Integration of phosphoproteomics using the Microwestern Array and PLSR-based network inference reveals new targets for the treatment of childhood Acute Lymphoblastic Leukemia

I. Training Project Summary. For my mentored research training as a postdoctoral fellow, I intend to develop a novel and transformative pipeline that integrates a new high-throughput technology with cutting-edge computational methods for improving drug discovery for childhood Acute Lymphoblastic Leukemia (ALL). This systems-approach uniquely integrates advances in biotechnology and experimental design with powerful computational strategies. Improving the prediction of computational models for new therapies would have invaluable impact on children suffering from complex diseases such as ALL and is a central goal of my research career. II. Aims. ALL is the most common cancer in children (Miller, Cancer 2006) where dysregulation of cell-signaling yields uncontrolled proliferation and differentiation. Understanding the mechanisms that modulate aberrant signaling in blood cell progenitors allows identification of new, effective, personalized, targeted cancer therapies. Many chromosomal translocations occur in ALL including the most common TEL/AML1 fusion (Stams, Clin. Cancer Research 2005). I propose identifying specific vulnerabilities in a stably transfected cell line containing the TEL/AML1 fusion as well as novel small molecules to exploit these vulnerabilities. This project would deliver (1) a quantitative assessment of the differential phosphorylation of 60 phosphosites of cell signaling proteins in a stably transfected cell line containing the TEL/AML1 fusion gene versus a wild-type control; (2) an inferred phosphorylation network in the mutant and wt cell lines highlighting the proposed mechanism by which the TEL/AML1 protein causes dysregulation in cell signaling; and (3) identification of small molecules that can be used to target vulnerabilities in this cell line thereby leading the afflicted cells to apoptosis. This project will involve me forging a productive collaboration and learning opportunity, combining the clinical expertise of Dr. Jonathan Licht in the Feinberg School of Medicine, the computational expertise of Dr. Neda Bagheri in the McCormick School of Engineering, and the breakthrough technology utilized by Dr. Chase Archer from the University of Chicago Institute for Genomics and Systems Biology. II. Significance. Understanding dynamic information flow within a signal transduction network is crucial to identifying how ALL can be effectively treated. During my doctoral studies, I pioneered the Microwestern Array (MWA) with Dr. Richard Jones in the Institute for Genomics and Systems Biology at the University of Chicago (Ciaccio et al., Nat Methods 2010). This technology creates an array of small Western blots on a single sheet of nitrocellulose, providing unprecedented insight on the regulation and complexity of signal transduction. My postdoctoral research in the Bagheri Lab has involved the development of a computationally efficient and statistically accurate method of inferring the architecture of signal transduction networks from phosphoproteomic data (Ciaccio et al., submitted to Nature Chemical Biology). Analysis of the cell signaling architecture from network inference (Ciaccio et al., Integrative and Comparative Biology 2014) can be employed to identify proteins that specifically contribute to cell viability of ALL, as well as identify small molecules that can modulate the significant phosphosites. III. Conclusion. In its relevance for young ALL patients, this transformative project aligns closely with the Hartwell Foundation’s mission to improve the clinical outcome and quality of life for children afflic