Polysomy Of Chromosome Research Articles

CDK4 gene copy number increase and concurrent genetic changes in acral melanoma of a Chinese cohort

Acral melanoma (AM) is the most common subtype of melanoma in Asian population. Abnormalities in the p16-cyclin D1-CDK4 signalling pathway play a crucial role in the development and progression of AM. However, the alterations of CDK4 gene copy number in AM are underreported. In this study, we investigated CDK4 gene copy number and concurrent molecular changes in a Chinese cohort with AM, in aim of exploring CDK4 gene alterations and its significance in AM. We examined copy number alterations of CDK4 with fluorescence in situ hybridisation (FISH) in 31 patients with AM. Six patients with CDK4 high-level copy number increase were examined by next-generation sequencing to detect concurrent molecular changes. Using FISH, 12 (12/31, 38.7%) cases showed CDK4 copy number increase, with 6 (6/31, 19.4%) low-level copy number increase and 6 (6/31, 19.4%) high-level copy number increase. Five of six CDK4 low-level copy number increase cases were accompanied by polysomy of chromosome 12, while one case was not. Two of six CDK4 high-level copy number increase cases were accompanied by polysomy of chromosome 12, while four cases were not. CDK4 copy number increase was significantly correlated with younger patient age. In six CDK4 high-level copy number increase cases, one case was found to be accompanied by NRAS mutation, one case was accompanied by HER2 mutation, one case was accompanied by BCL2L11 mutation ​and one case was accompanied by BRAF, HER2 and BCL2L11 mutations. Our study confirmed the presence of CDK4 copy number increase in AM cases. Detecting CDK4 copy number increase by FISH can be reliable in the diagnosis of AM. Some CDK4 copy number increases are the results of polysomy of chromosome 12. CDK4 high-level copy number increase coexists with other pathogenic mutations in AM. CDK4 appears to be a promising target for AM treatment and is expected to be combined with other targeted therapies.

DDIT3-amplified or low-polysomic pleomorphic sarcomas without MDM2 amplification: Clinicopathological review and immunohistochemical profile of nine cases

Several high-grade pleomorphic sarcoma cases that cannot be classified into any existing established categories have been reported. These cases were provisionally classified into undifferentiated pleomorphic sarcoma (UPS). Some dedifferentiated liposarcoma (DDLS) cases may also have been classified into the UPS category due to the absence of MDM2 amplification or an atypical lipomatous tumor/well-differentiated liposarcoma component. We retrieved and reviewed 77 high-grade pleomorphic sarcoma cases, initially diagnosed as UPS in 66 cases and DDLS in 11 cases. Fluorescence in situ hybridization (FISH) analyses of DDIT3 and MDM2 were performed for available cases. Of the cases successfully subjected to DDIT3 FISH (n = 56), nine (7 UPS and 2 DDLS) showed DDIT3 amplification but no MDM2 amplification. Two UPS cases showed both telomeric (5′) and centromeric (3′) amplification of DDIT3 or low polysomy of chromosome 12, whereas 5 UPS and 2 DDLS cases showed 5′-predominant DDIT3 amplification. Histopathologically, all cases showed UPS-like proliferation of atypical pleomorphic tumor cells. Immunohistochemically, only one case showed focal nuclear positivity for DDIT3, supporting the previous finding that DDIT3 expression was not correlated with DDIT3 amplification. All three cases with focal MDM2 expression involved 5′-predominant amplification, two of which showed DDLS-like histological features. The majority of cases (7/9) showed decreased expression in p53 staining, suggesting that DDIT3 amplification regulates the expression of TP53 like MDM2. From a clinicopathological perspective, we hypothesize that DDIT3-amplified sarcoma, especially with 5′-predominant amplification, can be reclassified out of the UPS category.

Clinical, Histopathologic and Genetic Features of Rhabdoid Meningiomas.

Rhabdoid meningiomas (RM) shows heterogeneous histological findings, and a wide variety of chromosomal copy number alterations (CNA) are associated with an unpredictable course of the disease. In this study, we analyzed a series of 305 RM samples from patients previously reported in the literature and 33 samples from 23 patients studied in our laboratory. Monosomy 22-involving the minimal but most common recurrent region loss of the 22q11.23 chromosomal region was the most observed chromosomal alteration, followed by losses of chromosomes 14, 1, 6, and 19, polysomies of chromosomes 17, 1q, and 20, and gains of 13q14.2, 10p13, and 21q21.2 chromosomal regions. Based on their CNA profile, RM could be classified into two genetic subgroups with distinct clinicopathologic features characterized by the presence of (1) chromosomal losses only and (2) combined losses and gains of several chromosomes. The latter displays a higher frequency of WHO grade 3 tumors and poorer clinical outcomes.

