucia Sergi Sergi, Stefania Merella, Alessandro Bulfone, Claudio Doglioni, Christof von Kalle, Yoon Jun Kim, Manfred Schmidt, Elia Stupka, Giovanni Tonon, Luigi Naldini, Eugenio Montini. Lentiviral vector-based insertional mutagenesis identifies new clinically relevant liver cancer genes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3169. doi:10.1158/1538-7445.AM2013-3169

Lung Tumor Microenvironment Induces Specific Gene Expression Signature in Intratumoral NK Cells

Natural killer (NK) cells are able to recognize and kill tumor cells, however whether they contribute to tumor immunosurveillance is still debated. Our previous studies demonstrated the presence of NK cells in human lung tumors. Their comparison with NK cells from non-tumoral lung tissues and with blood NK cells from the same individuals revealed a decreased expression of some NK receptors and impaired ex vivo cytotoxic functions occurring specifically in NK cells isolated from the tumor microenvironment. The aim of the present study was to characterize the transcriptional profile of such intratumoral NK cells, by comparative microarray analysis of sorted NK cells isolated from non-tumoral (Non-Tum-NK) and tumoral (Tum-NK) lung tissues of 12 Non-Small Cell Lung Cancer patients. Our results reveal a specific gene expression signature of Tum-NK cells particularly in activation processes and cytotoxicity, confirming that tumor environment induces modifications in NK cells biology. Indeed, intratumoral NK cells display higher expression levels of NKp44, NKG2A, Granzymes A and K, and Fas mRNA. A particular pattern of receptors involved in chemotaxis was also observed, with an overexpression of CXCR5 and CXCR6, and a lower expression of CX3CR1 and S1PR1 genes in Tum-NK as compared to Non-Tum-NK cells. The precise identification of the molecular pathways modulated in the tumor environment will help to decipher the role of NK cells in tumor immunosurveillance and will open future investigations to manipulate their antitumoral functions.

Abstract P5-03-06: Bisphenol A and mammary stem cells: implications in breast cancer susceptibility

Abstract It has been speculated that the increasing incidence of breast cancer might be linked to the increased exposure to environmental synthetic estrogens, such as bisphenol A (BPA), which is a most pervasive chemical in modern life as a component of polycarbonate plastics and epoxy resins used widely for food and beverage containers and dental sealants. Perinatal exposure to low, environmentally relevant doses of BPA in rodents resulted in the induction of pre-neoplastic ductal hyperplasia, carcinoma in situ, and increased susceptibility to tumorigenesis. However, the underlying mechanism for these observations is unclear. The murine mammary stem cells (MaSCs) are present in fetal mammary rudiments and could be the putative targets for BPA-induced tumorigenesis. More recently, MaSCs of different lineages have been matched with different subtypes of breast cancer by their specific gene-expression signatures. We thus hypothesize that mammary gland exposed to BPA at a susceptible window may lead to its susceptibility to tumorigenesis through a MaSC and/or stem cell niche mediated mechanism. To test this hypothesis, we exposed 21-day old Balb/C mice to BPA by gavage at 25 µg/kg/day during puberty for 3 weeks, and then isolated primary mammary cells at different time points (6-week, 2 and 4-month) for MaSC quantification using an in vitro mammosphere formation and 3D-ECM sphere differentiation assay as well as the in vivo cleared mammary fat pad regeneration assay. Our findings indicate that low dose BPA exposure at puberty can accelerate puberty onset, increase lateral branches and hyperplasia in adult mammary glands. Further, a single oral dose of DMBA at 30 mg/kg administrated at 2-month old resulted in a 2.4-fold increase in hyperplasia of mammary glands harvested at 4-month old when compared with BPA treated group without DMBA. Most significantly, puberty BPA exposure increased luminal MaSCs during gland development and this resulted in an increase of luminal cells in adult glands. In addition, puberty BPA exposure also altered basal MaSCs in such a way that regenerated glands from these basal MaSCs yielded higher preneoplastic lesion than control basal MaSCs, indicating puberty BPA exposure render basal MaSCs more susceptible to transformation. We also found significant increase of gene expression in steroid hormonal receptors (e.g. ERs and PR) in the stromal compartment (or stem cell niche), which suggest that the changes we observed above for the luminal and basal MaSCs may be caused indirectly through altered stromal environment upon BPA exposure during early life stage. Future studies are necessary to differentiate the effect of BPA exposure on MaSCs or the MaSC niche. In conclusion, our study showed that BPA-induced morphogenesis changes in mammary gland had a stem cell origin. More importantly, our findings suggest that BPA-induced susceptibility of mammary glands to tumorigenesis may also have a stem cell origin. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-03-06.

