Gain Of Chromosome Research Articles

Abstract 3842: Potent antitumor activity of the HSP90 inhibitor SNX-2112 in type 1 papillary renal cell carcinoma

Abstract Papillary renal-cell carcinoma (pRCC) is the second most common form of kidney cancer, accounting for 15 to 20% of all cases. There are currently no treatment options of proven benefit for patients with advanced pRCC. The type 1 subset of pRCC tumors are associated with gain of chromosome 7 and activating mutations of MET that could lead to aberrant MET pathway activation resulting in cell proliferation and anti-apoptotic signaling. While MET kinase inhibitors are active in some patients with type 1 pRCC, primary and acquired resistance is common, prompting us to investigate possible therapeutic alternatives. Heat shock protein 90 (Hsp90), which stabilizes numerous oncogenic proteins, including MET and several downstream mediators of MET activity, is an important regulator of cell proliferation and survival, and has attracted wide interest as a novel target for cancer therapy. Hsp90 inhibitors were also identified as molecules of interest based on antitumor activity against patient derived type 1 pRCC cell lines following quantitative high throughput screening (qHTS) with small molecule libraries. We hypothesized that inhibition of Hsp90 might provide a novel therapeutic approach for patients with pRCC tumors with MET pathway activation. SNX-2112 was chosen as a candidate Hsp90 inhibitor for further evaluation. Our data demonstrate that inhibition of the Hsp90 pathway is lethal to pRCC cell lines with MET pathway activation, and that treatment with SNX-2112 leads to the degradation of MET/pMET and its downstream signaling intermediates p-AKT, AKT, p-ERK. Furthermore, SNX-2112 leads to inhibition of critical downstream transcriptional targets of AKT and ERK, including VEGF, c-Myc and BIRC5. SNX-2112 has potent anti-tumor activity in vitro, inhibiting proliferation, clonogenicity and 3D-anchorage independent colony formation of MET activated pRCC cell lines. These data demonstrate that Hsp90 inhibition is a promising therapeutic strategy in Type 1 pRCC and is worthy of further preclinical and clinical evaluation. Citation Format: Roma Pahwa, Abhigya Giri, Carole Sourbier, Craig Thomas, W Marston Linehan, Len Neckers, Ramaprasad Srinivasan. Potent antitumor activity of the HSP90 inhibitor SNX-2112 in type 1 papillary renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3842.

Abstract 3369: Mosaic chromosome X copy-number aberrations in leukocytes of never-smoking lung cancer patients: The Female Lung Cancer Consortium in Asia (FLCCA)

Abstract Lung cancer (LC) is a global health burden that accounted for 1.69 million deaths worldwide in 2015. Asian women have high incidence rates of LC, with about half of all diagnoses occurring among never-smokers. Chromosomal copy-number (CN) aberrations can arise de novo in somatic cells with progressing age. These genomic alterations can change the dosage of critical genes and impact biological processes. Gains and losses of Chromosome X in a proportion of cells (ChrX mosaicism) are markers of genomic instability; however, their relationship with LC is unclear. We characterized leukocyte ChrX mosaicism among never-smoking Asian female LC patients and cancer-free controls. We investigated 5,137 LC cases (4,477 adenocarcinomas (AC) and 660 squamous cell carcinomas (SCC)) and 4,535 controls from 13 case-control studies and one cohort study in the Female Lung Cancer Consortium in Asia. Subjects were aged 19-91 years from China, Singapore, Taiwan, South Korea, and Japan. In case-control studies, blood was drawn after diagnosis and mostly before treatment. Leukocyte DNA was genotyped on Illumina 660W arrays, with a small subset on 610Q and 370K arrays. ChrX mosaicism was detected using normalized log R ratio (LRR) and B allele frequency (BAF) values from probes covering ChrX. ChrX was segmented for mosaic events (gains, losses, and copy-neutral) using circular binary segmentation on BAF values. Segments <2 Mb were excluded. Event CN state was assigned based on LRR values. LRR deviations of 0.01 and −0.01 were used to classify events as gain and losses, respectively, for ChrX-spanning mosaic events; while thresholds of 0.05 and −0.05 were used for those spanning a portion of ChrX. Mosaic proportions were estimated using deviation from the expected BAF given the LRR-defined CN state. Fisher's Exact tests on 2x3 and 2x2 tables were used to compare ChrX mosaic events between LC cases and controls. Exact logistic regression was used to assess associations between combined gain and loss events and AC. We found 18 detectable mosaic ChrX events (0.19%) in 12 women. LC cases had 5 gains, 3 losses, and 4 copy-neutral mosaic events; while controls had no gains, 1 loss, and 5 copy-neutral events (p=9.8E-2). AC patients had significantly more combined gains and losses (n=7) and fewer copy-neutral events (n=0) compared to controls who had 1 combined gain and loss and 5 copy-neutral events (p=4.7E-3). Notably, all 5 gains were among AC and none among controls (p=3.5E-3). Women with combined gain and loss events had 7 times the odds of AC compared to those without them (p=3.8E-2). Our preliminary findings suggest a possible role of leukocyte ChrX mosaicism, particularly CN gains, in the biological mechanism of LC development. However, given the rarity of these events and possible disease-effect, larger studies are needed to further evaluate ChrX mosaicism as a risk factor for future occurrence of LC. Citation Format: Jason Y. Wong, Mitchell Machiela, Weiyin Zhou, Wei Jie Seow, Bryan Bassig, Jinming Zhang, Meredith Yeager, Wei Zheng, Xiao-Ou Shu, Hongbing Shen, Keitaro Matsuo, Chao Agnes Hsiung, Maria P. Wong, Yun-Chul Hong, Jiu-cun Wang, Yi-Long Wu, Baosen Zhou, Robert Klein, Zhihua Yin, Tangchun Wu, Pan-Chyr Yang, Yong-Bing Xiang, Adeline Seow, Yu-Tang Gao, Chen Wu, Jianjun Liu, Zhibin Hu, Laurie Burdett, Qiuyin Cai, Juncheng Dai, Dongxin Lin, Kexin Chen, Stephen Chanock, Nathaniel Rothman, Qing Lan. Mosaic chromosome X copy-number aberrations in leukocytes of never-smoking lung cancer patients: The Female Lung Cancer Consortium in Asia (FLCCA) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3369.

