Chromosomal Comparative Genomic Hybridization Research Articles

Establishment and characterization of a novel ovarian high-grade serous carcinoma cell line\u2014IPO43

BackgroundEpithelial ovarian cancer (EOC) is an aggressive and lethal malignancy and novel EOC cell lines with detailed characterization are needed, to provide researchers with diverse helpful resources to study EOC biological processes and cancer experimental therapies.MethodsThe IPO43 cell line was established from the ascitic fluid of a patient with a diagnosis of high-grade serous carcinoma (HGSC) of the ovary, previously treated with chemotherapy.Cell immortalization was achieved in 2D cell culture and growth obtained in 2D and 3D cell cultures. The characterization of immortalized cells was done by immunocytochemistry, flow cytometry, cell proliferation, chromosomal Comparative Genomic Hybridization (cCGH), STR profile and Next Generation Sequencing (NGS).ResultsCharacterization studies confirmed that IPO43 cell line is of EOC origin and maintains morphological and molecular features of the primary tumor. cCGH analysis showed a complex profile with gains and losses of specific DNA regions in both primary ascitic fluid and cell line IPO43. The cell line was successfully grown in a 3D system which allows its future application in more complex assays than those performed in 2D models. IPO43 cell line is resistant to standard drug treatment in vitro.ConclusionsIPO43 is available for public research and we hope it can contribute to enrich the in vitro models addressing EOC heterogeneity, being useful to investigate EOC and to develop new therapeutic modalities.

Novel biallelic loss-of-function variants in CEP290 cause Joubert syndrome in two siblings

BackgroundJoubert syndrome (JS) is a rare genetic disorder, which can be defined by brain stem malformation, cerebellar vermis hypoplasia, and consequent “molar tooth sign” (MTS). JS always shares variety of phenotypes in development defects. With the development of next-generation sequencing, dozens of causative genes have been identified to JS so far. Here, we investigated two male siblings with JS and uncovered a novel pathogenesis through combined methods.ResultsThe siblings shared similar features of nystagmus, disorders of intellectual development, typical MTS, and abnormal morphology in fourth ventricle. Whole-exome sequencing (WES) and chromosome comparative genomic hybridization (CGH) were then performed on the proband. Strikingly, a maternal inherited nonsense variant (NM_025114.3: c.5953G>T [p.E1985*]) in CEP290 gene and a paternal inherited deletion in 12q21.32 including exons 1 to 10 of CEP290 gene were identified in the two affected siblings. We further confirmed the two variants by in vitro experiments: quantitative PCR and PCR sequencing.ConclusionsIn this study, we first reported a novel causative mechanism of Joubert syndrome: a copy number variation (CNV) combined with a single-nucleotide variant in CEP290 gene, which can be helpful in the genetic diagnosis of this disease.

Chromosomal Evolution and Evolutionary Relationships of Lebiasina Species (Characiformes, Lebiasinidae).

We present the first cytogenetic data for Lebiasina bimaculata and L. melanoguttata with the aim of (1) investigating evolutionary events within Lebiasina and their relationships with other Lebiasinidae genera and (2) checking the evolutionary relationships between Lebiasinidae and Ctenoluciidae. Both species have a diploid number 2n = 36 with similar karyotypes and microsatellite distribution patterns but present contrasting C-positive heterochromatin and CMA3+ banding patterns. The remarkable interstitial series of C-positive heterochromatin occurring in L. melanoguttata is absent in L. bimaculata. Accordingly, L. bimaculata shows the ribosomal DNA sites as the only GC-rich (CMA3+) regions, while L. melanoguttata shows evidence of a clear intercalated CMA3+ banding pattern. In addition, the multiple 5S and 18S rDNA sites in L. melanogutatta contrast with single sites present in L. bimaculata. Comparative genomic hybridization (CGH) experiments also revealed a high level of genomic differentiation between both species. A polymorphic state of a conspicuous C-positive, CMA3+, and (CGG)n band was found only to occur in L. bimaculata females, and its possible relationship with a nascent sex chromosome system is discussed. Whole chromosome painting (WCP) and CGH experiments indicate that the Lebiasina species examined and Boulengerella maculata share similar chromosomal sequences, thus supporting the relatedness between them and the evolutionary relationships between the Lebiasinidae and Ctenoluciidae families.

