Aneusomy Of Chromosome Research Articles

Prevalence, molecular markers, and outcome of bronchial squamous carcinoma in situ in high-risksubjects.

Bronchial squamous carcinoma in situ (CIS) is a preinvasive lesion that is thought to precede invasive carcinoma. We conducted prospective autofluorescence and white light bronchoscopy trials between 1992 and 2016 to assess the prevalence, molecular markers, and outcome of individuals with CIS and other preneoplastic bronchial lesions. Biopsies were evaluated at multiple levels and selected biopsies were tested for aneuploidy and DNA sequenced for TP53 mutation. Thirty-one individuals with CIS were identified. Twenty-two cases of CIS occurred in association with concurrent invasive carcinomas. Seven of the invasive tumors were radiographically occult. In two cases, CIS spread from the focus of invasive carcinoma into contralateral lung lobes, forming secondary invasive tumors. In nine cases, CIS occurred as isolated lesions and one progressed to invasive squamous carcinoma at the same site 40 months after discovery. In a second case, CIS was a precursor of carcinoma at a separate site in a different lobe. In seven cases CIS regressed to a lower grade or disappeared. High level chromosomal aneusomy was often associated with TP53 mutation and with invasive carcinoma. CIS most often occurs in association with invasive squamous carcinoma and may extend along the airways into distant lobes. In rare cases, CIS may be observed to directly transform into invasive carcinoma. CIS may be indicative of invasive tumor at a separate distant site. Isolated CIS may regress. Molecular changes parallel histological changes in CIS and may be used to map clonal expansion in the airways.

DNA methylation alterations in the genome of a toddler with cri‐du‐chat syndrome

Key Clinical MessageThis manuscript reports on genomewide epigenetic alterations in cri‐du‐chat syndrome related to a partial aneusomy of chromosome 5. A systematic analysis of these alterations will open up new possibilities for the prognostic evaluation of CDCS patients and the development of new therapeutic interventions for reducing the severity of the disease.

Analysis of Chromosomal Alterations in Urothelial Carcinoma.

Here, we describe the use of complementary techniques applicable to different types of samples to analyze chromosomal alterations in urothelial carcinoma. By a conventional chromosome analysis on fresh biopsies, it is possible to delineate the status of ploidy and rough chromosomal aberrations. The multi-target fluorescence in situ hybridization (FISH) UroVysion test, for the rapid detection of chromosomal aneusomy of chromosomes 3, 7, and 17 and/or deletion of 9p21 locus, is applicable to urine specimens as well as to formalin-fixed paraffin-embedded (FFPE) specimens and fresh biopsies. Finally, array comparative genomic hybridization (array-CGH) gives the possibility of analyzing the DNA in a single experiment from a biopsy of the tumor but also from FFPE specimens; this technique is able to detect alterations at the genome level not excluding any chromosome.

Clinical Utility of Chromosomal Aneusomy in Individuals at High Risk of Lung Cancer

IntroductionLow-dose computed tomography screening for lung cancer has a high false-positive rate with frequent discovery of indeterminate pulmonary nodules. Noninvasive biomarkers are needed to reduce false positives and improve risk stratification. A retrospective longitudinal evaluation was performed to assess chromosomal aneusomy in sputum by fluorescence in situ hybridization (CA-FISH) in four nested case-control studies. MethodsReceiver operating characteristic analysis resulted in two grouped cohorts: a high-risk cohort (Colorado High-Risk Cohort and Colorado Nodule Cohort [68 case patients and 69 controls]) and a screening cohort (American College of Radiology Imaging Network/National Lung Screening Trial and Pittsburgh Lung Screening Study [97 case patients and 185 controls]). The CA-FISH assay was a four-target DNA panel encompassing the EGFR and v-myc avian myelocytomatosis viral oncogene homolog (MYC) genes, and the 5p15 and centromere 6 regions or the fibroblast growth factor 1 gene (FGFR1) and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha gene (PIK3CA). A four-category scale (normal, probably normal, probably abnormal, and abnormal) was applied. Sensitivity, specificity, and positive and negative likelihood ratios (LRs) (with 95% confidence intervals [CIs]) were estimated for each cohort. ResultsSensitivity and specificity were, respectively, 0.67 (95% CI: 0.55–0.78) and 0.94 (95% CI: 0.85–0.98) for high-risk participants and 0.20 (95% CI: 0.13–0.30) and 0.84 (95% CI: 0.78–0.89) for screening participants. The positive and negative LRs were, respectively, 11.66 (95% CI: 4.44–30.63) and 0.34 (95% CI: 0.24–0.48) for high-risk participants and 1.36 (95% CI: 0.81–2.28) and 0.93 (95% CI: 0.83–1.05) for screening participants. ConclusionThe high positive LR of sputum CA-FISH indicates that it could be a useful adjunct to low-dose computed tomography for lung cancer in high-risk settings. For screening, however, its low positive LR limits clinical utility. Prospective assessment of CA-FISH in the incidentally identified indeterminate nodule setting is ongoing in the Colorado Pulmonary Nodule Biomarker Trial.

