MicroRNA-based assay for differential diagnosis of mesothelioma

e22079

Background: Malignant mesothelioma is an aggressive pleural neoplasm, strongly linked to environmental exposures such as asbestos. Mesothelioma can be difficult to differentiate from other tumors in the lung or pleura such as primary lung adenocarcinoma presenting with pleural effusion or metastatic adenocarcinoma from extrathoracic sites. We addressed the increasing need for accurate differential diagnosis of these tumors by developing a diagnostic assay based on expression levels of microRNAs, a family of small, non-coding RNAs whose tissue-specificity has proven applicability for identification of cancer tissue type and histology. Methods: We developed protocols for extraction of high-quality RNA that retain the microRNA fraction from FFPE tissue samples. Microarrays were used for initial profiling. qRT-PCR was used to validate results and to develop a diagnostic assay. Results: We identified microRNAs that are differentially expressed between mesothelioma, lung adenocarcinoma, and other confounding tumor types. A diagnostic assay (miRview™ meso) was developed, that utilizes qRT-PCR measurement of a small set of microRNAs to differentiate between mesothelioma and non-mesothelioma samples. After establishing this profile in more than 30 mesotheliomas and 200 samples of confounding tumors, the microRNA biomarkers were measured using a standardized protocol on a blinded test set. The assay had accuracy greater than 90% in differentiating mesothelioma from other confounding tumor types. More than ¾ of samples were classified with high confidence, and these samples were all correctly identified. Conclusions: MicroRNAs are emerging as effective cancer biomarkers. A robust and simple assay based on the expression level of a few microRNA biomarkers can accurately differentiate mesothelioma from other possible tumors in the lung and pleura. This assay provides an important new tool for diagnosing mesothelioma.

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Use of microRNAs to distinguish small from non-small lung cancer

e22061

Background: Lung tumors are divided to two main classes: non-small cell lung cancer (NSCLC) that accounts for ∼80–85% of all lung primary tumors, and tumors from neuroendocrine origin - mainly small cell lung carcinoma and lung carcinoid. The classification of lung tumors can present a diagnostic challenge. New markers for different subtypes may aid in diagnosing difficult cases, can improve the accuracy of classification and could be important for selecting proper treatment. Here we studied the utility of microRNA as biomarkers for this differential diagnosis. MicroRNAs, a family of short non-coding regulatory RNAs, are highly tissue-specific and are well preserved in routinely prepared formalin-fixed, paraffin-embedded (FFPE) specimens, making them promising candidates as biomarkers for tissue and tumor classification. Methods: We used proprietary protocols for extracting high-quality RNA from FFPE samples. We used microRNA microarrays to profile more than a hundred samples from different histological subtypes of lung cancer including small cell, lung carcinoid and various types of NSCLC. Differential microRNA expression was verified using a microRNA qRT- PCR platform. Results: We found that several microRNAs are significantly differentially expressed between different subtypes of lung cancers. Specifically, using combinations of few microRNAs, we were able to accurately differentiate between neuroendocrine and NSCLC. Small cell and carcinoid tumors can be further distinguished using the signals of additional microRNAs, with very high sensitivity and specificity. Conclusions: Our results underscore the potential of microRNA expression for classification of tumor subtypes. We found that combinations of small numbers of microRNAs can successfully aid in the differential diagnosis of lung tumors, and provide a basis for the development of simple and reliable assays for clinical oncology.

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Identification of tumor tissue origin by a microRNA-based molecular assay

11036

Background: Hundreds of thousands of patients are diagnosed each year with metastatic cancer. For ∼10% of these, the tumor primary site is never identified, and they are defined as Cancer of Unknown Primary (CUP). Identification of tumor tissue-of- origin has significant therapeutic implications and presents a major diagnostic challenge. In previous work we showed that by combining expression profiles of tissue-specific microRNAs with a biologically-motivated classification scheme, tumor tissue-of-origin can be identified with high accuracy. Here we describe the development of this approach into a practical diagnostic assay. Methods: We developed protocols for extraction of high-quality RNA that retain the microRNA fraction from FFPE archival tissue samples. Proprietary, highly specific qRT-PCR was used to profile microRNA expression levels in hundreds of samples. Results: A training set of nearly 400 primary and metastatic tumors samples with known primary sites, representing 25 different tumor types, was used to define a standardized diagnostics assay (miRview mets). The assay uses a qRT-PCR protocol to measure a panel of 48 microRNA biomarkers. The assay was validated on a test set of nearly 200 primary and metastatic tumors whose primary sites were blinded. The classification protocol identifies either a single, high-confidence origin or two possible low-confidence predictions. Overall, correct primary site was identified for 83% of the tumors. For 70% of the cases a single high-confidence prediction was made; these cases had a higher accuracy: 90% of the primary sites predicted with high confidence were accurately identified. Conclusions: Previous studies highlighted the tissue-specificity of microRNA expression. We developed this potential into a diagnostic assay that identifies tumor origins with high accuracy. This assay provides an important new tool for diagnosing tumor tissue origin.

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Independently-addressable micron-sized biosensor elements

With the continuing development of micro-total analysis systems and sensitive biosensing technologies, it is often desirable to immobilize biomolecules onto a surface in a small well-defined area. A novel method was developed to electrochemically attach DNA probes to micron-sized regions of a gold surface using biotin-LC-hydrazide (BH). Previously, we have found that the radical produced during the oxidation of BH will attach to a wide variety of electroactive surfaces. An array of micron-sized gold band electrodes (75 microm wide) was fabricated onto glass microscope slides and BH was deposited onto each electrode through the application of an oxidizing potential. Subsequent attachment of avidin to the biotinylated surface created the 'molecular sandwich' architecture necessary for further immobilization of biotinylated biomolecules to the surface. In this work, we utilized biotinylated DNA probes of varying sequence to illustrate the specificity of the attachment scheme. The immobilization of avidin, DNA probe, and hybridization of DNA target is visualized with fluorescence tags and the spatially selective attachment and hybridization of unique DNA sequences is demonstrated.

[Changes of the dose at the surface in oblique incidence of high energy photon beams]

For oblique incident photon beams, the absorbed dose is markedly different from normal incident beams. Our aim was to study the changes of the dose at the surface and in the build-up region for oblique incident 4, 6, 10, 15, 25 MV photon beams angled 0 degree to 80 degrees for square fields ranging from 5 x 5 to 30 x 30 cm2. All doses were measured as a function of the depth along the beam axis and used to define an obliquity factor. For all energies investigated, we have studied the obliquity factor as a function of depth, field sizes, energy and angle of incidence. Our results show that the obliquity factor is highly dependent on these different parameters. In addition, by considering the equivalent squares of the entrance fields distorted by obliquity, an analytical method has been developed to predict the dose at the surface of high energy photon beams for various angles and field sizes.