Ite Laird-Offringa Ph.D.

This grant is being fully funded by the Thomas G. Labrecque Foundation, through the Joan’s Legacy Grant Program.

Lay Description

The Laird-Offringa laboratory is focused on identifying changes in the genetic material (DNA) of lung cancer cells, to help us understand how lung cancer develops, and to use as markers for early detection. The kind of molecular change we study is called DNA methylation. DNA methylation is a chemical modification of DNA that doesn’t change the genetic sequence, but does change the way the DNA looks to a cell. Excessive methylation leads to the silencing or inactivation of genes. In cancer cells, DNA methylation is now recognized as a key molecular mechanism for the inactivation of so-called “tumor suppressor genes”. If one thinks of the genetic material as a very thick textbook, with instructions for the cell, DNA methylation can be thought of as post-it notes stuck to the beginning of certain chapters, instructing these chapters to be skipped. The pattern of methylation, or the “methylation profile”, is not the same for all types of cancer. Thus, abnormal methylation changes could provide important insights into the changes that lead to a particular kind of cancer. In addition, they could yield powerful biomarkers that may help the detection of different kinds of cancer.

At USC, we have developed a sensitive, accurate, automated DNA methylation analysis technique called MethyLight®. It uses a robot to analyze large numbers of samples per day, so that the presence of methylation at many different genes can be studied in a short amount of time. Using this assay, we have recently identified genes that are more highly methylated in lung adenocarcinoma than in a healthy, non-cancerous section of the lung of the same patient. Here we propose to examine when these changes first occur: whether they are present in atypicial adenomatous hyperplasia (AAH) and/or bronchioalveolar carcinoma (BAC), which are the pre-invasive lesions thought to precede lung adenocarcinoma. In addition, we will carry out detailed characterization of genes that specifically become methylated as BAC transitions to invasive adenocarcinoma. We are able to carry out such studies through our collaboration with Dr. Keith Kerr, a pathologist who is an expert in early lung lesions such as AAH and BAC. He is giving us access to a unique sample collection that he has collected over many years. The proposed studies will help clarify the molecular changes that cause pre-invasive changes in the lung, and the subsequent changes that cause progression to invasive lesions. The identification of sequential changes in methylation will provide insights that may be applicable to the development of targeted drugs. In addition, such DNA methylation changes will be powerful markers for early detection and patient classification, helping guide clinical decisions about treatment.

Scientific Abstract

Lung cancer is the leading cause of cancer death in the United States and Western Europe. Adenocarcinoma, the histological subtype most frequently seen in never smokers and former smokers, is now the most common type of lung cancer in men and women in the United States. The increasing incidence of lung adenocarcinoma and its lethal nature underline the importance of understanding the development and progression of this disease, and the need for the development of accurate tools for early diagnosis. Atypical adenomatous hyperplasia (AAH) and bronchioalveolar carcinoma (BAC), defined as non-invasive lesions, are thought to be sequential precursors along the path of progression to lung adenocarcinoma. Elucidation of the molecular changes underlying the development and progression of lung adenocarcinoma is of great importance for devising targeted drugs and methods of early detection.

DNA hypermethylation at promoter CpG islands is now recognized as a key mechanism for tumor suppressor gene inactivation in cancer. Identification of abnormal methylation changes could provide important insights into the mechanism of cancer development, and in addition could yield powerful biomarkers for cancer. At USC, we have developed a sensitive, quantitatively accurate, automated DNA methylation analysis technique based on real time polymerase chain reaction (PCR) with methylation-specific primers (MethyLight®). Using this high-throughput assay we have recently identified fifteen loci that show highly significant differences in methylation between lung adenocarcinoma and adjacent non-tumor tissue from the same patient (P<<0.0001 for 13/15 markers, Wilcoxon signed rank test). The identified loci represent genes with functions in cell cycle, differentiation, cell-cell contacts, signaling, and apoptosis. To determine the role of the methylation of these genes during the progression from AAH to BAC and to invasive disease, we have initiated a collaboration with expert lung pathologist Dr. Keith Kerr, one of the world’s top authorities in pre-invasive lesions preceding adenocarcinoma. Dr. Kerr will provide a unique collection of normal adjacent lung, pre-invasive lesions (AAH and BAC), mixed adenocarcinoma samples with a BAC component, and adenocarcinoma, representing adenocarcinoma in its different developmental stages. This collection will form the basis for the proposed study. We will use MethyLight to determine the methylation status of the previously identified markers (and any new ones we uncover during our ongoing studies) in these different samples. In a subset of representative samples, we will analyze the methylation of the loci in more detail through bisulfite genomic sequencing. This allows the examination of methylation along single DNA strands, and may provide information on the mechanism by which methylation spreads to new loci. The identification of sequential epigenetic alterations during progression to lung adenocarcinoma will broaden our molecular understanding of the disease, providing insights that may be applicable to the development of targeted drugs. Equally important, such DNA methylation changes will be powerful markers for early detection and patient classification. We envision that the data from this proposal will support a future R01 grant application that will be aimed at a detailed elucidation of the mechanistic role of DNA methylation in adenocarcinoma development and progression.