KRAS and aneusomy of chromosomes 4, 10 and 12 in colorectal carcinomas

AimsKRAS mutation status has predictive significance in EGFR-antibody treatment of colorectal adenocarcinoma. The aim of the study was the evaluation of KRAS mutation status in correlation to KRAS copy numbers and ploidy status. MethodsColorectal adenocarcinomas (n=52) were assembled into a TMA and analyzed by FISH. Probes for centromeres 4 and 10 were applied as surrogate markers for the ploidy status. In addition, a dual color FISH probe set for the centromere of chromosome 12 and the KRAS gene was applied to the TMA to analyze numerical alterations and KRAS gene copy numbers. Further we analyzed DNA sequence profiles of KRAS codons 12 and 13 to assess the allele status of the mutation within the tumor samples. ResultsKRAS mutation was confirmed in 24 cases, while 28 cases showed a wild-type KRAS status. The majority of cases showed diploid FISH signals for chromosomes 4 and 10. Near triploid FISH signals were observed in only 2 cases, 12 cases were hypodiploid, and 8 cases were hyperdiploid. In 6 cases, trisomy 12 could be ascertained. In total, aneuploidy could be detected in 28 cases, including cases with trisomy 12 and hyposomy 10. Tumors with aneuploid chromosomal content had a worse prognosis compared to euploid tumors, however, without reaching statistical significance (p=0.231). Hypodiploid carcinomas carried the worst prognosis. Specifically, monosomy 10 was significantly associated with reduced survival (p=0.039). Increased FISH signals of KRAS did not correlate significantly with relapse (p=0.916). ConclusionsFISH analysis can be used as a surrogate marker for the ploidy status. Loss of chromosome 10 may serve as a potential adverse prognostic marker being indicative for tumor progression.

Abstract P4-15-07: HER2 positive (HER2/CEP17 ratio≥2.0) invasive mammary carcinomas with average <4.0 HER2 and <2.0 CEP17 signals/cell: Clinicopathologic features, correlation with HER2 immunohistochemistry and response to neoadjuvant chemotherapy

