Opening the archives for state of the art tumour genetic research: sample processing for array-CGH using decalcified, formalin-fixed, paraffin-embedded tissue-derived DNA samples

<p>Abstract</p> <p>Background</p> <p>Molecular genetic studies on rare tumour entities, such as bone tumours, often require the use of decalcified, formalin-fixed, paraffin-embedded tissue (dFFPE) samples. Regardless of which decalcification procedure is used, this introduces a vast breakdown of DNA that precludes the possibility of further molecular genetic testing. We set out to establish a robust protocol that would overcome these intrinsic hurdles for bone tumour research.</p> <p>Findings</p> <p>The goal of our study was to establish a protocol, using a modified DNA isolation procedure and quality controls, to select decalcified samples suitable for array-CGH testing. Archival paraffin blocks were obtained from 9 different pathology departments throughout Europe, using different fixation, embedding and decalcification procedures, in order to preclude a bias for certain lab protocols. Isolated DNA samples were subjected to direct chemical labelling and enzymatic labelling systems and were hybridised on a high resolution oligonucleotide chip containing 44,000 reporter elements.</p> <p>Genomic alterations (gains and losses) were readily detected in most of the samples analysed. For example, both homozygous deletions of 0.6 Mb and high level of amplifications of 0.7 Mb were identified.</p> <p>Conclusions</p> <p>We established a robust protocol for molecular genetic testing of dFFPE derived DNA, irrespective of fixation, decalcification or sample type used. This approach may greatly facilitate further genetic testing on rare tumour entities where archival decalcified, formalin fixed samples are the only source.</p

Primary vascular tumors of bone: a spectrum of entities?

Vascular tumors of bone are a heterogeneous group. Numerous terms have been introduced as well as different classification systems. None of the classification schemes have been accepted due to lack of consistent terminology, accepted histologic criteria, and limited correlation with clinical outcome. It is acknowledged that vascular tumors of bone originate from endothelial cells, resulting in variable expression of endothelial markers. None of these markers are useful to discriminate between benign and malignant lesions. Although radiologic appearance is not specific, radiologic multifocality should trigger to include a vascular neoplasm in the differential diagnosis. This review gives an overview of current literature by describing all different histologic subtypes in correspondence with clinical, radiologic and genetic data. We propose the classification of vascular tumors of bone according to the three-tiered World Health Organization classification scheme for soft tissue tumors dividing entities into a benign, intermediate and malignant category. Hemangioma is the most often and commonly recognized benign lesion. Epithelioid hemangioma has been better defined over the past few years. Based on its locally aggressive behavior and occurrence of lymph node metastases, classification within the intermediate category could be considered. Angiosarcoma is the only accepted term for high-grade malignant vascular tumor of bone and so far, epithelioid hemangioendo-thelioma is the only accepted low-grade malignant vascular tumor of bone. It is still unclear whether other low-grade malignant vascular tumors of bone (e.g. hemangioendothelioma) truly exist. Unfortunately, molecular / genetic studies of vascular tumors of bone which might support the proposed classification are very sparse

Active TGF-β signaling and decreased expression of PTEN separates angiosarcoma of bone from its soft tissue counterpart

Angiosarcomas constitute a heterogeneous group of highly malignant vascular tumors. Angiosarcoma of bone is rare and poorly characterized. For angiosarcoma of soft tissue, some pathways seem to be involved in tumor development. Our aim was to evaluate the role of these pathways in angiosarcoma of bone. We collected 37 primary angiosarcomas of bone and used 20 angiosarcomas of soft tissue for comparison. Immunohistochemistry was performed on constructed tissue microarrays to evaluate expression of CDKN2A, TP53, PTEN, BCL2, CDK4, MDM2, cyclin D1, β-catenin, transforming growth factor-β (TGF-β), CD105, phospho-Smad1, phospho-Smad2, hypoxia-inducible factor-1α, plasminogen activator inhibitor type 1 (PAI-1), VEGF, CD117 and glucose transporter--1. PIK3CA was screened for hotspot mutations in 19 angiosarcomas. In nearly 55% of the angiosarcoma of bone, the retinoblastoma (Rb) pathway was affected. Loss of CDKN2A expression was associated with a significantly worse prognosis. No overexpression of TP53 or MDM2 was found, suggesting that the TP53 pathway is not important in angiosarcoma of bone. Angiosarcoma of bone showed highly active TGF-β signaling with immunoreactivity for phospho-Smad2 and PAI-1. Although the phosphatidylinositol 3-kinase (PI3K)/Akt pathway seems to be active in both tumor groups, different mechanisms were involved: 41% of angiosarcoma of bone showed a decrease in expression of PTEN, whereas in angiosarcoma of soft tissue overexpression of KIT was found (90%). PIK3CA hotspot mutations were absent. In conclusion, the Rb pathway is involved in tumorigenesis of angiosarcoma of bone. The PI3K/Akt pathway is activated in both angiosarcoma of bone and soft tissue, however, with a different cause; PTEN expression is decreased in angiosarcoma of bone, whereas angiosarcomas of soft tissue show overexpression of KIT. Our findings support that angiosarcomas are a heterogeneous group of vascular malignancies. Both angiosarcoma of bone and soft tissue may benefit from therapeutic strategies targeting the PI3K/Akt pathway. However, interference with TGF-β signaling may be specifically relevant in angiosarcoma of bone.Modern Pathology advance online publication, 19 April 2013; doi:10.1038/modpathol.2013.56