Integrated Copy Number Research Articles

Genome‐wide expression and copy number analysis identifies driver genes in gingivobuccal cancers

The molecular mechanisms contributing to the development and progression of gingivobuccal complex (GBC) cancers-a sub-site of oral cancer, comprising the buccal mucosa, the gingivobuccal sulcus, the lower gingival region, and the retromolar trigone-remain poorly understood. Identifying the GBC cancer-related gene expression signature and the driver genes residing on the altered chromosomal regions is critical for understanding the molecular basis of its pathogenesis. Genome-wide expression profiling of 27 GBC cancers with known chromosomal alterations was performed to reveal differentially expressed genes. Putative driver genes were identified by integrating copy number and gene expression data. A total of 315 genes were found differentially expressed (P ≤ 0.05, logFC > 2.0) of which 11 genes were validated by real-time quantitative reverse transcriptase-PCR (qRT-PCR) in tumors (n = 57) and normal GBC tissues (n = 18). Overexpression of LY6K, in chromosome band 8q24.3, was validated by immunohistochemical (IHC) analysis. We found that 78.5% (2,417/3,079) of the genes located in regions of recurrent chromosomal alterations show copy number dependent expression indicating that copy number alteration has a direct effect on global gene expression. The integrative analysis revealed BIRC3 in 11q22.2 as a candidate driver gene associated with poor clinical outcome. Our study identified previously unreported differentially expressed genes in a homogeneous subtype of oral cancer and the candidate driver genes that may contribute to the development and progression of the disease. © 2011 Wiley Periodicals, Inc.

Abstract A26: Multi-Reg: An integrative parallel approach to uncover drivers of cancer

Abstract Tumor samples harbor a vast number of genomic alterations of various kinds, and it is not easy to distinguish driver alterations that contribute to oncogenesis from passenger alterations. Most computational methods attempt to identify driver alternations by focusing on the most frequent alterations. Previous work in our lab has led to the development of CONEXIC, a Bayesian framework for integrating copy number and gene expression to identify candidate driver genes in cancer and to link them to gene expression signatures they regulate (Akavia et al, Cell, 2010). This framework was applied to data from melanoma cell lines, where it correctly identified known drivers (MITF) and connected them to their known targets. In addition, it predicted novel tumor dependencies not previously implicated in melanoma, which were confirmed experimentally. In general, current algorithms identify only one driver (the strongest) controlling a gene expression signature. However, drivers may act in parallel, where not only the strongest one is important. For example, either PTEN deletion or AKT activation can lead to a similar expression signature and phenotype. Therefore, we developed a new algorithm, based on the same principles as CONEXIC with multiple improvements. The new algorithm (called Multi-Reg) is capable of detecting multiple candidate regulators that can all act in parallel to regulate an expression signature. This algorithm can integrate mutations in addition to copy number and expression. Finally, we have designed Multi-Reg to be easier and quicker to run and more robust. We applied Multi-Reg to glioblastoma data from The Cancer Genome Atlas (TCGA). This data includes copy number, gene expression and mutations for hundreds of primary tumor samples. We found 84 candidate regulators that were missed by CONEXIC, but discovered by Multi-Reg. Because of Multi-Reg's ability to search for genes working in parallel, it identified FGFR3, PDGFRA and NF1, in addition to EGFR & MET (identified by CONEXIC), as important candidate drivers. Additionally, Multi-Reg results identified RHPN2 as a novel oncogenic factor controlling a gene expression signature related to invasion and migration. Validation has shown that RHPN2 has limited effect on cell proliferation but induces invasiveness in glioblastoma cell lines. Our results correctly identify known drivers of glioblastoma progression, including oncogenes such as EGFR, MET, CEBPB and tumor suppressors such as p16 and NF1. Multi-Reg also has the capability to identify more regulators than CONEXIC, and has correctly linked RHPN2 to the oncogenic phenomena it controls. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr A26.