Abstract Background: ASCO/CAP guidelines for the determination of HER2 amplification have recently been revised in an attempt to clarify which patients will benefit from HER2 directed therapy. Patients with HER2/CEP17 ratios ≥2.0 were eligible for the first generation trials of adjuvant trastuzumab regardless of the average number of HER2 signals/cell. Array CGH and FISH studies have since demonstrated the presence of complex segmental aneusomy of chromosome 17 in a subset of breast tumors. These focal copy number gains and losses can skew the HER2/CEP17 ratio and result in discordant results with HER2 immunohistochemistry (IHC). There is limited data on the clinicopathologic features, HER2 protein expression and response to therapy for tumors showing a HER2/CEP17 ratio ≥2.0 and average <4.0 HER2 signals/cell. Methods: All cases with HER2/CEP17 ratio ≥2.0 and average <4 HER2 signals/cell were identified from our database from 2009-2013. HER2 IHC was performed and scored on all identified cases. Tumor grade, histologic subtype, hormone receptor status and menopausal status were recorded. For patients receiving neoadjuvant chemotherapy, response was measured using residual cancer burden (RCB) class and yAJCC pathologic stage. Results: 70 (1.5%) of 4659 FISH cases met criteria for inclusion in the study. 22 (31%) of the 70 patients were premenopausal. All tumors were ductal (no special type) with the following features features: low-grade 14%, intermediate-grade 40%, high-grade 45%, estrogen receptor positive 79% and progesterone receptor positive 65%. HER2 protein evaluation demonstrated 52 (74%) negative (0-1+), 16 (23%) equivocal (2+) and 2 (3%) positive (3+) results. Most tumors (83%) showed 1+ or 2+ staining. 12 patients received neoadjuvant chemotherapy (see table). Six of these patients did not receive trastuzumab as part of their therapy due to congestive heart failure (n=1) or uncertainty about the patient's HER2 status (n=5). Neoadjuvant chemotherapy patient summaryPatient # (regimen)RatioHER2 copy#CEP17 copy#HER2 IHCER/PRyAJCCRCB classPatient 1 (AC+TH)2.23.91.81++/+ypT0 N0(i+)1Patient 2 (TCH)2.23.81.71++/-ypT0 N00Patient 3 (TCH)2.23.81.72++/+ypTis N00Patient 4 (AC+TH)2.33.01.30+/+ypT2 N2a2Patient 5 (TCH)2.23.71.71+-/-ypT1c N01Patient 6 (TCH)2.23.91.82+-/-ypTis N00Patient 7 (TC)*2.03.41.70-/-ypT0 N00Patient 8 (AC+T)2.23.61.71++/-ypT1c N02Patient 9 (TC)2.13.91.91+-/-ypT0 N00Patient 10 (AC)2.53.41.41++/+ypT1b N1a2Patient 11 (TAC)2.43.61.52+-/-ypT3 N1mi2Patient 12 (AC)2.03.31.61+-/-ypT1c N1a2*Congestive heart failure Conclusions: HER2 FISH positive invasive mammary carcinomas with a HER2/CEP17 ratio ≥2.0 and average <4.0 HER2 signals/cell are rare (1.5% in this study) and frequently show 1+ or 2+ staining by IHC. Treatment decisions for these patients were impacted by the uncertainty of HER2 status under the previous guidelines. In this small data set, these tumors demonstrated a good response to neoadjuvant trastuzumab-based chemotherapy and further support the recent modifications of ASCO/CAP guidelines to determine HER2 amplification. Citation Format: Chad A Livasy, Kimberly Limentani, Benjamin C Calhoun, Steven Limentani. HER2 positive (HER2/CEP17 ratio≥2.0) invasive mammary carcinomas with average <4.0 HER2 and <2.0 CEP17 signals/cell: Clinicopathologic features, correlation with HER2 immunohistochemistry and response to neoadjuvant chemotherapy [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-15-07.

MYC amplification and overexpression in primary cutaneous angiosarcoma: a fluorescence in-situ hybridization and immunohistochemical study

MYC, a proto-oncogene located on chromosome 8q24, is involved in the control of cell proliferation and differentiation. Previous studies have documented high-level MYC gene amplification and MYC overexpression by immunohistochemistry (IHC) in post-irradiation angiosarcomas, but not in primary cutaneous angiosarcoma (AS-C) or in other radiation-associated vascular proliferations, such as atypical vascular lesions. Prompted by our recent finding of MYC amplification in a primary hepatic AS, we analyzed a large number of well-characterized AS-C for MYC amplification and protein overexpression. Formalin-fixed, paraffin-embedded blocks from 38 AS-C were retrieved from our archives and were examined by IHC analysis and fluorescence in-situ hybridization (FISH), using a commercially available antibody and probe. For FISH analysis, the number of copies of MYC was compared with the control gene, CEN8 (MYC/CEN8 ratio). All cases occurred on sun-exposed skin; no patient was known to have a history of therapeutic irradiation. Possible associations between survival and a wide variety of clinicopathological variables were evaluated using the log-rank test. By IHC analysis, MYC overexpression was present in 9/38 (24%) AS-C (2–3+: 6 cases, 16%; 1+: 3 cases, 8%). By FISH analysis, 2/5 (40%) informative cases with 2–3+ immunostaining showed high-level gene amplification. One additional case with 3+ immunostaining showed higher level aneusomy of chromosome 8 (5–8 MYC and CEN8). Two out of fourteen (14%) IHC-negative cases also carried MYC amplification (one high level and one lower level). Low copy number gain of chromosome 8 (3–5 MYC and CEN8) was observed in AS-C with or without MYC expression. MYC amplification and MYC protein overexpression were not correlated with clinical outcome. We have shown, for the first time, MYC gene amplification and protein overexpression in primary (non-radiation-associated) AS of the skin. MYC protein overexpression in cases lacking gene amplification likely reflects other mechanisms of MYC activation. The study of a larger number of AS-C showing MYC amplification may be necessary to determine whether the behavior of such cases differs from their more common non-amplified counterparts.