Human embryos secrete microRNAs into culture media—a potential biomarker for implantation

To determine whether human blastocysts secrete microRNA (miRNAs) into culture media and whether these reflect embryonic ploidy status and can predict in vitro fertilization (IVF) outcomes. Experimental study of human embryos and IVF culture media. Academic IVF program. 91 donated, cryopreserved embryos that developed into 28 tested blastocysts, from 13 couples who had previously completed IVF cycles. None. Relative miRNA expression in IVF culture media. Blastocysts were assessed by chromosomal comparative genomic hybridization analysis, and the culture media from 55 single-embryo transfer cycles was tested for miRNA expression using an array-based quantitative real-time polymerase chain reaction analysis. The expression of the identified miRNA was correlated with pregnancy outcomes. Ten miRNA were identified in the culture media; two were specific to spent media (miR-191 and miR-372), and one was only present in media before the embryos had been cultured (miR-645). MicroRNA-191 was more highly concentrated in media from aneuploid embryos, and miR-191, miR-372, and miR-645 were more highly concentrated in media from failed IVF/non-intracytoplasmic sperm injection cycles. Additionally, miRNA were found to be more highly concentrated in ICSI and day-5 media samples when compared with regularly inseminated and day-4 samples, respectively. MicroRNA can be detected in IVF culture media. Some of these miRNA are differentially expressed according to the fertilization method, chromosomal status, and pregnancy outcome, which makes them potential biomarkers for predicting IVF success.

Agenesis of the Corpus Callosum Associated with a large Ocular Lipodermoid in a Neonate: A Case Report and Literature Review

Agenesis of the corpus callosum is the most common brain malformation. It may be an isolated malformation or a component of a malformation syndrome. Associated Central Nervous System (CNS) and non-CNS malformations have been broadly reviewed. However, the coexistence of a large ocular lipodermoid has never been mentioned. We reported a female newborn with multiple congenital anomalies, including complete agenesis of the corpus callosum with intracranial midline lipoma, a large epibulbar lipodermoid over the entire left cornea and a large Ventricular Septal Defect (VSD). No clinical neurological or cardiac symptoms or signs were noted during admission. She received an ocular tumor excision with amniotic membrane transplantation on the left eye at 10 days old. Limbal dermoids/lipodermoids are hallmarks of Goldenhar syndrome; however, our patient did not have preauricular tag, microtia, or vertebral anomalies. In addition, a chromosome study and comparative genomic hybridization array in this patient revealed no significant abnormalities. To the best of our knowledge, this is the first report of a case with a combination of agenesis of the corpus callosum, an ocular lipodermoid, and VSD.

Comparative Genomic Hybridization Studies on Mesothelioma Show a Parallel Fate of 1p21-1p22 and 9p21 Bands and a Chromosomally Stable Sub-Group

Malignant Pleural Mesothelioma (MPM) is a cancer whit a poor prognosis. The landscape of the chromosomal rearrangements in MPM was approached by several authors but robust conclusions could not be made, given the limited sample sets analyzed within each study. In order to improve the knowledge on the field, we retrieved and pooled all the results deriving from published studies where comparative genomic hybridization (CGH) was employed. A total of 283 tissues (149 epithelioid, 53 sarcomatoid, 78 biphasic, and 3 unclassified) were analysed, 179 with classical chromosome CGH (cCGH), and 104 with arrayed-CGH (aCGH). Some chromosomal bands were involved in aberrations with a frequency exceeding 20% (-1p21, -9p, -14q, and -22q for the epithelioid, -4, +5p, +8q21ter, -9p, -13, and -14q for the sarcomatoid, and -9p, -14q, and -22q for the biphasic type). We found a statistical significant association between contemporary losses at 9p21 and 1p21-1p22 (21% of the samples showed losses at both bands, P=7.74x10-8), whose significance should be elucidated with further studies. Candidate cancer genes involved in MPM were suggested. Finally, 15% of epithelioid, 13% of sarcomatoid, and 13% of biphasic MPM tissues did not show any genomic alteration. Only two previous studies suggested a less aggressive behavior of MPM in relation to a low degree of chromosomal alterations. Thus, more work is warranted to understand whether chromosomal rearrangements could be included as prognostic biomarker in the clinical practice.