Abstract 2189: Genomic dynamics in breast cancer progression analyzed by miFISH analysis

Abstract Our previous studies of synchronous Ductal Carcinomas in Situ (DCIS) and Invasive Ductal Carcinomas (IDC) often showed a high degree of chromosomal instability already in DCIS, and frequently a direct clonal evolution from DCIS to IDC. We now asked the question whether this degree of instability is also present in DCIS that did not progress to IDC. In collaboration with Englewood Hospital and Medical Center, we are therefore conducting a retrospective study analyzing FFPE material from 20 DCIS patients with low-grade or high-grade DCIS who did not present with invasive breast carcinoma during their follow-up (5-10 years) and compared the findings to 10 DCIS patients who presented with synchronous IDC. Using our novel multiplex interphase FISH (miFISH) assay, we are able to determine copy number changes of five oncogenes (COX2, MYC, CCND1, HER2, ZNF217) and three tumor suppressor genes (DBC2, CDH1, TP53) and assessed intratumor heterogeneity (ITH) and clonal evolution during disease progression. The miFISH analysis showed that low-grade DCIS displayed mostly stable patterns of gene copy numbers in a diploid genome, while high-grade DCIS frequently had increased nuclear DNA content (ploidy) associated with a higher degree of ITH. However, some low-grade DCIS exhibited complex and unstable patterns with higher ploidy. Also, a few high-grade DCIS were defined by few copy number changes, e.g., the gain of a whole chromosome 8 (DBC and MYC), resulting in a clonal population with a low instability index. DCIS and their synchronous IDC often displayed very similar miFISH patterns indicating direct expansion of dominant clones. Of note, the DCIS cells of one case were defined by the well described 1q gain/16q loss pattern and acquired subsequently a chromosome 8 gain in the IDC, confirming our previous observation that the gain of MYC is a pivotal step in breast cancer progression. Our data also show that DCIS with or without synchronous IDC exhibited similar patterns. This could indicate that DCIS in general, regardless of grading, should be treated as lesions with progressive potential. Phylogenetic tree modeling with our custom FISHtrees software will further elucidate the dynamics of DCIS lesions. In summary, miFISH analysis and phylogenetic tree modeling allow an in-depth characterization of precursor lesions and their evolutionary trajectory. We anticipate that this approach will ultimately help to stratify progression risk in patients with DCIS. Citation Format: Irianna Marie Torres, Leanora Hernandez, Jausheng Tzeng, Russell Schwartz, Alejandro Schaffer, Edward Michael Gertz, Daniela Hirsch, Steven Brower, Miguel Sanchez, Gert Auer, Kerstin Heselmeyer-Haddad, Thomas Ried. Genomic dynamics in breast cancer progression analyzed by miFISH analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2189.