Detection and Inheritance Pattern of Copy Number Variations (CNVs) in Children with Multiple Congenital Anomalies

Microscopically visible chromosomal alterations or segmental aneusomy are one of the major causes for congenital anomalies and require cytogenetic investigations. Conventional G-banding analysis is limited to the detection of imbalances greater than 5-10 Mb. Expressivity of a phenotype generally correlates with the degree of genetic imbalance, therefore, patients with a greater genetic imbalance are more likely to be investigated, which creates a diagnostic bias. This does not reflect the full range of phenotypic presentation that may be associated with an imbalance of a particular chromosomal segment. Systematic clinical diagnosis of a rare syndrome can be carried out using FISH to characterize known deletion/duplication breakpoints or by screening for known micro-deletion syndromes and sub-telomeric imbalances where routine banding technique suggests “normal” karyotype. In the past decade, array- Comparative Genomic Hybridization (a-CGH) has made it feasible to detect cryptic imbalances in more number of cases with apparently normal chromosomal makeup in addition to characterize structurally rearranged chromosome. The study of inheritance pattern by a combination of conventional cytogenetic and a-CGH techniques has helped to determine the imbalance as either de novo or inherited. a-CGH could also provide information on whether an imbalance is pathogenic or polymorphic, which could aid in calculating the recurrent risk for future pregnancies. It provides several advantages over conventional cytogenetic techniques such as whole genome coverage in a single experiment with resolution of 20-150 kb, faster turnaround time, higher sensitivity and specificity and non-requirement of dividing cells. Having an extensive coverage of the genome and high resolution, this technique has been pinned as the “first line genetic test” to study cryptic genetic imbalances in cases with developmental delay and congenital anomalies, where G-banded karyotype is “normal”.

Intratumoral, not circulating, endothelial progenitor cells share genetic aberrations with glial tumor cells

Literature data indicate that glioma stem cells may give rise to both tumor cells and endothelial progenitor cells (EPCs). Malignant glioma patients usually have increased levels of circulating (EPCs) and these cells are known to contribute to the glioma neovasculature. In this study we compared the intratumoral and circulating EPCs of glioma patients for a set of common glioma genotypical aberrations (amplification of EGFR; deletion of PTEN and aneusomy of chromosomes 7 and 10). We found that the EPCs present in the tumor tissues, not the circulating EPCs, share genetic aberrations with the tumor cells. EPCs with EGFR amplification were found in 46% and with PTEN deletion in 36% of the cases. EPCs with polysomy 7 and monosomy 10 were detected in 56% and 38% of the cases while centrosomal abnormalities in EPCs were found in 68% of the cases. The presence of genetic aberrations of glioma cells in intratumoral EPCs may point to transdifferentiation of glioma stem cells into EPCs. However, the tissue specific CD133 splice variant of blood EPCs was detected in the glioma tissues but not in control brains, suggestive of a blood origin of at least part of the intratumoral EPCs. The findings highlight the complexity of the cellular constituents of glioma neovascularization which should be taken into account when developing anti-angiogenic strategies for gliomas.

Landscape of chromosome number changes in prostate cancer progression

Both genetic instability resulting in aneuploidy and increased proliferative activity are common features of tumor development and progression. Cytometric evaluation of tumor ploidy status was recently suggested as a prognostic marker. However, in prostate cancer (PCa), a chromosome-specific evaluation is lacking. With the present study, we sought to identify distinct chromosomal changes to complement cytometric results concerning the diagnosis and prognosis of PCa patients. We assessed a cohort of 428 PCa specimens (186 localized PCa, 75 lymph node metastasized PCa, 125 lymph node metastases, 42 hormone-refractory distant metastases) for numerical alterations of all 24 chromosomes by using fluorescence in situ hybridization (FISH). Conducting immunohistochemistry with phosphorylated histone H3 (PHH3) and Ki-67, we quantified the proliferation rate. FISH results were fit in a linear model and tested for predictive power. As expected, we observed a significant increase in aneuploidy with advancing tumor stage. Similarly, an increased expression of the mitotic marker PHH3 was significantly associated with aneuploidy and higher pT-stage. We found aneusomy of chromosomes 4, 6, 20, and X to be indicative of lymph node metastasized PCa. However, with an AUC of 65%, this set of chromosomal changes was poorly suited to distinguish non-metastasized and lymph node metastasized primary tumors. Our results provide thorough insight into the so far incompletely elucidated chromosomal landscape of PCa. While overall ploidy status and PHH3 expression in primary tumors indicate advanced disease, a FISH-based test for distinct alterations does not seem to be beneficial for diagnostic or prognostic decisions.