Microarray-based gene expression profiling in patients with cryopyrin-associated periodic syndromes defines a disease-related signature and IL-1-responsive transcripts

ObjectiveTo analyse gene expression patterns and to define a specific gene expression signature in patients with the severe end of the spectrum of cryopyrin-associated periodic syndromes (CAPS). The molecular consequences...

B-Cell-Specific Transcription Factor BACH2 Involved in the Clinical Behavior Heterogeneity of Waldenström Macroglobulinemia

AbstractAbstract 1288 Background.Approximately 30% of the patients who fulfil the criteria of Waldenström macroglobulinemia (WM) are diagnosed while asymptomatic, and will not require immediate therapy; these cases are called indolent WM (IWM). However, patients with a disease-related event will be considered for therapy, these cases are called symptomatic or aggressive WM (AWM). The physiopathology of these 2 groups remains unclear, and the mechanisms of progression have not been fully understood so far. We hypothesized that a gene signature that differentiates these two categories could be identified to better understand the underlying mechanisms of progression of WM. Methods.Seventeen patients diagnosed with WM (8 IWM and 9 AWM) were included in this study. We selected tumour cells from the bone marrow (BM) using mononuclear cell isolation, then B cell enrichment (B cell isolation kit, Myltenyi-Biotec, USA). The purity was confirmed by flow cytometry. Total RNA was extracted using the Trizol method. Gene expression profiling was performed using U133A arrays (Affymetrix, USA). Gene expression was normalized using the RMA algorithm. We ranked genes by fold-change of expression levels on a first series of 11 patients (5 IWM and 6 AWM) calculated with the ‘limma' package in R. Next, we used a supervised classification to establish a gene expression profile to distinguish IWM from AWM. Therewith, we validated this profile on an independent set of 6 patients (3 IWM and 3 AWM). We then performed a pathway analysis using Ingenuity® analysis software. We confirmed gene expression deregulation with qRT-PCR on 3 candidate genes in the first series of patients. Genome-wide detection of copy number alteration and loss of heterozygosity were performed on 13 of the 17 WM cases, using the Genome-Wide Human SNP Array 6.0 (Affymetrix, USA). Finally, we investigated the functional consequences of the deregulation of these candidate genes in BCWM1 and MWCL1, both B cell lines originated from WM. Survival was studied using a colorimetric method with MTS (Promega, USA). Proliferation was analyzed using incorporation of a nucleoside analog (EdU) into DNA during active DNA synthesis (Invitrogen, USA). Results.The differential analysis has identified 82 probes, corresponding to 48 genes, significantly deregulated and capable of differentiating samples from IWM and AWM in an unsupervised classification. Moreover, with a supervised classification, this gene expression profile accurately classified 94% of the 17 WM samples, including the 6 WM of the independent validation set. The two molecular networks that appeared to play a major role in the physiopathology of IWM versus AWM were the plasma cell differentiation pathway and the AKT pathway. We have then identified 3 key genes in those 2 pathways, BACH2 and CIITA on the one hand and PTEN, respectively. We have then confirmed the deregulation of these gene expression levels by qRT-PCR in 3 IWM and 4 AWM; these 3 genes were over-expressed in IMW relatively to AMW. BACH2 is a B-cell-specific transcription factor known to be a tumour suppressor gene. It was shown that BACH2 reduces proliferation and induces cell death when over-expressed in B lymphoma tumour cells. We have thus pharmacologically over-expressed BACH2 in BCWM1 and MWCL1 and significantly reduced the proliferation and the survival of the two cell-lines. Further studies using BACH2 specific overexpression with lentiviral infection are underway, in vitro. The data will be presented at ASH. In order to further study the mechanisms of deregulation of BACH2 in IWM and AWM, we have conducted a genome wide SNP array study of 13 patients. Among those, 7 patients (4 IWM and 3 AWM) demonstrate a deletion of long arm of chromosome 6 (del6q), the most frequent chromosomal abnormality in WM. BACH2 gene is located on the 6q15 locus. Interestingly, we found that 3 out of the 3 AWM had a del6q that took in the 6q15 region, whereas 3 out of 4 of the IWM had a del6q preserving the 6q15 region. Therefore, haploinsufficiency could participate in the under-expression of BACH2 in aggressive WM; this hypothesis will be verified by using DNA qRT-PCR of BACH2. Conclusion.To the best of our knowledge, we have identified for the first time a specific gene expression signature that differentiates IWM and AWM. We have exposed several genes from this dataset, including BACH2, which is a candidate to better understand the underlying mechanisms of progression of WM. Disclosures:No relevant conflicts of interest to declare.