Abstract LB-026: iDEP: integrated differential expression and pathway analysis of RNA-Seq data

Abstract Analysis and interpretation of RNA-Seq data remain a challenge for bench scientists. We aim to develop a user-friendly web application for exploratory data analysis (EDA), differential expression, and pathway analysis using summarized gene-level data from RNA-Seq, DNA microarray or other platforms. The key idea of iDEP (integrated Differential Expression and Pathway analysis) is to make many powerful R/Bioconductor packages easily accessible by wrapping them under a graphical interface, alongside annotation databases. For EDA, it performs hierarchical clustering, k-means clustering, and principal component analysis. iDEP detects differentially expressed genes using the limma and DESeq2 packages. For a group of co-expressed genes, it identifies enriched gene ontology (GO) terms as well as transcription factor binding motifs in promoters. Pathway analysis can be performed using packages like GAGE, GSEA, PGSEA, or ReactomePA. iDEP can also detect chromosomal gain or loss using the PREDA package. iDEP uses annotation of 163 metazoa and 45 plant genomes in Ensembl for ID mapping and GO functional categorization. Common gene IDs including microarray probe names can be automatically recognized. Pathway information was also compiled from databases like KEGG, Reactome, MSigDB, GSKB, GeneSetDB, and araPath. As an example, we analyzed an RNA-Seq dataset involving siRNA-mediated Hoxa1 knockdown in lung fibroblasts, and identified the downregulation of cell-cycle genes, in agreement with previous studies. Our analyses also reveal the possible roles of E2F1 and its target genes, including microRNAs, in blocking G1/S transition, and the upregulation of genes related to cytokines, lysosome, and neuronal parts. iDEP enables users to conduct in-depth bioinformatics analysis of transcriptomic data through a graphical interface. Freely available at http://gelab.org/idep/ Citation Format: Steven X. Ge. iDEP: integrated differential expression and pathway analysis of RNA-Seq data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-026.

CDKN2A loss and PIK3CA mutation in myoepithelial-like metaplastic breast cancer.

Metaplastic breast carcinoma comprises a heterogeneous group of tumours with poorly understood pathogenesis. A subset of metaplastic breast cancers show myoepithelial differentiation and constitute a morphological spectrum with ill-defined borders from fibromatosis-like spindle cell carcinoma to myoepithelial carcinoma. In a series of 34 metaplastic breast cancers with spindle cell and myoepithelial differentiation, we found recurrent genetic aberrations, which set them apart from other metaplastic breast cancers and suggest a unique pathogenesis. The majority of cases (28 of 34 patients; 82.4%) showed distinct chromosomal loss in the 9p21.3 region, including CDKN2A and CDKN2B. Biallelic loss of the CDKN2A/B region was found in 50% of deleted cases. Expression of the cyclin-dependent kinase inhibitor CDKN2A (p16) was missing in all samples affected by 9p21.3 loss. Other genomic alterations frequently occurring in triple-negative and metaplastic breast cancer were absent or found in only a minority of cases. Gains of whole chromosome 5 and chromosomal region 5p were observed in nine cases, and were associated with recurrences (p < 0.001). In 64.3% of cases, 9p21.3 loss was accompanied by concurrent PIK3CA mutation. Both genomic abnormalities were also detectable in adenomyoepitheliomas (4/12), which are considered to represent the precursor lesion of myoepithelial metaplastic breast cancer. In adenomyoepithelioma, PIK3CA mutation was present in both luminal epithelial and myoepithelial cells, whereas p16 loss was found only in the latter. We conclude that 9p21.3 (CDKN2A) loss and PIK3CA mutation characterize a subgroup of metaplastic breast cancers with myoepithelial and spindle cell differentiation. Myoepithelial cells in adenomyoepithelioma may show identical aberrations. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

X chromosome gain is related to increased androgen receptor expression in male breast cancer.

X chromosome gain has been previously described in male breast cancer (MBC). Androgen receptor (AR) gene is located on X chromosome. The aim of this study was to investigate the role of the X chromosome gain in the development of MBC and its relation with AR gene copy number and expression.The X chromosome status was assessed in 66 cases of male invasive and in situ duct breast carcinoma, in 34 cases of gynecomastia associated with cancer, and in 11 cases of tumor-free gynecomastia. Cases were tested by fluorescence in situ hybridization (FISH) to assess the X chromosome status and AR amplification. AR expression was studied by immunohistochemistry (IHC). In addition, AR methylation status was assessed.X chromosome gain was observed in 74.7% of invasive duct carcinoma, in 20.6% of in situ duct carcinoma, and in 14.6% of gynecomastia when associated with cancer, while all cases of tumor-free gynecomastia showed wild X chromosome asset. AR gene copy number when increased paralleled the number of X chromosomes. AR IHC expression was observed in 100% of MBC tested. AR gene methylation status revealed low level or absence of methylation.These data suggest that X chromosome can play a role in the neoplastic transformation of male breast epithelium. X chromosome gain is paralleled by AR gene polysomy. Polysomic AR genes show low methylation levels and high AR protein expression on IHC. These data should be taken into consideration for MBC treatment planning.