Establishment and evaluation of digital PCR methods for HER2 copy number variation in breast cancer

Accurate measurement of human epidermal growth factor receptor 2 (HER2) copy number variation (CNV) is very important for guiding the tumor target therapy in breast cancer. Digital PCR (dPCR) is a sensitive and an absolute quantitative method, which can be used to detect HER2 CNV. Three HER2 exon-specific digital PCR assays along with three new reference genes assays (homo sapiens ribonuclease P RNA component H1 (RPPH1), glucose-6-phosphate isomerase (GPI), and chromosome 1 open reading frame 43 (C1ORF43), on different chromosomes) were established and validated by using standard reference material, 8 different cell lines and 110 clinical Formalin-fixed and paraffin-embedded (FFPE) samples. DPCR can achieve precise quantification of HER2 CNV by calculating the ratio of HER2/reference gene. The positive and negative coincidence rates were 98% (53/54) and 95% (53/56), respectively, compared with fluorescence in situ hybridization (FISH) diagnostic result 110 of FFPE samples. The common reference gene CEP17 used for FISH diagnostic was not suitable as single reference gene for HER2 CNV measurements by dPCR. The best practice of HER2 CNV determination by dPCR is to conduct the three duplex assays of H1 (HER2 exon 4) with the proposed three new reference genes, with a positive cut-off value of H1/RPPH1 ≥ 2.0 or H1/averaged reference gene ≥ 2.0. The proposed dPCR method in our study can accurately provide absolute copy number of HER2 and reference gene on an alternative chromosome, thus avoiding false negative caused by polysomy of chromosome 17. The improved molecular typing and diagnosis of breast cancer will better guide clinical medication.

Addition of Chromosome 17 Polysomy and HER2 Amplification Status Improves the Accuracy of Clinicopathological Factor-Based Progression Risk Stratification and Tumor Grading of Non-Muscle-Invasive Bladder Cancer.

Simple SummaryThe addition of chromosome 17 polysomy/HER2 amplification status to the updated EAU and AUA scores improves their accuracy, allowing molecular reclassification of EAU high-risk NMIBCs and G2 tumors. Based on this, we propose to reclassify the non-HER2 amplified, non-polysomic EAU 3–4 (high- and very high-risk) cases to the EAU 2 (intermediate) risk group to prevent unnecessarily strict follow-up and treatment for these patients. Furthermore, to classify Chr17 polysomic and/or HER2 amplified G2 tumors as high-grade (HG) and non-HER2 amplified, non-polysomic G2 tumors as low-grade (LG) NMIBCs (G1 and G3 tumors remain graded as low- and high-grade, respectively). Thus, the implementation of Chr17 polysomy/HER2 amplification testing would provide an immediate and simple solution to further refine the prognostic risk assessment of NMIBCs in the uro-oncology practice.Progression of non-muscle-invasive bladder cancer (NMIBC) to muscle-invasive disease (MIBC) significantly worsens life expectancy. Its risk can be assessed by clinicopathological factors according to international guidelines. However, additional molecular markers are needed to refine and improve the prediction. Therefore, in the present study, we aimed to predict the progression of NMIBCs to MIBC by assessing p53 expression, polysomy of chromosome 17 (Chr17) and HER2 status in the tissue specimens of the tumors of 90 NMIBC patients. Median follow-up was 77 months (range 2–158). Patients with Chr17 polysomy or HER2 gene amplification had a higher rate of disease progression (hazard ratio: 7.44; p < 0.001 and 4.04; p = 0.033, respectively; univariate Cox regression). Multivariable Cox regression models demonstrated that the addition of either Chr17 polysomy or HER2 gene amplification status to the European Association of Urology (EAU) progression risk score increases the c-index (from 0.741/EAU/ to 0.793 and 0.755, respectively), indicating that Chr17 polysomy/HER2 amplification status information improves the accuracy of the EAU risk table in predicting disease progression. HER2/Chr17 in situ hybridization can be used to select non-progressive cases not requiring strict follow-up, by reclassifying non-HER2-amplified, non-polysomic NMIBCs from the high- and very high-risk groups of EAU to the intermediate-risk group.