Array Comparative Genomic Hybridization of Keratoacanthomas and Squamous Cell Carcinomas: Different Patterns of Genetic Aberrations Suggest Two Distinct Entities

Keratoacanthoma (KA) is a benign keratinocytic neoplasm that spontaneously regresses after 3-6 months and shares features with squamous cell carcinomas (SCCs). Furthermore, there are reports of KAs that have metastasized, invoking the question of whether KA is a variant of SCC (Hodak et al., 1993). To date, no reported criteria are sensitive enough to discriminate reliably between KA and SCC, and consequently there is a clinical need for discriminating markers. Our previous study analyzed 132 KAs and 29 SCCs and revealed significantly different regions of genomic aberrations using chromosomal comparative genomic hybridization (CGH). In the present study, we applied array CGH to investigate 98 KAs and 22 SCCs from the above samples. The result shows that all KAs and SCCs have some degree of genetic aberrations. The distribution of numbers of aberrant clones per sample differed significantly between KAs and SCCs (P<0.02), which also demonstrated recurrent aberrations that differed significantly (P<0.001), as illustrated by unsupervised cluster analysis. Classifiers for clinicopathological parameters of KAs were established based on t-test statistics and permutation tests. Tumor size, fibrosis, and inflammation, which are related to the developmental stages of KAs, showed significant (t-test, permutation test) associations with aberrations of selected genomic regions. This suggests chromosomal instability during the whole life cycle of KAs.

Genetic characterization of dogs via chromosomal analysis and array-based comparative genomic hybridization (aCGH)

The results of cytogenetic and molecular cytogenetic investigations revealed similarities in genetic background and biological behaviour between tumours and genetic diseases of humans and dogs. These findings classify the dog a good and accepted model for human cancers such as osteosarcomas, mammary carcinomas, oral melanomas and others. With the appearance of new studies and advances in canine genome sequencing, the number of known homologies in diseases between these species raised and still is expected to increase. In this context, array-based comparative genomic hybridization (aCGH) provides a novel tool to rapidly characterize numerical aberrations in canine tumours or to detect copy number aberrations between different breeds. As it is possible to spot probes covering the whole genome on each chip to discover copy number aberrations of all chromosomes simultaneously, this method is time-saving and cost-effective - considering the relation of costs and the amount of data obtained. Complemented with traditional methods like karyotyping and fluorescence in situ hybridization (FISH) analyses, the aCGH is able to provide new insights into the underlying causes of canine carcinogenesis.

Identification of the first germline HRPT2 whole‐gene deletion in a patient with primary hyperparathyroidism

Germline mutations in the HRPT2 gene are associated with the hereditary hyperparathyroidism-jaw tumour syndrome (HPT-JT) and a subset of familial isolated hyperparathyroidism (FIHP). Somatic HRPT2 mutations are detected in sporadic parathyroid carcinomas and less frequently in cystic adenomas. The purpose of this study was to investigate the underlying HRPT2 defect in a young patient with symptomatic hyperparathyroidism due to an apparently sporadic parathyroid adenoma with cystic features. HRPT2 mutations in the patient's genomic and parathyroid tumour DNA were screened by PCR-based sequencing. Tumour loss of heterozygosity (LOH) at the HRPT2 locus was assessed with microsatellite markers. A large germline HRPT2 deletion was investigated by real-time quantitative PCR analysis (qPCR). Genomic DNA losses were also appraised by chromosomal comparative genomic hybridization (cCGH). No germline HRPT2 point mutation was detected by direct sequencing. A novel hemizygous HRPT2 somatic mutation (c.32delA) was identified in the tumour. Apparent constitutional homozygosity for HRPT2 flanking microsatellite markers, and absence of LOH at a distal marker, suggested a large germline deletion. Gene dose mapping by qPCR unveiled a de novo deletion of the whole HRPT2 gene and adjacent loci (<9·3 Mb in size). cCGH confirmed germline DNA loss involving the HRPT2 locus. We report the first large germline deletion of the HRPT2 gene, which was not detectable by conventional PCR-based sequencing methods. This finding emphasizes that qPCR should be implemented in HRPT2 molecular analysis, which may improve genetic assessment and clinical management of patients with FIHP and HPT-JT.