49. A case study of trisomy 13 mosaicism

A newborn male infant presented to the neonatal intensive care unit with respiratory distress, congenital heart disease (VSD, ASD, PDA), neonatal teeth, polydactyly in feet and hands, and undescended testes. Pregnancy was complicated by late prenatal care and history of substance abuse. Chromosomal microarray analysis (CMA) was performed on a peripheral blood specimen from this infant. Initially, the CMA software called a modest copy gain of 8 Mb with a mean log ration of 0.2, a value below our cutoff of >0.4. Upon closer examination of the scatter plot, a larger copy number gain of chromosome 13 was suspected. FISH was therefore ordered with probes for the long arm of chromosome 13 and results showed trisomy in 13% of cells, with the abnormal cells showing a der(13;13). Conventional cytogenetic analysis was subsequently performed and revealed a karyotype of 46,XY,der(13)t(13;13)(p11.2;q13) in 20% of cells examined.

Mps1 inhibitors synergise with low doses of taxanes in promoting tumour cell death by enhancement of errors in cell division

BackgroundChromosomal instability (CIN) is a common trait of cancer characterised by the continuous gain and loss of chromosomes during mitosis. Excessive levels of CIN can suppress tumour growth, providing a possible therapeutic strategy. The Mps1/TTK kinase has been one of the prime targets to explore this concept, and indeed Mps1 inhibitors synergise with the spindle poison docetaxel in inhibiting the growth of tumours in mice.MethodsTo investigate how the combination of docetaxel and a Mps1 inhibitor (Cpd-5) promote tumour cell death, we treated mice transplanted with BRCA1−/−;TP53−/− mammary tumours with docetaxel and/or Cpd-5. The tumours were analysed regarding their histopathology, chromosome segregation errors, copy number variations and cell death to understand the mechanism of action of the drug combination.ResultsThe enhanced efficacy of combining an Mps1 inhibitor with clinically relevant doses of docetaxel is associated with an increase in multipolar anaphases, aberrant nuclear morphologies and cell death. Tumours treated with docetaxel and Cpd-5 displayed more genomic deviations, indicating that chromosome stability is affected mostly in the combinatorial treatment.ConclusionsOur study shows that the synergy between taxanes and Mps1 inhibitors depends on increased errors in cell division, allowing further optimisation of this treatment regimen for cancer therapy.

Chromosome Segregation Is Biased by Kinetochore Size

SummaryChromosome missegregation during mitosis or meiosis is a hallmark of cancer and the main cause of prenatal death in humans. The gain or loss of specific chromosomes is thought to be random, with cell viability being essentially determined by selection. Several established pathways including centrosome amplification, sister-chromatid cohesion defects, or a compromised spindle assembly checkpoint can lead to chromosome missegregation. However, how specific intrinsic features of the kinetochore—the critical chromosomal interface with spindle microtubules—impact chromosome segregation remains poorly understood. Here we used the unique cytological attributes of female Indian muntjac, the mammal with the lowest known chromosome number (2n = 6), to characterize and track individual chromosomes with distinct kinetochore size throughout mitosis. We show that centromere and kinetochore functional layers scale proportionally with centromere size. Measurement of intra-kinetochore distances, serial-section electron microscopy, and RNAi against key kinetochore proteins confirmed a standard structural and functional organization of the Indian muntjac kinetochores and revealed that microtubule binding capacity scales with kinetochore size. Surprisingly, we found that chromosome segregation in this species is not random. Chromosomes with larger kinetochores bi-oriented more efficiently and showed a 2-fold bias to congress to the equator in a motor-independent manner. Despite robust correction mechanisms during unperturbed mitosis, chromosomes with larger kinetochores were also strongly biased to establish erroneous merotelic attachments and missegregate during anaphase. This bias was impervious to the experimental attenuation of polar ejection forces on chromosome arms by RNAi against the chromokinesin Kif4a. Thus, kinetochore size is an important determinant of chromosome segregation fidelity.

Combined somatic mutation and copy number analysis in the survival of familial CLL.

