M. Ben Major, Ph.D.
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Associate Professor
- B.S., Michigan State University, 1997
- Ph.D., Huntsman Cancer Institute, 2004
- Postdoc, University of Washington, 2004-2009
- Joined the Department in 2009
Research Interests
Although initiated by genetic mutation, the unchecked proliferation, aberrant differentiation, and altered motility of cancer cells depends upon the integrity and activation state of specific signal transduction pathways. Our laboratory is interested in understanding how alterations in these signaling pathways contribute to human cancer, and whether exploitation of that understanding can aid in the development of new diagnostics, prognostics and therapeutic intervention strategies. To this end, we employ a global “systems level” integrative discovery platform, one that has as a foundation mass spectrometry-based proteomic interaction networks. More specifically, through LC/MS/MS, we define the physical interaction network for a signaling pathway of oncogenic interest. By small molecule and functional genomic screening, we then annotate the human genome for functional contribution to the pathway of interest. Integration of these data with cancer-associated mutation data and cancer-associated gene expression data yields a powerful tool for oncogenic discovery—a cancer annotated physical/functional map for a specific signaling pathway of interest. The models and hypotheses produced though integrative screening are challenged through mechanistic studies employing cultured human cancer cells, zebrafish, mice and in vitro biochemical systems. With this general approach, we are currently pursuing the following projects:
Development of Integrative Functional Genomic and Proteomic Discovery Technologies.A central tenet of my research program is discovery-based science, founded largely upon mass spectrometry-driven proteomics, functional genomics and disease annotation. The integration of these disparate data types eliminates false positives, rescues false negatives, and highlights neighborhoods within the global network of phenotypic, mechanistic and disease importance. My team developed a machine learning approach and web interface to probabilistically score and functionally annotate protein-protein interactions (SPOTLITE). We have also recently reported an improved MS data acquisition simulator, which facilitates the development of new algorithms for improved protein sequencing. We are also developing new functional genomic screening technologies, but rather than continue with the more traditional loss-of-function approaches (siRNA, CRISPR), our efforts are focused on gain-of-function genome annotation. To this end, we recently developed a mass spectrometry-coupled genome-wide hypermorphic functional annotation technology called CDt/MS.
Keap1/Nrf2 Signal Transduction. Keap1 is an E3 ubiquitin ligase important for cellular defense against genotoxic stress, and in that context contributes fundamentally to aging and a myriad of human cancers, most notably lung cancer. Keap1 functions by ubiquitinating the Nrf2 transcription factor, which ultimately results in the proteosomal degradation of Nrf2. In an effort to better understand Keap1 in an oncogenic contect, I completed quantitative proteomic analysis of the Keap1 protein complex as well as functional genomic screen of the Keap1/Nrf2 pathway. The resulting integrative map has identified numerous novel proteins which both physically associate with keap1 as well as functional regulate Keap1/Nrf2 signaling. Ongoing work in the lab is focused on understanding the mechanisms by which these proteins control Keap1 function as well as uncovering new cancer connections.
Mechanistic Studies of WNT/β-catenin Signaling. Of the relatively small number of signaling pathways that function as master regulators of development, adult tissue homeostasis and cancer, the β-catenin dependent Wnt pathway (Wnt/β-catenin) figures prominently; it regulates the growth and fate of neoplastic cells in tissues of diverse origin, notably the colon, kidney, breast and skin. My group has performed an array of proteomic an functional genomic studies of WNT signaling, including protein-protein interaction screens, kinase activity profiling, phospho-proteomics, siRNA and haploid mutagenesis loss-of-function screens, and more recently, novel gain-of-function screens. Integration of these data has and continues to reveal mechanistic insight and new disease-relevant regulators of pathway activity. As an example, our gain-of-function genomic screens demonstrated that the FOXP1 transcription factor activates β-catenin dependent transcription. Proteomic analyses demonstrated that FOXP1 binds the β-catenin transcriptional complex on chromatin. Disease-focused studies in mice and human clinical samples demonstrated that FOXP1 overexpression in B-cell lymphoma activates WNT signaling to promote tumor growth. We are now evaluating WNT inhibitors as a possible therapy for FOXP1-high lymphomas.
E3 Ubiquitin Ligases and Ubiquitin specific proteases. E3 ubiquitin ligase complexes provide specificity and catalysis for the transfer of ubiquitin to target proteins, a post-translational modification that results in proteosome-mediated degradation, altered subcellular localization or changes in protein interaction. As such, E3 ubiquitin ligases regulate every facet of cell biology, and importantly, are frequently perturbed in disease states such as cancer. While defining protein-protein interactions within the Wnt/β-catenin pathway, we performed tandem affinity purification and mass spectrometry on βTrCP, the E3 ubiquitin ligase responsible for β-catenin degradation. As the E3 complex is catalytic in action, many of the known βTrCP substrates were not identified by LC/MS/MS. As such we designed and implemented an approach which stabilizes the E3-substrate interaction. Using this strategy, we have identified novel substrates for both the βTrCP and the KEAP1 E3 ubiquitin ligases. Work in my laboratory is exploiting this system to identify substrates for uncharacterized E3 ubiquitin ligases, specifically those with established connections to oxidative stress signaling, Wnt signaling and human disease.
