Recurrent Rearrangements Research Articles

Interstitial NORs, Fragile Sites, and Chromosome Evolution: A Not So Simple Relationship - The Example of Melolontha melolontha and Genus Protaetia (Coleoptera: Scarabaeidae)

In the present study, the origin of recurrent rearrangements involving chromosome 6 in 3.2% of cells of Melolontha melolontha (Coleoptera, Scarabaeidae) was investigated. Various chromosome staining techniques, including C-banding, Giemsa and silver staining, as well as fluorescence in situ hybridization with a human 28S rDNA probe, were applied to M. melolontha chromosome spreads. In addition, related species of the genera Melolontha and Protaetia were studied. On chromosome 6 of M. melolontha, there is a fragile site-like structure which corresponds to an interstitial nucleolus organizer region (NOR). Despite this instability, the NOR remains unique and interstitial in this species, as well as in the other species studied. It is proposed that the intercalary position of the NOR both facilitates the detection of its fragile site-like instability and correlates with its relative stability during evolution. We explain this apparent paradox by strong counter-selection for imbalances of the chromosome fragment distal to the interstitial NORs, which would recurrently occur in the progeny of translocation carriers. Thus, the frequent telomeric position of the NORs in most animal and plant taxa would have no functional rationale but would be the consequence of selection against the meiotic transmission of chromosome imbalances.

Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region.

Recurrent rearrangements of Chromosome 8p23.1 are associated with congenital heart defects and developmental delay. The complexity of this region has led to inconsistencies in the current reference assembly, confounding studies of genetic variation. Using comparative sequence-based approaches, we generated a high-quality 6.3-Mbp alternate reference assembly of an inverted Chromosome 8p23.1 haplotype. Comparison with nonhuman primates reveals a 746-kbp duplicative transposition and two separate inversion events that arose in the last million years of human evolution. The breakpoints associated with these rearrangements map to an ape-specific interchromosomal core duplicon that clusters at sites of evolutionary inversion (P = 7.8 × 10−5). Refinement of microdeletion breakpoints identifies a subgroup of patients that map to the same interchromosomal core involved in the evolutionary formation of the duplication blocks. Our results define a higher-order genomic instability element that has shaped the structure of specific chromosomes during primate evolution contributing to rearrangements associated with inversion and disease.

NUP98 is rearranged in 3.8% of pediatric AML forming a clinical and molecular homogenous group with a poor prognosis.

Pediatric acute myeloid leukemia (AML) is a rare disease whose prognosis is highly variable according to factors such as chromosomal abnormalities. Recurrent genomic rearrangements are detected in half of pediatric AML by karyotype. NUcleoPorin 98 (NUP98) gene is rearranged with 31 different fusion partner genes. These rearrangements are frequently undetected by conventional cytogenetics, as the NUP98 gene is located at the end of the chromosome 11 short arm (11p15). By screening a series of 574 pediatric AML, we detected a NUP98 rearrangement in 22 cases (3.8%), a frequency similar to CBFB-MYH11 fusion gene (4.0%). The most frequent NUP98 fusion gene partner is NSD1. These cases are homogeneous regarding their biological and clinical characteristics, and associated with bad prognosis only improved by bone marrow transplantation. We detailed the biological characteristics of these AML by exome sequencing which demonstrated few recurrent mutations (FLT3 ITD, WT1, CEBPA, NBPF14, BCR and ODF1). The analysis of the clonal structure in these cases suggests that the mutation order in the NUP98-rearranged pediatric AML begins with the NUP98 rearrangement leading to epigenetic dysregulations then followed by mutations of critical hematopoietic transcription factors and finally, activation of the FLT3 signaling pathway.

Recurrent NTRK1 Gene Fusions Define a Novel Subset of Locally Aggressive Lipofibromatosis-like Neural Tumors

The family of pediatric fibroblastic and myofibroblastic proliferations encompasses a wide spectrum of pathologic entities with overlapping morphologies and ill-defined genetic abnormalities. Among the superficial lesions, lipofibromatosis (LPF), composed of an admixture of adipose tissue and fibroblastic elements, in the past has been variously classified as infantile fibromatosis or fibrous hamartoma of infancy. In this regard, we have encountered a group of superficial soft tissue tumors occurring in children and young adults, with a notably infiltrative growth pattern reminiscent of LPF, variable cytologic atypia, and a distinct immunoprofile of S100 protein and CD34 reactivity, suggestive of neural differentiation. SOX10 and melanocytic markers were negative in all cases tested. In contrast, a control group of classic LPF displayed bland, monomorphic histology and lacked S100 protein immunoreactivity. To define the pathogenetic abnormalities in these seemingly distinctive groups, we performed RNA sequencing for fusion gene discovery in 2 cases each, followed by screening for any novel alterations identified in a larger cohort representing both entities. The 2 index LPF-like neural tumors (LPF-NT) showed TPR-NTRK1 and TPM3-NTRK1 gene fusions, which were further validated by fluorescence in situ hybridization (FISH) and reverse transcription polymerase chain reaction. Subsequent FISH screening of 14 LPF-NT identified recurrent NTRK1 gene rearrangements in 10 (71%) cases. Of the NTRK1-negative LPF-NT cases, 1 case each showed ROS1 and ALK gene rearrangements. In contrast, none of the 25 classic LPFs showed NTRK1 gene rearrangements, although regional abnormalities were noted in the 1q21-22 region by FISH in a majority of cases. Furthermore, NTRK1 immunostaining was positive only in NTRK1-rearranged S100-positive LPF-NT but negative in classic LPF. These results suggest that NTRK1 oncogenic activation through gene fusion defines a novel and distinct subset of soft tissue tumors resembling LPF, but displaying cytologic atypia and a neural immunophenotype, provisionally named LPF-like neural tumors.