Genome-wide copy number analyses identified novel cancer genes in hepatocellular carcinoma

A powerful way to identify driver genes with causal roles in carcinogenesis is to detect genomic regions that undergo frequent alterations in cancers. Here we identified 1,241 regions of somatic copy number alterations in 58 paired hepatocellular carcinoma (HCC) tumors and adjacent nontumor tissues using genome-wide single nucleotide polymorphism (SNP) 6.0 arrays. Subsequently, by integrating copy number profiles with gene expression signatures derived from the same HCC patients, we identified 362 differentially expressed genes within the aberrant regions. Among these, 20 candidate genes were chosen for further functional assessments. One novel tumor suppressor (tripartite motif-containing 35 [TRIM35]) and two putative oncogenes (hairy/enhancer-of-split related with YRPW motif 1 [HEY1] and small nuclear ribonucleoprotein polypeptide E [SNRPE]) were discovered by various in vitro and in vivo tumorigenicity experiments. Importantly, it was demonstrated that decreases of TRIM35 expression are a frequent event in HCC and the expression level of TRIM35 was negatively correlated with tumor size, histological grade, and serum alpha-fetoprotein concentration. These results showed that integration of genomic and transcriptional data offers powerful potential for identifying novel cancer genes in HCC pathogenesis.

Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer

Copy number alterations (CNAs) associated with cancer are known to contribute to genomic instability and gene deregulation. Integrating CNAs with gene expression helps to elucidate the mechanisms by which CNAs act and to identify the transcriptional downstream targets of CNAs. Such analyses can help to sort functional driver events from the many accompanying passenger alterations. However, the way CNAs affect gene expression can vary in different cellular contexts, for example between different subtypes of the same cancer. Thus, it is important to develop computational approaches capable of inferring differential connectivity of regulatory networks in different cellular contexts. We propose a statistical deregulation model that integrates copy number and expression data of different disease subtypes to jointly model common and differential regulatory relationships. Our model not only identifies CNAs driving gene expression changes, but at the same time also predicts differences in regulation that distinguish one cancer subtype from the other. We implement our model in a penalized regression framework and demonstrate in a simulation study the feasibility and accuracy of our approach. Subsequently, we show that this model can identify both known and novel aspects of cross-talk between the ER and NOTCH pathways in ER-negative-specific deregulations, when compared with ER-positive breast cancer. This flexible model can be applied on other modalities such as methylation or microRNA and expression to disentangle cancer signaling pathways. The Bioconductor-compliant R package DANCE is available from www.markowetzlab.org/software/ yinyin.yuan@cancer.org.uk; florian.markowetz@cancer.org.uk.

Correction: Identification of Candidate Growth Promoting Genes in Ovarian Cancer through Integrated Copy Number and Expression Analysis

Correction: Identification of Candidate Growth Promoting Genes in Ovarian Cancer through Integrated Copy Number and Expression Analysis

Heterozygous deletion at the RLN1 locus in a family with testicular germ cell cancer identified by integrating copy number variation data with phenome and interactome information

To search for disease-related copy number variations (CNVs) in families with a high frequency of germ cell tumours (GCT), we analysed 16 individuals from four families by array comparative genomic hybridization (aCGH) and applied an integrative systems biology algorithm that prioritizes risk-associated genes among loci targeted by CNVs. The top-ranked candidate, RLN1, encoding a Relaxin-H1 peptide, although only detected in one of the families, was selected for further investigations. Validation of the CNV at the RLN1 locus was performed as an association study using qPCR with 106 sporadic testicular GCT patients and 200 healthy controls. Observed CNV frequencies of 1.9% among cases and 1.5% amongst controls were not significantly different and this was further confirmed by CNV data extracted from a genome-wide analysis of 189 cases and 380 controls, where similar frequencies of 2.2% were observed in both groups (p=1). Immunohistochemistry for Relaxin-H1 (RLN1), Relaxin-H2 (RLN2) and their cognate receptor, RXFP1, detected one, and in some cases both, of the relaxins in Leydig cells, Sertoli cells and a subset of neoplastic germ cells, whereas the receptor was present in Leydig cells and spermatids. Collectively, the findings show that a heterozygous loss at the RLN1 locus is not a genetic factor mediating high population-wide risk for testicular germ cell tumour, but do not exclude a contribution of this aberration in some cases of cancer. The preliminary expression data suggest a possible role of the relaxin peptides in spermatogenesis and warrant further studies.

