High-resolution Genomic Analysis Research Articles

High Resolution Genomic Analysis In CLL Demonstrates Genomic Stability In Untreated Patients and Novel Markers of Progression In Treated Patients

AbstractAbstract 2426Chronic lymphocytic leukemia is the most common leukemia of adults but still incurable. Prognosis at diagnosis is widely variable, and the key cytogenetic abnormalities determined by FISH remain one of the best predictors of prognosis and treatment response. We therefore undertook very high resolution genomic analysis of 161 CLLs with matched germline samples using Affymetrix 6.0 SNP arrays, in an effort to identify additional predictors of prognosis, and have also performed gene expression profiling on most of this patient cohort. The median age at diagnosis for the cohort was 55 (31–79), and the median time to sampling was 4.6 months (0.5–291). 22% of the cohort was previously treated, with an additional 21% of patients receiving treatment during the follow-up period, for a total of 43% treated, with a median time from diagnosis to treatment of 41 months (0.4-161.2 months). The genomic data were analyzed both by GISTIC, which identifies significant deletions and amplifications based on analysis of the frequency and amplitude of each aberration in the tumor samples alone, as well as by paired copy number analysis of each tumor and its cognate germline, using Birdseed, PLINK and PennCNV. Our results show that the CLL genome is overall quite stable, with a median of only one acquired copy number aberration per sample, excluding rearrangements at the immunoglobulin gene loci. GISTIC analysis on the entire population identified the known common CLL abnormalities at frequencies that would be expected in a largely untreated cohort: 57% del 13q, 6.2% deletion 11q, 5.0% deletion 17p, and 12% trisomy 12. The presence of two or more acquired copy number aberrations (CNAs) of any type was associated with a significantly shorter time to first therapy (p<0.0001). A higher number of CNAs was strongly associated with deletions of 11q or 17p, but the predictive power of a higher number of CNAs was still present in those CLLs without deletions 11q or 17p. Detailed analysis of 13q deletion revealed no association of longer deletions or homozygous deletions with time to first therapy. However, any additional somatic copy number aberration in addition to 13q deletion significantly reduced the time to first therapy, making it comparable to non-13q patients. In order to identify genetic markers of progression, we compared treated to untreated patients using GISTIC. This analysis revealed that untreated patients showed peaks largely limited to deletion 13q and trisomy 12. Treated patients however showed three additional significant peaks: a deletion peak at 8p, as well as significant amplification peaks at 3q26.32 and 8q24.21. The deletion peak at 8p was observed in 8 of 161 samples tested (5.0%), and was large, with a common region of deletion spanning 11.0–29.6 Mb. Six of eight of these patients were untreated at the time of sampling but had a very short time to treatment thereafter, independent of whether they had coexistent deletions of 17p or 11q, suggesting that this deletion carries a very poor prognosis in itself. Another notable region of amplification was found on 3q26.32 in nine patients (9/161 or 5.6%). Although many of these amplified regions were large, three of the nine patients carrying this amplification demonstrated focal somatic amplification of the final exon of PIK3CA, the alpha catalytic subunit of PI3K. Finally the amplification on 8q24 was present in 6 of 161 CLLs (3.7%), two of which were focal and amplified only the gene desert region previously implicated in CLL risk by genome-wide association study and located approximately 335 kb centromeric to MYC. Analysis of gene expression profiling comparing patients with and without amplifications demonstrated upregulation of MYC mRNA expression and alteration of downstream targets of MYC in samples with amplification. We conclude that very high resolution copy number analysis with matched germline comparison in CLL reveals a quite stable genome in untreated patients, and identifies amplifications of 3q26 and MYC at 8q24 as progression events. Disclosures:No relevant conflicts of interest to declare.

Mandibulofacial dysostosis, microtia, and limb anomalies in a newborn: a new form of acrofacial dysostosis syndrome?