Thymidylate synthase polymorphisms and risk of conotruncal heart defects

In this study, we investigated whether the two TYMS functional variants (28 bp VNTR and 1494del6) (275 cases and 653 controls) and six selected SNPs (265 case infants, 535 control infants; 169 case mothers and 276 control mothers) were associated with risks of conotruncal heart defects. Further, we evaluated interaction effects between these gene variants and maternal folate intake for risk of CTD. Cases with diagnosis of single gene disorders or chromosomal aneusomies were excluded. Controls were randomly selected from area hospitals in proportion to their contribution to the total population of live-born infants. DNA samples were collected using buccal brushes or drawn from the repository of newborn screening blood specimens when available. Genetic variants were treated as categorical variables (homozygous referent, heterozygote, homozygous variant). Odds ratios and 95% confidence intervals (CI) were computed to estimate risks among all subjects, Hispanic and non-Hispanic whites, respectively, using logistic regression. Gene-folate interactions were assessed for these variants by adding an interaction term to the logistic model. A dichotomized composite variable, "combined folate intake," was created by combining maternal peri-conceptional use of folic acid-containing vitamin supplements with daily dietary intake of folate. In general, the results do not show strong gene-only effects on risk of CTD. We did, however, observe a 3.6-fold increase in CTD risk (95% CI: 1.1-11.9) among infants who were homozygotes for the 6 bp deletion in the 3'-untranslated region (UTR) (1694del6) and whose mothers had low folate intake during the peri-conceptional period.

Defining a FISH chromosomal aneusomy panel for predicting lung cancer in the setting of CT-detected lung nodules.

10580 Background: Early detection of lung cancer by CT is supported by the National Lung Screening Trial; but while sensitivity of CT is high, specificity is low. Biomarkers to predict the malignant nature of CT detected lung nodules would have great clinical utility. We previously found in a nested case-control study that a 4-target chromosomal aneusomy (CA) FISH panel exhibited sensitivity/specificity of 76%/88% in sputum samples of heavy smokers obtained within 18 months of lung cancer diagnosis. We hypothesized that CA-FISH may be an effective biomarker to assist with clinical decisions in the setting of CT detected lung nodules of indeterminate etiology and attempted to identify a more effective reagent. Methods: Homebrew probes encompassing genomic sequences of EGFR, NXK2-1, PIK3CA, MYC, BRF2, SOX2, PPMID, FGFR1 and the commercial reagent LSI D5S721/D5S23 (Abbott Molecular) were combined in 2-4-target FISH assays to investigate tissue copy number in early stage lung squamous cell carcinoma (SCC, N=19) and adenocarcinoma (AC, N=20). Logistic regression models were used to estimate predictive discrimination [sensitivity, specificity, area under the ROC curve (AUC)]. Results: Copy number gain was largely detected for all markers (mean range 3.39 - PPMID to 4.67 - MYC). Mean copy number of PI3CA, BRF2, SOX2 and FGFR1 were significantly higher in SCC than AC, while NKX2 and MYC were marginally higher in AC than SCC. Gene amplification was detected for all 9 markers, most frequently for SOX2 and FGFR1 (6 and 5 cases) with significant overlap between FGFR1/BRF2 and SOX2/PIK3CA. Based on the AUC results and the existence of targeted inhibitors, the probe set EGFR/FGFR1/MYC/PIK3CA was selected as a candidate for further development as an adjunct to CT screening for early detection. For this selected set,the optimal cutoff based in the linear predictor from logistic regression yields a sensitivity and specificity of 0.85. Conclusions: A highly sensitive/specific CA-FISH probe set was identified which may well complement CT screening in the early diagnosis of lung cancer. This probe set will be tested in the setting of CT detected lung nodules. (Supported by LUNGevity and NCI-Lung Cancer SPORE grants).