Similar cytogenetic findings in two synchronous secondary peripheral chondrosarcomas in a patient with multiple osteochondromas

Secondary peripheral chondrosarcoma is a malignant chondroid tumor arising in a benign precursor, either an osteochondroma or an enchondroma. Multiple osteochondromas syndrome (MO) is an autosomal dominant skeletal disorder associated with bony growths in the form of osteochondromas that occasionally undergo malignant transformation to secondary peripheral chondrosarcomas. We describe the genetic examination of three secondary peripheral chondrosarcomas that had arisen synchronously from osteochondromas in a patient with MO by chromosome banding, high resolution chromosomal comparative genomic hybridization, and mutation analysis of the EXT1 and EXT2 genes. In two of the tumors (the third was not genetically informative), very similar chromosome abnormalities were found, indicating that they must somehow be part of the same neoplastic process in spite of being anatomically distinct.

DNA copy number aberrations associated with the clinicopathological features of colorectal cancers: Identification of genomic biomarkers by array-based comparative genomic hybridization

The aim of the present study was to investigate the chromosomal aberrations that are linked with the crucial clinicopathological features of colorectal cancer (CRC) and its prognosis by array-based comparative genomic hybridization (CGH). Fresh-frozen tumor tissues of 94 cases of CRC were analyzed by using bacterial artificial chromosome (BAC) CGH slides spotted with 4030 human BAC clones, which covered the whole range of the human genome at an average interval of 0.83 mega base pairs. DNA copy number aberrations (DCNAs) were identified in association with clinicopathological features: a gain of 8q24.3 and losses of 9q33.1 and 20p12.2 were associated with lymph node metastasis, gain of 8q24.3 and loss of 9q33.1 with disease stage, gain of 8q21.11 and loss of 10q21.3 with lymphovascular invasion and losses of 3p25.1, 10p15.3, 12q15 and 17p13.1 for venous invasion. These aberrations can be regarded as genomic biomarkers to predict the clinical outcome of patients with CRC, and are expected to serve to individualize the treatment of CRC patients.

Molecular-Microscopical Correlation in Dermatopathology

Molecular-Microscopical Correlation in Dermatopathology

Cytogenetic characterization of head and neck squamous cell carcinoma cell lines as model systems for the functional analyses of tumor‐associated genes

Head and neck squamous cell carcinoma (HNSCC) is a solid malignant neoplasm exhibiting aggressive phenotypes and high recurrence rates. To improve its clinical management, understanding the molecular basis of HNSCC development is of critical importance. For the investigation of tumor-associated genes, functional analyses in well-characterized tumor cell systems are required. To establish an experimental platform, a set of 20 HNSCC cell lines was screened for genetic imbalances by chromosomal comparative genomic hybridization (cCGH). Frequent DNA copy number gains were detected on 3q26.3-qter, 5p, 7p11-p13, 8q23-qter, 9p11-p13, 9q31-qter, 11q13 and 20q13.1, whereas copy number losses were found on 3p, 4p, 4q32.1-qter, 8p11-p12 and 18q22 in agreement with previous observations on genetic aberrations detected in primary HNSCC specimens. Subsequent mRNA expression analysis of 11q13 candidate genes CCND1 and CTTN revealed that HNSCC cell lines exhibiting a DNA copy number gain on 11q13 had a higher transcript level of CCND1 and CTTN compared with HNSCC cell lines without 11q13 copy number gain (P = 0.014 and P = 0.009, respectively). Furthermore, CCND1 and CTTN amplification as detected by fluorescence in situ hybridization correlated with protein expression as assessed by immunocytochemistry. In summary, the cytogenetic characterization illustrates that this set of HNSCC cell lines is representative for the HNSCC genome and provides tumor model systems for detailed analysis of genes with a possible role in the pathomechanism of head and neck tumors.