Recurrent large-scale somatic copy number alterations (SCNAs), and somatic point mutations can be analysed to stratify patients with chronic lymphocytic leukaemia (CLL) into distinct prognostic groups. To investigate the relationship between SCNAs and somatic mutations, we performed whole-exome sequencing and single nucleotide polymorphism microarray analyses on 98 CLL patients from 40 families with a high burden of CLL. Overall, 69 somatic mutations in 29 CLL driver genes were detected among 45 subjects (46%), with the most frequently mutated genes being TP53 (8·2%), NOTCH1 (8·2%) and ATM (5·1%). Additionally, 142 SCNAs from 54 subjects (57%) were detected, including losses of chromosome 13q14 (28·9%), 11q (5·6%), 17p (2·1%), and gain of chromosome 12 (4·2%). We found that patients having both an adverse point mutation in a CLL driver gene and an unfavourable SCNA tended to have poorer survival (Hazard ratio [HR]=3·17, 95% confidence interval [CI]=0·97-10·35; P=0·056) than patients having either a point mutation (HR=1·34, 95%CI=0·66-2·71; P=0·42) or SCNAs (HR=2·65, 95%CI=0·77-9·13; P=0·12). TP53 mutation carriers were associated with the poorest overall survival (HR=4·39, 95%CI=1·28-15·04; P=0·018). Our study suggests that combining SCNA and mutational data could contribute to predicting outcome in familial CLL.

Comparison of EpCAMhighCD44+ cancer stem cells with EpCAMhighCD44− tumor cells in colon cancer by single-cell sequencing

ABSTRACTCancer stem cells (CSCs) are considered to be responsible for tumorigenesis and cancer relapse. EpCAMhighCD44+ tumor cells are putative colorectal CSCs that express high levels of stem cell genes, while the EpCAMhighCD44− population mostly contains differentiated tumor cells (DTCs). This study aims to determine whether single CSC (EpCAMhighCD44+) and DTC (EpCAMhighCD44−) can be distinguished in terms of somatic copy number alterations (SCNAs). We applied fluorescence-activated cell sorting to isolate the CD45−EpCAMhighCD44+ and CD45−EpCAMhighCD44− populations from two primary colon tumors, on which low-coverage single-cell whole-genome sequencing (WGS) was then performed ∼0.1x depth. We compared the SCNAs of the CSCs and DTCs at single-cell resolution. In total, 47 qualified single cells of the two populations underwent WGS. The single-cell SCNA profiles showed that there were obvious SCNAs in both the CSCs and DTCs of each patient, and each patient had a specific copy number alteration pattern. Hierarchical clustering and correlation analysis both showed that the SCNA profiles of CSCs and DTCs from the same patient had similar SCNA pattern, while there were regional differences in the CSCs and DTCs in certain patient. SCNAs of CSCs in the same patient were highly reproducible. Our data suggest that major SCNAs occurred at an early stage and were inherited steadily. The similarity of ubiquitous SCNAs between the CSCs and DTCs might have arisen from lineage differentiation. CSCs from the same patient had reproducible SCNA profiles, indicating that gain or loss in certain chromosome is required for colon cancer development.

Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups

BackgroundMolecular data of histologically classified oligodendrogliomas are available offering the possibility to stratify these human brain tumors into clinically relevant molecular subtypes.MethodsGene copy number, mutation, and expression data of 193 histologically classified oligodendrogliomas from The Cancer Genome Atlas (TCGA) were analyzed by well-established computational approaches (unsupervised clustering, statistical testing, network inference).ResultsWe applied hierarchical clustering to tumor gene copy number profiles and revealed three molecular subgroups within histologically classified oligodendrogliomas. We further screened these subgroups for molecular glioma markers (1p/19q co-deletion, IDH mutation, gain of chromosome 7 and loss of chromosome 10) and found that our subgroups largely resemble known molecular glioma subtypes. We excluded glioblastoma-like tumors (7a10d subgroup) and derived a gene expression signature distinguishing histologically classified oligodendrogliomas with concurrent 1p/19q co-deletion and IDH mutation (1p/19q subgroup) from those with predominant IDH mutation alone (IDHme subgroup). Interestingly, many signature genes were part of signaling pathways involved in the regulation of cell proliferation, differentiation, migration, and cell-cell contacts. We further learned a gene regulatory network associated with the gene expression signature revealing novel putative major regulators with functions in cytoskeleton remodeling (e.g. APBB1IP, VAV1, ARPC1B), apoptosis (CCNL2, CREB3L1), and neural development (e.g. MYTIL, SCRT1, MEF2C) potentially contributing to the manifestation of differences between both subgroups. Moreover, we revealed characteristic expression differences of several HOX and SOX transcription factors suggesting the activity of different glioma stemness programs in both subgroups.ConclusionsWe show that gene copy number profiles alone are sufficient to derive molecular subgroups of histologically classified oligodendrogliomas that are well-embedded into general glioma classification schemes. Moreover, our revealed novel putative major regulators and characteristic stemness signatures indicate that different developmental programs might be active in these subgroups, providing a basis for future studies.