Awards and Honors
2010: NIH Directors New Innovator Award (DP2)
2010: Sidney Kimmel Cancer Foundation Award
2015: V Foundation Translational Science Award
2015: Gabrielle’s Angel Foundation Award
Clinical Interests
- non-small cell lung cancer
- head and neck squamous cell carcinoma
- B-cell lymphoma (DLBCL)
Selected Recent Publications
Computational Proteomics and Informatics:
- Dennis Goldfarb, Bridgid Hast, Wei Wang and Michael B. Major. Spotlite: An Improved Algorithm and Web Application for Predicting Co-Complexed Proteins from Affinity Purification – Mass Spectrometry Data. Journal of Proteome Research, 2014 Oct 10th
- Dennis Goldfarb, Wei Wang and Michael B. Major. MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics. Bioinformatics. 2015 Dec. 17th.
Wnt Signaling:
- Babita Madan, Matthew P. Walker, Robert Young, Laura Quick, Kelly A. Orgel, Meagan Ryan, Priti Gupta, Ian C. Henrich, Marc Ferrer, Shane Marine, Brian S. Roberts, William T. Arthur, Jason D. Berndt, Victor Kwan Min Lee, Andre M. Oliveira, Randall T. Moon, David M. Virshup, Margaret M. Chou and Michael B. Major. The USP6 Oncogene Promotes Wnt Signaling by Deubiquitylating Frizzleds. Proceedings of the National Academy of Sciences, 2016. May 9th.
- Matthew P. Walker, Charles M. Stopford, Maria Cederlund, Fang Fang, Christopher Jahn, Alex D. Rabinowitz, Dennis Goldfarb, David M. Graham, Feng Yan, Allison M. Deal, Yuri Fedoriw, Kristy L. Richards, Ian J. Davis, Gilbert Weidinger, Blossom Damania, and Michael B. Major. FOXP1 Potentiates Wnt/b-catenin Signaling in Diffuse Large B-cell Lymphoma. Science Signaling. 2015 Feb. 3rd
- Priscila F. Siesser, Marta Motolese, Matthew P. Walker, Dennis Goldfarb, Kelly Gewain, Feng Yan, Rima M. Kulikauskas, Andy J. Chien, Linda Wordeman and Michael B. Major. FAM123A Binds Microtubules and Inhibits the Guanine Nucleotide Exchange Factor ARHGEF2 to Decrease Actomyosin Contractility. Science Signaling. 2012 Sep 4; 240(5):ra64.
KEAP1/NRF2 Signaling:
- Gurkan Guntas, Steven M. Lewis, Kathleen M. Mulvaney, Erica W. Cloer, Ashutosh Tripathy, Thomas R. Lane, Michael B. Major, Brian Kuhlman. Engineering a genetically encoded competitive inhibitor of the KEAP1-NRF2 interaction via structure-based design and phage-display. Protein Engineering and Design. 2015 Jan;29(1):1-9
- Bridgid E. Hast, Erica W. Cloer, Dennis Goldfarb, Heng Li, Priscila F. Siesser, Feng Yan, Vonn Walter, Ning Zheng, D. Neil Hayes and Michael B. Major. Cancer-derived mutations in KEAP1 impair NRF2 degradation but not ubiquitination. Cancer Research, 2013, Dec. 9, 2013
- Bridgid E. Hast, Dennis Goldfarb, Kathleen M. Mulvaney, Michael A. Hast, Priscila F. Siesser, Feng Yan, D. Neil Hayes and Michael B. Major. Proteomic analysis of ubiquitin ligase KEAP1 reveals associated proteins that inhibit NRF2 ubiquitination. Cancer Research, Apr 1st, 2013;73(7):2199-210.
Ubiquitin Ligases and Ubiquitin Specific Proteases:
- Tai Young Kim, Priscila Siesser, Kent L Rossman, Dennis Goldfarb, Kathryn Mackinnon, Feng Yan, XianHua Yi, Michael MacCoss, Randall T. Moon , Channing .J Der and Michael B. Major. Substrate Trapping Proteomics Reveals Targets of the βTrCP2/FBXW11 Ubiquitin Ligase. Molecular and Cellular Biology, 2014 Oct 22nd
- Babita Madan, Matthew P. Walker, Robert Young, Laura Quick, Kelly A. Orgel, Meagan Ryan, Priti Gupta, Ian C. Henrich, Marc Ferrer, Shane Marine, Brian S. Roberts, William T. Arthur, Jason D. Berndt, Victor Kwan Min Lee, Andre M. Oliveira, Randall T. Moon, David M. Virshup, Margaret M. Chou and Michael B. Major. The USP6 Oncogene Promotes Wnt Signaling by Deubiquitylating Frizzleds. Proceedings of the National Academy of Sciences, 2016. May 9th