Abstract 4906: A systems approach into studying the changes in genetic regulation during prostate cancer progression

Abstract Prostate cancer (PC) is a complex disease that is currently the most common malignancy in males, and the second most frequent cause of cancer-related mortality in developed countries. Despite its high prevalence, the molecular mechanisms that induce PC progression are not well understood. The most common alterations affecting genetic regulation in PC are TMPRSS2:ERG gene fusions, 8q24 amplifications (including MYC-oncogene), and androgen receptor (AR) mutations and amplifications in castration-resistant (late stage) tumors. In normal prostatic tissue, local androgen metabolism maintains a balance between the proliferation and apoptotic cell death of prostatic epithelial cells. However in PC, androgen metabolism drives malignant transformation. The exact mechanisms which cause the imbalance in proliferation and apoptosis are not known, but likely include dysregulation of AR/MYC/ERG-regulated transcription factors (TFs) and/or microRNAs. Using a systems biology approach, we jointly studied the accumulation of expression and copy number differences of TFs and microRNAs during PC progression. We first established a generic regulatory network consisting of transcription factors and microRNAs using three sets of sequence-based binding site predictions. First, TF binding sites were predicted by scanning the sequences upstream from gene transcription start sites for binding motifs from Transfac database, second, TF binding to microRNA promoters was predicted with ProbTF, and third, microRNA binding sites were obtained from Targetscan predictions. The inferred generic network was then adapted for studying PC by pruning it based on a set of publicly available gene expression, microRNA expression data. That is, we only considered those hypothetical regulatory connections that were supported by the data. By dividing these data into normal prostate tissue, primary PC's of different grade, and metastatic tumors, we were able to study the changes in regulation during different stages of the disease. We uncovered putative regulatory motifs consisting of differentially expressed TFs and microRNAs. Another level of regulatory information was added by integrating copy number information to the regulatory motifs. We concentrated on the motifs that could be associated to AR-, ERG-, or MYC-signaling, due to their relevance in prostate cancer, or to molecules that are known to be regulated by these TFs. We found previously unknown microRNAs and TFs that may directly bound to the promoters of the TFs and therefore may have a critical effect to the malignancy of prostate cancers. The experimental validations of the most promising new candidate TF/microRNA regulatory connections are currently underway. We demonstrated here an application of a systems biology based method to prostate cancer which was used to gain insights into the changes in genetic regulation during progression of the disease. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4906. doi:10.1158/1538-7445.AM2011-4906

Improvement of resistance to maize dwarf mosaic virus mediated by transgenic RNA interference

To overcome the low efficiency of agronomic protection from maize dwarf mosaic disease, susceptible maize inbred line was transformed by Agrobacterium tumefaciens harboring hpRNA expression vectors containing inverted-repeat sequences of different lengths targeting coat protein gene ( CP) of maize dwarf mosaic virus (MDMV). After PCR screening and Southern blotting, the flanking sequences of the integration sites were amplified by thermal asymmetric interlaced PCR (TAIL-PCR) and used for analysis of T-DNA integration patterns. The T 2 plant lines were evaluated for their MDMV resistance in field inoculation trials under two environments. Of the nineteen T 2 plant lines positive in Southern blotting, six were evaluated as resistant to MDMV, and four of them had resistance non-significantly different from the highly resistant control “H9-21”, while the resistance of the other eleven was proved to be significantly improved when compared to their non-transformed parent line. These improvements in MDMV resistance were verified by the relative amount of virus CP gene expression measured by quantitative real time PCR. Comparing the results of Southern blotting and TAIL-PCR analysis, different integration patterns of one or two copies of the inverted-repeat sequences were identified from non-repetitive and repetitive sequences of the maize genome. The MDMV resistance mediated by RNA interference is relative to the length of the inverted-repeat sequence, the copy number of T-DNA integration and the repeatability of integration sites. A longer hpRNA expression construct shows more efficiency than a shorter one.