Increased HOXA5 expression provides a selective advantage for gain of whole chromosome 7 in IDH wild-type glioblastoma.

Glioblastoma is the most frequently occurring and invariably fatal primary brain tumor in adults. The vast majority of glioblastomas is characterized by chromosomal copy number alterations, including gain of whole chromosome 7 and loss of whole chromosome 10. Gain of whole chromosome 7 is an early event in gliomagenesis that occurs in proneural-like precursor cells, which give rise to all isocitrate dehydrogenase (IDH) wild-type glioblastoma transcriptional subtypes. Platelet-derived growth factor A (PDGFA) is one gene on chromosome 7 known to drive gliomagenesis, but, given its location near the end of 7p, there are likely several other genes located along chromosome 7 that select for its increased whole-chromosome copy number within glioblastoma cells. To identify other potential genes that could select for gain of whole chromosome 7, we developed an unbiased bioinformatics approach that identified homeobox A5 (HOXA5) as a gene whose expression correlated with gain of chromosome 7 and a more aggressive phenotype of the resulting glioma. High expression of HOXA5 in glioblastoma was associated with a proneural gene expression pattern and decreased overall survival in both human proneural and PDGF-driven mouse glioblastoma. Furthermore, HOXA5 overexpression promoted cellular proliferation and potentiated radioresistance. We also found enrichment of HOXA5 expression in recurrent human and mouse glioblastoma at first recurrence after radiotherapy. Overall, this study implicates HOXA5 as a chromosome 7-associated gene-level locus that promotes selection for gain of whole chromosome 7 and an aggressive phenotype in glioblastoma.

Correction: Molecular Subtypes in Head and Neck Cancer Exhibit Distinct Patterns of Chromosomal Gain and Loss of Canonical Cancer Genes.

[This corrects the article DOI: 10.1371/journal.pone.0056823.].

The deregulated microRNAome contributes to the cellular response to aneuploidy

BackgroundAneuploidy, or abnormal chromosome numbers, severely alters cell physiology and is widespread in cancers and other pathologies. Using model cell lines engineered to carry one or more extra chromosomes, it has been demonstrated that aneuploidy per se impairs proliferation, leads to proteotoxic as well as replication stress and triggers conserved transcriptome and proteome changes.ResultsIn this study, we analysed for the first time miRNAs and demonstrate that their expression is altered in response to chromosome gain. The miRNA deregulation is independent of the identity of the extra chromosome and specific to individual cell lines. By cross-omics analysis we demonstrate that although the deregulated miRNAs differ among individual aneuploid cell lines, their known targets are predominantly associated with cell development, growth and proliferation, pathways known to be inhibited in response to chromosome gain. Indeed, we show that up to 72% of these targets are downregulated and the associated miRNAs are overexpressed in aneuploid cells, suggesting that the miRNA changes contribute to the global transcription changes triggered by aneuploidy. We identified hsa-miR-10a-5p to be overexpressed in majority of aneuploid cells. Hsa-miR-10a-5p enhances translation of a subset of mRNAs that contain so called 5’TOP motif and we show that its upregulation in aneuploids provides resistance to starvation-induced shut down of ribosomal protein translation.ConclusionsOur work suggests that the changes of the microRNAome contribute on one hand to the adverse effects of aneuploidy on cell physiology, and on the other hand to the adaptation to aneuploidy by supporting translation under adverse conditions.

Targeted Genomic Profiling Reveals Recurrent KRAS Mutations in Mesonephric-like Adenocarcinomas of the Female Genital Tract.