The acrofacial dysostoses (AFDs) are a heterogeneous group of disorders involving craniofacial dysostosis and limb anomalies. Depending on the type of limb defects, two major groups have been defined: Nager syndrome with predominant preaxial anomalies and Miller syndrome with postaxial malformations. Genomic copy number variation, a common type of genomic variability, can influence gene expression by disrupting coding sequences, perturbing long-range gene regulation, or altering gene dosage, and these effects could contribute to phenotypic variations or disease risk. We present a distinct AFD case with mandibulofacial dysostosis, microtia and limb malformations but without limb defects, which may represent a new form of AFD. To investigate the etiology of the phenotype, whole genomic high-resolution array comparative genomic hybridization analysis was carried out, revealing two cryptic duplications, 1p36.33 and 1q21.3-q22 duplications. Two genes, VWA1 and PYGO2, contained in the two duplications, respectively, are likely to be the candidate genes for the phenotype of our patient.

161 HUMAN ES AND IPS CELL DIFFERENTIATION TO NEURAL PHENOTYPES

applications, we have taken a systems biology approach. In order to identify features characteristic of pluripotent cells, we have performed high-resolution genomic, epigenomic, and gene expression analyses on diverse pluripotent, multipotent, and differentiated cell types. Integrative analysis of these complex datasets has allowed us to identify networks of interacting factors that maintain the pluripotent state. In the course of our work, we have also discoveredmechanisms regulating such fundamental cellular activities as transcription, splicing, and silencing of repetitive elements.

160 DISEASE MODELING USING HUMAN IPS CELLS

applications, we have taken a systems biology approach. In order to identify features characteristic of pluripotent cells, we have performed high-resolution genomic, epigenomic, and gene expression analyses on diverse pluripotent, multipotent, and differentiated cell types. Integrative analysis of these complex datasets has allowed us to identify networks of interacting factors that maintain the pluripotent state. In the course of our work, we have also discoveredmechanisms regulating such fundamental cellular activities as transcription, splicing, and silencing of repetitive elements.

A molecular portrait of gastrointestinal stromal tumors: an integrative analysis of gene expression profiling and high-resolution genomic copy number

In addition to KIT and PDGFRA mutations, sequential accumulation of other genetic events is involved in the development and progression of gastrointestinal stromal tumors (GISTs). Until recently, the significance of these other alterations has not been thoroughly investigated. We report the first study that integrates gene expression profiling and high-resolution genomic copy number analyses in GIST. Fresh tissue specimens from 25 patients with GIST were collected, and gene expression profiling and high-resolution genomic copy number analyses were performed, using Affymetrix U133Plus and SNP array 6.0. We found that all 21 mutant GIST patients showed both macroscopic cytogenetic alterations and cryptic microdeletions or amplifications, whereas 75% (three of four) of wild-type patients with GIST did not show genomic imbalances. The most frequently observed chromosomal alterations in patients with mutant GIST included 14q complete or partial deletion (17 of 25), 1p deletion (14 of 25) and 22q deletion (10 of 25). Genetic targets of the chromosomal aberrations were selected by integrated analysis of copy number and gene expression data. We detected the involvement of known oncogenes and tumor suppressors including KRAS in chr 12p amplification and KIF1B, PPM1A, NF2 in chr 1p, 14q and 22p deletions, respectively. The genomic segment most frequently altered in mutated samples was the 14q23.1 region, which contains potentially novel tumor suppressors, including DAAM1, RTN1 and DACT1. siRNA-mediated RTN1 downregulation showed evidence for the potential role in GIST pathogenesis. The combination of gene expression profiling and high-resolution genomic copy number analysis offers a detailed molecular portrait of GISTs, providing an essential comprehensive knowledge necessary to guide the discovery of novel target genes involved in tumor development and progression.

