Professional Education

  • Bachelor of Science, Stanford University, BIOL-BSH (1999)
  • Doctor of Philosophy, University of California San Francisco (2007)
  • Doctor of Medicine, University of California San Francisco (2009)

Stanford Advisors

Research & Scholarship

Lab Affiliations


Graduate and Fellowship Programs

  • Hematology (Fellowship Program)
  • Oncology (Fellowship Program)


Journal Articles

  • Protein turnover and inclusion body formation AUTOPHAGY Mitra, S., Tsvetkov, A. S., Finkbeiner, S. 2009; 5 (7): 1037-1038


    In a recent study, we investigated the relationship between inclusion body (IB) formation and the activity of the ubiquitin-proteasome system (UPS) in a primary neuron model of Huntington disease. We followed individual neurons over the course of days and monitored the level of mutant huntingtin (htt) (which causes Huntington disease), IB formation, UPS function, and neuronal toxicity. The accumulation of UPS substrates and neuronal toxicity increased with increasing levels of proteasome inhibition. The UPS was more impaired in neurons that subsequently formed IBs than in those that did not; however, after IBs formed, UPS function improved. These findings suggest that IB formation is a protective cellular response mediated in part by increased degradation of intracellular protein.

    View details for Web of Science ID 000272691100015

    View details for PubMedID 19838079

  • Single Neuron Ubiquitin-Proteasome Dynamics Accompanying Inclusion Body Formation in Huntington Disease JOURNAL OF BIOLOGICAL CHEMISTRY Mitra, S., Tsvetkov, A. S., Finkbeiner, S. 2009; 284 (7): 4398-4403


    The accumulation of mutant protein in intracellular aggregates is a common feature of neurodegenerative disease. In Huntington disease, mutant huntingtin leads to inclusion body (IB) formation and neuronal toxicity. Impairment of the ubiquitin-proteasome system (UPS) has been implicated in IB formation and Huntington disease pathogenesis. However, IBs form asynchronously in only a subset of cells with mutant huntingtin, and the relationship between IB formation and UPS function has been difficult to elucidate. Here, we applied single-cell longitudinal acquisition and analysis to monitor mutant huntingtin IB formation, UPS function, and neuronal toxicity. We found that proteasome inhibition is toxic to striatal neurons in a dose-dependent fashion. Before IB formation, the UPS is more impaired in neurons that go on to form IBs than in those that do not. After forming IBs, impairment is lower in neurons with IBs than in those without. These findings suggest IBs are a protective cellular response to mutant protein mediated in part by improving intracellular protein degradation.

    View details for DOI 10.1074/jbc.M806269200

    View details for Web of Science ID 000263134400039

    View details for PubMedID 19074152

  • Inclusion body formation reduces levels of mutant huntingtin and the risk of neuronal death NATURE Arrasate, M., Mitra, S., Schweitzer, E. S., Segal, M. R., Finkbeiner, S. 2004; 431 (7010): 805-810


    Huntington's disease is caused by an abnormal polyglutamine expansion within the protein huntingtin and is characterized by microscopic inclusion bodies of aggregated huntingtin and by the death of selected types of neuron. Whether inclusion bodies are pathogenic, incidental or a beneficial coping response is controversial. To resolve this issue we have developed an automated microscope that returns to precisely the same neuron after arbitrary intervals, even after cells have been removed from the microscope stage. Here we show, by survival analysis, that neurons die in a time-independent fashion but one that is dependent on mutant huntingtin dose and polyglutamine expansion; many neurons die without forming an inclusion body. Rather, the amount of diffuse intracellular huntingtin predicts whether and when inclusion body formation or death will occur. Surprisingly, inclusion body formation predicts improved survival and leads to decreased levels of mutant huntingtin elsewhere in a neuron. Thus, inclusion body formation can function as a coping response to toxic mutant huntingtin.

    View details for DOI 10.1038/nature02998

    View details for Web of Science ID 000224435500037

    View details for PubMedID 15483602

  • Disease-Associated Polyglutamine Stretches in Monomeric Huntingtin Adopt a Compact Structure JOURNAL OF MOLECULAR BIOLOGY Peters-Libeu, C., Miller, J., Rutenber, E., Newhouse, Y., Krishnan, P., Cheung, K., Hatters, D., Brooks, E., Widjaja, K., Tina Tran, T., Mitra, S., Arrasate, M., Mosquera, L. A., Taylor, D., Weisgraber, K. H., Finkbeiner, S. 2012; 421 (4-5): 587-600


    Abnormal polyglutamine (polyQ) tracts are the only common feature in nine proteins that each cause a dominant neurodegenerative disorder. In Huntington's disease, tracts longer than 36 glutamines in the protein huntingtin (htt) cause degeneration. In situ, monoclonal antibody 3B5H10 binds to different htt fragments in neurons in proportion to their toxicity. Here, we determined the structure of 3B5H10 Fab to 1.9 Å resolution by X-ray crystallography. Modeling demonstrates that the paratope forms a groove suitable for binding two ?-rich polyQ strands. Using small-angle X-ray scattering, we confirmed that the polyQ epitope recognized by 3B5H10 is a compact two-stranded hairpin within monomeric htt and is abundant in htt fragments unbound to antibody. Thus, disease-associated polyQ stretches preferentially adopt compact conformations. Since 3B5H10 binding predicts degeneration, this compact polyQ structure may be neurotoxic.