ОПРЕДЕЛЕНИЕ РАДИОЧУВСТВИТЕЛЬНОСТИ БОЛЬНЫХ РАКОМ СЛИЗИСТОЙ ОБОЛОЧКИ ПОЛОСТИ РТА ПО ЧАСТОТЕ КЛЕТОК С ПОЛИСОМИЕЙ ХРОМОСОМ 7 И 11 ПРИ ФРАКЦИОНИРОВАННОЙ ГАММА-ЛУЧЕВОЙ ТЕРАПИИ

Purpose: To study the dynamics of frequency of tumor cells with polysomy 7 and 11 chromosomes in patients with oral cancer during fractionated gamma-radiotherapy. Material and methods: The study was carried out using fluorescence in situ hybridization (FISH) on smears of 19 patients with oral cancer before treatment, after first total focal dose of gamma-radiotherapy (up to 18 Gy) and after second total focal dose (up to 32 Gy). As for control oral smears of 12 healthy donors were taken. Molecular cytogenetic abnormalities were examined in taken samples. Results: The average group frequency of cell with polysomy 7 and 11 chromosomes in controls was 0.7 ± 0.2 % and 0.3 ± 0.1 % respectively. The average frequency of cells with chromosome 7 polysomy in group oral cancer patients before treatment was 32.3 ± 4.5 %, after first focal dose was 15.7 ± 2.9 % and after second focal dose was 8.0 ± 2.3 %. Dynamics analysis of these values revealed the significant decreasing (р &lt; 0.05) in cells with chromosome 7 polysomy during radiotherapy. The average group frequency of cells with polysomy 11 in cancer patients before treatment was 25.8 ± 5.6 %, 12.2 ± 2.4 % and 5.4 ± 0.9 % after first and second focal dose respectively. These values was significantly (р &lt; 0.01) higher compare with the one in the control group. After radiotherapy the 16 (84 %) patients with polysomy chromosomes 7 and/or 11 had significant decreasing (р &lt; 0.05) in aberrant levels. Some of them (6 persons – 32 %) had decreasing frequency up to the control levels. 4 persons (21 %) observed firstly the increasing of cells with polysomy but after there was the reduction. 5 patients (26 %) over full course of gamma-radiotherapy demonstrated the gain in frequency of cells with polysomy or the same value as it was before treatment. Conclusion: Thus, the study of molecular cytogenetic abnormalities in cells of oral cancer patients before and after radiotherapy was shown the polysomy of chromosomes being the marker of genome instability could indicate the tumor response ongoing therapy.

Characteristics of HER2 Gene Amplification by Fluorescence In Situ Hybridization in Endometrial Serous Carcinoma.

Targeted anti-human epidermal growth factor receptor 2 (HER2) therapy has recently become the standard for advanced-stage and recurrent HER2-positive endometrial serous carcinoma (ESC) in the United States, and an endometrial carcinoma-specific HER2 testing algorithm has been proposed. However, comprehensive studies on the specific features of HER2 gene amplification in these tumors are lacking. To evaluate the characteristics of HER2 amplification in ESC in the context of breast and gastric HER2 fluorescence in situ hybridization (FISH) guidelines. Ninety-four ESCs with available HER2 immunohistochemistry (IHC) and FISH were included. HER2 IHC was scored according to the proposed endometrial carcinoma-specific algorithm and FISH was evaluated by using the 2018 ESC clinical trial criteria, the American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) 2016 gastric criteria, and ASCO/CAP 2013 and 2018 breast criteria. Most tumors (90.4%; 85 of 94) had a 2+ HER2 IHC score. Polysomy of chromosome 17 was present in 16% (15 of 94) and monosomy 17 was seen in 2% (2 of 94) of tumors. HER2 FISH interpretation per the clinical trial criteria (HER2/CEP17 ratio ≥ 2.0) showed 99% concordance with the current gastric and breast HER2 FISH interpretations. Our results support the clinical trial criteria for HER2 FISH in ESC with a modification to include HER2 IHC 2+ and HER2/CEP17 ratio less than 2.0 and average HER2 copy number of 6.0 or greater in the HER2-positive category. Future prospective clinical investigations are necessary to assess the correlation between specific HER2 FISH result categories and therapeutic response.