The molecular basis of T cell acute lymphoblastic leukemia

T cell acute lymphoblastic leukemias (T-ALLs) arise from the malignant transformation of hematopoietic progenitors primed toward T cell development, as result of a multistep oncogenic process involving constitutive activation of NOTCH signaling and genetic alterations in transcription factors, signaling oncogenes, and tumor suppressors. Notably, these genetic alterations define distinct molecular groups of T-ALL with specific gene expression signatures and clinicobiological features. This review summarizes recent advances in our understanding of the molecular genetics of T-ALL.

Early gene expression differences in inbred mouse strains with susceptibility to pulmonary adenomas

Lung cancer is the most common cause of cancer-related deaths in both men and women, and effective preventatives are rare due to the difficulty of early detection. Specific gene expression signatures have been identified in individuals that already developed lung cancer. To identify if gene expression differences could be detected in individuals before the onset of the disease, we obtained lung tissues for microarray analysis from young, healthy mice of 9 inbred strains with known differences in their susceptibility to spontaneous pulmonary adenomas when aged. We found that the most common differentially expressed genes among all possible 36 strain comparisons showed significant associations with cancer- and inflammation-related processes. Significant expression differences between susceptible and resistant strains were detected for Aldh3a1, Cxcr1 and 7, Dpt, and Nptx1—genes with known cancer-related functions, and Cd209, Cxcr1 and 7, and Plag2g1b—genes with known inflammatory-related functions. Whereas Aldh3a1, Cd209, Dpt, and Pla2g1b had increased expression, Cxcr1 and 7, and Nptx1 had decreased expression in strains susceptible to pulmonary adenomas. Thus, our study shows that expression differences between susceptible and resistant strains can be detected in young and healthy mice without manifestation of pulmonary adenomas and, thus, may provide an opportunity of early detection. Finally, the identified genes have previously been reported for human non-small cell lung cancer suggesting that molecular pathways may be shared between these two cancer types.

Imaging the Clear Cell Renal Cell Carcinoma Proteome

A key barrier to identifying tissue biomarkers of clear cell renal cell carcinoma is the heterogeneity of protein expression in tissue. However, by providing spectra for every 0.05 mm(2) area of tissue, imaging mass spectrometry reveals the spatial distribution of peptides. We determined whether this approach could be used to identify and map protein signatures of clear cell renal cell carcinoma. We constructed 2 tissue microarrays with 2 cores each of matched tumor and normal tissue from the nephrectomy specimens of 70 patients with clear cell renal cell carcinoma. Samples were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. In each tissue microarray peptide signatures were identified that differentiated cancer from normal tissue. The signatures were then cross validated. Mass spectrometry/mass spectrometry sequencing was performed to determine the identity of select, differentially expressed peptides. Immunohistochemistry was used for validation. In each tissue microarray peptide signatures were identified that had 94.7% to 98.5% classification accuracy for each 0.05 mm(2) spot (spectrum) and 96.9% to 100% accuracy for each tissue core. Cross validation across tissue microarrays revealed a classification accuracy of 82.6% to 84.7% for each spot and 88.9% to 92.4% for each core. We identified vimentin, histone 2A.X and α-enolase as proteins with greater expression in cancer tissue. This was validated by immunohistochemistry. Imaging mass spectrometry identified and mapped specific peptides that accurately distinguished malignant from normal renal tissue. This demonstrates its potential as a novel, high throughput approach to clear cell renal cell carcinoma biomarker discovery. Given the multiple pathways and known heterogeneity involved in tumors such as clear cell renal cell carcinoma, multiple peptide signatures that maintain their spatial relationships may outperform traditional protein biomarkers.