CNAmet: an R package for integrating copy number, methylation and expression data

Gene copy number and DNA methylation alterations are key regulators of gene expression in cancer. Accordingly, genes that show simultaneous methylation, copy number and expression alterations are likely to have a key role in tumor progression. We have implemented a novel software package (CNAmet) for integrative analysis of high-throughput copy number, DNA methylation and gene expression data. To demonstrate the utility of CNAmet, we use copy number, DNA methylation and gene expression data from 50 glioblastoma multiforme and 188 ovarian cancer primary tumor samples. Our results reveal a synergistic effect of DNA methylation and copy number alterations on gene expression for several known oncogenes as well as novel candidate oncogenes. CNAmet R-package and user guide are freely available under GNU General Public License at http://csbi.ltdk.helsinki.fi/CNAmet.

Unexpectedly High Copy Number of Random Integration but Low Frequency of Persistent Expression of the Sleeping Beauty Transposase After Trans Delivery in Primary Human T Cells

We have shown that the Sleeping Beauty (SB) transposon system can mediate stable expression of both reporter and therapeutic genes in human primary T cells and that trans delivery (i.e., transposon and transposase are on separate plasmids) is at least 3-fold more efficient than cis delivery. One concern about trans delivery is the potential for integration of the transposase-encoding sequence into the cell genome with the possibility of continued expression, transposon remobilization, and insertional mutagenesis. To address this concern, human peripheral blood lymphocytes were nucleofected with transposase plasmid and a DsRed transposon. Eighty-eight stable DsRed(+) T cell clones were generated and found to be negative for the transposase-encoding sequence by PCR analysis of genomic DNA. Genomic PCR was positive for transposase in 5 of 15 bulk T cell populations that were similarly transfected and selected for transgene expression where copy numbers were unexpectedly high (0.007-0.047 per cell) by quantitative PCR. Transposase-positive bulk T cells lacked transposase plasmid demonstrated by Hirt (episomal) extracted DNA and showed no detectable transposase by Southern hybridization, Western blot, and quantitative RT-PCR analyses. Cytogenetic and array comparative genomic hybridization analyses of the only identified transposase-positive clone (O56; 0.867 copies per cell) showed no chromosomal abnormality or tumor formation in nude mice although transposon remobilization was detected. Our data suggest that SB delivery via plasmid in T cells should be carried out with caution because of unexpectedly high copy numbers of randomly integrated SB transposase.

Expression of an immunogenic F1-V fusion protein in lettuce as a plant-based vaccine against plague.

Yersinia pestis is a pathogenic agent that causes the bubonic and pneumonic plague. The development of an efficient and low-cost oral vaccine against these diseases is highly desirable. In this study, the immunogenic fusion protein F1-V from Y. pestis was introduced into lettuce via Agrobacterium-mediated transformation, and putative transgenic lines were developed. The presence of the transgene in these putative transgenic lines was determined using polymerase chain reaction (PCR), and transgene integration and transgene copy number were confirmed following Southern blot analysis. The presence of specific F1-V transcripts was confirmed by reverse-transcriptase (RT)-PCR. Using monoclonal antibodies, ELISA and western blot analysis revealed that the expected antigenic F1-V protein was successfully expressed in transgenic lines. Mice immunized subcutaneously with lettuce expressing the F1-V antigen developed systemic humoral responses as 'proof of concept' of using lettuce as a production platform for the F1-V immunogen that could be used as a candidate plant-based vaccine against plague.

Abstract 3086: Gain of chromosome 13 is a cause of CDK8 overexpression associated with colorectal adenoma to carcinoma progression