Chromosomal aberrations, visualized using UroVysion® fluorescence in-situ hybridization assay, can predict poor prognosis in formalin-fixed paraffin-embedded tissues of cholangiocarcinoma patients

Cholangiocarcinoma (CCA) is a highly aggressive malignant tumor that has highest incidence in northeastern Thailand. The survival rate of CCA patients after receiving surgical treatment is quite low. Recently, genetic alterations including chromosome abnormalities have been studied as predictive factors and to aid planning for further treatment. This study aims to investigate the association between chromosomal aberrations, clinical data, and overall survival time of CCA patients. Formalin-fixed paraffin-embedded (FFPE) tissues from 194 CCA patients were examined. The copy numbers of chromosomes 3, 7, 17 and 9p21 were investigated using the UroVysion® fluorescence in-situ hybridization (FISH) assay. The overall survival time (OS) of CCA patients with or without polysomy of chromosomes 3, 7, 17 and/or loss of 9p21 were statistically analyzed in association with their clinicopathological parameters. Kaplan-Meier analysis was performed. The OS of patients with polysomy of chromosomes 3+7 was significantly shorter than those without this polysomy (log-rank P=0.006; median OS 14.79 vs. 19.62 months). Moreover, patients with polysomy of chromosomes 3+7+17 and heterozygous for 9p21 loss have significantly shorter survival time than those without such chromosomal aberrations (log-rank P=0.001; median OS 15.74 vs. 37.57 months). Interestingly, multivariate analysis revealed that polysomy of chromosomes 3+7 and of chromosomes 3+7+17 with 9p21 heterozygous loss were independent predictive factors of a poor OS (P=0.027; P=0.008, respectively).The chromosomal aberrations patterns which we evaluated using FISH; 1) polysomy of chromosomes 3+7 and 2) polysomy of chromosomes 3+7+17 with 9p21 heterozygous loss, have strong potential as indicators of poor prognosis in CCA patients.

Abstract PD4-03: Characterization of HER2 amplification in the cerebrospinal fluid of patients with Leptomeningeal Disease in stage IV patients with breast cancer

Abstract Introduction. Breast cancers that metastasize to the central nervous system (BrM) and progress to leptomeningeal disease (LMD) are commonly HER2 amplified. Triple negative breast cancer (TNBC) also may also acquire HER2 amplification and/or copy number changes (HER2+) in BrM and LMD due to genetic heterogeneity. LMD has a dismal prognosis if untreated, but advances in anti-HER2 therapy have been highly effective for improving outcomes in patients with HER2+ LMD. Current methods for evaluating HER2 status in LMD are extremely limited. Cerebrospinal fluid (CSF) cytology is of limited sensitivity with poor cellular yield and preservation due to technical artifacts of preparation that severely limit evaluation of HER2 by FISH or IHC. We evaluated the ability of CNSide™ to selectively enrich CSF tumor cells (CSF-TCs) and assess HER2 gene amplification or copy number gain in breast cancer patients with LMD. Methods. CSF specimens from 77 unique breast cancer patients with suspected LMD were collected using CEE-Sure™ CSF collection tubes and analyzed using the CNSide assay, both produced by Biocept, Inc (San Diego CA). CSF tumor cells (CSF-TCs) stabilized at ambient temperature in CEE-Sure for shipping. In the CLIA laboratory CSF-TCs are labeled using a proprietary mouse anti-human antibody cocktail with secondary biotinylated anti-mouse Ig. All CSF cells are then captured in a streptavidin-coated micro-fluidic channel and fluorescently labeled with DAPI, streptavidin, keratin and CD45 to discriminate nucleated CSF-TCs that are SA+ and cytokeratin+, but CD45 negative. CSF-TCs are digitally imaged, localized and counted with specific X-Y coordinates in the channel that allow further characterization of the HER2 status of each cell using FISH probes for centromere 17 and HER2. Results. Of 77 unique patient CSF specimens, 74.0% (57/77) demonstrated the presence of metastatic tumor cells (defined as cells which were DAPI positive, streptavidin positive, and CD45 negative). HER2 cells ranged from fewer than 10 cells to tens of thousands of cells recovered from a single collection tube of CSF. Of the 57 specimens in which malignant cells were identified, 56.1% (32/57) demonstrated HER2 amplification by FISH (defined as HER2:CEP17 ≥ 2.0 or ≥ 6 HER2 signals) and 43.9% (25/57) did not demonstrate HER2 amplification by FISH. Ten (10) patients also had polysomy of chromosome 17 as well as other gene alterations. Conclusion: HER2 amplification is frequently found in breast cancer patients with LMD and can be reliably detected in tumor cells isolated from CSF. Evaluation of HER2 status in CSF-TCs allows treating physicians the opportunity to rapidly confirm the presence of this biomarker and select a more effective targeted therapy against HER2 in patients who present with life-threatening complications of breast cancer. Additional studies are needed to fully establish the clinical utility of CNSide when using various anti-HER2 therapies or therapy combinations to treat breast cancer patients with LMD. Citation Format: Michael Dugan, Deanna Fisher, Nathan Sweed, Barbara Blouw, Julie Mayer. Characterization of HER2 amplification in the cerebrospinal fluid of patients with Leptomeningeal Disease in stage IV patients with breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD4-03.