Genomic and Cytogenetic Localization of the Carotenoid Genes in the Aphid Genome

Data published in the scientific literature suggests a possible link between chromosomal rearrangements involving autosomes 1 and 3 and the presence of red morphs in the peach-potato aphid Myzus persicae (Sulzer). In order to begin a study of this relationship, we analysed the genomic and chromosomal location of genes involved in carotenoid biosynthesis in M. persicae and the pea aphid, Acyrthosiphon pisum (Harris), since carotenoids are the basis of the colour in many aphid species. Genomic analysis identified a DNA sequence containing carotenoid genes in synteny between the 2 species. According to the results obtained using in situ PCR, carotenoid genes were located in a subterminal portion of autosome 1 in both species. The same localization has also been observed in the onion aphid Neotoxoptera formosana Takahashi that, as M. persicae and A. pisum, belongs to the tribe Macrosiphini, thereby suggesting a synteny of this chromosomal region in aphids. In situ PCR experiments performed on 2 M. persicae asexual lineages bearing heterozygous translocations involving autosomes 1 and 3 revealed that carotenoid genes were located within chromosomal portions involved in recurrent rearrangements. We also verified by bioinformatics analyses the presence of fragile sites that could explain these recurrent rearrangements in M. persicae.

Cytogenetics in the management of lymphomas and lymphoproliferative disorders in adults and children: an update by the Groupe francophone de cytogénétique hématologique (GFCH).

Non-Hodgkin's lymphomas and lymphoproliferative disorders include a high number of heterogeneous entities, described in the 2008 WHO classification. This classification reflects the crucial role of a multidisciplinary approach which integrates cytogenetic results both for the notion of clonality and for differential diagnosis between these entities. The prognostic impact of some cytogenetic abnormalities or genome complexity is also confirmed for many of these entities. Novel provisional entities have been described, such as BCLU (B-cell lymphoma unclassifiable with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma) for which karyotype is critical to distinguish BCLU from Burkitt's lymphoma. The karyotype can be established from any tumour or liquid infiltrated by lymphoma cells. Recent adaptations of technics for cellular cultures according to the subtype of known (or suspected) lymphoma have significantly improved the percentage of informative karyotypes. Conventional karyotypes remain the best technical approach recommended for most of these subtypes. Interphase and/or metaphase FISH also represents a solid and rapid approach, because of the significant number of recurrent (sometimes specific) rearrangements of these entities. Next generation sequencing technologies contribute to enrich genomic data and substantially improve the understanding of oncogenic mechanisms underlying these lymphoid malignancies. Some molecular biomarkers are already part of the diagnostic process (for example, somatic mutation of MYD88 in Waldenström disease) thus reinforcing the essential principle of a multidisciplinary approach for the diagnosis of all the mature lymphoid malignancies.

Genomic alterations in neuroendocrine cancers of the ovary.

BackgroundAs we have previously reported, small cell carcinoma of the ovary (SCCO) is a rare, aggressive form of ovarian cancer associated with poor outcomes. In an effort to identify new treatment options, we utilized comprehensive genomic profiling to assess the potential for novel therapies in SCCO.MethodsPatients with SCCO, SCCO-HT (hypercalcemic type), neuroendocrine tumors of the ovary (NET-O), and small cell carcinoma of the lung (SCLC) profiled by Caris Life Sciences between 2007–2015 were identified. Tumors were assessed with up to 21 IHC stains, in situ hybridization of cMET, EGFR, HER2 and PIK3CA, and next-generation sequencing (NGS) as well as Sanger sequencing of selected genes.ResultsForty-six patients with SCCO (10 SCCO, 18 SCCO-HT, 18 NET-O) were identified as well as 58 patients with SCLC for comparison. Patients with SCCO and SCCO-HT were younger (median 42 years [range 12–75] and 26 years [range 8–40], respectively) than patients with NET-O 62 [range 13–76] or SCLC 66 [range 36–86]. SCCO patients were more likely to be metastatic (70 %) than SCCO-HT (50 %) or NET-O (33 %) patients, but at a similar rate to SCLC patients (65 %). PD1 expression varied across tumor type with SCCO (100 %), SCCO-HT (60 %), NET-O (33 %) vs SCLC (42 %). PDL1 expression also varied with SCCO (50 %), SCCO-HT (20 %), NET-O (33 %) and SCLC (0 %). No amplifications were identified in cMET, EGFR, or HER2 and only 1 was found in PIK3CA (NET-O). Actionable mutations were rare with 1 patient with SCCO having a BRCA2 mutation and 1 patient with NET-O having a PIK3CA mutation. No other actionable mutations were identified.ConclusionsNo recurrent actionable mutations or rearrangements were identified using this platform in SCCO. IHC patterns may help guide the use of chemotherapy in these rare tumors.

