Karyotypic changes detected by comparative genomic hybridization in a stillborn infant with chorioangioma and liver hemangioma

Genetic Analysis of Copy Number Variation in Large Chorangiomas

INTRODUCTION

Chorangioma (CA) is the most common nontrophoblastic, vascular tumor-like lesion of the placenta with a reported incidence of 0.5% to 1% in all examined placentas. The underlying molecular mechanisms of CAs are still poorly elucidated, and a systematic investigation of the genetic background of CAs has not previously been done.

MATERIALS AND METHODS

Tissue biopsies from 8 large (>40 mm) histologically confirmed CAs and 8 unaffected matched placenta controls, along with standard control DNA samples were analyzed for large genomic deletions and duplications using array comparative genomic hybridization (array-CGH) method.

RESULTS

Array-CGH analysis revealed no rare or novel copy number variants in the CA samples compared with either standard control DNA or unaffected placenta DNA from the same individual.

DISCUSSION

In this study, a systematic genetic investigation of 8 large CAs failed to demonstrate any large-scale pathogenic genetic changes. This lack of association might support a nongenetic, nontumorous origin of these lesions; however, additional genetic studies focusing on smaller genomic alterations are required to fully assess any possible genetic contribution.

Giant Hepatic Hemangioma and Placental Chorangiosis: A Unique Case of Stillbirth?

INTRODUCTION

Hepatic hemangiomas (HH) are benign vascular tumors, and when large, may contribute to fetal morbidity/mortality. Chorangiosis is placental villus capillary hypervascularity, probably linked with fetal hypoxia.

CASE REPORT

We present a macrosomic stillbirth at 39 + 3 weeks of gestation with congestive heart failure (CHF) and myocardial infarction. A giant right hepatic lobe HH was present, along with placental chorangiosis.

CONCLUSION

A common pathogenetic pathway between congenital HH and placental chorangiosis has not been reported. Our case suggests that the effects of HH and chorangiosis increase the risk of late fetal loss due to the high-output CHF.

Enrichment of the embryonic stem cell reprogramming factors Oct4, Nanog, Myc, and Sox2 in benign and malignant vascular tumors

Background

The “stem cell theory of cancer” states that a subpopulation of cells with stem cell-like properties plays a central role in the formation, sustainment, spread, and drug resistant characteristics of malignant tumors. Recent studies have isolated distinct cell populations from infantile hemangiomas that display properties equivalent to aberrant progenitor cells, suggesting that, in addition to malignant tumors, benign tumors may also contain a stem cell-like component.

Methods

In this study, the expression levels of the embryonic stem cell reprogramming factors Oct4, Nanog, Myc, Sox2, and Klf4 were examined via immunohistochemistry in a panel of 71 benign, borderline, and malignant vascular tumors including capillary hemangioma, cavernous hemangioma, granulomatous hemangioma, venous hemangioma, hemangioendothelioma, hemangiopericytoma, and angiosarcoma. Antigenicity for each protein was quantified based on staining intensity and percentage of tissue positive for each antigen, and subsequently compared to data obtained from two control tissue sets: 10 vascular tissues and a panel of 58 various malignant sarcomas.

Results and discussion

With the exception of Myc (which was only present in a subset of benign, borderline, and malignant tumors), Oct4, Nanog, Sox2, and Klf4 were detectable at variable levels across both normal and diseased tissues. Semi-quantitative evaluation of our immunohistochemical staining revealed that protein expression of Oct4, Nanog, Myc, and Sox2, but not Klf4, was significantly increased in benign, borderline, and malignant vascular tumors relative to non-diseased vascular tissue controls. Interestingly, the enhanced levels of Oct4, Nanog, Myc, and Sox2 protein were approximately equivalent between benign, borderline, and malignant vascular tumors.

Conclusions

These findings provide supporting evidence that enrichment for proteins involved in pluripotency is not restricted solely to malignant tumors as is suggested by the “stem cell theory of cancer”, but additionally extends to common benign vascular tumors such as hemangiomas.