Genomic characterization of Imatinib resistance in CD34 + cell populations from chronic myeloid leukaemia patients

To ascertain genomic alterations associated with Imatinib resistance in chronic myeloid leukaemia, we performed high resolution genomic analysis of CD34 + cells from 25 Imatinib (IM) resistant and 11 responders CML patients. Using patients’ T-cells as reference, we found significant association between number of acquired cryptic copy number alterations (CNA) and disease phase ( p = 0.036) or loss of IM response for patients diagnosed in chronic phase (CP) ( p = 0.04). Recurrent cryptic losses were identified on chromosomes 7, 12 and 13. On chromosome 7, recurrent deletions of the IKZF1 locus were detected, for the first time, in 4 patients in CP.

Clonal selection of 11q CN-LOH and CBL gene mutation in a serially studied patient during MDS progression to AML

By conventional metaphase and SNP array cytogenetics we serially studied a patient affected by high-risk myelodysplastic syndrome (MDS), documenting the conversion from partial trisomy 8q to trisomy 8 and partial tetrasomy 8q during progression to acute myeloid leukemia (AML). Moreover, the serial application of high resolution genomic array analysis at different disease stages allowed the description of cryptic abnormalities and the demonstration of their enrichment in the AML phase. In particular the detection and quantification of a copy-neutral loss of heterozygosity region located in chromosome 11q guided the search for point mutations in the CBL gene, thus allowing the escription of the novel missense mutation K382E and the demonstration of its selection during progression to secondary AML.

ANO1 amplification and expression in HNSCC with a high propensity for future distant metastasis and its functions in HNSCC cell lines

Background:Head and neck squamous cell carcinoma (HNSCC) is associated with poor survival. To identify prognostic and diagnostic markers and therapeutic targets, we studied ANO1, a recently identified calcium-activated chloride channel (CaCC).Methods:High-resolution genomic and transcriptomic microarray analysis and functional studies using HNSCC cell line and CaCC inhibitors.Results:Amplification and overexpression of genes within the 11q13 amplicon are associated with the propensity for future distance metastasis of HPV-negative HNSCC. ANO1 was selected for functional studies based on high correlations, cell surface expression and CaCC activity. ANO1 overexpression in cells that express low endogenous levels stimulates cell movement, whereas downregulation in cells with high endogenous levels has the opposite effect. ANO1 overexpression also stimulates attachment, spreading, detachment and invasion, which could account for its effects on migration. CaCC inhibitors decrease movement, suggesting that channel activity is required for the effects of ANO1. In contrast, ANO1 overexpression does not affect cell proliferation.Interpretation:ANO1 amplification and expression could be markers for distant metastasis in HNSCC. ANO1 overexpression affects cell properties linked to metastasis. Inhibitors of CaCCs could be used to inhibit the tumourigenic properties of ANO1, whereas activators developed to increase CaCC activity could have adverse effects.

Abstract A20: FGFR1-amplified squamous cell lung cancers depend on FGFR1

Abstract In lung adenocarcinomas of never-smokers EGFR mutations or EML4-ALK gene fusions are frequent genomic events that both expose prime therapeutic targets. By contrast, squamous cell lung cancer (SQLC) is almost invariably associated with smoking; in this subgroup of patients, no attractive therapeutic target has so far been identified. In order to identify such a therapeutically exploitable target in SQLC, we performed high-resolution genomic analyses of over 300 lung tumor specimens. Using 6.0 Affymetrix SNP-arrays we identified high-level focal amplifications of FGFR1 in 10% of over 150 primary SQLC specimens. Importantly, FGFR1 amplification was almost exclusively restricted to SQLC of smokers and almost never observed in adenocarcinomas. We also performed high-throughput cell line screening of 82 genomically annotated lung cancer cell lines using the FGFR inhibitor PD170374 and identified the presence of focal FGFR1 -amplifications as the strongest predictor of PD170374 activity. Biochemical kinase profiling across 108 kinases suggested that PD170374 was highly selective with only one of the kinases being inhibited to a similar extend as FGFR1 itself. Treatment with PD173074 induced apoptosis and inhibited MAPK- and, to a lesser extend, PI3K signaling in cell lines with focal amplification of FGFR1. In order to validate FGFR1 as a critical target in FGFR1 -amplified cells we employed retroviral expression of the gatekeeper mutant allele of FGFR1 (V561M) and thus the PD173074-sensitive cells were rendered resistant. Additionally, lentiviral-mediated knockdown of FGFR1 in FGFR1 -amplified cell lines confirmed FGFR1 as a critical target for FGFR1 inhibition in these cells. Finally, successful treatment of mice engrafted with FGFR1 -amplified lung cancer cell lines with PD173074 confirmed its on-target activity in vivo. Overall, our work demonstrates the functional relevance of amplification of FGFR1 in lung cancer and suggests that inhibition of FGFR with targeted therapeutics might be an effective strategy in squamous cell carcinoma patients with focal amplification of FGFR1. Citation Information: Clin Cancer Res 2010;16(14 Suppl):A20.