Additional activation of the AR gene may be involved in the development of the castration resistance phenotype in prostate cancer

IntroductionSeveral studies have already shown that changes in the AR gene may be associated with a more aggressive disease phenotype and even castration-resistant prostate cancer. Thus, we investigated cytogenetic and molecular alterations linked to AR. Materials and methodsTo evaluate AR methylation, we performed a cytogenetic-molecular analysis using fluorescence in situ hybridization that uses specific probes for the AR gene (Xq11.12) and the X chromosome centromere. For AR activity, we performed a qualitative analysis of human androgen receptor activity. To analyze the expression of AR in PC3 and LNCaP cell lines, we used qPCR assays. ResultsIn the qPCR assay, we found downregulation of AR in the PC3 cell line compared with the LNCaP. We found the presence of X chromosome polysomy in PC-3 and LNCaP cell lines by FISH assay. In the HUMARA-Q assay, we found two X chromosomes/cell and the activity of both AR in the PC-3 cell line. In LNCaP cells, we found two X chromosomes/cell and methylation of only one AR. ConclusionCastration-resistant prostate cancer phenotype represents a significant challenge in the setting of urological management. The X chromosomes and AR-linked alterations may contribute to a better understanding of the disease. However, further studies should be performed in an attempt to elucidate as much as possible the role of AR in the castration-resistant prostate cancer phenotype.

Papel de la activación adicional del gen RA en el desarrollo del fenotipo resistente a la castración en el cáncer de próstata

IntroductionSeveral studies have already shown that changes in the AR gene may be associated with a more aggressive disease phenotype and even castration-resistant prostate cancer. Thus, we investigated cytogenetic and molecular alterations linked to AR. Materials and methodsTo evaluate AR methylation, we performed a cytogenetic-molecular analysis using fluorescence in situ hybridization that uses specific probes for the AR gene (Xq11.12) and the X chromosome centromere. For AR activity, we performed a qualitative analysis of human androgen receptor activity. To analyze the expression of AR in PC3 and LNCaP cell lines, we used qPCR assays. ResultsIn the qPCR assay, we found downregulation of AR in the PC3 cell line compared with the LNCaP. We found the presence of X chromosome polysomy in PC-3 and LNCaP cell lines by FISH assay. In the HUMARA-Q assay, we found two X chromosomes/cell and the activity of both AR in the PC-3 cell line. In LNCaP cells, we found two X chromosomes/cell and methylation of only one AR. ConclusionCastration-resistant prostate cancer phenotype represents a significant challenge in the setting of urological management. The X chromosomes and AR-linked alterations may contribute to a better understanding of the disease. However, further studies should be performed in an attempt to elucidate as much as possible the role of AR in the castration-resistant prostate cancer phenotype.

Divergent leukaemia subclones as cellular models for testing vulnerabilities associated with gains in chromosomes 7, 8 or 18

Haematopoietic malignancies are frequently characterized by karyotypic abnormalities. The development of targeted drugs has been pioneered with compounds against gene products of fusion genes caused by chromosomal translocations. While polysomies are equally frequent as translocations, for many of them we are lacking therapeutic approaches aimed at synthetic lethality. Here, we report two new cell lines, named MBU-7 and MBU-8, that differ in complete trisomy of chromosome18, a partial trisomy of chromosome 7 and a tetrasomy of the p-arm of chromosome 8, but otherwise share the same mutational pattern and complex karyotype. Both cell lines are divergent clones of U-937 cells and have the morphology and immunoprofile of monocytic cells. The distinct karyotypic differences between MBU-7 and MBU-8 are associated with a difference in the specific response to nucleoside analogues. Taken together, we propose the MBU-7 and MBU-8 cell lines described here as suitable in vitro models for screening and testing vulnerabilities that are associated with the disease-relevant polysomies of chromosome 7, 8 and 18.

