James Shorter

faculty photo
Associate Professor of Biochemistry and Biophysics
Fellow, Institute on Aging (IOA)
Faculty Member, The Institute for Translational Medicine and Therapeutics (ITMAT)
Mentor, Penn Summer Undergraduate Internship Program (SUIP)
Primary Trainer, Center for Neurodegenerative Research (CNDR)
Faculty Member, Chemistry-Biology Interface (CBI), Wistar Institute and The University of Pennsylvania
Faculty Member, Penn Center for AIDS Research (CFAR)
Member, Internal Advisory Board of Penn Institute on Aging
Mentor, Penn Clinical and Translational Sciences Award (CTSA) summer undergraduate internship program
Department: Biochemistry and Biophysics

Contact information
Department of Biochemistry and Biophysics
Perelman School of Medicine
University of Pennsylvania
805b Stellar-Chance Laboratories
422 Curie Boulevard
Philadelphia, PA 19104
Office: 215-573-4256
Fax: 215-898-4217
Lab: 215-573-4257
Education:
B.A. (Biology)
University of Oxford, 1995.
Ph.D. (Cell Biology)
University of London, 2000.
Permanent link
 

Description of Research Expertise

Life demands that proteins fold into elaborate structures to perform the overwhelming majority of biological functions. We investigate how components of the proteostasis (protein homeostasis) network enable cells to achieve successful protein folding. In particular, we seek to understand how cells prevent, reverse, or even promote the formation of diverse misfolded conformers, encompassing: prions, amyloids, fibrillar structures, amorphous aggregates and toxic soluble oligomers.

Amyloid fibers are self-templating protein conformers. They self-replicate their specific ‘cross-β’ conformation at their growing ends, by converting other copies of the same protein to the ‘cross-β’ amyloid form. When amyloid fibers grow and divide with high efficiency they can be infectious, and are then termed prions (Cushman et al., 2010; Shorter & Lindquist, 2005; Shorter, 2010). Cells have evolved a sophisticated machinery to alleviate such aberrant protein aggregation. For example, protein disaggregases resolve protein aggregates, molecular chaperones prevent protein aggregation, osmolytes act as chemical chaperones, and degradation systems eliminate misfolded proteins (Shorter, 2008; Vashist et al. 2010).

Nonetheless, these safeguards can be breached, especially as organisms age, and the consequences are often fatal. Prion and amyloid formation are associated with some of the most devastating neurodegenerative diseases confronting humankind, including Alzheimer’s disease, Parkinson's disease, variant Creutzfeldt-Jakob disease, and Huntington's disease (Cushman et al., 2010; Jackrel & Shorter, 2011). Yet, surprisingly, it is becoming increasingly clear that prions and amyloids are not always a problem. In fact, several have been harnessed during evolution for adaptive purposes and feature in some of the most revolutionary new concepts in biology and evolution, including protein-based genetic elements, long-term memory formation, melanosome biogenesis, evolutionary capacitance and the revelation of cryptic genetic variation (Shorter & Lindquist, 2005; Watt et al., 2009; Shorter, 2010). We employ biochemistry and genetics to understand the enigmatic mechanistic interfaces that exist between protein disaggregases, molecular chaperones, small molecules and amyloid/prion fibers or other misfolded species, and how these interfaces can be manipulated to divert pathogenic and promote beneficial phenotypic trajectories. Specifically, we are pursuing the following goals:

1) Defining the structural and mechanistic basis for Hsp104 function. One major focus concerns Hsp104, a protein disaggregase of the AAA+ superfamily from yeast, which disaggregates denatured proteins and returns them to normal function (Shorter, 2008; Vashist et al. 2010; DeSantis & Shorter, 2012). Hsp104 is also essential for the formation and inheritance of several yeast prions; protein-based genetic elements comprised of amyloid fibers that self-perpetuate alterations in protein form and function. Hsp104 can both construct and deconstruct self-replicating amyloid forms of Sup35, which comprise the yeast prion [PSI+], and Ure2, which comprise the yeast prion [URE3] (Shorter & Lindquist, 2004; Shorter & Lindquist, 2006). We aim to elucidate the hexameric structure of Hsp104 (Wendler et al., 2007; Wendler et al., 2009; Sweeny et al., 2011). We also strive to understand the mechanistic basis of how Hsp104 structure enables these disaggregation activities and other prion-regulatory functions (DeSantis et al., 2012; DeSantis and Shorter, 2012).

