Validation of 34betaE12 immunoexpression in clear cell papillary renal cell carcinoma as a sensitive biomarker.

Clear cell papillary renal cell carcinoma (CCPRCC) is a recently recognised neoplasm with a broad spectrum of morphological characteristics, thus representing a challenging differential diagnosis, especially with the low malignant potential multicystic renal cell neoplasms and clear cell renal cell carcinoma. We selected 14 cases of CCPRCC with a wide spectrum of morphological features diagnosed on morphology and CK7 immunoreactivity and analysed them using a panel of immunohistochemical markers, focusing on 34βE12 and related CKs 1,5,10 and 14 and several molecular analyses such as fluorescence in situ hybridisation (FISH), array comparative genomic hybridisation (aCGH), VHL methylation, VHL and TCEB1 sequencing and multiplex ligation-dependent probe amplification (MLPA). Twelve of 13 (92%) CCPRCC tumours were positive for 34βE12.

Differentiating soft tissue leiomyosarcoma and undifferentiated pleomorphic sarcoma: A miRNA analysis.

The rare and highly aggressive adult soft tissue sarcomas leiomyosarcoma (LMS) and undifferentiated pleomorphic sarcoma (UPS) contain complex genomes characterized by a multitude of rearrangements, amplifications, and deletions. Differential diagnosis remains a challenge. MicroRNA (miRNA) profiling was conducted on a series of LMS and UPS samples to initially investigate the differential expression and to identify specific signatures useful for improving the differential diagnosis.

Renal cell carcinoma with smooth muscle stroma lacks chromosome 3p and VHL alterations.

Renal cell carcinoma with prominent smooth muscle stroma is a rare neoplasm composed of an admixture of epithelial cell with clear cytoplasm arranged in small nest and tubular structures and a stroma composed of smooth muscle. In the epithelial component, loss of chromosome 3p detected by fluorescence in situ hybridization (FISH) has been reported and on this basis these neoplasms have been viewed as variants of clear cell renal cell carcinoma. To test the validity of this classification, we have evaluated the chromosome 3 and VHL status of three of these tumors using FISH, array comparative genomic hybridization, gene sequencing, and methylation-specific multiplex ligation-dependent probe amplification analysis.

MicroRNA expression profiles in Kaposi's sarcoma.

Kaposi's sarcoma (KS) is a mesenchymal tumor, caused by Human herpesvirus 8 (HHV8) with molecular and cytogenetic changes poorly understood. To gain further insight on the underlying molecular changes in KS, we performed microRNA (miRNA) microarray analysis of 17 Kaposi's sarcoma specimens. Three normal skin specimens were used as controls.

True 3q chromosomal amplification in squamous cell lung carcinoma by FISH and aCGH molecular analysis: impact on targeted drugs.

Squamous lung carcinoma lacks specific "ad hoc" therapies. Amplification of chromosome 3q is the most common genomic aberration and this region harbours genes having role as novel targets for therapeutics. There is no standard definition on how to score and report 3q amplification.

MicroRNA expression profiles in metastatic and non-metastatic giant cell tumor of bone.

Giant cell tumor of bone (GCTB) is a skeletal neoplasm, a locally aggressive tumor that occasionally metastasizes to the lungs. To identify novel biomarkers associated with GCTB progression and metastasis, we performed a miRNA microarray on ten primary tumors of GCTB, of which five developed lung metastases and the rest remained metastasis-free. Between metastatic and non-metastatic GCTB, 12 miRNAs were differentially expressed (such as miR-136, miR-513a-5p, miR-494, miR-224, and miR-542-5p).

MicroRNA profiling predicts survival in anti-EGFR treated chemorefractory metastatic colorectal cancer patients with wild-type KRAS and BRAF.

Anti-EGFR monoclonal antibodies (anti-EGFRmAb) serve in the treatment of metastatic colorectal cancer (mCRC), but patients with a mutation in KRAS/BRAF and nearly one-half of those without the mutation fail to respond. We performed microRNA (miRNA) analysis to find miRNAs predicting anti-EGFRmAb efficacy. Of the 99 mCRC patients, we studied differential miRNA expression by microarrays from primary tumors of 33 patients who had wild-type KRAS/BRAF and third- to sixth-line anti-EGFRmAb treatment, with/without irinotecan.