Abstract Introduction: Colorectal adenomas are common precursors of colorectal cancer (CRC). About only 5% of adenomas progress to cancer and this progression is mostly associated with overall onset/increase of chromosomal instability. Gain of 13q is often implicated in this progression of adenoma to carcinoma (1). Until recently however no genes were identified to be the drivers of this amplicon. Recently, Firestein and collaborators (2) showed that cyclin 8 (CDK8), at 13q12.13, functions as an oncogene in CRC. The aim of this study was to evaluate CDK8 gene dosage effects in colorectal adenoma to carcinoma progression. Material and methods: Sixty seven colorectal tumours (34 adenomas and 28 carcinomas) were analysed by array CGH (5k BAC platform, including contig coverage of 13q) and by expression microarray (30k Compugen library). Integration of DNA copy number dosage and gene expression was performed using the Ace-it tool (3). Results: In the tumours analysed we observed 13q copy number gain in 9% and 46% of adenomas and carcinomas, respectively. Integrating copy number and mRNA expression with the differential upregulation of genes between carcinomas and adenomas, provided us with a list of 43 genes. Within this list, CDK8 ranked 7th in significancy (p=0.003). Conclusions: Copy number gain of 13q has a gene dosage effect on CDK8 mRNA expression, indicating a role of this gene in colorectal adenoma to carcinoma progression. (1) Hermsen M, Postma C, Baak J, Weiss M, Rapallo A, Sciutto A, Roemen G, Arends JW, Williams R, Giaretti W, De Goeij A, Meijer G. Colorectal adenoma to carcinoma progression follows multiple pathways of chromosomal instability. Gastroenterology 2002 Oct;123(4):1109-19. (2) Firestein R, Bass AJ, Kim SY, Dunn IF, Silver SJ, Guney I, Freed E, Ligon AH, Vena N, Ogino S, Chheda MG, Tamayo P, Finn S, Shrestha Y, Boehm JS, Jain S, Bojarski E, Mermel C, Barretina J, Chan JA, Baselga J, Tabernero J, Root DE, Fuchs CS, Loda M, Shivdasani RA, Meyerson M, Hahn WC. CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity. Nature 2008 Sep 25;455(7212):547-51. (3) van Wieringen WN, Belien JA, Vosse SJ, Achame EM, Ylstra B. ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data. Bioinformatics. 2006 Aug 1;22(15):1919-20. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3086.

Overexpression of aveBIV leading to the improvement of 4′-epidaunorubicin production in Streptomyces coeruleorubidus strain SIPI-A0707

The 4'-epidaunorubicin is the semisynthesis precursor of epirubicin which is a clinically useful antitumor drug thought to have slightly less cardiotoxicity than doxorubin. The 4'-epidaunorubicin was formed by overexpression of heterologous Streptomyces avermitilis aveBIV in Streptomyces coeruleorubidus SIPI-A0707 dnmV mutant blocked in the biosynthesis of daunosamine, the deoxysugar component of daunorubicin. But there was a low-yield production of 4'-epidaunorubicin. In our study, product yields were enhanced considerably by increasing aveBIV gene copy number or changing means of aveBIV integration. The 4'-epidaunorubicin titer was improved by around threefold in the recombinant strain DYG1006 with the aveBIV increased threefold copy numbers. The transcript levels of aveBIV gene meet the expectation of fermentation levels of 4'-epidaunorubicin. The method described here provides the means to produce 4'-epidaunorubicin efficiently on an industrial scale.

Identification of Candidate Growth Promoting Genes in Ovarian Cancer through Integrated Copy Number and Expression Analysis

Ovarian cancer is a disease characterised by complex genomic rearrangements but the majority of the genes that are the target of these alterations remain unidentified. Cataloguing these target genes will provide useful insights into the disease etiology and may provide an opportunity to develop novel diagnostic and therapeutic interventions. High resolution genome wide copy number and matching expression data from 68 primary epithelial ovarian carcinomas of various histotypes was integrated to identify genes in regions of most frequent amplification with the strongest correlation with expression and copy number. Regions on chromosomes 3, 7, 8, and 20 were most frequently increased in copy number (>40% of samples). Within these regions, 703/1370 (51%) unique gene expression probesets were differentially expressed when samples with gain were compared to samples without gain. 30% of these differentially expressed probesets also showed a strong positive correlation (r≥0.6) between expression and copy number. We also identified 21 regions of high amplitude copy number gain, in which 32 known protein coding genes showed a strong positive correlation between expression and copy number. Overall, our data validates previously known ovarian cancer genes, such as ERBB2, and also identified novel potential drivers such as MYNN, PUF60 and TPX2.