Haplotype analysis reveals that the recurrent BRCA1 deletion of exons 23 and 24 is a Greek founder mutation.

A recurrent large genomic rearrangement (LGR) encompassing exons 23 and 24 of the BRCA1 gene has been identified in breast-ovarian cancer families of Greek origin. Its breakpoints have been determined as c.5406 + 664_*8273del11052 (RefSeq: NM_007294.3) and a diagnostic polymerase chain reaction (PCR) has been set up for rapid screening. In a series of 2,092 high-risk families completely screened for BRCA1 and BRCA2 germline mutations, we have found the deletion in 35 families (1.68%), representing 7.83% of the mutations identified in both genes and 10.3% of the total BRCA1 mutations. In order to characterize this deletion as a founder mutation, haplotype analysis was conducted in 60 carriers from 35 families, using three BRCA1 intragenic microsatellite markers and four markers surrounding the BRCA1 locus. Our results demonstrate a common shared core disease-associated haplotype of 2.89Mb. Our calculations estimate that the deletion has originated from a common ancestor 1450 years ago, which most probably inhabited the Asia Minor area. The particular (LGR) is the third mutation of such type that is proven to have a Greek founder effect in the Greek population, illustrating the necessity for LGRs testing in individuals of Greek descent.

Abstract A03: Analyses of a prostate cancer patient-derived xenografts series, a resource for translational research

Abstract Patients with metastatic prostate cancer (PCa) have effective therapy options, but none of them are curative. Thus, their mortality rates are persistently high. Essential to furthering our progress in PCa research and therapy development is a spectrum of models that reflect the heterogeneity of the disease at each tumor site as well as the different histological variants of PCa (e.g., adenocarcinoma, small cell carcinoma). To address this challenge, we developed a strategy to establish PCa patient-derived xenografts (PDXs), using PCa tissue specimens taken from PCa sites demonstrating clinical progression. This approach provided a diverse repository of PDXs that can be linked prospectively with clinical progression and led to the identification of clinically relevant therapy targets and have proven valuable for testing drugs. We studied the first 50 PDXs developed under our program to a) define the histopathological features of paired human PCa and corresponding PDXs applying the clinically defined morphological characterization groupings of human cancer to the PDX tumors; b) assess the expression of genes known to play roles in PCa pathogenesis (e.g., androgen receptor, PTEN, ETS gene fusions) in PDXs and the human tumors of origin using immunohistochemistry and fluorescence in situ hybridization and c) perform array comparative genomic hybridization to 42 PDXs. We found that the histopathological and molecular pattern of these PDXs maintain the fidelity with the human tumor of origin. Furthermore, of the 50 cases studied, 32 (64%) were adenocarcinomas, and 16 (32%) were small cell carcinomas, poorly differentiated neuroendocrine carcinomas or mixed adenocarcinoma/ small cell carcinomas. In our cohort, we also have one sarcomatoid tumor and one ductal adenocarcinoma. Of the 32 adenocarcinomas in this cohort, 26 were AR-positive (81%), and 11 of the 27 AR-positive adenocarcinomas (41%) had aberrant expression of genes frequently involved in recurrent rearrangement (e.g., ERG, ETV1, ETV5). Also, SCCs and poorly differentiated neuroendocrine carcinomas did not express AR and were negative for ERG. This distribution recapitulates that of human PCa in the general population. Comparative genomic hybridization demonstrated gains and losses previously reported in PCa with a defined cluster of genomic aberrations. Significant differences in oncogenic pathways activation in pairs of PDXs derived from different areas of the same tumor suggesting divergent cellular progression. Finally, using this platform, we identified a focal deletion of speckle-type POZ protein-like (SPOPL) gene in 7/28 PDX. SPOPL is a MATH-BTB protein that shares an overall 85% sequence identity with SPOP (a SPOPL paralog). SPOP was recently reported to be mutated in about 8% of PCa and to define a molecular subclass of PCa. No mutations were found in SPOP in our cohort. In support of our findings, deletions on SPOPL were also found in about 7% of the PCa in TCGA data suggesting that our cohort is a reliable platform for discovery. In conclusion, we have developed a dynamic repository of clinically annotated samples that can be used as a discovery platform. Furthermore, these clinically annotated samples can be linked prospectively to clinical progression/response to therapy and thus will help define therapeutic targets for subpopulations of men and to identify likely responders to previous and upcoming therapies. Citation Format: Nallasivam Palanisamy, Jun Yang, Xinhai Wan, Elsa M. li Ning Tapia, John C. Araujo, Eleni Efstathiou, Estefania Labanca, Louis Pisters, Ana Aparicio, Ritu Bhalla, Scott Tomlins, Lakshmi P. Kunju, Arul Chinnaiyan, Christopher J. Logothetis, Patricia Troncoso, Nora M. Navone. Analyses of a prostate cancer patient-derived xenografts series, a resource for translational research. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr A03.

Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.

Genetic differences that specify unique aspects of human evolution have typically been identified by comparative analyses between the genomes of humans and closely related primates1, including more recently the genomes of archaic hominins2,3. Not all regions of the genome, however, are equally amenable to such study. Recurrent copy number variation (CNV) at chromosome 16p11.2 accounts for ~1% of autism cases4,5 and is mediated by a complex set of segmental duplications, many of which arose recently during human evolution. We reconstructed the evolutionary history of the locus and identified BOLA2 (bolA family member 2) as a gene duplicated exclusively in Homo sapiens. We estimate that a 95 kbp segment containing BOLA2 duplicated across the critical region ~282 thousand years ago (kya), one of the latest among a series of genomic changes that dramatically restructured the locus during hominid evolution. All humans examined carry one or more copies of the duplication, which nearly fixed early in the human lineage—a pattern unlikely to have arisen so rapidly in the absence of selection (p < 0.0097). We show that the duplication of BOLA2 led to a novel, human-specific in-frame fusion transcript and that BOLA2 copy number correlates with both RNA expression (r = 0.36) and protein level (r = 0.65), with the greatest expression difference between human and chimpanzee in experimentally derived stem cells. Analyses of 152 patients carrying a chromosome 16p11.2 rearrangement showed that >96% of breakpoints occur within the Homo sapiens-specific duplication. In summary, the duplicative transposition of BOLA2 at the root of the Homo sapiens lineage ~282 kya simultaneously increased copy number of a gene associated with iron homeostasis and predisposed our species to recurrent rearrangements associated with disease.

Abstract 118: A comprehensive profile of the genomic architecture of curable prostate cancer

Abstract There is an urgent need to develop novel biomarkers of treatment response for precision medicine in prostate cancer, particularly in the setting of localized, non-indolent disease, which represents the vast majority of cases at initial clinical presentation. The Canadian Prostate Cancer Genome Network (CPC-GENE) - a member of the International Cancer Genome Consortium - aims to identify multi-modal prognostic and predictive signatures of therapeutic outcome based on intrinsic tumour genomics, transcriptomics, and epigenomics, which are being incorporated into novel clinical trials of treatment escalation/de-escalation for image-guided radiotherapy and/or radical prostatectomy. Herein we report the results of the largest prostate cancer whole-genome sequencing study to date, consisting of 194 patients and whole-exome sequencing of 479 patients with localized, potentially curable disease; a sample size that allows for saturating discovery of genes mutated at ≥1% frequency. We show that tumours treated by curative local therapy have a paucity of clinically-actionable mutations relative to high-risk localized or metastatic disease, but instead harbor a significant number of recurrent non-coding aberrations and genomic rearrangements, including a novel inversion - and an associated reduction in gene expression - of the PTEN tumour suppressor gene on chromosome 10. The median tumour contains three distinct driver mutations, with &amp;gt;86% of tumours possessing at least one known driver. Importantly, multiple driver aberrations are associated with patient outcome, including copy number aberrations and methylation events, but notably excluding well-described recurrent events such as TMPRSS2:ERG fusions and SPOP point mutations. Localized hypermutation events (e.g. kataegis) were detected in &amp;gt;20% of tumours, and were strongly enriched for aggressive disease. Taken together, these data provide a comprehensive analysis of the genomic landscape of localized, non-indolent prostate cancer. Moreover, our results strongly suggest that specific molecular aberrations may serve as useful biomarkers for improved pre-treatment stratification of patients with localized, low/intermediate risk disease into escalation/de-escalation protocols, and support the development of clinical trials to assess this hypothesis, based on patient-specific molecular profiles. Citation Format: Michael E. Fraser, Theodorus van der Kwast, John McPherson, Colin C. Collins, Yves Fradet, Bernard Tetu, Alain Bergeron, Rob G. Bristow, Paul C. Boutros. A comprehensive profile of the genomic architecture of curable prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 118.