Structural and numerical abnormalities resolved in one-step analysis: the most common chromosomal rearrangements detected by comparative genomic hybridization in childhood acute lymphoblastic leukemia

Comparative genomic hybridization (CGH) is a technique that permits detection of chromosomal imbalances. This method allows the detection of gains and losses of genetic material at a resolution lower than 5 Mb. The limitations of conventional cytogenetic studies, such as morphologically insufficient quality of metaphases or the mitotic index, can be eliminated by use of CGH. It is particularly important in the diagnosis of leukemias, and CGH could be a useful tool enabling more precise cytogenetic analysis of leukemic cells. A group of 89 children with acute lymphoblastic leukemia was studied by means of CGH using bone marrow obtained from all consecutive pediatric patients. CGH experiments were performed according to the manufacturer's instruction with minor modifications. In addition, each sample was examined with standard GTG technique and fluorescence in situ hybridization. The conventional cytogenetics failed in 12 patients (13.5%), and 22 patients (24.7%) had a normal karyotype. Structural and numerical changes were found in 55 cases (61.8%) displaying a different abnormalities including deletions, trisomies, tetrasomies, isochromosomes, and markers with unknown origin. However, all samples were successfully analyzed by CGH. We have shown that high-resolution comparative genomic hybridization analysis is a reliable and relatively quick one-step method to identify main aberrations that would not be detected by either conventional G banding or by conventional fluorescence in situ hybridization. It should be considered to establish CGH as a routine analysis for screening patients with acute lymphoblastic leukemia.

A co‐segregating microduplication of chromosome 15q11.2 pinpoints two risk genes for autism spectrum disorder

High resolution genomic copy-number analysis has shown that inherited and de novo copy-number variations contribute significantly to autism pathology, and that identification of small chromosomal aberrations related to autism will expedite the discovery of risk genes involved. Here, we report a microduplication of chromosome 15q11.2, spanning only four genes, co-segregating with autism in a Dutch pedigree, identified by SNP microarray analysis, and independently confirmed by FISH and MLPA analysis. Quantitative RT-PCR analysis revealed over 70% increase in peripheral blood mRNA levels for the four genes present in the duplicated region in patients, and RNA in situ hybridization on mouse embryonic and adult brain sections revealed that two of the four genes, CYFIP1 and NIPA1, were highly expressed in the developing mouse brain. These findings point towards a contribution of microduplications at chromosome 15q11.2 to autism, and highlight CYFIP1 and NIPA1 as autism risk genes functioning in axonogenesis and synaptogenesis. Thereby, these findings further implicate defects in dosage-sensitive molecular control of neuronal connectivity in autism. However, the prevalence of this microduplication in patient samples was statistically not significantly different from control samples (0.94% in patients vs. 0.42% controls, P = 0.247), which suggests that our findings should be interpreted with caution and indicates the need for studies that include large numbers of control subjects to ascertain the impact of these changes on a population scale.

High-resolution genomic and expression analyses of copy number alterations in HER2-amplified breast cancer.