Ganglioside synthase knockout in oncogene-transformed fibroblasts depletes gangliosides and impairs tumor growth

Biologically active membrane gangliosides, expressed and released by many human tumors, are hypothesized to significantly impact tumor progression. Lack of a model of complete and specific tumor ganglioside depletion in vivo, however, has hampered elucidation of their role. Here we report the creation of a novel, stable, genetically induced tumor cell system resulting in specific and complete blockade of ganglioside synthesis. Wild type (WT) and GM3 synthase/GM2 synthase double knockout (DKO) murine embryonic fibroblasts were transformed using amphotropic retrovirus-transduced oncogenes (pBABE-c-MycT58A+H-RasG12V). The transformed cells, WTt and DKOt respectively, evidenced comparable integrated copy numbers and oncogene expression. Ganglioside synthesis was completely blocked in the DKOt cells, importantly without triggering an alternate pathway of ganglioside synthesis. Ganglioside depletion (to <0.5 nmol/107 cells from 9-11 nmol/107 WTt or untransfected normal fibroblasts) did not adversely affect cell proliferation kinetics but did reduce cell migration on fibronectin-coated wells, consistent with our previous observations in ganglioside-depleted normal human fibroblasts. Strikingly, despite similar oncogene expression and growth kinetics, DKOt cells evidenced significantly impaired tumor growth in syngeneic immunocompetent mice, underscoring the pivotal role of tumor cell gangliosides and providing an ideal system for probing their mechanisms of action in vivo.

Mathematical model of the rate‐limiting steps for retrovirus‐mediated gene transfer into mammalian cells

A quantitative understanding of the process of retrovirus-mediated gene transfer into mammalian cells should assist the design and optimization of transduction protocols. We present a mathematical model of the process that incorporates the essential rate-limiting transduction steps including diffusion, convection and decay of viral vectors, their binding at the cell surface and entry into the cell cytoplasm, reverse transcription of uncoated RNA to form DNA intermediates, transport of the latter through the cytosol to the cell nucleus and, finally, nuclear import and integration of the delivered DNA into the target cell genome. Cell and virus population balances are used to account for the kinetics of multiple vector infections which influence the transduction efficiency and govern the integrated copy number. The mathematical model is validated using gibbon ape leukemia virus envelope pseudotyped retroviral vectors and K562 target cells. Viral intermediate complexes derived from the internalized retroviral vectors are found to remain stable inside the K562 cells and the cytoplasmic trafficking time is consistent with the time scale for retrovirus uncoating, reverse transcription and transport to the cell nucleus. The model predictions of transduction efficiency and integrated copy number agree well with experimental data for both static (i.e., standard gravity) and centrifugation-based gene transfer protocols. The formulation of the model can also be applied to transduction protocols involving lenti- or foamy-viruses and so should prove to be useful for the optimization of several types of gene transfer processes.

Integrative approach for prioritizing cancer genes in sporadic colon cancer

The current multistep carcinogenesis models of colon cancer do not fully capture the genetic heterogeneity of the disease, which is additionally complicated by the presence of passenger and driver genetic alterations. The aim of this study was to select in the context of this significant heterogeneity additional genes functionally related to colon cancer development. High-throughput copy number and gene expression data of 36 microsatellite stable sporadic colon cancers resected from patients of a single institution characterized for mutations in APC, KRAS, TP53 and loss of 18q were analyzed. Genes whose expression correlated with the underlying copy number pattern were selected, and their association with the above listed mutations and overall survival was evaluated. Gain of 20q was strongly associated with TP53 mutation, and overall survival with alterations on 7p, 8p, 13q, 18q, and 20q. An association with 18q loss and gain of 8q24 was also observed. New candidate genes with a potential role in colon cancer are PLCG1 on 20q, DBC1 on 8q21, and NDGR1 on 8p24. In addition, an unexpected pattern of loss and mutability was found in the region upstream of the KRAS gene. By integrating copy number alterations with gene expression and mutations in colon cancer associated genes, we have developed a strategy that identifies previously known molecular features and additional players in the molecular landscape of colon cancer.

