Integrated Proteomic and Metabolic Analysis of Breast Cancer

Institution: Scripps Research Institute
Investigator(s): Kyle Chiang, Ph.D. -
Award Cycle: 2005 (Cycle 11) Grant #: 11GB-0078 Award: $59,121
Award Type: Dissertation Award
Research Priorities
Biology of the Breast Cell>Pathogenesis: understanding the disease



Initial Award Abstract (2005)
The molecular features special to metastatic breast carcinomas that support their motile and invasive behavior are complex and poorly defined. Although one generally accepted notion assigns proteins, such as proteases, a central role in promoting the aggressive properties of metastatic breast tumors, the actual functions played by individual enzymes in breast cancer remain elusive. Indeed, many proteases and their endogenous inhibitors show altered expression patterns during breast tumorigenesis; however, the overall functional outcome of such changes remain unclear. To better understand how proteases and related enzymes impact breast cancer, we have developed a novel chemical proteomics method termed activity-based protein profiling (ABPP) that allows large enzyme families to be analyzed for changes in their activity directly in whole cell, tissue and fluid samples. From our analysis of human cancer cell lines and tissue we have identified a novel enzyme, KIAA1363, as an invasiveness related serine hydrolase. We hypothesize that this enzyme may potentially be a new diagnostic marker or therapeutic target important for the detection and treatment of aggressive breast cancer.

We will use ABPP, a competitive ABPP strategy and various biochemical, cell biology, and mouse genetic models to study the potential therapeutic target KIAA1363. We propose to: (1) optimize selective inhibitors of KIAA1363 and use these reagents to test the function of this hydrolase in breast cancer models, (2) characterize breast tumorigenesis in KIAA1363(-/-) mice, and (3) Identify endogenous substrates of KIAA1363 by global metabolite profiling. Conventional genomic and proteomic methods measure changes in transcript and protein abundance, respectively, and therefore provide only an indirect assessment of protein function. Numerous posttranslational forms of enzyme regulation remain undetected by these approaches. In this research project, we are addressing the utility of higher-order functional proteomics technologies by developing and applying chemical probes that measure protein activity rather than abundance.

The proteomics methods we are applying in this application can discover new therapeutic targets and lead compounds for treating breast cancer, we believe these methods have the great potential to accelerate the discovery of drugs that increase breast cancer survival and therefore reduce the stress and anxiety associated with this disease. Thus, we believe that our proteomics method, through identifying new drug targets and lead inhibitors for breast cancer, could overcome difficulties associated with treating this disease.


Final Report (2006)
Previous studies using our chemical proteomic technology, called activity-based protein profiling (ABPP), have identified enzyme activity signatures that distinguish human cancer cells based on biological properties, such as states of invasiveness. A primary component of this enzyme activity signature was KIAA1363, a novel enzyme activity increased in aggressive cancer cells from multiple tissues of origin including breast carcinomas. The focus of this work is to apply an integrated proteomic and metabolomic approach (i.e., analyzing the complete set of small-molecule metabolites, such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites) to characterize the molecular and cellular function that KIAA1363 plays in supporting breast cancer pathogenesis.

We have identified a potent and selective inhibitor of KIAA1363 and have utilized this chemical tool to inactivate the enzyme in living systems. This inhibitor is adequate for in situ studies in human cancer cell lines but has thus far displayed poor pharmacokinetic properties in vivo. In future studies we intend to synthesize analogs of our inhibitor that maintain selectivity for KIAA1363 while reducing overall reactivity in an attempt to improve the short half life seen in rodent plasma.

To study KIAA1363’s role in tumorigenesis we used MDA-MB-231 breast cancer cell lines and SKOV-3 ovarian cancer cell lines with reductions in KIAA1363 expression achieved using short-hairpin RNA (shRNA) interference. These experiments revealed that targeted interference of KIAA1363 resulted in significant reductions in tumor growth rates in mouse xenograft models. We are currently focused on investigating models of human breast cancer tumorigenesis and metastasis in KIAA1363 (-/-) mice.

In summary, we have utilized an integrated proteomic and metabolomic platform to determine that KIAA1363, an enzyme of previously unknown function, is a key regulator of a lipid signaling network that contributes to cancer pathogenesis. Considering further that reduction in KIAA1363 activity were found to impair tumor growth in vivo, we postulate that inhibitors of this enzyme may prove of value for the treatment of multiple types of cancer. More generally, our “systems biology” strategy should facilitate the assignment of functions to many of the uncharacterized enzymes that currently populate the human proteome. Assembly of these enzymes into metabolic and signaling networks that contribute to complex human pathologies, like breast cancer, should reveal new molecular markers and targets for disease diagnosis and treatment.


Symposium Abstract (2005)
The molecular features special to metastatic breast carcinomas that support their motile and invasive behavior are complex and poorly defined. Although one generally accepted notion assigns proteins, such as proteases, a central role in promoting the aggressive properties of metastatic breast tumors, the actual functions played by individual enzymes in breast cancer remain elusive. Indeed, many proteases and their endogenous inhibitors show altered expression patterns during breast tumorigenesis; however, the overall functional outcome of such changes remain unclear. To better understand how proteases and related enzymes impact breast cancer, we have developed a novel chemical proteomics method termed activity-based protein profiling (ABPP) that allows large enzyme families to be analyzed for changes in their activity directly in whole cell, tissue and fluid samples. Conventional genomic and proteomic methods measure changes in transcript and protein abundance, respectively, and therefore provide only an indirect assessment of protein function. Numerous posttranslational forms of enzyme regulation remain undetected by these approaches. In this research project, we are addressing the utility of higher-order functional proteomics technologies by developing and applying chemical probes that measure protein activity rather than abundance.

From our analysis of human cancer cell lines and tissue we have identified a novel enzyme, KIAA1363, as invasiveness related serine hydrolase. We hypothesize that this enzyme may potentially be a new diagnostic marker or therapeutic target important for the detection and treatment of aggressive breast cancer.

We will use ABPP, a competitive ABPP strategy, and various biochemical, cell biology, and mouse genetic models to study the potential therapeutic target KIAA1363. We propose to: (1) optimize selective inhibitors of KIAA1363 and use these reagents to test the function of this hydrolase in breast cancer models, (2) characterize breast tumorigenesis in KIAA1363(-/-) mice, and (3) Identify endogenous substrates of KIAA1363 by global metabolite profiling.The proteomics methods we are applying in this application can discover new therapeutic targets and lead compounds for treating breast cancer, we believe these methods have the great potential to accelerate the discovery of drugs that increase breast cancer survival and therefore reduce the stress and anxiety associated with this disease. Thus, we believe that our proteomics method, through identifying new drug targets and lead inhibitors for breast cancer, could overcome difficulties associated with treating this disease.

An enzyme that regulates ether lipid signaling pathways in cancer annotated by multidimensional profiling. (2006) Chem. Bio. 131041-50. Comment in Chem. Biol. 13, 1013-1017, Chem. Eng. News 84, 12, and Nat. Methods 4,8-9 Hydrolase expressed and bc
Periodical:Chemistry and Biology
Index Medicus: Chem Biol
Authors: Chiang KP, Niessen S, Saghatelian A, Cravatt BF
Yr: 2006 Vol: 12 Nbr: Abs: Pg:1041-1050