Abstract 782: Characterization of genetic changes in oligodendroglial tumors including glioblastomas with oligodendroglial component

Abstract In contrast to astrocytic tumors including glioblastomas (GBM), oligodendrogliomas (O) show a better prognosis and increased responsiveness to chemotherapy. Interestingly, a small subgroup of glioblastomas contains areas with histological features of oligodendroglial differentiation. In the current WHO classification (2007) these tumors are now included as a variant of glioblastomas and are called glioblastomas with oligodendroglial component (GBMO). However, definitive diagnostic criteria still do not exist. In this study we used a genome wide approach (chromosomal comparative genomic hybridization (CGH) and molecular karyotyping) in combination with interphase fluoreszence in situ hybridization (FISH) (regions 1p, 1q, 7q, 10q, 17p, 19q, cen18, 21q) to genetically characterize GBMO and “classical” O. We analyzed the oligodendroglial and the astrocytic glioblastoma parts of 13 GBMO separately by chromosomal CGH of microdissected paraffin embedded tumor tissue and interphase FISH on paraffin sections. Furthermore, freshly frozen material of six oligodendrogliomas (4 WHO grade II, 6 WHO-grade III) was examined genome wide by using the standard Agilent 244A chip. We identified four distinct genetic subtypes in GBMO: an “astrocytic” subtype (9/13) characterized by +7/-10; an “oligodendroglial” subtype with −1p/-19q (1/13); an “intermediate” subtype showing +7/-1p (1/13), and an “other” subtype having none of the former aberrations typical for gliomas (2/13). In contrast, most “classical” O (5/6) showed combined 1p/19q deletion, corresponding genetically to the “oligodendroglial” subtype. Four of the O with 1p/19q codeletion showed additional aberrations (e. g. −4, −14, −9, −18). The different histological tumor parts of GBMO revealed common genetic changes in all tumors and showed additional aberrations specific for their oligodendroglial and astrocytic parts. These findings demonstrate the monoclonal origin of the tumor followed by the formation of the astrocytic and oligodendroglial components. We are currently evaluating the array CGH results of six oligodendrogliomas, which will also be presented. The diagnostic determination of these genetic signatures may allow for a better prognostication of the patients. Our results underline the importance of molecular cytogenetic analyses to supplement the histological diagnosis of gliomas. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 782.

A simple method for enhancing hybridization efficiency in chromosome and array comparative genomic hybridization

The accuracy of comparative genomic hybridization (CGH) analysis is affected by hybridization efficiency. We describe here a simple method for enhancing hybridization efficiency. The hybridization procedure is essentially the same as that of conventional methods. Hybridization solution containing denatured DNA probe mixture was applied to a metaphase chromosome slide or DNA chip slide and covered with a coverslip. In the new method, however, the slide was inverted by turning the coverslip downward prior to hybridization. We termed this method the inverted slide method. To estimate the efficiency of the new method, metaphase chromosome slides and DNA chip slides were treated by both the conventional and inverted slide methods and incubated in a moist chamber at 37°C for 12, 24, 48, and 72 h. Hybridization signals were approximately 1.5 to 2 times brighter on the slides using the inverted slide method than those using the conventional method after 48 and 72 h of incubation. Furthermore, topographical differences in fluorescence intensity were smaller in slides using the inverted-slide method than in those prepared by the conventional method. The inverted slide method is methodologically very simple and improves the resolution of CGH.

Array‐Based Genomics in Glioma Research

Over the years, several relevant biomarkers with a potential clinical interest have been identified in gliomas using various techniques, such as karyotype, microsatellite analysis, fluorescent in situ hybridization and chromosome comparative genomic hybridization. Despite their pivotal contribution to our understanding of gliomas biology, clinical application of these approaches has been limited by technological and clinical complexities. In contrast, genomic arrays (array-based comparative genomic hybridization and single nucleotide polymorphisms array) have emerged as promising technologies for clinical use in the setting of gliomas. Indeed, their feasibility and reliability have been rigorously assessed in gliomas and are discussed in this review. The well-known genomic biomarkers in gliomas are in fact readily and reliably identified using genomic arrays. Moreover, it detects a multitude of new cryptic genomic markers, with potential biological and/or clinical significances. The main studies dedicated to genomic characterization of gliomas using genomic arrays are reviewed here. Interestingly, several recurrent genomic signatures have been reported by different teams, suggesting the validity of these genomic patterns. In light of this, genomic arrays are relatively simple and cost-effective techniques whose implementation in molecular diagnostic laboratories should be encouraged as a valuable clinical tool for management of glioma patients.