Comprehensive Analysis of CD4+ T Cells in the Decision between Tolerance and Immunity In Vivo Reveals a Pivotal Role for ICOS

We have established a comprehensive in vivo mouse model for the CD4(+) T cell response to an "innocuous" versus "dangerous" exogenous Ag and developed an in vivo test for tolerance. In this model, specific gene-expression signatures, distinctive upregulation of early T cell-communication molecules, and differential expansion of effector T cells (Teff) and regulatory T cells (Treg) were identified as central correlates of T cell tolerance and T cell immunity. Different from essentially all other T cell-activation molecules, ICOS was found to be induced in the immunity response and not by T cells activated under tolerogenic conditions. If expressed, ICOS did not act as a general T cell costimulator but selectively caused a massive expansion of effector CD4(+) T cells, leaving the regulatory CD4(+) T cell compartment largely undisturbed. Thus, ICOS strongly contributed to the dramatic change in the balance between Ag-specific Teff and Treg from ∼1:1 at steady state to 21:1 at the height of the immune response. This newly defined role for the balance of Teff to Treg, together with its known key function in T cell help for B cells, establishes ICOS as a central mediator of immunity. Given its exceptionally selective induction on CD4(+) T cells under inflammatory, but not tolerogenic, conditions, ICOS emerges as a pivotal effector molecule in the early decision between tolerance and immunity to exogenous Ag.

Abstract A35: Predicting drugs effect on transcription factor activity by regulatory network analysis of drug perturbed cellular states

Abstract Phenotypic changes during pathophysiological processes can be efficiently captured by genome-wide gene expression signatures or molecular phenotypes. Transcription factors (TFs) are the key components of the transcriptional regulatory network that integrates intracellular and extracellular stimuli and generates a response in the form of specific gene expression signatures. We have shown the existence and dissected the components of this integrative logic layer in several pathologic and physiologic processes. Moreover, perturbation of key components of this machinery can be efficiently used to induce desired phenotypic changes. However, TFs have been rather elusive targets for pharmacological intervention. Here, by using a cell-context specific network-based approach, we generated a comprehensive map between small compounds and TF activity. We leveraged the large collection of expression profiles in response to small molecule perturbagens from CMAP to first reverse-engineer transcriptionally regulatory networks in 3 different cellular context (Breast: MCF7, Prostate:PC3 and Myeloma:HL60) by the ARACNe algorithm, and then interrogate these networks with the MARINa algorithm to identify TFs whose activity is affected by the profiled compounds. We show two different evidences that validate our method. First, we correctly identified ESR1 as the very top TF whose activity is affected by the estrogen antagonists tamoxifen, raloxifen and clomifene. Second, we selected 10 compounds from the 1,400 represented in the MCF7 CMAP dataset that our method predict as STAT3 perturbagens. From these, 4 showed a significant inhibition of STAT3 activity in a cell-based STAT3 reported assay. Citation Format: Yao Shen, Mariano Alvarez, Sergey Pampou, Jorida Coku, Andrea Califano. Predicting drugs effect on transcription factor activity by regulatory network analysis of drug perturbed cellular states [abstract]. In: Proceedings of the AACR Special Conference on Chemical Systems Biology: Assembling and Interrogating Computational Models of the Cancer Cell by Chemical Perturbations; 2012 Jun 27-30; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2012;72(13 Suppl):Abstract nr A36.

Igf2 pathway dependency of the Trp53 developmental and tumour phenotypes.

Insulin-like growth factor 2 (IGF2) and the transformation related protein 53 (Trp53) are potent regulators of cell growth and metabolism in development and cancer. In vitro evidence suggests several mechanistic pathway interactions. Here, we tested whether loss of function of p53 leads to IGF2 ligand pathway dependency in vivo. Developmental lethality occurred in p53 homozygote null mice that lacked the paternal expressed allele of imprinted Igf2. Further lethality due to post-natal lung haemorrhage occurred in female progeny with Igf2 paternal null allele only if derived from double heterozygote null fathers, and was associated with a specific gene expression signature. Conditional deletion of Igf2fl/fl attenuated the rapid tumour onset promoted by homozygous deletion of p53fl/fl. Accelerated carcinoma and sarcoma tumour formation in p53+/− females with bi-allelic Igf2 expression was associated with reductions in p53 loss of heterozygosity and apoptosis. Igf2 genetic dependency of the p53 null phenotype during development and tumour formation suggests that targeting the IGF2 pathway may be useful in the prevention and treatment of human tumours with a disrupted Trp53 pathway.