MicroRNA profiling differentiates colorectal cancer according to KRAS status.

Recent studies have shown the important role of microRNAs (miRNAs) in a variety of biological processes, and in its ability to distinguish tumors according to their prognostic and predictive properties. To identify miRNA signatures associated with colorectal carcinoma (CRC) and with KRAS status, we studied, using Agilent's miRNA microarrays, miRNA expression in primary tumors from 55 metastatic CRC patients, including 15 with mutant and 40 with wild-type KRAS. Comparing these with normal colon tissue, we identified 49 miRNAs--including 19 novel miRNAs--significantly deregulated in tumor tissue.

miRNA expression profiles in myelodysplastic syndromes reveal Epstein-Barr virus miR-BART13 dysregulation.

Recently, the microRNA (miRNA) signature has been used for better characterization and understanding of the pathogenesis of different malignancies, including myelodysplastic syndromes (MDS). MDS are a heterogeneous group of stem cell disorders in which the genetic and molecular defects are not well defined. In the present study, we applied array based miRNA profiling to study 19 bone marrow cell samples of de novo MDS compared with eight healthy individuals.

Integrative analysis of microRNA, mRNA and aCGH data reveals asbestos- and histology-related changes in lung cancer.

Lung cancer has the highest mortality rate of all of the cancers in the world and asbestos-related lung cancer is one of the leading occupational cancers. The identification of asbestos-related molecular changes has long been a topic of increasing research interest. The aim of this study was to identify novel asbestos-related molecular correlates by integrating miRNA expression profiling with previously obtained profiling data (aCGH and mRNA expression) from the same patient material.

MicroRNA microarrays on archive bone marrow core biopsies of leukemias--method validation.

Due to availability of bone marrow core biopsies (CB) in many pathology laboratories, we evaluated the quality and the biological information of the miRNA profiling using 9 acute lymphoblastic leukemia (ALL) and 9 chronic myeloid leukemia (CML) matched CB and bone marrow aspirates (BA). Technical replicates showed reproducible results across platforms and clustered together in hierarchical clustering analysis; and matched samples showed similar biological content having common differentially expressed miRNAs against the same control samples. We showed, that CBs, which have underwent decalcification in addition to formalin-fixation, are suitable for miRNA profiling.

Unique microRNA profile in Dupuytren's contracture supports deregulation of β-catenin pathway.

Dupuytren's contracture, a proliferative disease of unknown origin, is characterized by an abnormal fibroblast proliferation process. Evidence from numerous microRNA (miRNA) studies shows that miRNAs have a vital function in many biological processes, for instance, in cellular signaling networks, cell growth, tissue differentiation, and cell proliferation. Our aim was to characterize, to our knowledge for the first time, the miRNA-expression profile of Dupuytren's contracture.

High-resolution oligonucleotide array comparative genomic hybridization study and methylation status of the RPS14 gene in de novo myelodysplastic syndromes.

In myelodysplastic syndromes (MDS), close to one half of patients do not have any visible karyotypic change. In order to study submicroscopic genomic alterations, we applied high-resolution array comparative genomic hybridization techniques (aCGH) in 37 patients with de novo MDS. Furthermore, we studied the methylation status of the RPS14 gene in 5q deletion (5q21.

JAK2V617F mutation and spontaneous megakaryocytic or erythroid colony formation in patients with essential thrombocythaemia (ET) or polycythaemia vera (PV).

The in vitro cultures of erythroid (BFU-E) and megakaryocytic (CFU-Meg) progenitors have been useful diagnostic tools in myeloproliferative disorders (MPD). However, after the discovery of the JAK2V617F mutation, their diagnostic role has been uncertain. In this single-centre retrospective study we analyzed JAK2V617F mutation in 58 ET and 42 PV patients diagnosed according to WHO criteria and compared the results with those of colony forming assays with special emphasis on CFU-Meg growth.

CanGEM: mining gene copy number changes in cancer.

The use of genome-wide and high-throughput screening methods on large sample sizes is a well-grounded approach when studying a process as complex and heterogeneous as tumorigenesis. Gene copy number changes are one of the main mechanisms causing cancerous alterations in gene expression and can be detected using array comparative genomic hybridization (aCGH). Microarrays are well suited for the integrative systems biology approach, but none of the existing microarray databases is focusing on copy number changes.