IntroductionHER2 gene amplification and protein overexpression (HER2+) define a clinically challenging subgroup of breast cancer with variable prognosis and response to therapy. Although gene expression profiling has identified an ERBB2 molecular subtype of breast cancer, it is clear that HER2+ tumors reside in all molecular subtypes and represent a genomically and biologically heterogeneous group, needed to be further characterized in large sample sets.MethodsGenome-wide DNA copy number profiling, using bacterial artificial chromosome (BAC) array comparative genomic hybridization (aCGH), and global gene expression profiling were performed on 200 and 87 HER2+ tumors, respectively. Genomic Identification of Significant Targets in Cancer (GISTIC) was used to identify significant copy number alterations (CNAs) in HER2+ tumors, which were related to a set of 554 non-HER2 amplified (HER2-) breast tumors. High-resolution oligonucleotide aCGH was used to delineate the 17q12-q21 region in high detail.ResultsThe HER2-amplicon was narrowed to an 85.92 kbp region including the TCAP, PNMT, PERLD1, HER2, C17orf37 and GRB7 genes, and higher HER2 copy numbers indicated worse prognosis. In 31% of HER2+ tumors the amplicon extended to TOP2A, defining a subgroup of HER2+ breast cancer associated with estrogen receptor-positive status and with a trend of better survival than HER2+ breast cancers with deleted (18%) or neutral TOP2A (51%). HER2+ tumors were clearly distinguished from HER2- tumors by the presence of recurrent high-level amplifications and firestorm patterns on chromosome 17q. While there was no significant difference between HER2+ and HER2- tumors regarding the incidence of other recurrent high-level amplifications, differences in the co-amplification pattern were observed, as shown by the almost mutually exclusive occurrence of 8p12, 11q13 and 20q13 amplification in HER2+ tumors. GISTIC analysis identified 117 significant CNAs across all autosomes. Supervised analyses revealed: (1) significant CNAs separating HER2+ tumors stratified by clinical variables, and (2) CNAs separating HER2+ from HER2- tumors.ConclusionsWe have performed a comprehensive survey of CNAs in HER2+ breast tumors, pinpointing significant genomic alterations including both known and potentially novel therapeutic targets. Our analysis sheds further light on the genomically complex and heterogeneous nature of HER2+ tumors in relation to other subgroups of breast cancer.

Abstract 331: A comprehensive high-resolution genomic analysis of primary central nervous system lymphomas (PCNSL) shows a highly complex karyotype characterized by abnormalities affecting multiple genes involved in critical pathways associated with lymphocyte maturation and survival

Abstract Introduction. PCNSL is an aggressive primary brain tumor characterized by a perivascular accumulation of malignant cells that have lymphoid characteristics. As there is significantly less information regarding the molecular pathogenesis of PCNSL in comparison with systemic lymphomas the aim of this study was to perform a comprehensive high-resolution genomic analysis in a cohort of PCNSL cases to better characterize the disease at chromosomal and gene level. Material and Methods. Specimens from 7 EBV- and HIV-negative and presumed immunocompetent PCNSL patients with sufficient frozen tissue for DNA extraction were studied. Copy-number abnormalities were analyzed by array CGH using SurePrint G3 (1 million probes) microarray (Agilent). B-cell differentiation status was characterized by immunostains for CD10, MUM-1, and CD138. Results. PCNSL cases were characterized by highly complex genomes with a median of 23 copy-number abnormalities per patient (range 16-49). Twenty-four chromosomal regions were affected in recurrent deletions and 19 in copy-number gains. Gain of 12q12-q24.33 and losses of 9p21.3 and 6q were the most common abnormalities, found in five of the seven patients. There was not a deleted region on 6q unique to all cases, with 6q14.1-q14.3, 6q16.3-q22.2 and 6q25.3-q26 losses being found in 4 out of 5 cases with 6q deletions. Two regions of interest were biallelically deleted. CDKN2A was the sole gene included in all cases with 9p21.3, being biallelically deleted in two out of 5 cases. TOX and CD58, genes associated with the development and activation of T cells, were also biallelically affected. Focal monoallelic deletions affecting negative regulators of the NFkB signaling pathway (MAP4K1, TANK, TAX1BP1, TRIB3), cell cycle (RB1) and immune-cell regulation (SIRPB1, CBLB, NFATC2) were also identified. Overall, a total of 22 genes were included in homozygous deletions in at least one case. Several chromosomal breakpoints were identified inside genes that encode transcription factors previously identified as being part of fusion protein in other hematological malignancies (FOXP1, ETV6 and NCOA2). Conclusion. This pilot study showed evidence for a highly complex genome, mainly characterized by abnormalities affecting a plethora of genes involved in lymphocyte development, activation and NF-kB signaling pathways regulation. 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 331.