Gene variants in the folate‐mediated one‐carbon metabolism (FOCM) pathway as risk factors for conotruncal heart defects

We evaluated 35 variants among four folate-mediated one-carbon metabolism pathway genes, MTHFD1, SHMT1, MTHFR, and DHFR as risk factors for conotruncal heart defects. Cases with a diagnosis of single gene disorders or chromosomal aneusomies were excluded. Controls were randomly selected from area hospitals in proportion to their contribution to the total population of live-born infants. Odds ratios (OR) and the 95% confidence intervals (CI) were computed for each genotype (homozygous variant or heterozygote, vs. homozygous wildtype) and for increase of each less common allele (log-additive model). Interactions between each variant and three folate intake variables (maternal multivitamin use, maternal dietary folate intake, and combined maternal folate intake) were also evaluated under the log-additive model. In general, we did not identify notable associations. The A allele of MTHFD1 rs11627387 was associated with a 1.7-fold increase in conotruncal defects risk in both Hispanic mothers (OR = 1.7, 95% CI = 1.1-2.5) and Hispanic infants (OR = 1.7, 95% CI = 1.2-2.3). The T allele of MTHFR rs1801133 was associated with a 2.8-fold increase of risk among Hispanic women whose dietary folate intake was ≤ 25th centile. The C allele of MTHFR rs1801131 was associated with a two-fold increase of risk (OR = 2.0, 95% CI = 1.0-3.9) only among those whose dietary folate intake was >25th centile. Our study suggested that MTHFD1 rs11627387 may be associated with risk of conotruncal defects through both maternal and offspring genotype effect among the Hispanics. Maternal functional variants in MTHFR gene may interact with dietary folate intake and modify the conotruncal defects risk in the offspring.

Correlations between the percentage of tumor cells showing an anaplastic lymphoma kinase (ALK) gene rearrangement, ALK signal copy number, and response to crizotinib therapy in ALK fluorescence in situ hybridization–positive nonsmall cell lung cancer

AbstractBACKGROUND:Fluorescence in situ hybridization (FISH), using break‐apart red (3′) and green (5′) ALK (anaplastic lymphoma kinase) probes, consistently shows rearrangements in <100% of tumor cells in ALK‐positive (ALK+) nonsmall cell lung cancer (NSCLC). Increased copy numbers of fused and rearranged signals also occur. Here, correlations are explored between the percentage of ALK+ cells and signal copy number and their association with response to ALK inhibition.METHODS:Ninety ALK+ NSCLC cases were evaluated. The percentage of positive cells, pattern of positivity (split, single red, or both), and copy number of fused, isolated red and green signals were recorded. Thirty patients had received crizotinib.RESULTS:Increased isolated red signal copy number (contributing to both single red and split patterns of positivity) correlated with a higher percentage of ALK+ cells (r = 0.743, P < .0001). Mean fused copy number was negatively associated with isolated red signal copy number (r = −0.409, P < .0001). Neither percentage of positive cells (r = 0.192, P = .3), nor copy number of isolated red signal (r = 0.274, P = .195) correlated with maximal tumor shrinkage with crizotinib.CONCLUSIONS:The strong association between increased copy number of key ALK signals and percentage of positive cells suggests that the <100% rate of cellular positivity in ALK+ tumors is due to technical factors, not biological factors. In ALK+ tumors, neither the percentage of positive cells nor signal copy number appear to be informative variables for predicting benefit from ALK inhibition. The inverse relationship between fused and isolated red copy number suggests ALK+ may be a distinct “near‐diploid” subtype of NSCLC that develops before significant chromosomal aneusomy occurs. Cancer 2012. © 2012 American Cancer Society.

Comparable levels of folate-induced aneusomy in B-lymphoblasts from oral-cleft patients and controls

Background Peri-conceptional use of folic acid contributes to protection against congenital malformations, such as neural tube defects and cleft lip with or without cleft palate (CL/P). Previous studies showed that low folate levels cause DNA damage, leading to chromosomal instability and aneusomy. This study seeks to confirm this finding and investigates whether the in vitro sensitivity towards aneusomy of chromosome 17 and 21 in the folate-deficient state differs between CL/P patients and controls. Methods Epstein–Barr virus-immortalized B-lymphoblasts derived from 15 CL/P children and 15 controls, were cultured in medium with high and low concentrations – approximately 40 nM and 5 nM – of 5-methyltetrahydrofolate, respectively. Fluorescence in situ hybridization was used to detect specific fluorescence signals for chromosomes 17 and 21. Results A significant increase in aneusomy of chromosomes 17 (2.3% vs 7.6%; p ≤ 0.001) and 21 (2.5% vs 7.0%; p ≤ 0.001) was observed after 10 days of culturing in low folate. These results were comparable in cell lines from patients and controls. Interestingly, for chromosome 17 the folate deficiency mainly resulted in an increase of monosomy (6%, p ≤ 0.001), while for chromosome 21 the increase of trisomy was larger (4.9%, p ≤ 0.001). Conclusions These data suggest that folate deficiency is a significant risk factor in the development of aneusomy and may affect the distribution of chromosomes during cell division. The comparable aneusomy frequencies in CL/P and in controls suggest that other folate-related processes are involved in the pathogenesis of CL/P, and additional investigations are needed to identify the causal mechanisms.