High-purity enrichment of functional cardiovascular cells from human iPS cells

A variety of human inherited heart diseases affect the normal functions of cardiomyocytes (CMs), endothelial cells (ECs), or smooth muscle cells (SMCs). To study human heart disease and generate cardiac cells for basic and translational research, an efficient strategy is needed for production of cardiac lineages from human stem cells. In the present study, a highly reproducible method was developed that can simultaneously enrich a large number of CMs and cardiac SMCs and ECs from human induced pluripotent stem (iPS) cells with high purity. Human multipotent cardiovascular progenitor cells were generated from human iPS cells, followed by selective differentiation of the multipotent cardiovascular progenitor cells into CMs, ECs, and SMCs. With further fluorescence-activated cell sorting, each of the three cardiovascular cell types could be enriched with high purity (>90%). These enriched cardiovascular cells exhibited specific gene expression signatures and normal functions when assayed both in vitro and in vivo. Moreover, CMs purified from iPS cells derived from a patient with LEOPARD syndrome, a disease characterized by cardiac hypertrophy, showed the expected up-regulated expression of genes associated with cardiac hypertrophy. Overall, our technical advance provides the means for generating a renewable resource of pure human cardiovascular cells that can be used to dissect the mechanisms of human inherited heart disease and for the future development of drug and cell therapeutics for heart disease.

Abnormal Wnt and PI3Kinase Signaling in the Malformed Intestine of lama5 Deficient Mice

Laminins are major constituents of basement membranes and are essential for tissue homeostasis. Laminin-511 is highly expressed in the intestine and its absence causes severe malformation of the intestine and embryonic lethality. To understand the mechanistic role of laminin-511 in tissue homeostasis, we used RNA profiling of embryonic intestinal tissue of lama5 knockout mice and identified a lama5 specific gene expression signature. By combining cell culture experiments with mediated knockdown approaches, we provide a mechanistic link between laminin α5 gene deficiency and the physiological phenotype. We show that laminin α5 plays a crucial role in both epithelial and mesenchymal cell behavior by inhibiting Wnt and activating PI3K signaling. We conclude that conflicting signals are elicited in the absence of lama5, which alter cell adhesion, migration as well as epithelial and muscle differentiation. Conversely, adhesion to laminin-511 may serve as a potent regulator of known interconnected PI3K/Akt and Wnt signaling pathways. Thus deregulated adhesion to laminin-511 may be instrumental in diseases such as human pathologies of the gut where laminin-511 is abnormally expressed as it is shown here.

Slow freezing and vitrification differentially modify the gene expression profile of human metaphase II oocytes

Cryopreservation is now considered as an efficient way to store human oocytes to preserve fertility. However, little is known about the effects of this technology on oocyte gene expression. The aim of this study was to examine the effect of the two cryopreservation procedures, slow freezing and vitrification, on the gene expression profile of human metaphase II (MII) oocytes. Unfertilized MII oocytes following ICSI failure were cryopreserved either by slow freezing or by the Cryotip method for vitrification. After thawing, total RNA was extracted and analyzed using Affymetrix Human Genome U133 Plus 2.0 GeneChip arrays. The gene expression profiles and associated biological pathways in slowly frozen/thawed and vitrified MII oocytes were determined and compared with those of non-cryopreserved MII oocytes used as controls. Both cryopreservation procedures negatively affected the gene expression profile of human MII oocytes in comparison with controls. However, slowly frozen and vitrified MI oocytes displayed specific gene expression signatures. Slow freezing was associated with down-regulation of genes involved in chromosomal structure maintenance (KIF2C and KIF3A) and cell cycle regulation (CHEK2 and CDKN1B) that may lead to a reduction in the oocyte developmental competence. In vitrified oocytes, many genes of the ubiquitination pathway were down-regulated, including members of the ubiquitin-specific peptidase family and subunits of the 26S proteasome. Such inhibition of the degradation machinery might stabilize the maternal protein content that is necessary for oocyte developmental competence. The low pregnancy rates commonly observed when using human MII oocytes after slow freezing-thawing may be explained by the alterations of the oocyte gene expression profile.

The chemopreventive effect of mifepristone on mammary tumorigenesis is associated with an anti-invasive and anti-inflammatory gene signature.

