Publications

Publications

Yumanity Therapeutics’ integrated discovery platforms have been described in multiple, peer-reviewed publications, including three recent Science papers co-authored by Yumanity’s founding research team, Drs. Khurana, Chung and Tardiff. Additional references for select publications generated from the lab of Yumanity’s scientific founder, Dr. Susan Lindquist, are included below.

Recent Publications Describing Yumanity’s Integrated Platforms:

  1. Treusch S, Hamamichi S, Goodman JL, Matlack KES, Chung CY, Baru V, Shulman JM, Parrado A, Bevis BJ, Valastyan JS, Han H, Lindhagen-Persson M, Reiman EM, Evans DA, Bennett DA, Olofsson A, DeJager PL, Tanzi RE, Caldwell KA, Caldwell GA, Lindquist S, 2011. Functional links between Aβ toxicity, endocytic trafficking and Alzheimer’s Disease risk factors in yeast. Science 334(6060): 1241-5.
  2. Tardiff DF, Jui NT, Khurana V, Tambe MA, Thompson ML, Chung CY, Kamadurai HB, Kim HT, Lancaster AK, Caldwell KA, Caldwell GA, Rochet J-C, Buchwald SL and Lindquist S, 2013. Yeast Reveal a “Druggable” Rsp5/Nedd4 network that ameliorates α-synuclein toxicity in neurons. Science, 342(6161): 979-83.
  3. Chung CY, Khurana V, Auluck PK, Tardiff DF, Mazzulli JR, Soldner F, Baru V, Lou Y, Freyzon Y, Cho S, Mungenast AE, Muffat J, Mitalipova M, Pluth MD, Jui, NT, Schule B, Lippard SJ, Tsai L-H, Krainc D, Buchwald SL, Jaenisch R and Lindquist S, 2013. Identification and rescue of α-synuclein toxicity in Parkinson patient–derived neurons. Science, 342(6161): 983-87.
  4. Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn S, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, Costanzo M, San Luis B-J, Schoendorf D, Inmaculada Barrasa M, Ehsani S, Sanjana N, Zhong Q, Gasser T, Bartel D, Vidal M, Deleidi M, Boone C, Fraenkel E, Berger B, and Lindquist S, 2017. Genome-Scale Networks Link Neurodegenerative Disease Genes to a-Synuclein through Specific Molecular Pathways. Cell Systems, 228, 1-14.

Supportive Publications:

  1. Chung CY, Khurana V, Yi S, Sahni N, Loh K, Auluck P, Baru V, Udeshi N, Freyzon Y, Carr S, Hill D, Vidal M, Ting A, and Lindquist S, 2017. In Situ Peroxidase Labeling and Mass-Spectrometry Connects Alpha-Synuclein Directly to Endocytic Trafficking and mRNA Metabolism in Neurons. Cell Systems, 232, 1-9.
  2. Sahni, Yi, Taipale, Fuxman Bass, Coulombe-Huntington, Yang, Peng, Weile, Karras, Wang, Kovács, Kamburov, Krykbaeva, Lam, Tucker, Khurana, Sharma, Liu, Yachie, Zhong, Shen, Palagi, San-Miguel, Fan, Balcha, Dricot, Jordan, Walsh, Shah, Yang, Stoyanova, Leighton, Calderwood, Jacob, Cusick, Salehi-Ashtiani, Whitesell, Sunyaev, Berger, Barabási, Charloteaux, Hill, Hao, Roth, Xia, Walhout, Lindquist, Vidal. Widespread macromolecular interaction perturbations in human genetic disorders. Cell. 161(3):647-60. doi: 10.1016/j.cell.2015.04.013.
  3. Tsvetkov, Mendillo, Zhao, Carette, Merrill, Cikes, Varadarajan, van Diemen, Penninger, Goldberg, Brummelkamp, Santagata, Lindquist. Compromising the 19S proteasome complex protects cells from reduced flux through the proteasome. PMID: 26327695; PMCID: PMC4551903
  4. Khurana V, Tardiff DF, Chung CY, Lindquist S., 2015. Toward stem cell-based phenotypic screens for neurodegenerative diseases. Nat Rev Neuro doi:10.1038/nrneurol.2015.79
  5. Caraveo G, Auluck PK, Whitesell L, Chung CY, Baru V, Mosharov EV, Yan X, Johny MB, Soste M, Picotti P, Kim H, Caldwell KA, Caldwell GA, Sulzer D, Yue DT, Lindquist S, 2014. Calcineurin determines toxic versus beneficial responses to α-synuclein. Proc Natl Acad Sci doi:10.1073/pnas.1413201111.
  6. Taipale M, Tucker G, Peng J, Krykbaeva I, Lin ZY, Larsen B, Choi H, Berger B, Gingras AC, Lindquist S, 2014. A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways. Cell, 158(2): 434-48.
  7. Matlack KES, Tardiff DF, Narayan P, Hamamichi S, Caldwell KA, Caldwell GA, and Lindquist S, 2014. Clioquinol promotes the degradation of metal-dependent amyloid-β (Aβ) oligomers to restore endocytosis and ameliorate Aβtoxicity. Proc Natl Acad Sci, 111 (11): 4013-18.
  8. Taipale M, Krykbaeva I, Whitesell L, Santagata S, Zhang J, Liu Q, Gray NS, Lindquist S, 2013. Chaperones as thermodynamic sensors of drug::target interactions in living cells. Nat Biotech, 31(7): 630-7.
  9. Krishnan R, Goodman JL, Mukhopadhyay S, Pacheco CD, Lemke EA, Deniz AA, Lindquist S, 2012. Conserved features of intermediates in amyloid assembly determine their benign or toxic states. Proc Natl Acad Sci 109(28): 11172-77.
  10. Tardiff DF, Tucci ML, Caldwell KA, Caldwell GA, Lindquist S, 2012. Different 8-hydroxyquinolines Protect Models of TDP-43, α-synuclein, and Polyglutamine Proteotoxicity through Distinct Mechanisms. J Biol Chem 287(6): 4107-20.
  11. Su LJ, Auluck PK, Outeiro TF, Yeger-Lotem E, Kritzer JA, Tardiff DF, Strathearn KE, Liu F, Cao S, Hamamichi S, Hill KJ, Caldwell KA, Bell GW, Fraenkel E, Cooper AA, Caldwell GA, McCaffery JM, Rochet J-C, Lindquist S, 2010. Compounds from an unbiased chemical screen reverse both ER-to-Golgi trafficking defects and mitochondrial dysfunction in Parkinson disease models. Dis Model Mech 3: 194-208.
  12. Kritzer JA, Hamamichi S, McCaffery JM, Santagata S, Naumann TA, Caldwell KA, Caldwell GA, Lindquist S, 2009. Rapid Selection of Cyclic Peptides that Reduce Alpha-Synuclein Toxicity in Yeast and Animal Models. Nat Chem Biol 5: 655-63.
  13. Yeger-Lotem E, Riva L, Su LJ, Gitler AD, Cashikar A, King OD, Auluck PK, Geddie ML, Valastyan JS, Karger DR, Lindquist S, Fraenkel E, 2009. Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat Genet 41: 316-23.
  14. Gitler AD, Chesi A, Geddie ML, Strathearn KE, Hamamichi S, Hill KJ, Caldwell KA, Caldwell GA, Cooper AA, Rochet J-C, Lindquist S, 2009. α-Synuclein is part of a diverse and highly conserved interaction network that includes PARK9 and manganese toxicity. Nat Genet 41: 308-15.
  15. Gitler AD, Bevis BJ, Shorter J, Strathearn KE, Hamamichi S, Su LJ, Caldwell KA, Caldwell GA, Rochet JC, McCaffery JM, Barlowe C, Lindquist S, 2008. The Parkinson’s disease protein {alpha}-synuclein disrupts cellular Rab homeostasis. Proc Natl Acad Sci USA 105: 145-50.
  16. Cooper AA, Gitler AD, Cashikar A, Haynes CM, Hill KJ, Bhullar B, Liu K, Xu K, Strathearn KE, Liu F, Cao S, Caldwell KA, Caldwell GA, Marsischky G, Kolodner RD, LaBaer J, Rochet JC, Bonini NM, Lindquist S, 2006. α-Synuclein blocks ER-Golgi traffic and Rab 1 rescues neuron loss in Parkinson’s models. Science 313: 324-28.
  17. Outeiro TF, Lindquist S, 2003. Yeast cells provide insight into Alpha-synuclein biology and pathobiology. Science 302: 1772-75.
  18. Parsell D, Kowal A, Singer MA, Lindquist S, 1994. Protein disaggregation mediated by heat-shock protein HSP104. Nature 372: 475-78.