Detection of circulating tumor cells with chromosomes 7 and 8 polysomy in non-small cell lung cancer and its correlation with epidermal growth factor receptor mutations in cancer tissue

Objective: To investigate the value of chromosomes 7 and 8 polysomy in circulating tumor cells (CTCs) for the diagnosis of non-small cell lung cancer, and the correlation of CTCs with clinical pathological characteristics and epidermal growth factor receptor (EGFR) mutations in cancer tissue. Methods: Fifty-seven patients with non-small cell lung cancer and 21 patients with benign lung diseases were enrolled at Beijing Chaoyang Hospital, Capital Medical University, Beijing, China from November 2017 to October 2020. Negative enrichment combined with immunofluorescence in situ hybridization (imFISH) was used to identify CTCs polysomy on chromosomes 7 and 8. EGFR mutations in 56 lung cancer patients was detected using ARMS-PCR. Results: CTCs were detected in 93.0% (53/57) of non-small cell lung cancers and 28.6% (6/21) benign lung lesions. The difference between lung cancer patients and the control cohort was statistically significant (P<0.01). Receive operator curve (ROC) analyses showed that, when the cut-off value was 1 cell/3.2 mL, Youden index had the highest sensitivity of 93.0% and specificity of 71.4% (AUC=0.906, 95%CI:0.833-0.980, P<0.01). The positive rate of CTCs in stage Ⅲ-Ⅳ cancers was significantly higher than that in stage Ⅰ-Ⅱ (P=0.023). No significant correlation was observed between positive rate of CTCs or chromosome polysomy and age, gender, smoking status, pathologic types and EGFR mutation status. The number of CTCs in EGFR mutated group was higher than that in the non-mutated group (6.5±1.1 vs. 3.7±0.7, P=0.045). The detection rate for CTCs ≥5 in the EGFR mutated group was also higher than the EGFR non-mutated group (52.0% vs. 19.4%,P=0.010). Conclusion: Detection of CTCs with chromosomes 7 and 8 polysomy has potential value in auxiliary diagnosis of non-small cell lung cancer, and the number of CTCs is correlated to TNM stage and EGFR gene mutation status.

Renal cell carcinomas with tubulopapillary architecture and oncocytic cells: Molecular analysis of 39 difficult tumors to classify

So-called oncocytic papillary renal cell carcinoma (OPRCC) is a poorly defined variant of papillary renal cell carcinoma. Since its first description, several studies were published with conflicting results, and thus precise definition is lacking.A cohort of 39 PRCCs composed of oncocytic cells were analyzed. Cases were divided into 3 groups based on copy number variation (CNV) pattern. The first group consisted of 23 cases with CNV equal to renal oncocytoma. The second group consisted of 7 cases with polysomy of chromosomes 7 and 17 and the last group of 9 cases included those with variable CNV.Epidemiologic, morphologic and immunohistochemical features varied among the groups. There were not any particular histomorphologic features correlating with any of the genetic subgroups. Further, a combination of morphologic, immunohistochemical, and molecular-genetic features did not allow to precisely predict biologic behavior.Owing to variable CNV pattern in OPRCC, strict adherence to morphology and immunohistochemical profile is recommended, particularly in limited samples (i.e., core biopsy). Applying CNV pattern as a part of a diagnostic algorithm can be potentially misleading.OPRCC is a highly variable group of tumors, which might be misdiagnosed as renal oncocytoma. Using the term OPRCC as a distinct diagnostic entity is, thanks to its high heterogeneity, questionable.

Assessment of isochromosome 12p and 12p abnormalities in germ cell tumors using fluorescence in situ hybridization, single-nucleotide polymorphism arrays, and next-generation sequencing/mate-pair sequencing

The identification of isochromosome 12p [i(12p)] and 12p gains have significant clinical utility in the diagnosis of germ cell tumors (GCTs). We have summarized the results of fluorescence in situ hybridization (FISH) assays to identify i(12p), performed in a Clinical Laboratory Improvement Amendments (CLIA)-validated setting for 536 specimens. In addition, the American Association for Cancer Research (AACR) Project GENIE registry and The Cancer Genome Atlas (TCGA) data sets were evaluated for chromosome 12p gains, and a limited number of cases were concurrently evaluated using FISH, single-nucleotide polymorphism (SNP) arrays and next-generation sequencing (NGS; including mate-pair sequencing). Specimens submitted for FISH testing were frequently from potential sites of metastases (male: 70.9% and female: 69.3%), and polysomy of chromosome 12 with or without concurrent i(12p) was a frequent finding, seen in 3% (16/536) and 35% (186/536) of cases, respectively. Our analysis suggests that 12p gains are likely to be present in approximately 73% of male GCTand in 32% of female GCT (AACR GENIE, n=555). When comparing TCGA cases of testicular GCT (n=149) to combined cases of sarcoma, colorectal, prostate, and urothelial carcinoma (n=1754), 12p gains had a sensitivity of 77.2% and specificity of 97.3% for GCT. Some advantages of FISH over SNP arrays/NGS include relatively lower cost, rapid turnaround time, the ability to analyze biopsy material with a limited number of tumor cells (50cells), and the ability to distinguish i(12p) from polysomy. The ability to spatially restrict the analysis to cells of interest is critical, as specimens submitted for testing often have low tumor purity. Disadvantages include false negative results due to an inability to detect segmental gains due to FISH probe design. With the availability of numerous testing modalities, including FISH, SNP arrays, and NGS-based assays, a nuanced understanding of the advantages and disadvantages of each methodology, as has been presented in this study, may inform appropriate testing strategies.

