Identification of a sensitive and specific panel of DNA methylated markers to imp

University Of Southern California, Los Angeles CA

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Abstract

DESCRIPTION (provided by applicant): The clinical management of small renal masses (SRMs) is challenging since the current methods for distinguishing between benign masses and malignant renal cell carcinomas (RCCs) are frequently inaccurate or inconclusive. High false negative rates increase the risk of cancer progression and indeterminate diagnoses result in unnecessary and potentially morbid surgical procedures. The long-term goal is to improve the clinical management of patients with SRMs. The objective in this particular application is to identify DNA methylation markers that can improve the diagnostic value of renal needle biopsies. The central hypothesis is that differentially methylated DNA markers can be used definitively distinguish between malignant and benign SRMs and complement histological findings to allow for more accurate RCC diagnosis. The rationale for the proposed research is that since changes in DNA methylation can occur prior to histological changes and can be detected in small amounts of tissue, measurement of DNA methylation markers in needle biopsy material would be able to identify malignant SRMs. This hypothesis will be tested by pursuing two specific aims: 1) Select and validate a panel of candidate markers that are differentially methylated in RCCs compared to adjacent normal tissues and normal renal epithelia; and 2) Determine the sensitivity and specificity of these markers in distinguishing malignant from benign small renal masses in needle biopsies. Under the first aim, DNA methylation patterns in matched tumors and normal tissues will be compared in order to identify a panel of markers that are specific to each of the three most common subtypes of RCC and a panel that is general to RCC. These markers will be validated using a different quantitative assay on an independent set of benign lesions and RCC tumors with matched normal tissues. Under the second aim, the presence of the validated markers in both needle biopsies and matched bulk tumors will be confirmed as a control. Then the DNA methylation marker results and histological findings from the needle biopsies will be compared with the histopathological profiles of the bulk tumors in order to evaluate the sensitivity and specificity of this combinatoral approach in comparison to histological profiling of the needle biopsies alone. The approach is innovative because it represents a significant departure from the current method of characterizing SRMs. The proposed research is significant because it is expected to considerably increase the diagnostic accuracy of renal needle biopsy. Ultimately, such knowledge has the potential to improve the clinical management of patients with SRMs.