HER2 gene amplification occurs frequently in the micropapillary variant of urothelial carcinoma: analysis by dual-color in situ hybridization

Human epidermal growth factor receptor-2 (HER2) is a well-recognized growth-promoting factor in cancer, although its application to urothelial carcinoma has been limited because of a low frequency of gene amplification. We evaluated HER2 protein expression and gene amplification in micropapillary carcinoma, a rare but highly aggressive variant of urothelial carcinoma by dual-color in situ hybridization. Gene amplification was defined by a HER2:CHR17 ratio of ≥2.2; low and high levels of amplification were further defined as <2.5 and ≥2.5, respectively. Immunohistochemistry was used to determine HER2 protein expression using the American Society of Clinical Oncology/College of American Pathologists Guidelines of HER2 staining. Protein expression, gene amplification, and chromosome 17 aneusomy were compared by Jonchkeere–Terpstra and Cochran–Armitage trend tests. In all, 19 of the 20 micropapillary carcinoma samples yielded usable dual-color in situ hybridization and immunohistochemistry results for evaluation. Overall, 68% (n=13) demonstrated HER2 protein expression of 2+ to 3+ staining. Gene amplification was present in 42% of samples (n=8), with 100% correlation with 2+ and 3+ protein expression. Gene amplification and protein expression were significantly associated (P=0.01). Overall, 53% of samples (n=10) had aneusomy of chromosome 17. Chromosome 17 aneusomy was present in approximately half of the samples evaluated, suggesting inherent genomic instability in this variant of urothelial carcinoma. However, increased HER2:CHR17 ratios demonstrate increased HER2 expression due to amplification in the majority of micropapillary carcinomas. These results suggest that HER2-targeted therapy may be successful on the genomic level in patients with this disease.

A new isolation method for peripheral blood circulating solid tumor cells with EpCAM antibody linked nanobeads

Objective To establish an isolation method for solid GTC in peripheral blood using EpCAM antibody-linked nanobeads and evaluate the sensitivity of the method and its application significance. Methods Five, ten, twenty, fifty and one hundred MCF7 (breast cancer), KYSE70 (esophageal cancer), BxPC-3 (pancreatic cancer) and 9811P (stomach cancer) cells were added into 7. 5 ml erythrocyte lysed peripheral blood obtained from healthy volunteers respectively. EpCAM antibodylinked nanobeads were used to enrich cancer cells. The recovery rates of the in vitro added cancer cells were evaluated by fluorescence microscopy. Then, the untreated thirty cases of esophageal cancer (six cases at stage Ⅰ and Ⅱ, twenty-four cases at stage Ⅲ and Ⅳ), thirty-five cases of breast cancer (fifteen cases at stage Ⅰ and Ⅱ , twenty cases at stage Ⅲ and Ⅳ), thirty cases of pancreatic cancer (five cases at stage Ⅰ and Ⅱ , twenty-five cases at stage Ⅲ and Ⅳ), thirty-three gastric cancer (thirteen cases for stage Ⅰ and Ⅱ ,twenty cases at stage Ⅲ and Ⅳ) were enrolled to enrich the peripheral blood CTC. Thirty healthy volunteers and thirty gastritis patients served as two groups of control. Meanwhile the enriched CTC was identified by IF and HE staining. FISH was used to analyze the copy number of chromosome 8 and chromosome 20 in two hundred esophageal cancer, breast cancer, pancreatic caner and gastric cancer CTC. Results After DAPI staining and mixing with 7.5 ml peripheral blood from healthy donors, the average cell recovery rates of KYSE70, MCF7, BxPC-3 and 9811P cells evaluated under fluorescence microscope were 87%, 87%, 86% and 88% (within group), and the recovery rates of 5 gradient dilution levels were 88%, 85%, 87%, 88% and 87% (intergroup). With a high sensitivity, this method was able to isolate one cancer cell in 107 white blood cells of peripheral blood. The positive rates of more than 2 CTC in the peripheral blood detected by this method were 50% (15/30) of esophageal cancer, 63% (22/35) of breast cancer, 70% (21/30) of pancreatic cancer and 61% (20/33) gastric cancer patients respectively,but no CTC was detected in the peripheral blood of healthy volunteers and gastritis patients (P = 0. 000).The aneusomy of chromosome 8 and chromosome 20 were found in 80% esophageal cancer, 75% breast cancer, 65% pancreatic cancer and 59% gastric cancer. Conclusions The CTC isolation technique with EpCAM antibody-linked nanobeads is sensitive and accurate. The aneusomy of chromosome 8 and 20 is frequent in CTC from esophageal cancer, breast cancer, pancreatic cancer and gastric cancer. Key words: Antigens,neoplasm; Cell adhesion molecules; Nanoparticles; Neoplasm circulating cells; Cell line,tumor