Hereditary gastrointestinal stromal tumors sharing the KIT Exon 17 germline mutation p.Asp820Tyr develop through different cytogenetic progression pathways

Hereditary gastrointestinal stromal tumor (GIST) syndrome is a rare autosomal dominant genetic disorder originated by germline mutations in the KIT or PDGFRA genes. We report the third family with hereditary predisposition to GIST due to the KIT Exon 17 germline mutation p.Asp820Tyr and characterize the cytogenetic progression pathways followed by different GIST sharing the same primary genetic event, using a combination of chromosome banding, comparative genomic hybridization (CGH), and fluorescence in situ hybridization (FISH) analyses. The missense mutation p.Asp820Tyr was detected in the proband's rectal and gastric GIST, as well as in his aunt's GIST epiplon metastasis. The mutation p.Asp820Tyr was subsequently also found in the proband's peripheral blood DNA, as well as in that of 4 of 10 relatives thus far analyzed. CGH analysis revealed loss of 14q and 15q in the proband's gastric lesion, whereas FISH analysis of the proband's rectal GIST did not detect loss of 14q and 15q, but instead loss of 4q and 22q and gain of 20q, indicating that the two tumors were independent GIST. Chromosome banding and CGH analyses of the aunt's GIST epiplon metastasis revealed multiple cytogenetic alterations, including 1p loss, but none in common with the two proband's GIST. We conclude that, although the patients share the same KIT Exon 17 germline mutation, the multiple GIST analyzed followed different pathogenetic progression pathways, each of which did not significantly differ from what has been described in sporadic GIST.

DNA Copy Number Aberrations in Breast Cancer by Array Comparative Genomic Hybridization

Array comparative genomic hybridization (CGH) has been popularly used for analyzing DNA copy number variations in diseases like cancer. In this study, we investigated 82 sporadic samples from 49 breast cancer patients using 1-Mb resolution bacterial artificial chromosome CGH arrays. A number of highly frequent genomic aberrations were discovered, which may act as “drivers” of tumor progression. Meanwhile, the genomic profiles of four “normal” breast tissue samples taken at least 2 cm away from the primary tumor sites were also found to have some genomic aberrations that recurred with high frequency in the primary tumors, which may have important implications for clinical therapy. Additionally, we performed class comparison and class prediction for various clinicopathological parameters, and a list of characteristic genomic aberrations associated with different clinicopathological phenotypes was compiled. Our study provides clues for further investigations of the underlying mechanisms of breast carcinogenesis.

Genomic characteristics of soft tissue sarcomas

Studies on the molecular mechanisms behind soft tissue sarcoma development have disclosed that these malignancies are as genetically heterogeneous as they are clinically and morphologically diverse. Much of the genetic information on soft tissue sarcomas is still limited to the genomic level, as detected by chromosome banding analysis or comparative genomic hybridization. Based on the results of such studies, soft tissue sarcomas may be broadly dichotomized into one group, accounting for approximately 20% of the cases, characterized by specific balanced translocations, and one group typically showing massive chromosomal rearrangements leading to recurrent, but non-specific, structural and numerical rearrangements. As summarized in this review, the genomic characterization of soft tissue sarcomas has not only provided cell biologists with decisive information on the parts of the genome that may harbor genes that are essential for tumor development but also given the clinicians involved in the management of these patients a valuable diagnostic tool.

The Chromosomal Aberrations in the Head and Neck Squamous Cell Carcinoma Cell Lines: PCI-1, PCI-13 and PCI-50

Background and ObjectivesZZThe knowledge about chromosomal aberrations manifestated in cancer has been spotlighted recently. The genetic analyses based on the knowledge about chromosomal aberrations are important for the development of diagnotic methods and evaluation of prognostic factors in cancers. Comparative genomic hybridization (CGH) is a powerful tool for evaluating chromosomal aberrations and array CGH significantly enhances these diagnostic effectiveness. The incidence of head and neck squamous cell carcinoma (HNSCC) has been increasing worldwide but the treatment outcomes still have been limited. The aim of this study is to evaluate the location of chromosomal aberrations in HNSCC cell lines with the combination of CGH and array CGH.