Abstract 2430: Neuroblastoma: Telomere elongation is responsible for aggressive behavior

Abstract Neuroblastoma (NB) is a highly malignant pediatric tumor of the sympathetic nervous system that commonly displays low overall mutation frequency. We searched for new structural rearrangements in a series of 275 NBs of all stages using high density SNP microarrays. Exome sequencing was also performed on 15 tumor/constitutional DNA pairs and 25 additional tumors, mainly high-risk NBs, using paired-end sequencing on Illumina instrument. Normalized coverage data were used to generate array comparative genomic hybridization (CGH)-like profiles. Structural rearrangements leading to gain of TERT gene were observed in 15 of 275 neuroblastomas as judged by SNP microarray. 12 out of these 15 tumors with TERT rearrangement belong to 11q-deleted subgroup of NB patients that marks tumors with a poor prognosis. These rearrangements occurred only in high-risk NBs in an almost mutually exclusive fashion with MYCN amplifications, which is a known genetic event in this tumor type. Furthermore, in the small series of NBs analyzed by exome sequencing, we detect extensive structural rearrangements of chromosome 2, 5 and 7 leading to amplification of MYCN, TERT and CDK6 respectively in one tumor. The exome sequencing approach detected at average 14 (range 2-77) somatic protein-changing alterations per tumor. Combining structural and mutational data from the exome sequencing show recurrent alterations in ATRX gene. In our NB cohort we see alterations of ATRX in four non MYCN-amplified tumors: two focal deletions, one nonsense mutation and one deleterious missense mutation. ATRX inactivation results in alternative lengthening of telomeres (ALT). This means that high-risk neuroblastomas cancer cells can preserve their telomeres by ALT or by activation of telomerase reverse transcriptase (encoded by TERT). Alterations in TERT and ATRX were mutually exclusive, which is in agreement with the independent activation by these genes of telomere lengthening. Moreover, three cases with chromothripsis of chromosome 5 with rearrangements affecting the TERT were identified through SNP microarrays. These results identify TERT as at least one of the target genes activated by chromothripsis of chromosome 5. This remodeling of the genomic context likely abrogates transcriptional silencing of TERT in high-risk neuroblastoma and places telomerase activation in the centre of transformation in a large fraction of these tumors. This study identifies recurrent TERT and ATRX rearrangements and telomere lengthening as an important mechanism characterizing high-risk tumors and it supports the pharmacological inhibition of these targets to improve the outcome for this patient group. Citation Format: Niloufar Javanmardi, Susanne Fransson, Rose-Marie Sjöberg, Anna Djos, Per Kogner, Tommy Martinsson. Neuroblastoma: Telomere elongation is responsible for aggressive behavior. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2430.

16 - Genomic Profiling of Plasmablastic Lymphoma Reveals Recurrent Copy Number Alterations and MYC Rearrangement as Common Genetic Abnormalities

16 - Genomic Profiling of Plasmablastic Lymphoma Reveals Recurrent Copy Number Alterations and MYC Rearrangement as Common Genetic Abnormalities

23 - Utility of Genome-Wide Characterization of B-Cell Acute Lymphoblastic Leukemia Using SNP-Based Microarray

Pediatric B-cell acute lymphoblastic leukemia (B-ALL) is the most common childhood malignancy, and although event free survival has approached 90%, variability in disease outcomes still persists. At time of diagnosis, cytogenetic analysis of the leukemic clone currently dictates disease risk stratification, optimal therapeutic selection and overall prognosis. Cytogenetic analysis via conventional G-banded chromosome studies and fluorescence in situ hybridization (FISH) for the detection of recurrent rearrangements and characteristic gains and losses is the current gold standard. With the implementation of single nucleotide polymorphism (SNP)-based microarray tools within clinical laboratories (CytoScanHD and OncoScan/Affymetrix), a more precise characterization of B-ALL clones can be achieved. Here we demonstrate the utility of a SNP microarray in 4 illustrative pediatric patient cases seen at the Mayo Clinic Cytogenetics Laboratory to appropriately classify a variety of clinically significant B-ALL clones, including distinguishing hyperdiploidy versus pseudo-hyperdiploidy resulting from a doubled hypodiploid clone, identifying partial homozygous microdeletions of clinically-significant genes (e.g. CDNK2A/B and IKZF1) that fall below the resolution of FISH, and clarifying intrachromosomal amplification of chromosome 21 (iAMP21) unresolved by chromosome and FISH evaluation. These data indicate that the integration of a SNP-based microarray, along with concurrent chromosome and FISH evaluations, offers the most comprehensive cytogenetic analysis of a B-ALL clone.