    View details for DOI 10.1016/j.jmb.2012.01.034

    View details for Web of Science ID 000308383800013

    View details for PubMedID 22306738

  • Identifying polyglutamine protein species in situ that best predict neurodegeneration NATURE CHEMICAL BIOLOGY Miller, J., Arrasate, M., Brooks, E., Libeu, C. P., Legleiter, J., Hatters, D., Curtis, J., Cheung, K., Krishnan, P., Mitra, S., Widjaja, K., Shaby, B. A., Lotz, G. P., Newhouse, Y., Mitchell, E. J., Osmand, A., Gray, M., Thulasiramin, V., Saudou, F., Segal, M., Yang, X. W., Masliah, E., Thompson, L. M., Muchowski, P. J., Weisgraber, K. H., Finkbeiner, S. 2011; 7 (12): 925-934


    Polyglutamine (polyQ) stretches exceeding a threshold length confer a toxic function to proteins that contain them and cause at least nine neurological disorders. The basis for this toxicity threshold is unclear. Although polyQ expansions render proteins prone to aggregate into inclusion bodies, this may be a neuronal coping response to more toxic forms of polyQ. The exact structure of these more toxic forms is unknown. Here we show that the monoclonal antibody 3B5H10 recognizes a species of polyQ protein in situ that strongly predicts neuronal death. The epitope selectively appears among some of the many low-molecular-weight conformational states assumed by expanded polyQ and disappears in higher-molecular-weight aggregated forms, such as inclusion bodies. These results suggest that protein monomers and possibly small oligomers containing expanded polyQ stretches can adopt a conformation that is recognized by 3B5H10 and is toxic or closely related to a toxic species.

    View details for DOI 10.1038/NCHEMBIO.694

    View details for Web of Science ID 000297166200016

    View details for PubMedID 22037470

  • Quantitative Relationships between Huntingtin Levels, Polyglutamine Length, Inclusion Body Formation, and Neuronal Death Provide Novel Insight into Huntington's Disease Molecular Pathogenesis JOURNAL OF NEUROSCIENCE Miller, J., Arrasate, M., Shaby, B. A., Mitra, S., Masliah, E., Finkbeiner, S. 2010; 30 (31): 10541-10550


    An expanded polyglutamine (polyQ) stretch in the protein huntingtin (htt) induces self-aggregation into inclusion bodies (IBs) and causes Huntington's disease (HD). Defining precise relationships between early observable variables and neuronal death at the molecular and cellular levels should improve our understanding of HD pathogenesis. Here, we used an automated microscope that tracks thousands of neurons individually over their entire lifetime to quantify interconnected relationships between early variables, such as htt levels, polyQ length, and IB formation, and neuronal death in a primary striatal model of HD. The resulting model revealed that mutant htt increases the risk of death by tonically interfering with homeostatic coping mechanisms rather than producing accumulated damage to the neuron, htt toxicity is saturable, the rate-limiting steps for inclusion body formation and death can be traced to different conformational changes in monomeric htt, and IB formation reduces the impact of the starting levels of htt of a neuron on its risk of death. Finally, the model that emerges from our quantitative measurements places critical limits on the potential mechanisms by which mutant htt might induce neurodegeneration, which should help direct future research.

    View details for DOI 10.1523/JNEUROSCI.0146-10.2010

    View details for Web of Science ID 000280789600028

    View details for PubMedID 20685997

  • The ubiquitin-proteasome pathway in Huntington's disease THESCIENTIFICWORLDJOURNAL Mitra, S., Finkbeiner, S. 2008; 8: 421-433


    The accumulation of mutant protein is a common feature of neurodegenerative disease. In Huntington's disease, a polyglutamine expansion in the huntingtin protein triggers neuronal toxicity. Accompanying neuronal death, mutant huntingtin aggregates in large macromolecular structures called inclusion bodies. The function of the machinery for intracellular protein degradation is linked to huntingtin toxicity and components of this machinery colocalize with inclusion bodies. An increasing body of evidence implicates the ubiquitin-proteasome pathway in the failure of cells to degrade mutant huntingtin. A number of potential mechanisms that link compromised ubiquitin-proteasome pathway function and neurodegeneration have been proposed and may offer opportunities for therapeutic intervention.

    View details for DOI 10.1100/tsw.2008.60

    View details for Web of Science ID 000255276800006

    View details for PubMedID 18454252

  • AMPA receptors regulate transcription of the plasticity-related immediate-early gene Arc NATURE NEUROSCIENCE Rao, V. R., Pintchovski, S. A., Chin, J., Peebles, C. L., Mitra, S., Finkbeiner, S. 2006; 9 (7): 887-895


    Learning and memory depend critically on long-term synaptic plasticity, which requires neuronal gene expression. In the prevailing view, AMPA receptors mediate fast excitatory synaptic transmission and effect short-term plasticity, but they do not directly regulate neuronal gene expression. By studying regulation of Arc, a gene required for long-term plasticity, we uncovered a new role for AMPA receptors in neuronal gene expression. Spontaneous synaptic activity or activity induced by brain-derived neurotrophic factor (BDNF) elicited Arc expression in cultures of rat cortical neurons and in organotypic brain slices. Notably, inhibiting AMPA receptors strongly potentiated activity-dependent Arc expression. We found that AMPA receptors negatively regulate Arc transcription, but not translation or stability, through a mechanism involving a pertussis toxin-sensitive G protein. These results provide insights into the activity-dependent mechanisms of Arc expression and suggest that, in addition to effecting short-term plasticity, AMPA receptors regulate genes involved in long-term plasticity.

    View details for DOI 10.1038/nn1708

    View details for Web of Science ID 000238590800014

    View details for PubMedID 16732277

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