Whole-Genome Profiling of Pediatric Diffuse Intrinsic Pontine Gliomas Highlights Platelet-Derived Growth Factor Receptor α and Poly (ADP-ribose) Polymerase As Potential Therapeutic Targets

Diffuse intrinsic pontine glioma (DIPG) is one of the most devastating of pediatric malignancies and one for which no effective therapy exists. A major contributor to the failure of therapeutic trials is the assumption that biologic properties of brainstem tumors in children are identical to cerebral high-grade gliomas of adults. A better understanding of the biology of DIPG itself is needed in order to develop agents targeted more specifically to these children's disease. Herein, we address this lack of knowledge by performing the first high-resolution single nucleotide polymorphism (SNP) -based DNA microarray analysis of a series of DIPGs. Eleven samples (nine postmortem and two pretreatment surgical samples), the largest series thus far examined, were hybridized to SNP arrays (250 k or 6.0). The study was approved by the research ethics board at our institution. All array findings were validated using quantitative polymerase chain reaction, fluorescence in situ hybridization, immunohistochemistry, and/or microsatellite analysis. Analysis of DIPG copy number alterations showed recurrent changes distinct from those of pediatric supratentorial high-grade astrocytomas. Thirty-six percent of DIPGs had gains in platelet-derived growth factor receptor alpha (PDGFRA; 4 to 18 copies) and all showed PDGFR-alpha expression. Low-level gains in poly (ADP-ribose) polymerase (PARP) -1 were identified in three cases. Pathway analysis revealed genes with loss of heterozygosity were enriched for DNA repair pathways. To our knowledge, our data provides the first, comprehensive high-resolution genomic analysis of pediatric DIPG. Our findings of recurrent involvement of the PDGFR pathway as well as defects in DNA repair pathways coupled with gain of PARP-1 highlight two potential, biologically based, therapeutic targets directed specifically at this devastating disease.

Identification of Two Critically Deleted Regions within Chromosome Segment 7q35-q36 in EVI1 Deregulated Myeloid Leukemia Cell Lines

Chromosomal rearrangements involving the EVI1 proto-oncogene are a recurrent finding in myeloid leukemias and are indicative of a poor prognosis. Rearrangements of the EVI1 locus are often associated with monosomy 7 or cytogenetic detectable deletions of part of 7q. As EVI1 overexpression alone is not sufficient to induce leukemia, loss of a 7q tumour suppressor gene might be a required cooperating event. To test this hypothesis, we performed high-resolution array comparative genomic hybridization analysis of twelve EVI1 overexpressing patients and three EVI1 deregulated cell lines to search for 7q submicroscopic deletions. This analysis lead to the delineation of two critical regions, one of 0.39 Mb on 7q35 containing the CNTNAP2 gene and one of 1.33 Mb on chromosome bands 7q35–q36 comprising nine genes in EVI1 deregulated cell lines. These findings open the way to further studies aimed at identifying the culprit EVI1 implicated tumour suppressor genes on 7q.

Combined High Resolution Genomic and Expression Profiles Microarray Analysis in Sezary Syndrome.