A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets †

The integration of high-throughput genomic data represents an opportunity for deciphering the interplay between structural and functional organization of genomes and for discovering novel biomarkers. However, the development of integrative approaches to complement gene expression (GE) data with other types of gene information, such as copy number (CN) and chromosomal localization, still represents a computational challenge in the genomic arena. This work presents a computational procedure that directly integrates CN and GE profiles at genome-wide level. When applied to DNA/RNA paired data, this approach leads to the identification of Significant Overlaps of Differentially Expressed and Genomic Imbalanced Regions (SODEGIR). This goal is accomplished in three steps. The first step extends to CN a method for detecting regional imbalances in GE. The second part provides the integration of CN and GE data and identifies chromosomal regions with concordantly altered genomic and transcriptional status in a tumor sample. The last step elevates the single-sample analysis to an entire dataset of tumor specimens. When applied to study chromosomal aberrations in a collection of astrocytoma and renal carcinoma samples, the procedure proved to be effective in identifying discrete chromosomal regions of coordinated CN alterations and changes in transcriptional levels.

Somatic Cell Nuclear Transfer to Create a Miniature Swine Model of Retinitis Pigmentosa

Retinitis pigmentosa is a group of genetic eye conditions for which the most common autosomal dominant form is a P23H substitution in the rhodopsin gene. Our objective was to create a P23H rhodopsin model in miniature swine with different founding animals demonstrating variation in disease severity. We used a 17.5 kb fragment of the human genome containing the P23H affected coding sequence and genomic regulatory regions. The DNA fragment was transfected into fetal fibroblast of NIH miniature swine with or without a selectable marker. Clonal cell colonies with stable integration were utilized for somatic cell nuclear transfer. Six transgenic founder animals were produced from five pregnancies. Clinical examination at 0.5, 3 and 6 months and a standard ISCEV ERG protocol at dark‐ and light‐adapted levels was used at 3 (n=6) and 6 months (n=2) of age to assess phenotype. No fundus abnormalities were detected although significant variation in ERG response was observed among founders. At 3 months, two founders had severely compromised dark‐ and light‐adapted responses. Changes in the two founders evaluated again at 6 months indicated disease progression. Phenotype variation in the founders is likely due to integration site and copy number and may not be affected by the utilization of a co‐transfected marker gene. Support: NIH U42‐RR18877 and R24EY015636, USDA 35205‐05309, Discovery Eye Foundation.

Integrated gene copy number and expression microarray analysis of gastric cancer highlights potential target genes

We performed an integrated array comparative genomic hybridization (aCGH) and expression microarray analysis of 8 normal gastric tissues and 38 primary tumors, including 25 intestinal and 13 diffuse gastric adenocarcinomas to identify genes whose expression is deregulated in association with copy number alteration. Our aim was also to identify molecular genetic alterations that are specific to particular clinicopathological characteristics of gastric cancer. Distinct molecular genetic profiles were identified for intestinal and diffuse gastric cancers and for tumors obtained from 2 different locations of the stomach. Interestingly, the ERBB2 amplification and gains at 20q13.12-q13.33 almost exclusively discriminated intestinal cancers from the diffuse type. In addition, the 17q12-q25 gain was characteristic to cancers located in corpus and the 20q13.12-q13.13 gain was more common in the antrum. Statistical analysis was performed using integrated copy number and expression data to identify genes showing differential expression associated with a copy number alteration. Genes with the highest statistical significance included ERBB2, MUC1, GRB7, PPP1R1B and PPARBP with concomitant changes in copy number and expression. Immunohistochemical analysis of ERBB2 and MUC1 on a tissue microarray containing 78 independent gastric tissues showed statistically significant differences (p < 0.05 and <0.001) in immunopositivity in the intestinal (31 and 70%) and diffuse subtypes (14 and 41%), respectively. In conclusion, our results demonstrate that intestinal and diffuse type gastric cancers as well as cancers located in different sites of the stomach have distinct molecular profiles which may have clinical value.