48 - Getting to Know Your LCRs: Recognizing and Interpreting Atypical CNVs in Recurrent Syndromic Microdeletion/Duplication Regions Mediated by Alternative Low Copy Repeat Elements

Regions of the genome containing multiple low copy repeats (LCRs) are well known for recurrent deletions and duplications. The routine use of array-based technologies has expanded our understanding of the complexity and diversity of these recurrent rearrangements, historically detected by FISH. It is now clear that in addition to the common and clinically well-defined microdeletions/duplications, other CNVs in these regions are mediated by alternative LCRs. Interpretation of these atypical CNVs within regions of syndromic microdeletions/duplications is often challenging, especially when the critical genes for the phenotypes are not well defined. Additionally, identification of relevant patients from the medical literature can be cumbersome, as most historical papers refer to previously established LCR nomenclature rather than genomic coordinates. Additional care must be taken when reporting these results and referencing relevant literature, as there can be significant clinical differences between typical and atypical deletions/duplications. Focusing on genomic regions containing recurrent CNVs mediated by LCRs, we have curated .bed and .aed files to illustrate the position and conventional names of both common and atypical breakpoint LCRs in those regions. This allows for rapid recognition of typical and atypical deletions/duplications, and also provides an easy reference to both LCR nomenclature and current genomic coordinates. We will review the current clinical understanding of both typical and atypical CNVs in recurrent microdeletion/duplication regions (e.g. 22q11.2, 15q11.2-13, and 7q11.23), provide a collection of relevant literature to aid interpretations, and highlight the utility of this easy to use resource when interpreting typical and atypical recurrent LCR-mediated copy number variation.

Biphenotypic sinonasal sarcoma: an expanded immunoprofile including consistent nuclear β-catenin positivity and absence of SOX10 expression

Biphenotypic sinonasal sarcoma (BSNS) is a recently recognized low-grade sarcoma that exhibits both neural and myogenic differentiation. This unique dual phenotype stems from recurrent rearrangements in PAX3, a transcription factor that promotes commitment along both lineages. While identification of PAX3 rearrangements by fluorescence in situ hybridization (FISH) can confirm a BSNS diagnosis, this assay is not widely available. This study evaluates whether an expanded immunohistochemical panel can facilitate recognition of BSNS without molecular analysis. Eleven cases of BSNS were identified from the surgical pathology archives of two academic medical centers. In 8 cases, the diagnosis was confirmed by FISH using custom probes for PAX3. In 3 cases, FISH failed but histologic and immunophenotypic findings were diagnostic for BSNS. All 11 BSNS (100%) were at least focally positive for S100 as well as calponin and/or smooth muscle actin. In addition, 10 (91%) of 11 expressed nuclear β-catenin, 8 (80%) of 10 expressed factor XIIIa, 4 (36%) of 11 expressed desmin, and 3 (30%) of 10 expressed myogenin. All 11 tumors were negative for SOX10. While no single marker resolves immunohistochemical overlap between BSNS and its histologic mimickers such as nerve sheath tumors, an extended immunohistochemical panel that includes β-catenin and SOX10 helps to support the diagnosis of BSNS without the need for gene rearrangement studies.

MP90-06 FULL EXOME SEQUENCING, COPY NUMBER VARIATION AND TRANSCRIPTOME ANALYSES REVEALS DIVERSITY AND MUTATIONAL EVOLUTION IN A LONGITUDINAL SERIES OF SURGICAL PROSTATE CANCER BONE METASTASES FROM A PATIENT WITH PROGRESSIVELY THERAPY-RESISTANT CANCER.