S2275 All at Once: Dual Novel Diagnosis of Crohn’s Disease and Colonic Adenocarcinoma in a 22-Year-Old Man

INTRODUCTION: Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the United States. Mucinous adenocarcinoma makes up 10-15% of all CRC and disproportionately affects younger adults. One study found that those aged 25 and younger who developed CRC present acutely and when compared to older adults, were diagnosed at a more advanced stage and carried a poorer prognosis.[1] Crohn’s disease frequently presents in ages 20-29 and can increase risk of CRC. CASE DESCRIPTION/METHODS: A 22 year old male with no significant past medical history presented to ED with intermittent abdominal pain, diarrhea and weight loss. Initial labs revealed leukocytosis, elevated CRP/ESR and positive fecal occult blood test. CT imaging revealed hepatic flexure stricture with dilation of the ascending colon and distal ileum with enlarged ileocolic lymph nodes (Figure 1). Colonoscopy revealed moderate stenosis at the hepatic flexure with significant inflammation and ulceration which prevented a pediatric colonscopy from traversing. Descending colon had scattered moderate inflammation. Two days following the colonoscopy, the patient developed a bowel perforation which required emergent exploratory laparotomy with open right hemicolectomy and diverting loop ileostomy. Surgical findings included terminal ileum perforation, dense stricture at the hepatic flexure with adherence to the underlying duodenum without fistula. Pathology report revealed adenocarcinoma in the ascending colon invading into the visceral peritoneal surface, with extensive lymphovascular invasion. The cancer was staged at G3pT4aN2a. The uninvolved terminal ileum revealed active inflammation consistent with Crohn’s disease. Genetic testing was only positive for polysomy of chromosome 17. He was ultimately diagnosed with mucinous adenocarcinoma with signet ring cell features in the setting of newly diagnosed Crohn’s disease (Figure 2). DISCUSSION: This is a rare case of advanced mucinous adenocarcinoma with signet ring features of the ascending colon in a 22-year-old with previously undiagnosed Crohn’s disease. This demonstrates the importance and difficulty of considering CRC in the differential when working up a young adult for GI symptoms as the newly diagnosed Crohn’s disease seemed to fit our patient’s presentation perfectly.Figure 1.: Stricture at the hepatic flexure with dilation of the ascending colon and distal ileum.Figure 2.: Signet ring cells.

Evaluation of UroVysion for Urachal Carcinoma Detection.

Background: Patients with hematuria who are positive for urinary fluorescence in situ hybridization (FISH) are generally considered to have urothelial carcinoma. We determined whether UroVysion FISH could be used for the diagnosis of urachal carcinoma.Methods: Seven cases of urachal carcinoma with haematuria subjected to FISH analysis were retrospectively analyzed in our hospital from May 2012 to November 2019. Paraffin-embedded tissue sections from one FISH-positive and one FISH-negative urachal carcinoma were processed in strict accordance with the instructions of the UroVysion kit. Meanwhile, FISH data from the other 414 hematuria patients were collected as controls.Results: All 7 patients with urachal carcinoma were diagnosed with adenocarcinoma. According to Sheldon stage, six patients had stage IIIa and one patient had stage IVb. The sensitivity and specificity of urinary FISH for the diagnosis of urachal carcinoma were 71.43% (5/7) and 94.61% (281/297), respectively. The rates of polysomy for chromosomes 3 and 7 in positive patients were both 100% (5/5), whereas the rate of polysomy for chromosome 17 was 40% (2/5), and the chromosome 9p21 region (p16) gene deletion rate was 20% (1/5). Histological assessment and cytological FISH were consistent for urachal carcinoma. No significant difference was observed in the diagnostic efficacy between urachal carcinoma and urothelial carcinoma (71.43 vs. 87.18%, P = 0.245).Conclusions: Taken together, UroVysion FISH was found to be positive in a high proportion of pathologically confirmed urachal carcinoma of late stage with hematuria. Its chromosomal aberrations may be different from those of urothelial carcinoma, but more studies are needed to clarify their genetic background. Not all tumors showing abnormalities by FISH are urothelial carcinomas.