Abstract 3238Poster Board III-175We have used single nucleotide polymorphism (SNP) and comparative genomic hybridization array (aCGH) to study DNA copy number (CN) changes and loss of heterozygosity (LOH) in a series of 28 patients affected by Sézary syndrome (SS), a rare form of cutaneous-T-cell lymphoma (CTCL). Our data identified, further confirming previous studies, recurrent losses of 17p13.2-p11.2 and 10p12.1-q26.3 occurring in 71 and 68% of cases respectively; common gains were detected for 17p11.2-q25.3 (64%) and chromosome 8/8q (50%). Moreover, we identified novel genomic lesions recurring in more than 30% of tumours: loss of 9q13-q21.33 and gain of 10p15.3-10p12.2. Individual chromosomal aberrations did not show a significant correlation with prognosis, however when more than three recurrent chromosomal alterations (gain or loss) were considered, a statistical association was observed using Kaplan-Meier survival analysis. Crossing genomic data mapping with those obtained from gene expression profiles of matching samples we were able to identify a total of 113 deregulated transcripts in aberrant chromosomal regions that included cancer related genes such as members of the NF-kB pathway (NKIRAS2, PSMD3, BAG4, BTRC, TRAF2) that might explain its constitutive activation in CTCL. Matching this list of genes with those discriminating patients with different survival times we identify several common candidates that might exert critical roles in SS, like PIP5K1B and BUB3. Taken together this study confirms and maps more precisely the regions of gain and loss and, combined to transcriptional profiles, suggest a novel set of genes of potential interest in SS. DisclosuresNo relevant conflicts of interest to declare.

A Comprehensive High-Resolution Genomic Analysis of Primary Central Nervous System Lymphomas Shows a Highly Complex Karyotype Characterized by Abnormalities Affecting Multiple Genes Involved in Critical Pathways Associated with Lymphocyte Maturation and Survival.

Abstract 4637Primary central nervous system lymphoma (PCNSL) is an aggressive form of extra-nodal, high-grade, non-Hodgkin B-cell neoplasm. It originates in the brain, leptomeninges, spinal cord or eyes and typically remains confined to the CNS. Further immunophenotypic characterization has revealed that these tumors have overlapping features of germinal center and activated B-cell differentiation. Although the cells of origin are lymphocytes, PCNSL should be considered a brain tumor because its therapeutic challenges resemble those of other brain tumors. Regarding the molecular pathogenesis of PCNSL, there is significantly less information in comparison with systemic lymphomas. The aim of this study was to perform a comprehensive high-resolution genomic analysis in a cohort of PCNSL cases to better characterize the disease at chromosomal and gene level. Copy-number abnormalities were analyzed in seven PCNSL by array-based comparative genomic hybridization (aCGH) using SurePrint G3 (1 million probes, ∼4 Kb resolution) microarray (Agilent). Overall, PCNSL cases were characterized by highly complex genomes with a median of 23 copy-number abnormalities per patient (range 16-49). The whole genomic regions affected in abnormalities correspond to areas between 3% and 29% of the human genome. Globally, 43 chromosomal regions were affected in a recurrent fashion (24 areas involved in recurrent deletions and 19 in copy-number gains). Gain of 12q12-q24.33 and losses of 9p21.3 and 6q were the most common abnormalities found in 71% patients each (5 out of 7). There was not a unique deleted region on 6q to all patients, with 6q14.1-q14.3, 6q16.3-q22.2 and 6q25.3-q26 losses being found in 4 out of 5 cases with 6q deletions. None of these regions include PTPRK, which has been previously proposed as a potential modulator of PCNSL progression. CDKN2A was the sole gene included in all cases with 9p21.3, being biallelically deleted in two out of 5 cases. Minimal deleted genes were also delineated in 3p21.1 (minimal affected area of 0.03Mb) and 3q26.32 (0.27Mb) in 44% of cases each. Those regions included PRKCD (inhibits B-cell growth through transcriptional regulation of IL-6) and TBL1XR1 (corepressor of nuclear hormone receptor), respectively. Overall, a total of 22 genes were included in homozygous deletions in at least one case. Besides CDKN2A (cell cycle), other genes of interest associated with the development and activation of T cells (TOX, CD58) were biallelically affected. Focal monoallelic deletions affecting negative regulators of the NFkB signaling pathway (MAP4K1, TANK, TAX1BP1, TRIB3), cell cycle (RB1) and immune-cell regulation (SIRPB1, CBLB, NFATC2) were also identified. Of interest, no copy-number abnormalities were identified affecting TP53 in any patient. Several chromosomal breakpoints were identified inside genes that encodes transcription factors previously identified as being part of fusion protein in other hematological malignancies (FOXP1, ETV6 and NCOA2) thus suggesting the potential existence of fusion proteins including these genes. Cytogenetic and genetic approaches are being currently used to validate this hypothesis. This is the first study characterizing a cohort of PCNSL cases by using this comprehensive high-resolution approach. Regarding the small number of cases analyzed so far, we can confirm the existence of a highly complex genome, mainly characterized by abnormalities affecting a plethora of genes involved in lymphocyte development, activation and NF-kB signaling pathways regulation. Molecular analyses are ongoing to validate these findings in a larger cohort of PCNSL patients. Disclosures:Fonseca:Otsuka: Consultancy; BMS: Consultancy; Amgen: Consultancy; Medtronic : Consultancy; Genzyme: Consultancy.