You have accessJournal of UrologyProstate Cancer: Basic Research & Pathophysiology IV1 Apr 2016MP90-06 FULL EXOME SEQUENCING, COPY NUMBER VARIATION AND TRANSCRIPTOME ANALYSES REVEALS DIVERSITY AND MUTATIONAL EVOLUTION IN A LONGITUDINAL SERIES OF SURGICAL PROSTATE CANCER BONE METASTASES FROM A PATIENT WITH PROGRESSIVELY THERAPY-RESISTANT CANCER. Christina Jamieson, Michelle Muldong, Michael A. Liss, Seung Chol Park, Theresa Mendoza, Abigail Gallegos, Lee Edsall, Unwanaobong Nseyo, Olga Miakicheva, Brittany Burton, Danielle Burner, Amy Strasner, Christopher J. Kane, Anna A. Kulidjian, and Theresa Gaasterland Christina JamiesonChristina Jamieson More articles by this author , Michelle MuldongMichelle Muldong More articles by this author , Michael A. LissMichael A. Liss More articles by this author , Seung Chol ParkSeung Chol Park More articles by this author , Theresa MendozaTheresa Mendoza More articles by this author , Abigail GallegosAbigail Gallegos More articles by this author , Lee EdsallLee Edsall More articles by this author , Unwanaobong NseyoUnwanaobong Nseyo More articles by this author , Olga MiakichevaOlga Miakicheva More articles by this author , Brittany BurtonBrittany Burton More articles by this author , Danielle BurnerDanielle Burner More articles by this author , Amy StrasnerAmy Strasner More articles by this author , Christopher J. KaneChristopher J. Kane More articles by this author , Anna A. KulidjianAnna A. Kulidjian More articles by this author , and Theresa GaasterlandTheresa Gaasterland More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2016.02.2550AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Prostate cancer metastasizes to bone in 50-90% of patients with advanced disease yet relatively little is known about genome-wide genetic alterations in prostate cancer bone metastases. Recent whole genome, exome and transcriptome sequencing studies on prostate cancer have identified recurrent mutations and gene rearrangements such as the TMPRSS2-ERG fusion and variants of the androgen receptor (AR). Here we determined bone metastatic prostate cancer genomic and transcriptomic variation in a longitudinal series of surgical bone metastasis samples from the same patient. METHODS We collected surgical prostate cancer bone metastases samples at the time of orthopaedic repair surgery with matched peripheral blood and prostatectomy tissue and established a new bone-niche xenograft model with a primary patient surgical prostate cancer bone metastasis, PCSD1 (Prostate Cancer San Diego 1). Next generation whole exome sequencing was performed on genomic DNA extracted from flash frozen samples or single cell suspensions of surgical bone metastasis specimens, peripheral blood mononuclear cells and from primary FFPE archived prostatectomy tissue. DNA libraries were prepared using the NimbleGen DNA Sample Preparation kit and sequencing was performed on the Illumina HiSeq 2000 sequencing platform. Affymetrix Oncoscan analysis was used to determine genome-wide copy number and loss-of-heterozygosity (LOH) profiles. Whole transcriptome analysis was performed using Affymetrix GeneChip Human Transcriptome Array 2.0. RESULTS We generated full exome sequences to determine the impact of acquired somatic mutations driving lethal and recurrent bone metastatic CRPC, as well as impact of treatment first with androgen deprivation therapy (ADT), then additional radiation plus docetaxel and, lastly, abiraterone plus cabazitaxel from sequential surgeries in a single patient. We also sequenced the whole exome of PCSD1 intra-femoral xenograft tumors to determine the impact of in vivo xenograft models on the exomic integrity of prostate cancer bone metastasis. Sequence analysis has identified SNVs, small insertion and deletions, translocations and additional gene rearrangements that are shared as well as unique to each bone metastatic sample. Integration of exome sequencing, CNV and microarrays revealed activation of WNT5a in prostate cancer bone metastases. CONCLUSIONS This is a whole exome and transcriptome report on a unique set of samples from one patient: blood (germ line), primary tumor, surgical bone metastasis sample #1 after ADT, bone metastasis #2 after ADT, radiation and docetaxel, bone metastasis #3 after abiraterone, radiation, plus cabazitaxel. Analysis of surgical prostate cancer bone metastases at different stages of treatment and progression in this patient provides a foundation to profile genomic diversity in recurrent bone metastatic prostate cancer. Mutations and activation of Wnt5a are being tested int the matched patient derived xenograft, PCSD1. © 2016FiguresReferencesRelatedDetails Volume 195Issue 4SApril 2016Page: e1146-e1147 Advertisement Copyright & Permissions© 2016MetricsAuthor Information Christina Jamieson More articles by this author Michelle Muldong More articles by this author Michael A. Liss More articles by this author Seung Chol Park More articles by this author Theresa Mendoza More articles by this author Abigail Gallegos More articles by this author Lee Edsall More articles by this author Unwanaobong Nseyo More articles by this author Olga Miakicheva More articles by this author Brittany Burton More articles by this author Danielle Burner More articles by this author Amy Strasner More articles by this author Christopher J. Kane More articles by this author Anna A. Kulidjian More articles by this author Theresa Gaasterland More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning

Somatic mutation in neurons is linked to neurologic disease and implicated in cell-type diversification. However, the origin, extent, and patterns of genomic mutation in neurons remain unknown. We established a nuclear transfer method to clonally amplify the genomes of neurons from adult mice for whole-genome sequencing. Comprehensive mutation detection and independent validation revealed that individual neurons harbor ∼100 unique mutations from all classes but lack recurrent rearrangements. Most neurons contain at least one gene-disrupting mutation and rare (0-2) mobile element insertions. The frequency and gene bias of neuronal mutations differ from other lineages, potentially due to novel mechanisms governing postmitotic mutation. Fertile mice were cloned from several neurons, establishing the compatibility of mutated adult neuronal genomes with reprogramming to pluripotency and development.

