Proteolytic pathways are prominent in virtually all human diseases and are common hallmarks of basic cellular functions ranging from differentiation to death. The long-term goal of this proposal is to develop a novel, rapid, quantitative platform to monitor the proteolytic activity associated with apoptosis in patients undergoing chemotherapy for hematologic malignancies. We hypothesize that products of caspase proteolysis are released from dying apoptotic cancer cells into the circulation and that a subset of these markers will be cell type-specific, and therefore malignancy-specific. A serum biomarker approach to monitoring chemotherapy represents a paradigm shift in clinical management of cancer, which mostly relies upon radiographic imaging and laboratory tests. Because these studies are typically performed weeks to months after the start of therapy, unnecessary or ineffective chemotherapy is often administered. Since current methods to identify, detect, and quantify proteolytic fragments are cumbersome, low-throughput, and costly, we propose to develop a platform that involves a hypothesis-driven discovery method, novel neo-epitope targeted antibodies, and a new multiplexed quantification method. To identify these apoptotic biomarkers, we will develop targeted mass spectrometric methods for identifying proteolysis products created by caspase activity upon induction of apoptosis in cell culture models of hematologic malignancies and plasma of patients undergoing chemotherapy for these cancers (Aim 1). This approach permits an unprecedented large-scale targeted way to detect and stratify apoptotic biomarkers in serum that can be used to monitor treatment of patients undergoing chemotherapy. However, the current lack of reliable and high-throughput methods to measure proteolytically- derived biomarker levels in plasma prevents such a real-time strategy and thus, we will develop antibodies specifically directed against the neo-epitopes of proteins cleaved by caspases during apoptosis (Aim 2). The phage-based methods developed here will enable quantification of apoptotic biomarkers in a multi-parameter fashion and transform the laborious and often uncertain process of generating monoclonal antibodies with high affinities and specificities into a well-defined, cheap, and renewable one. Finally, we will develop unique methods for biomarker quantification, including a novel highly multiplexed phage and next generation sequencing assay (PHANGS) (Aim 3). Application of these methods in a pilot study to correlate biomarker levels to treatment response in patients with diffuse large B-cell lymphoma and multiple myeloma will provide essential groundwork to further biomarker validation studies. These approaches and methods have vast biomedical applications, including biological imaging and detection of proteolysis in single cells and animals as well as novel therapeutic uses of neo-epitope antibodies. Furthermore, while focused on hematologic malignancies, these tools and technologies will significantly elucidate the crucial role of proteolysis in a spectrum of human diseases, such as cancer, infectious disease, and neurodegeneration.

Public Health Relevance

The proposed study will result in the development of a serum biomarker approach to permit rapid and real-time monitoring of chemotherapeutic response and efficacy that will represent a significant advance in clinical management of cancer. Furthermore, the novel technologies developed here will significantly advance the study of proteolysis in other human diseases.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project (R01)
Project #
Application #
Study Section
Enabling Bioanalytical and Biophysical Technologies Study Section (EBT)
Program Officer
Jessup, John M
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Francisco
Schools of Pharmacy
San Francisco
United States
Zip Code
Calvo, Sarah E; Julien, Olivier; Clauser, Karl R et al. (2017) Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast. Mol Cell Proteomics 16:512-523
Seaman, J E; Julien, O; Lee, P S et al. (2016) Cacidases: caspases can cleave after aspartate, glutamate and phosphoserine residues. Cell Death Differ 23:1717-26
Julien, Olivier; Zhuang, Min; Wiita, Arun P et al. (2016) Quantitative MS-based enzymology of caspases reveals distinct protein substrate specificities, hierarchies, and cellular roles. Proc Natl Acad Sci U S A 113:E2001-10
Koerber, James T; Hornsby, Michael J; Wells, James A (2015) An improved single-chain Fab platform for efficient display and recombinant expression. J Mol Biol 427:576-86
Wiita, Arun P; Seaman, Julia E; Wells, James A (2014) Global analysis of cellular proteolysis by selective enzymatic labeling of protein N-termini. Methods Enzymol 544:327-58
Wiita, Arun P; Hsu, Gerald W; Lu, Chuanyi M et al. (2014) Circulating proteolytic signatures of chemotherapy-induced cell death in humans discovered by N-terminal labeling. Proc Natl Acad Sci U S A 111:7594-9
Koerber, James T; Thomsen, Nathan D; Hannigan, Brett T et al. (2013) Nature-inspired design of motif-specific antibody scaffolds. Nat Biotechnol 31:916-21
Crawford, Emily D; Seaman, Julia E; Agard, Nick et al. (2013) The DegraBase: a database of proteolysis in healthy and apoptotic human cells. Mol Cell Proteomics 12:813-24
Shimbo, Kazutaka; Hsu, Gerald W; Nguyen, Huy et al. (2012) Quantitative profiling of caspase-cleaved substrates reveals different drug-induced and cell-type patterns in apoptosis. Proc Natl Acad Sci U S A 109:12432-7
Agard, Nicholas J; Mahrus, Sami; Trinidad, Jonathan C et al. (2012) Global kinetic analysis of proteolysis via quantitative targeted proteomics. Proc Natl Acad Sci U S A 109:1913-8