Multiple Whole Chromosomal Gains Define Angiomatous Meningiomas and Are Absent From the Tumor Vasculature.

Angiomatous meningioma is a variant with prominent vascularity that can mimic other highly vascularized tumors and present diagnostic challenges. Unlike most meningioma variants, where NF2 gene loss on chromosome 22 is the most common genetic abnormality, angiomatous meningiomas are unique in having multiple whole chromosome gains (polysomies). We analyzed 38 meningiomas, 9 angiomatous (including 2 atypical and 1 anaplastic), and 29 nonangiomatous meningiomas, using array comparative genomic hybridization (aCGH). Angiomatous meningiomas showed multiple chromosomal alterations including polysomies and copy neutral loss of heterozygosity in comparison to nonangiomatous variants. The most frequent gains were of chromosomes 5 and 20 (100% and 89% of cases, respectively); none showed chromosome 22 loss. Furthermore, using fluorescence in situ hybridization we show that the vasculature lacked chromosomal polysomy. While generally benign, we present 2 grade II and the first cytogenetically confirmed grade III angiomatous meningioma, demonstrating their potentially aggressive behavior. Thus, multiple polysomies define angiomatous meningioma and aCGH can distinguish this variant from nonangiomatous meningiomas and other histological mimics in diagnostically challenging cases. Furthermore, the prominent vasculature is not neoplastic and likely induced by angiogenic factors. Together, these findings suggest a distinct tumorigenic pathway in angiomatous meningiomas.

HER2, chromosome 17 polysomy and DNA ploidy status in breast cancer; a translational study

Breast cancer treatment depends on human epidermal growth factor receptor-2 (HER2) status, which is often determined using dual probe fluorescence in situ hybridisation (FISH). Hereby, also loss and gain of the centromere of chromosome 17 (CEP17) can be observed (HER2 is located on chromosome 17). CEP17 gain can lead to difficulty in interpretation of HER2 status, since this might represent true polysomy. With this study we investigated whether isolated polysomy is present and how this effects HER2 status in six breast cancer cell lines and 97 breast cancer cases, using HER2 FISH and immunohistochemistry, DNA ploidy assessment and multiplex ligation dependent probe amplification. We observed no isolated polysomy of chromosome 17 in any cell line. However, FISH analysis did show CEP17 gain in five of six cell lines, which reflected gains of the whole chromosome in metaphase spreads and aneuploidy with gain of multiple chromosomes in all these cases. In patients’ samples, gain of CEP17 indeed correlated with aneuploidy of the tumour (91.1%; p < 0.001). Our results indicate that CEP17 gain is not due to isolated polysomy, but rather due to widespread aneuploidy with gain of multiple chromosomes. As aneuploidy is associated with poor clinical outcome, irrespective of tumour grade, this could improve future therapeutic decision making.

MDM2 dual-color in situ hybridization (DISH) aids the diagnosis of intimal sarcomas.

Intimal sarcoma is a rare malignant mesenchymal tumor arising from the intima of the great vessels and the heart, and is associated with poor outcomes. As clinico-radiological findings and pathological features are often non-specific, the diagnosis of intimal sarcoma is challenging. Recently, MDM2 amplification was reported to be a characteristic genetic event in this tumor. In the present study, we examined MDM2 status by immunohistochemistry, and by fluorescence and dual-color in situ hybridization (FISH and DISH) using intimal sarcoma (10 tumors), angiosarcoma (5), pulmonary sarcomatoid carcinoma (p-SC) (14) and chronic pulmonary thrombosis (CPT) (3) to investigate MDM2 amplification for the diagnosis of intimal sarcoma. MDM2 and CDK4 were immunopositive in all 10 intimal sarcoma tumors, and high-level amplification of MDM2 was detected in eight tumors by both FISH and DISH. The other two tumors had polysomy of chromosome 12 and overexpression of p53 protein. Although MDM2 aberrations were observed in three p-SCs (two with amplification and one with polysomy), angiosarcomas and CPTs lacked MDM2 amplification. Furthermore, there was high concordance between FISH and DISH. In conclusion, we found that MDM2 amplification strongly supports the diagnosis of intimal sarcoma, and MDM2 DISH was a concordant method and an acceptable alternative to FISH. As MDM2 amplification and p53 overexpression were mutually exclusive, disruption of the MDM2-p53 pathway may be an essential genetic event for this malignant tumor.