Abstract PD2-05: Evaluating the role of recurrent ESR1-CCDC170 in breast cancer endocrine resistance

Abstract Background Recurrent gene fusions resulting from chromosome translocations are critical genetic aberrations causing cancer. In our previous study, we identified recurrent rearrangements between ESR1 and its neighbor, CCDC170, in 6-8% of luminal B tumors. Luminal B subtype is a more aggressive ER+ breast cancer, with a higher risk of early relapse after endocrine therapy. These rearrangements enable the expression of N-terminally truncated CCDC170 (ΔCCDC170) under ESR1 promoter. Consistent with the behavior of luminal B tumors, ectopic ΔCCDC170 expression in ER+ breast cancer cells, led to markedly increased cell motility, invasion, anchorage-independent growth, and reduced endocrine sensitivity in vitro, as well as enhanced xenograft growth in vivo. In the present study, we studied the role of ESR1-CCDC170 in breast cancer endocrine resistance in vivo and explored the potential mechanism. Methods To study endocrine resistance in vivo, we transplanted T47D cells stably overexpressing (OE) control (empty) construct or 2 ΔCCDC170 fusion variants (E2-E7 and E2-E10) bilaterally to 4-6 week old female athymic nude mice (supplemented with 17β-estradiol pellets). The tumor growth was monitored biweekly and tumor volume was measured by the formula 1/2(length × width2). When the tumors reach 150–200 mm3, mice were randomly allocated to vehicle or tamoxifen (tam) treatment groups. For ERE luciferase assay, cells were co-transfected with ERE luciferase reporter (ERE-TK-Luc) and pCMV β-galactosidase. The luciferase levels were measured and normalized to β-gal activity. For immunoblot analysis, T47D OE cells were estrogen-deprived, serum-starved, and treated with vehicle, estrogen (E2) or tam. Reverse Phase Protein Array (RPPA) analysis was performed using ∼200 validated antibodies against an array of key signaling molecules in cancer. Results Our in vivo endocrine sensitivity study showed that, while T47D vector control tumors mostly regressed after tam treatment, the regression of E2-E7 tumors was significantly slower. Moreover, E2-E10 tumors continued to grow despite tam treatment. These observations suggest that ΔCCDC170 may render the T47D xenografts less sensitive to tam in vivo. Kaplan–Meier analysis revealed a significantly worse progression-free survival (defined by tumor doubling time) for E2-E7 (p&amp;lt;0.01) and E2-E10 (p&amp;lt;0.001) tumors treated with tam compared to control tumors. ΔCCDC170 expression in T47D cells enhanced the ER transcriptional activity in the presence of E2 but not tam, suggesting that the fusion-mediated endocrine-sensitivity changes is unlikely due to restoration of classic ER activity. Immunoblot analysis of T47D OE cells revealed hyperactive growth factor signaling even after serum withdrawal, which was not significantly affected by tam treatment. Preliminary RPPA analysis revealed upregulation of key signaling molecules in T47D cells expressing ΔCCDC170, such as Her3, AMPK, Akt, Erk, c-Myc, and Src-3. Conclusion These data suggest a potential role of ESR1-CCDC170 in mediating breast cancer endocrine resistance, presumably due to hyperactive growth factor signaling endowed by this fusion. Further studies are required to elucidate the role of endogenous ESR1-CCDC170 in breast cancer endocrine resistance, and discover the precise engaged mechanisms. Citation Format: Hu Y, Veeraraghavan J, Wang X, Tan Y, Kim J, Schiff R, Wang X-S. Evaluating the role of recurrent ESR1-CCDC170 in breast cancer endocrine resistance. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr PD2-05.

The Current Status of Solitary Fibrous Tumor: Diagnostic Features, Variants, and Genetics.

Solitary fibrous tumor (SFT) is a fibroblastic mesenchymal tumor originally described in the pleura but now shown at almost every anatomic site. Histopathologically, SFT is characteristically a circumscribed neoplasm composed of variably cellular and patternless distributions of bland spindle and ovoid cells within prominent collagenous stroma and shows diffuse expression of CD34, but it has a broad spectrum of both morphology and of biologic behavior. Many different names (particularly hemangiopericytoma) were previously used in the course of our understanding of this neoplasm but are now subsumed under the term "SFT," and the putative cell of origin was debated. However, it is now recognized that SFT is a translocation-associated neoplasm, consistently associated with NAB2-STAT6 gene fusions arising from recurrent intrachromosomal rearrangements on chromosome 12q, and this translocation is a likely major contributor to its pathogenesis. While most SFT with classical morphologic features behave in an indolent manner and those with overtly malignant histologic features tend to be aggressive neoplasms that behave as high-grade sarcomas, the behavior of SFT is unpredictable, and it is important to be aware of the propensity for aggressive behavior in a minority of histologically classical SFT and to ensure adequate clinical follow-up. Surgical excision remains the treatment gold standard; while radiotherapy and conventional chemotherapeutic agents have only shown limited efficacy, further understanding of the molecular events underlying tumorigenesis may allow the development of novel targeted treatments. We review SFT, discussing the morphologic spectrum and variants, including malignant and dedifferentiated subtypes, clinicopathological aspects, recent molecular genetic findings, and the differential diagnosis.