Progesterone receptor (PR) antagonists are potent antitumor agents in carcinogen and progestin-dependent mammary tumorigenesis models through both PR- and non-PR-mediated mechanisms. The PR antagonist mifepristone/RU486 has been used primarily as an abortifacient possessing high affinity for both the PR and glucocorticoid receptors (GR). To determine whether mifepristone would be effective as a chemopreventive agent, we assessed its effect on progestin/7,12-dimethylbenz(a)anthracene (DMBA)-induced mammary carcinogenesis in wild-type (WT) and estrogen receptor-α-positive (ER(+)) transgenic mice expressing the dominant-negative Pax8PPARγ (Pax8) fusion protein. Mifepristone administered at a dose of 2.5 mg significantly delayed mammary tumorigenesis in WT, but not in Pax8 mice, whereas, a three-fold higher dose almost completely blocked tumorigenesis in both WT and Pax8 mice. The sensitivity of WT mice to 2.5 mg mifepristone correlated with an expression profile of 79 genes in tumors, 52 of which exhibited the opposite response in Pax8 mice, and corresponded primarily to the downregulation of genes associated with metabolism, inflammation, and invasion. These results suggest that the chemopreventive activity of mifepristone in WT mice correlates with a specific gene expression signature that is associated with multiple nuclear receptor signaling pathways.

Dependence of Wilms tumor cells on signaling through insulin-like growth factor 1 in an orthotopic xenograft model targetable by specific receptor inhibition

We have previously demonstrated an increased DNA copy number and expression of IGF1R to be associated with poor outcome in Wilms tumors. We have now tested whether inhibiting this receptor may be a useful therapeutic strategy by using a panel of Wilms tumor cell lines. Both genetic and pharmacological targeting resulted in inhibition of downstream signaling through PI3 and MAP kinases, G(1) cell cycle arrest, and cell death, with drug efficacy dependent on the levels of phosphorylated IGF1R. These effects were further associated with specific gene expression signatures reflecting pathway inhibition, and conferred synergistic chemosensitisation to doxorubicin and topotecan. In the in vivo setting, s.c. xenografts of WiT49 cells resembled malignant rhabdoid tumors rather than Wilms tumors. Treatment with an IGF1R inhibitor (NVP-AEW541) showed no discernable antitumor activity and no downstream pathway inactivation. By contrast, Wilms tumor cells established orthotopically within the kidney were histologically accurate and exhibited significantly elevated insulin-like growth factor-mediated signaling, and growth was significantly reduced on treatment with NVP-AEW541 in parallel with signaling pathway ablation. As a result of the paracrine effects of enhanced IGF2 expression in Wilms tumor, this disease may be acutely dependent on signaling through the IGF1 receptor, and thus treatment strategies aimed at its inhibition may be useful in the clinic. Such efficacy may be missed if only standard ectopic models are considered as a result of an imperfect recapitulation of the specific tumor microenvironment.

Abstract 5062: Integrated analysis of the whole exome sequencing (WES) identifies novel mutations and suggests patient selection hypothesis

Abstract Whole exome sequencing was done on 257 breast and 102 ovarian tumors using next generation sequencing. Seven gigabases of sequencing data were generated for each sample or 100x coverage of the whole exome, which enable to determine sequence variations with >99% confidence. The results of the mutation calls were compared with recently published TCGA breast and ovarian datasets. Genes with large number of passenger mutations were called out and frequency of passenger mutations per sample was linked to MMR signature. In ovarian tumors, a high prevalence of p53 and BRCA1 mutation was confirmed in serous tumors. A signature of BRCA1/2 deficient tumors was developed and cross-validated between the datasets. In no-serous tumors, a high prevalence of mutations MAPK pathway and beta-catenin pathway were found. FOXL2 mutation was identified in 100% of granulose ovarian tumors and linked to high levels of EMT signature. In addition we showed a significant overlap between genes found to be mutated in TCGA datasets and in our dataset, suggesting a larger number of potentially significantly mutated genes than previously reported. In breast tumors, known high frequency of mutations was confirmed in PIK3CA and TP53 genes and validated with respective pathway specific gene expression signatures. In addition, prevalent mutations were identified in MAPK and PI3K pathways and linked with respective pathway signatures. These findings strengthen and enrich our understanding of molecular subtypes of ovarian and breast tumors and can be used for identification of novel targets and for development of responder hypothesis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5062. doi:1538-7445.AM2012-5062