Phenotypic variability of a deletion and duplication 6q16.1 → q21 due to a paternal balanced ins(7;6)(p15;q16.1q21)

Constitutional insertional translocations are rare findings in clinical cytogenetics. Here, we report on the unbalanced segregation of a balanced paternal insertional translocation ins(7;6)(p15;q16.1q21) to three children. Investigations by conventional karyotyping, FISH with locus-specific probes, microsatellite marker analysis, and SNP-array based copy number analysis revealed a direct orientation of the inserted segment, a size of 11.3 Mb, and breakpoints between rs4370337 and rs12660854 and rs12110990 and rs4946730 on 6q16.1 and 6q21, respectively, as well as within BAC clone RP11-182J2 on 7p15. A 17-year-old daughter inherited the der(6) chromosome and was affected by severe mental retardation, obesity, and minor anomalies. Two further children inherited the der(7) chromosome. A daughter shows an almost unremarkable phenotype and only minor features in neuropsychological testing at 19 years of age. Her 14-year-old half-brother demonstrates a mild delay in cognitive development most likely jointly caused by the chromosomal rearrangement and asphyxia during delivery. The patient with the deletion confirms the previously reported phenotype of severe mental retardation and obesity in patients with del(6)(q16.2), while both patients with partial trisomy for the same segment of chromosome 6 are further examples for a generally less severe phenotype associated with duplications than with deletions, and even for the recent insight that chromosomal aneusomies of several megabases may go without major clinical consequences.

Gain of chromosome 7 by chromogenic in situ hybridization (CISH) in chordomas is correlated to c-MET expression

Chordomas are low to intermediate grade malignancies that arise from remnants of embryonic notochord. They often recur after surgery and are highly resistant to conventional adjuvant therapies. Recently, the development of effective targeted molecular therapy has been investigated in chordomas that show receptors for tyrosine kinase (RTKs) activation. Expression of specific RTKs such as Epidermal Growth Factor Receptor (EGFR) and Mesenchymal-epithelial transition factor (c-MET) in chordomas may offer valuable therapeutic options. We investigated changes in copy number of chromosome 7 and correlated it with EGFR gene status and EGFR and c-MET protein expression in 22 chordoma samples. Chromosome 7 copy number was evaluated by chromogenic in situ hybridization (CISH) and protein expression of EGFR and c-MET by immunohistochemistry. Tumors mostly showed conventional histopathologic features and were found mainly in sacral (41%) and cranial sites (54.5%). Aneusomy of chromosome 7 was seen in 73% of the samples, 62% of primary tumors and in all recurrent chordomas. EGFR and c-MET were both expressed, but only c-MET protein expression was significantly correlated with chromosome 7 aneusomy (P ≤ 0.001). c-MET overexpression may represent an early chromosome 7 alteration that could play an important role during chordoma pathogenesis. c-MET overexpression shows promise as a molecular marker of response to targeted molecular therapy in the treatment of chordomas.

Cellular aging and centrosome aberrations

The significant increase in chromosomal instability with aging is well known, but the underlying mechanism is not fully understood. Our earlier studies showed a high frequency of abnormal mitosis, such as mitotic slippage or incomplete mitosis in near-senescent human fibroblasts. This study examined the centrosome aberrations in mitotic and interphase cells from different passages of several strains of human fibroblasts. Analysis by laser scanning cytometry showed increased frequencies of abnormal mitotic cells with supernumerary (>2/cell) centrosomes and misaligned chromosomes in later passages in all strains examined. Numerical centrosome aberrations were prominent in a polyploid subpopulation. In metaphase cells, numerical centrosome aberrations were correlated significantly with chromosome misalignment. Fluorescent in situ hybridization analysis using a centromere-specific probe revealed a correlation between chromosome aneusomy and centrosome over-duplication. These results suggest that abnormal duplication of centrosomes in association with cellular aging may be responsible for the increase in chromosomal instability with aging.