Genomic disorders: mechanisms for copy number variation and clinical implementation of high-resolution genome analysis

Genomic disorders: mechanisms for copy number variation and clinical implementation of high-resolution genome analysis

Cyfip1 Is a Putative Invasion Suppressor in Epithelial Cancers

Identification of bona fide tumor suppressors is often challenging because of the large number of genetic alterations present in most human cancers. To evaluate candidate genes present within chromosomal regions recurrently deleted in human cancers, we coupled high-resolution genomic analysis with a two-stage genetic study using RNA interference (RNAi). We found that Cyfip1, a subunit of the WAVE complex, which regulates cytoskeletal dynamics, is commonly deleted in human epithelial cancers. Reduced expression of CYFIP1 is commonly observed during invasion of epithelial tumors and is associated with poor prognosis in this setting. Silencing of Cyfip1 disturbed normal epithelial morphogenesis in vitro and cooperated with oncogenic Ras to produce invasive carcinomas in vivo. Mechanistically, we have linked alterations in WAVE-regulated actin dynamics with impaired cell-cell adhesion and cell-ECM interactions. Thus, we propose Cyfip1 as an invasion suppressor gene.

Identification of targetable cellular subsets within melanoma tumors

9082 Background: Human tumors, including melanoma, are complex mixtures of individual, molecularly distinct subpopulations, or clones of cancer cells. Effective cancer therapy will likely require targeting of all tumor subsets within a given cancer. Understanding the tumor complexity and the ability to identify points of therapeutic vulnerability within the individual tumor subsets will be essential for development of effective personalized cancer therapies. Methods: We have developed an approach that combines identification of individual tumor subsets using a multiparameter nuclear flow cytometry coupled with a high-resolution genomic analysis using the array-based comparative genomic hybridization (aCGH). Melanoma nuclei were isolated from tumor tissues and subjected to flow cytomery using melanocyte-specific antibodies (to separate melanoma cells from stroma) and DNA content, to separate individual tumor subpopulations. DNA extracted from isolated nuclear subpopulations was extracted and analyzed by aCGH. This approach was adopted for both fresh-frozen and paraffin-embedded clinical specimens. Results: We initially demonstrate the feasibility of the outlined approach by successful separation of melanoma from stromal nuclei and separation of individual melanoma nuclear subpopulations by DNA content. aCGH analysis of the DNA derived from isolated tumor subpopulations allowed successful identification of potentially targetable molecular aberrations in individual subsets of tumor cells. Notably, such aberrations were often not detected in unsorted, bulk tumors analyzed by the same high-resolution aCGH approach. Conclusions: We demonstrate a feasible approach to in-depth molecular analysis of tumor subpopulations within a clinical cancer tissue. This approach allows identification of potentially targetable molecular aberrations within individual tumor subsets, thus opening a possibility for a broad tumor targeting through design of individually-tailored therapeutic approaches. No significant financial relationships to disclose.