Academic Appointments

Professional Education

  • Postdoctoral Fellow, University of California, San Francisco, Cellular and Molecular Pharmacology (2013)
  • Ph.D., Harvard University, Biological and Biomedical Sciences (2005)
  • B.S., University of Wisconsin, Madison, Biochemistry and Molecular Biology (1996)

Research & Scholarship

Current Research and Scholarly Interests

Endocytic Pathogens as Tools and Targets

Endocytic pathogens such as protein aggregates, viruses, protein toxins, and bacteria have evolved remarkable ways to enter the cell, disrupt homeostasis, and cause cell death. We use these agents both as probes to understand normal cellular trafficking and signaling events, and to find key targets for therapy.
As an example of this work, we have used high-coverage shRNA libraries and genetic interaction maps to explore the biology of the retrograde-trafficking toxin ricin. We have identified new proteins involved in retrograde trafficking, new components and functions for the vesicle tethering TRAPP complex, and a new role for the small ribosomal subunit RPS25, all of which are under current study.

Stress Signaling to the Cell Death Machinery

Cells have elaborate mechanisms of sensing diverse stresses (oxidative damage, nutrient deprivation, DNA breaks, etc), and must either repair damage or induce cell death. Misregulation of these pathways results in diseases such as cancer and Alzheimer’s. We would like to understand how these signals connect to the death pathway in health and disease in order to improve therapies.

Technology Development and Genetic Interaction Maps

Much of the work we do utilizes genetic screens enabled by novel high-coverage shRNA libraries (~25 shRNAs/gene) we have developed. The high coverage greatly reduces false positive and false negative results that have plagued traditional RNAi strategies. We use a pooled format that can be rapidly screened in large bioreactors, and analyze screens by deep sequencing to quantify changes in shRNA abundance.
Importantly, our library design allows us to knock down pairs of genes, and has facilitated the first systematic genetic interaction maps in mammalian cells. Using these maps, we can understand coordinated gene functions, predict new functions for uncharacterized genes, and identify drug targets. They also allow us to quickly identify synergistic interactions under stress conditions that we hope to exploit for combination therapies. Together with a broad network of collaborators, we are continuing to use this platform to develop new technologies for disrupting and interrogating gene function on a genomic scale.


2014-15 Courses

Postdoctoral Advisees

Graduate and Fellowship Programs


Journal Articles

  • Next-Generation NAMPT Inhibitors Identified by Sequential High-Throughput Phenotypic Chemical and Functional Genomic Screens CHEMISTRY & BIOLOGY Matheny, C. J., Wei, M. C., Bassik, M. C., Donnelly, A. J., Kampmann, M., Iwasaki, M., Piloto, O., Solow-Cordero, D. E., Bouley, D. M., Rau, R., Brown, P., McManus, M. T., Weissman, J. S., Cleary, M. L. 2013; 20 (11): 1352-1363


    Phenotypic high-throughput chemical screens allow for discovery of small molecules that modulate complex phenotypes and provide lead compounds for novel therapies; however, identification of the mechanistically relevant targets remains a major experimental challenge. We report the application of sequential unbiased high-throughput chemical and ultracomplex small hairpin RNA (shRNA) screens to identify a distinctive class of inhibitors that target nicotinamide phosphoribosyl transferase (NAMPT), a rate-limiting enzyme in the biosynthesis of nicotinamide adenine dinucleotide, a crucial cofactor in many biochemical processes. The lead compound STF-118804 is a highly specific NAMPT inhibitor, improves survival in an orthotopic xenotransplant model of high-risk acute lymphoblastic leukemia, and targets leukemia stem cells. Tandem high-throughput screening using chemical and ultracomplex shRNA libraries, therefore, provides a rapid chemical genetics approach for seamless progression from small-molecule lead identification to target discovery and validation.

    View details for DOI 10.1016/j.chembiol.2013.09.014

    View details for Web of Science ID 000328434700008

    View details for PubMedID 24183972

  • A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Cell Bassik, M. C., Kampmann, M., Lebbink, R. J., Wang, S., Hein, M. Y., Poser, I., Weibezahn, J., Horlbeck, M. A., Chen, S., Mann, M., Hyman, A. A., Leproust, E. M., McManus, M. T., Weissman, J. S. 2013; 152 (4): 909-22


    Genetic interaction (GI) maps, comprising pairwise measures of how strongly the function of one gene depends on the presence of a second, have enabled the systematic exploration of gene function in microorganisms. Here, we present a two-stage strategy to construct high-density GI maps in mammalian cells. First, we use ultracomplex pooled shRNA libraries (25 shRNAs/gene) to identify high-confidence hit genes for a given phenotype and effective shRNAs. We then construct double-shRNA libraries from these to systematically measure GIs between hits. A GI map focused on ricin susceptibility broadly recapitulates known pathways and provides many unexpected insights. These include a noncanonical role for COPI, a previously uncharacterized protein complex affecting toxin clearance, a specialized role for the ribosomal protein RPS25, and functionally distinct mammalian TRAPP complexes. The ability to rapidly generate mammalian GI maps provides a potentially transformative tool for defining gene function and designing combination therapies based on synergistic pairs.

    View details for DOI 10.1016/j.cell.2013.01.030

    View details for PubMedID 23394947

  • Rapid creation and quantitative monitoring of high coverage shRNA libraries. Nature methods Bassik, M. C., Lebbink, R. J., Churchman, L. S., Ingolia, N. T., Patena, W., LeProust, E. M., Schuldiner, M., Weissman, J. S., McManus, M. T. 2009; 6 (6): 443-5


    Short hairpin RNA libraries are limited by low efficacy of many shRNAs and by off-target effects, which give rise to false negatives and false positives, respectively. Here we present a strategy for rapidly creating expanded shRNA pools (approximately 30 shRNAs per gene) that are analyzed by deep sequencing (EXPAND). This approach enables identification of multiple effective target-specific shRNAs from a complex pool, allowing a rigorous statistical evaluation of true hits.

    View details for DOI 10.1038/nmeth.1330

    View details for PubMedID 19448642

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