Hsp104 is often assisted by a supporting cast of molecular chaperones to rescue aggregated polypeptides (Sweeny & Shorter, 2008). Most notably, Hsp70, Hsp40 and small heat shock proteins synergize with Hsp104 to promote the reactivation of protein aggregates (Duennwald et al., 2012). We wish to understand how these molecular chaperones achieve these synergistic activities (Doyle et al., 2007; Shorter & Lindquist, 2008; DeSantis & Shorter, 2012; Duennwald et al., 2012). Finally, we seek to define the natural substrates comprising the Hsp104 folding reservoir and determine the impact of specific Hsp104 clients on yeast biology.

2) Applying Hsp104 to disease-associated protein misfolding and aggregation. Inexplicably, Hsp104 has no known homologue or orthologue in metazoa. This deficiency is vexing, for it would seem that a protein that reverses protein aggregation and restores protein function, would be critical in our fight against several diseases caused by aberrant protein aggregation. Hence, we engineer, evolve and apply Hsp104 to metazoan systems to antagonize and reverse the proteotoxic aggregation pathways that are intimately connected with Parkinson’s, Alzheimer’s and Huntington’s disease as well as amyotrophic lateral sclerosis and HIV infection (Lo Bianco et al., 2008; Shorter, 2008; Vashist et al. 2010; Castellano and Shorter, 2012; DeSantis et al., 2012).

3) Defining the metazoan disaggregase machinery. The loss of Hsp104 from metazoan lineages is abrupt. The choanoflagellate protist, Monosiga brevicollis, one of the most advanced pre-metazoans has a clear Hsp104 homologue, whereas even early branching metazoans like the sea anemone, Nematostella vectensis do not. The reason underlying the loss of Hsp104 is unclear, especially because Hsp104 is well tolerated in animal systems. Whether mammals possess an analogous protein disaggregase (AAA+ protein or otherwise) has endured as an important open question. Recently, we have answered this question and identified a mammalian disaggregase system comprised of Hsp110, Hsp70 and Hsp40, which catalyzes the disaggregation and reactivation of chemically and thermally denatured aggregates, but is unable to rapidly remodel amyloid (Shorter, 2011). However, together with small heat shock proteins, Hsp110, Hsp70 and Hsp40 can slowly depolymerize amyloid fibers from their ends (Duennwald et al., 2012). We are now delineating the mechanism of Hsp110, Hsp70 and Hsp40 action . We are also interested in identifying additional metazoan disaggregases.

4) Defining how small molecules modulate amyloid folding trajectories. We employ a variety of small molecules as mechanistic probes to understand amyloid foldings pathways of Sup35 and Aβ42. These include 4,5-dianilinophthalimide (DAPH-1) and analogs, which dissolve Aβ42 fibers (that occur in Alzheimer's disease) and eliminate their neurotoxicity (Wang et al., 2008). DAPH-1 also disrupts Sup35 prion structure and function (Wang et al., 2008). We are interested in defining the mechanisms by which DAPH-1 and other small molecules modulate amyloid formation. Intriguingly, we have found that some small molecules select for the formation of drug-resistant prions or amyloids (Roberts et al., 2009; Shorter, 2010; Duennwald & Shorter, 2010). We have also discovered that specific small molecule combinations can preclude the formation of drug-resistant polymorphs or 'strains' (Roberts et al., 2009; Shorter, 2010; Duennwald & Shorter, 2010). Furthermore, we seek to elucidate synergies between small molecules and protein disaggregases that may accelerate the disruption of specific amyloid oligomers and fibers.

5) Defining the misfolding trajectories of RNA-binding proteins bearing prion-like domains in amyotrophic lateral sclerosis and other neurodegenerative disorders. Finally, we are investigating the mechanisms by which certain RNA-binding proteins, including TDP-43 and FUS, misfold and aggregate in various neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) with ubiquitin positive inclusions (FTLD-U) (Johnson et al., 2009; Sun et al., 2011). Intriguingly, using a bioinformaics approach we have discovered that TDP-43 and FUS harbor a prion-like domain similar to the domain in Sup35, Ure2 and other yeast prion proteins that confers prionogenicity (Cushman et al., 2010; Sun et al., 2011; Gitler and Shorter, 2011; King et al., 2012). Remarkably, our bioinformatics approach indicates that several RNA-binding proteins in the human genome harbor prion-like domains similar to FUS and TDP-43 (Gitler and Shorter, 2011; Couthouis et al., 2011; Couthouis et al., 2012; King et al., 2012). We have determined that two of these, TAF15 and EWSR1, are intrinsically aggregation prone and connected through pathology and genetics to ALS (Couthouis et al., 2011; Couthouis et al., 2012). We are interested to determine whether other RNA-binding proteins bearing prion-like domains misfold and contribute to other neurodegenerative disorders (King et al., 2012; Li et al., 2013). Indeed, we recently established that mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and amyotrophic lateral sclerosis (Kim et al., 2013). We aim to understand how the prion-like domain enables misfolding and whether these RNA-binding proteins access prion-like conformers (Li et al., 2013). We are also elucidating methods to prevent or reverse the misfolding of various RNA-binding proteins with prion-like domains and mitigate their toxicity (Sun et al., 2011; Armakola et al., 2012).