Electronic supplementary material

The online version of this article (doi:10.1186/s12907-015-0018-0) contains supplementary material, which is available to authorized users.

A new normalizing algorithm for BAC CGH arrays with quality control metrics

The main focus in pin-tip (or print-tip) microarray analysis is determining which probes, genes, or oligonucleotides are differentially expressed. Specifically in array comparative genomic hybridization (aCGH) experiments, researchers search for chromosomal imbalances in the genome. To model this data, scientists apply statistical methods to the structure of the experiment and assume that the data consist of the signal plus random noise. In this paper we propose "SmoothArray", a new method to preprocess comparative genomic hybridization (CGH) bacterial artificial chromosome (BAC) arrays and we show the effects on a cancer dataset. As part of our R software package "aCGHplus," this freely available algorithm removes the variation due to the intensity effects, pin/print-tip, the spatial location on the microarray chip, and the relative location from the well plate. removal of this variation improves the downstream analysis and subsequent inferences made on the data. Further, we present measures to evaluate the quality of the dataset according to the arrayer pins, 384-well plates, plate rows, and plate columns. We compare our method against competing methods using several metrics to measure the biological signal. With this novel normalization algorithm and quality control measures, the user can improve their inferences on datasets and pinpoint problems that may arise in their BAC aCGH technology.

Non-trophoblastic tumor of the placenta with combined histologic features of chorangioma and leiomyoma

Chorangioma is the most common non-trophoblastic tumor of the placenta, which represents an excessive vascular proliferation within chorionic villi. While the histologic picture of a chorangioma may vary greatly from lesion to lesion, the presence of abundant smooth muscle tissue within a chorangioma has not been previously reported. Herein we report a case of a 34-year-old primigravida woman with a peculiar mesenchymal placental tumor, characterized by combined features of chorangioma and leiomyoma; large lobules of numerous small blood vessels within loose stroma, separated by broad bundles of smooth muscle fibers. Genetic studies by means of PCR excluded maternal and confirmed placental origin of the lesion.

Challenges in array comparative genomic hybridization for the analysis of cancer samples

PURPOSE

To address some of the challenges facing the incorporation of array comparative genomic hybridization technology as a clinical tool, including archived tumor tissue, tumor heterogeneity, DNA quality and quantity, and array comparative genomic hybridization platform selection and performance.

METHODS

Experiments were designed to assess the impact of DNA source (e.g., archival material), quantity, and amplification on array comparative genomic hybridization results. Two microdissection methods were used to isolate tumor cells to minimize heterogeneity. These data and other data sets were used in a further performance comparison of two commonly used array comparative genomic hybridization platforms: bacterial artificial chromosome (Roswell Park Cancer Institute) and oligonucleotide (Agilent Technologies, Santa Clara, CA).

RESULTS

Array comparative genomic hybridization data from as few as 100 formalin-fixed, paraffin-embedded cells isolated by laser capture microdissection and amplified were remarkably similar to array comparative genomic hybridization copy number alterations detected in the bulk (unamplified) population. Manual microdissection from frozen sections provided a rapid and inexpensive means to isolate tumor from adjacent DNA for amplification and array comparative genomic hybridization. Whole genome amplification introduced no appreciable allele bias on array comparative genomic hybridization. The array comparative genomic hybridization results provided by the bacterial artificial chromosome and Agilent platforms were concordant in general, but bacterial artificial chromosome array comparative genomic hybridization showed far fewer outliers and overall less technical noise, which could adversely affect the statistical interpretation of the data.

CONCLUSIONS

This study demonstrates that copy number alterations can be robustly and reproducibly detected by array comparative genomic hybridization in DNA isolated from challenging tumor types and sources, including archival materials, low DNA yield, and heterogeneous tissues. Furthermore, bacterial artificial chromosome array comparative genomic hybridization offers the advantage over the Agilent oligonucleotide platform of presenting fewer outliers, which could affect data interpretation.