Mesonephric adenocarcinoma most commonly arises in the cervix and is presumed to be derived from normal or hyperplastic mesonephric remnants. It is characterized by recurrent KRAS mutations and lack of PIK3CA/PTEN alterations. Adenocarcinomas of the uterine corpus and ovary characterized by morphologic and immunophenotypic similarities to mesonephric adenocarcinoma have been reported. The pathogenesis of these tumors, which have been designated "mesonephric-like adenocarcinomas" is unknown, and it has been debated whether these represent mesonephric adenocarcinomas that arise in the endometrium/ovary or endometrioid adenocarcinomas that closely mimic mesonephric adenocarcinoma. The relationship at the molecular level between mesonephric adenocarcinomas and mesonephric-like adenocarcinomas is unknown. The aim of this study was to examine the molecular alterations in mesonephric-like adenocarcinomas to identify driver mutations and potential therapeutically targetable mutations, and to determine the relationship between mesonephric-like adenocarcinomas and mesonephric adenocarcinomas using targeted next-generation sequencing. Seven mesonephric-like adenocarcinomas (4 ovarian, 3 uterine corpus) underwent targeted next-generation sequencing to detect mutations, copy number variations and structural variants in exonic regions of 300 cancer genes, and 113 selected intronic regions across 35 genes. All 7 tumors (100%) harbored canonical activating KRAS mutations (4 G12D, 3 G12V). PIK3CA activating mutations were identified in 3 of 7 (43%) cases. There were no alterations in PTEN, ARID1A, or TP53 in any of the tumors. In copy number analysis, 5 of 7 (71%) tumors exhibited 1q gain, which was accompanied by 1p loss in 2 cases. In addition, 4 of 7 (57%) tumors had chromosome 10 gain, which was accompanied by gain of chromosome 12 in 3 cases. Mesonephric-like adenocarcinomas, similar to mesonephric adenocarcinomas, are characterized by recurrent KRAS mutations, gain of 1q, lack of PTEN mutations, and gains of chromosomes 10 and 12. PIK3CA mutations, which have not previously been identified in mesonephric adenocarcinoma, were found in 3 of 7 (43%) mesonephric-like adenocarcinomas in our study. Mesonephric-like adenocarcinomas exhibit strikingly similar molecular aberrations to mesonephric adenocarcinomas, but also frequently harbor PIK3CA mutations, demonstrating biological overlap with carcinomas of both mesonephric and Mullerian (endometrioid) differentiation. Given the previously documented association with endometriosis (ovarian neoplasms) and the prominent endometrial involvement (uterine corpus neoplasms), we believe these are best regarded as of Mullerian origin and representing adenocarcinomas which differentiate along mesonephric lines; as such, we propose the term mesonephric-like Mullerian adenocarcinoma.

Biphasic papillary renal cell carcinoma is a rare morphological variant with frequent multifocality: a study of 28 cases.

To further characterise biphasic squamoid renal cell carcinoma (RCC), a recently proposed variant of papillary RCC. We identified 28 tumours from multiple institutions. They typically showed two cell populations-larger cells with eosinophilic cytoplasm and higher-grade nuclei, surrounded by smaller, amphophilic cells with scanty cytoplasm. The dual morphology was variable (median 72.5% of tumour, range 5-100%); emperipolesis was found in all cases. The male/female ratio was 2:1, and the median age was 55 years (range 39-86 years). The median tumour size was 20 mm (range 9-65 mm). Pathological stage pT1a was found in 21 cases, pT1b in three, and pT3a and pT3b in one each (two not available). Multifocality was found in 32%: multifocal biphasic RCC in one case, biphasic + papillary RCC in two cases, biphasic + clear cell RCC in three cases, biphasic + low-grade urothelial carcinoma of the renal pelvis in one case, and biphasic + Birt-Hogg-Dubé syndrome in one case. Positive immunostains included: PAX8, cytokeratin (CK) 7, α-methylacyl-CoA racemase, epithelial membrane antigen, and vimentin. Cyclin D1 was expressed only in the larger cells. The Ki67 index was higher in the larger cells (median 5% versus ≤1%). Negative stains included: carbonic anhydrase 9, CD117, GATA-3, WT1, CK5/6, and CK20; CD10 and 34βE12 were variably expressed. Gains of chromosomes 7 and 17 were found in two evaluated cases. Follow-up was available for 23 patients (median 24 months, range 1-244 months): 19 were alive without disease, one was alive with recurrence, and one had died of disease (two had died of other causes). Biphasic papillary RCC is a rare variant of papillary RCC, and is often multifocal.

Cytogenetic study on some common bone tumours

This study aimed to detect the consistent chromosomal abnormalities of each type of common bone tumours . Thirty bone tumors specimens were processed for direct cytogenetic preparation , only (9 cases) showed success results for chromosomal preparation by banding technique , the results of cytogenetic study were 1- Osteosarcoma (4) cases revealed multiple numerical and structural changes with complex karyotype and pronounced cell to cell variation . chromosome 17 was the most frequent involved in these chromosomal alteration . Also loss or structural changes of chromosome 13 was found in (2) cases of osteosarcoma loss or gain of sex chromosome were detected in these cases , loss of Y chromosome in (2) cases ; loss of X chrosome in (1) case and gain of X chrosome in another case . 2- Osteochnodroma : reveled the simple numerical change with no structural change in one case . 3- Chondroblastoma : in this tumor structural and numerical abnormalities of chrosome 5 . 4- Chondrosarcoma : showed chromosomal aberration with multiple numerical and structural changes in chromosome (1) was of interest and monsomy 18 was reported in one case . 5- Giant cell tumors : It showed a complex changes and the range of chromosomal number was 50 – 58 with the characteristic telomeric fusion in malignant cases while simple numerical change only in benign giant cell tumor . Conclusion Cytogenetic study of both benign and malignant bone tumors have revealed abnormlities in the number and / or structures of chromosomes X, Y , 1,5,6,11 , 13,17,18 and complex chromosomal changes in malignant types of bone tumors .