Description of Itmat Expertise

Dr. Shorter's laboratory employs biochemistry and genetics to understand the enigmatic mechanistic interfaces that exist between protein-remodeling factors, molecular chaperones, small molecules and amyloid/prion fibers, and how these interfaces can be manipulated to divert pathogenic and promote beneficial phenotypic trajectories. Dr. Shorter is interested in translating these biochemical and genetic efforts into therapies for human patients.

Selected Publications

Jackrel, M.E., M.E. DeSantis, B.A. Martinez, L.M. Castellano, R.M. Stewart, K.A. Caldwell, G.A. Caldwell, and J. Shorter*: Potentiated Hsp104 variants antagonize diverse proteotoxic misfolding events. Cell 156: 170-182, January 2014 Notes: *Corresponding author.

Li, Y.R.*, O.D. King, J. Shorter*, and A.D. Gitler*.: Stress granules as crucibles of ALS pathogenesis. J. Cell Biol. 201: 361-372, April 2013 Notes: * Co-corresponding author.

Kim^, H.J., N.C.Kim^, Y.D. Wang^, E.A. Scarborough^, J. Moore^, Z. Diaz^, K.S. MacLea, B. Freibaum, S. Li, A. Molliex, A.P. Kanagaraj, R. Carter, K.B. Boylan, A.M. Wojtas, R. Rademakers, J.L. Pinkus, S.A. Greenberg, J.Q. Trojanowski, B.J. Traynor, B.N. Smith, S. Topp, A.S. Gkazi, J. Miller, C.E. Shaw, M. Kottlors, J. Kirschner, A. Pestronk, Y.R. Li, A.F. Ford, A.D. Gitler, M. Benatar, O.D. King, V.E. Kimonis, E.D. Ross, C.C. Weihl, J. Shorter*, and J.P. Taylor*.: Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS. Nature 495: 467–473, March 2013 Notes: ^Co-first author. *Co-corresponding author.

DeSantis, M.E., E.H. Leung, E.A. Sweeny, M.E. Jackrel, M. Cushman-Nick, A. Neuhaus-Follini, S. Vashist, M.A. Sochor, M.N. Knight and J. Shorter*: Operational Plasticity Enables Hsp104 to Disaggregate Diverse Amyloid and Non-Amyloid Clients. Cell 151: 778-793, Nov 2012 Notes: *Corresponding author. See also Preview: Hsp104 gives clients the individual attention they need. Murray, A.N, and J.W. Kelly. Cell. 151: 695-697.

DeSantis, M.E. and J. Shorter*.: Hsp104 Drives ‘Protein-Only’ Positive Selection of Sup35 Prion Strains Encoding Strong [PSI+] Chemistry & Biology 19: 1400–1410, November 2012 Notes: *Corresponding author.

Duennwald, M.L, A. Echeverria, and J. Shorter*.: Small Heat Shock Proteins Potentiate Amyloid Dissolution by Protein Disaggregases from Yeast and Humans. PLoS Biol. 9(6): e1001346, June 2012 Notes: *Corresponding author.

King, O.D.*, A.D. Gitler* and J. Shorter*. : The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease. Brain Res. 1462: 61-80, June 2012 Notes: *Co-corresponding author.

Sun, Z.^, Z. Diaz^, X. Fang, M.P. Hart, A. Chesi, J. Shorter* and A.D. Gitler*: Molecular determinants and genetic modifiers of aggregation and toxicity for the ALS disease protein FUS/TLS. PLoS Biol. 9(4): e1000614, April 2011 Notes: ^Co-first author. *Co-corresponding author.

Roberts B.E., M.L. Duennwald*, H. Wang, C. Chung, N.P. Lopreiato, E.A. Sweeny, M.N. Knight and J. Shorter*: A synergistic small-molecule combination directly eradicates diverse prion strain structures. Nat. Chem. Biol. 5(12): 936-946, December 2009 Notes: *Co-corresponding author.

Johnson, B.S., D. Snead, J.J. Lee, J. M. McCaffery, J. Shorter* and A.D. Gitler* : TDP-43 is intrinsically aggregation-prone, and amyotrophic lateral sclerosis-linked mutations accelerate aggregation and increase toxicity. J. Biol. Chem. 284(30): 20329-39, July 2009 Notes: * Co-corresponding author.

back to top
Last updated: 11/12/2014
The Trustees of the University of Pennsylvania