Translational Proteomics of Normal to Benign Breast Disease

Institution: John Wayne Cancer Institute
Investigator(s): David Hoon, MSc, Ph.D. - Armando Giuliano, M.D. - Lori Wilson, M.D. -
Award Cycle: 2003 (Cycle IX) Grant #: 9DB-0098 Award: $188,044
Award Type: TRC Pilot Award
Research Priorities
Biology of the Breast Cell>Biology of the Normal Breast: the starting point

Initial Award Abstract (2003)
The development of benign breast disease is an important clinical problem that is not well understood or diagnosed. It is our strong belief that understanding of the physiological changes in respect to the study of breast cell proteins (proteomics) will provide valuable progress in better diagnosing early stages of breast disease development. Proteins are the functional components of the cell that are directly responsible for disease development. To date this has been very difficult to assess however, with new innovative technology and clinical resources we can approach this field much easier now. Only through cross-multidisciplinary integration of the clinical and basic sciences can new developments be achieved with rapid application to patient care. Our approach is to address this problem examining proteomics of normal breast tissue change to benign (pre-cancer) disease. Identification of unique protein patterns associated with innovative proteomic technology will allow a better identification of those patients at increased risk developing breast cancer. The focus is on the earliest events of breast disease development. The understanding of the complexity of normal breast changes during different physiological stages of a woman during her lifetime that predispose to malignancy is advantageous. The proposal utilizes the collaborative effort of three co-PIs specialized in different aspects of breast cancer research.

The central hypothesis is that benign breast disease has a unique proteomic signature pattern(s) compared to normal breast tissue. The first major question to be answered is the feasibility of developing a proteomic signature profile of normal breast tissue during different stages of women physiology. The objective is to determine changes in normal breast proteins during physiologic changes that may be risk factors to cancer development. The second question will be to determine if proteomic profile signatures of various types of benign breast disease can be used for diagnosing early stages of pre-cancerous breast disease.

The primary methodology in the study is to use ProteinChip array technology to detect specific protein profiles. The study will assess normal breast and pre-cancer breast tissue biopsies from routine diagnostic surgeries to assess tissue protein profiles. This will allow assessment of normal breast tissue, benign breast tissue and early stages of pre-malignancy for unique signature proteins.

This project emphasis highly translational research that applies the novel basic science field of proteomic arrays to an important breast disease problem utilizing clinical tissues. The study addresses the development of proteomic signature profiles of normal breast at different stages in an adult woman’s lifetime as a baseline for comparison to early benign breast disease. The study allows us to develop new approaches of identifying more accurately early stages of benign breast disease and prognostic factors in normal breast that identify high risk for breast disease. The development of a proteomic signature assay will also provide new approaches to assess breast tissue biopsies for more accurate diagnosis.

Final Report (2006)
The onset of breast disease is an important clinical problem that is poorly understood or diagnosed. The development of better diagnostic tests that identify physiological changes in respect to breast cell proteins (proteomics) should provide us with important information as to improving diagnosis of early stages of breast disease. Proteins are the functional components of the normal cell whereby, at early stages of cancerous tissue development changes in specific proteins may be valuable signatures of disease development. Assessment of specific protein signatures in breast cancer has been a monumental task. However, with the mass spectrometry high-throughput assay (SELDI-TOF) we were able to address these problems much easier. We developed a proteomic profiling assay with specific ProteinChips to identify significant proteomic signatures in cancer versus normal breast tissue.

In the first aim of the study we collected breast tissue from normal, DCIS and tumors that were histopathology classified. We established a biorepository of catalogued frozen tissues. Overall in this aim we were able to accrue >500 tissue specimens for the biorepository. Specimens were cut into thin sections and meticulously microdissected to isolate normal from cancerous cell types. These samples were processed for proteomic profiling on two different types of ProteinChips of different specificity (IMAC-3 and WCX2). In the second aim we assessed proteomic profiling of normal versus cancer tissue and benign tissue. Using the IMAC-3 ProteinChip we identified several proteins in the cancer not present in normal breast tissue. An assay sensitivity of 81% and a specificity of 88% were obtained. Using the WCX2 ProteinChips we identified two major proteins in cancer tissues that had a specificity of 98% and sensitivity of 98%. From these studies we have identified several key proteins that are in breast cancer and not normal tissue. In the third aim a bioinformatics algorithm was developed to identify specific protein signatures that were significantly different in normal versus cancerous tissues. The studies were very successful overall in that specific proteomic signature peaks were identified using both types of ProteinChips to identify normal from cancerous tissue. The studies also allowed us to predict from primary tumors which were more aggressive and likely to spread to the draining lymph node such as the sentinel lymph node. Several proteins were identified that significantly predicted whether a tumor-draining lymph node has metastasis or not.

The understanding of the complexity of normal breast changes during different physiological stages of a woman during her lifetime that predispose to malignancy is advantageous. In our studies we have identified multiple significant protein differences in normal and cancerous tissues. This will allow us to identify these proteins and hopefully develop an assay system for early detection. Also the study allowed us to determine what primary tumors are likely to spread to the lymph node. These are important finding that will allow us to further characterize these specific proteins and develop detection assays. The study results are highly encouraging and very successful. The development of a proteomic based early detection assay is highly important to diagnose early breast disease development.