Abstract A29: Omics profile of two immortalized Brazilian glioblastoma cell cultures

Abstract Background: Glioblastomas are the most frequent and deadly brain tumors. Genomic alterations, as well as its high heterogeneity, are important features of these tumors. Despite the advances in the biology of these tumors, it is essential to develop models, such as primary tumor cell lines, that better mimic their genomic diversity and therapeutic behavior. We aimed to characterize the molecular profile of two (HCB2 and HCB151) established immortalized glioblastoma cell lines. Methods: Immortalized glioblastoma cell lines, HCB2 and HCB151, were established from Barretos Cancer Hospital patients diagnosed with glioblastoma. The cells were cultured with DMEM+10%BFS+1%PS and molecularly characterized, using arrayCGH, next-generation sequencing (Ion Torrent) and validated by Sanger sequencing, miRNA expression and CNV using the NanoString platform, and BD Lyoplate™ Human Cell Surface Marker Screening Panel using Accuri™ C6 flow cytometer. The tumorigenic capacity was further determined in vivo by the chicken chorioallantoic membrane (CAM) assay, and its response to temozolomide-based chemotherapy was done by MTS. Results: The aCGH analysis showed that the most frequent events was the gain of chromosome 7 and loss of chromosomes 10, 13, and 17p. HCB2 exhibited mutations in the TERT gene, while HCB151 showed mutations in the TP53, PTEN, LZTR1, and TERT genes. The immortalized cultures present an unique miRNA profile. The CAM assay showed that HCB2 and HCB151 were able to form vascularized tumors, with HCB151 more aggressive than HCB2. In addition, both HCB2 (IC50&amp;gt;1000 µM) and HCB151 (IC50=783 µM) showed resistance to TMZ when compared to commercial glioblastomas cell lines (23-441 µM). Conclusion: The present findings showed that the immortalized glioblastoma cell lines showed classic genomic features of glioblastomas and exhibited a similar biologic behavior, suggesting that these cell lines are a good model for glioblastoma preclinical studies. Citation Format: Adriana Cruvinel-Carloni, Renato José da Silva-Oliveira, Viviane Aline Oliveira-Silva, Marcela Nunes Rosa, Lucas Tadeu Bidinotto, Gustavo Noriz Berdinarelli, Raul Torrieri, Adriane Feijó Evangelista, Olga Catarina Martinho, Vera Mónica Gonçalves, Carlos Clara, Gisele Caravina de Almeida, Rui Manuel Reis. Omics profile of two immortalized Brazilian glioblastoma cell cultures [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A29.

Molecular insights turning game for management of ependymoma: A review of literature

Molecular biology of ependymoma is being extensively studied in recent years, providing insights into newer therapeutic strategies. The different anatomic subgroups of ependymoma, namely supratentorial, posterior fossa (PF), and spinal, pose entirely different clinical behavior and prognosis. Recently, nine molecular subgroups of ependymoma have been identified, one of which has been incorporated into the WHO classification. Further understanding of the molecular biology of ependymoma is vital to expand its clinical utility. Here, we performed a review of the literature on the molecular biology of ependymoma. Therapeutic avenues include: (1) targeted agents against – (a) chromothripsis-induced nuclear factor-kappa beta signaling, (b) gene silencing by DNA methylation, (c) increased telomerase activity, and (d) microRNA and (2) de-escalating treatment in good prognostic subgroup such as PFB. The prognostic value of different chromosomal gain or loss is being better understood and may serve as prognostic signatures in future. Faster adoption of molecular classification into clinical practice requires simpler identification techniques using immunohistochemical surrogates for molecular subgroups, for example, cell adhesion molecule L1 for v-rel reticuloendotheliosis viral oncogene homolog A (RELA) fusion, laminin subunit alpha 2, tenascin-C, and neural epidermal growth factor-like 2 for PFA and PFB. Identification of poor prognostic markers such as RELA fusion and PFA has necessitated future research impetus to be directed to find more efficacious treatment approach in these groups.